Multiple sequence alignment - TraesCS2D01G446900

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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 TraesCS2D01G446900 chr2D 100.000 4695 0 0 1 4695 556952789 556948095 0.000000e+00 8671
1 TraesCS2D01G446900 chr2D 90.909 110 9 1 2448 2557 622392476 622392368 3.790000e-31 147
2 TraesCS2D01G446900 chr2B 94.246 3615 155 26 552 4144 664222686 664219103 0.000000e+00 5474
3 TraesCS2D01G446900 chr2B 93.810 517 19 3 4178 4690 664219107 664218600 0.000000e+00 765
4 TraesCS2D01G446900 chr2B 88.739 222 7 5 273 476 664222909 664222688 6.030000e-64 255
5 TraesCS2D01G446900 chr2B 86.190 210 26 2 1 208 568027626 568027834 1.700000e-54 224
6 TraesCS2D01G446900 chr2A 94.441 3508 146 21 552 4035 696925980 696922498 0.000000e+00 5352
7 TraesCS2D01G446900 chr2A 92.649 653 27 14 4053 4695 696922452 696921811 0.000000e+00 920
8 TraesCS2D01G446900 chr2A 91.667 192 14 2 354 543 696926269 696926078 1.000000e-66 265
9 TraesCS2D01G446900 chr5B 83.094 278 43 3 1 274 295662343 295662620 2.800000e-62 250
10 TraesCS2D01G446900 chr5B 79.348 276 53 3 1 272 692746394 692746669 1.720000e-44 191
11 TraesCS2D01G446900 chr7D 83.032 277 43 3 1 274 82858233 82857958 1.010000e-61 248
12 TraesCS2D01G446900 chr7D 81.295 278 46 5 1 274 147195772 147196047 2.200000e-53 220
13 TraesCS2D01G446900 chr5D 82.784 273 41 6 1 270 36483589 36483858 6.070000e-59 239
14 TraesCS2D01G446900 chr5A 82.500 280 41 6 1 274 349620690 349620413 6.070000e-59 239
15 TraesCS2D01G446900 chr5A 82.609 161 14 7 117 274 475461268 475461417 3.810000e-26 130
16 TraesCS2D01G446900 chr6A 82.143 280 41 8 1 274 387209202 387208926 1.020000e-56 231
17 TraesCS2D01G446900 chr7B 80.755 265 48 3 1 263 14146526 14146789 2.210000e-48 204


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 TraesCS2D01G446900 chr2D 556948095 556952789 4694 True 8671.000000 8671 100.000 1 4695 1 chr2D.!!$R1 4694
1 TraesCS2D01G446900 chr2B 664218600 664222909 4309 True 2164.666667 5474 92.265 273 4690 3 chr2B.!!$R1 4417
2 TraesCS2D01G446900 chr2A 696921811 696926269 4458 True 2179.000000 5352 92.919 354 4695 3 chr2A.!!$R1 4341

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
258 259 0.108472 GACGGGTTTAAGAGGTCCGG 60.108 60.0 0.0 0.0 44.36 5.14 F
1098 1295 0.114168 TTTTGGAGTGATGGGTGGGG 59.886 55.0 0.0 0.0 0.00 4.96 F
1188 1385 0.323451 GGATCTTGGTGGTTGGGGAC 60.323 60.0 0.0 0.0 0.00 4.46 F
2171 2377 0.323725 GAAGGGGCTGCTTGATTCCA 60.324 55.0 0.0 0.0 0.00 3.53 F
2534 2740 2.090658 GCTGTACTTCATGACAACGTCG 59.909 50.0 0.0 0.0 34.95 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1325 0.032540 CCAGGAAACCAAGCAAGCAC 59.967 55.000 0.00 0.00 0.00 4.40 R
2171 2377 0.605589 CTCGACTTGCTCTCCACCTT 59.394 55.000 0.00 0.00 0.00 3.50 R
2681 2887 1.136147 CATTGTTCAGCGCCTCTGC 59.864 57.895 2.29 0.00 42.56 4.26 R
3313 3519 0.538057 CCTTTGCCTGCAAGTCCTCA 60.538 55.000 4.58 0.00 37.24 3.86 R
4040 4247 0.549950 AGAACATGCATGGGAGGGAG 59.450 55.000 29.41 3.17 0.00 4.30 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.369870 GTTCACACCGTAGCGATGG 58.630 57.895 3.14 3.14 37.80 3.51
19 20 0.108992 GTTCACACCGTAGCGATGGA 60.109 55.000 12.54 0.00 35.46 3.41
20 21 0.108992 TTCACACCGTAGCGATGGAC 60.109 55.000 12.54 0.00 35.46 4.02
21 22 1.214325 CACACCGTAGCGATGGACA 59.786 57.895 12.54 0.00 35.46 4.02
22 23 1.076533 CACACCGTAGCGATGGACAC 61.077 60.000 12.54 0.00 35.46 3.67
23 24 1.872234 CACCGTAGCGATGGACACG 60.872 63.158 12.54 0.00 35.46 4.49
24 25 2.042259 ACCGTAGCGATGGACACGA 61.042 57.895 12.54 0.00 36.53 4.35
25 26 1.585521 CCGTAGCGATGGACACGAC 60.586 63.158 0.00 0.00 36.53 4.34
26 27 1.933041 CGTAGCGATGGACACGACG 60.933 63.158 0.00 0.00 36.53 5.12
27 28 1.136147 GTAGCGATGGACACGACGT 59.864 57.895 0.00 0.00 0.00 4.34
28 29 0.860618 GTAGCGATGGACACGACGTC 60.861 60.000 5.18 5.18 44.57 4.34
59 60 3.249687 AGGTTTCCTGGCGCTTTAG 57.750 52.632 7.64 3.45 29.57 1.85
60 61 0.960861 AGGTTTCCTGGCGCTTTAGC 60.961 55.000 7.64 0.00 29.57 3.09
61 62 1.241315 GGTTTCCTGGCGCTTTAGCA 61.241 55.000 7.64 0.00 42.21 3.49
62 63 0.811281 GTTTCCTGGCGCTTTAGCAT 59.189 50.000 7.64 0.00 42.21 3.79
63 64 0.810648 TTTCCTGGCGCTTTAGCATG 59.189 50.000 7.64 0.00 42.21 4.06
64 65 1.031571 TTCCTGGCGCTTTAGCATGG 61.032 55.000 7.64 0.33 42.21 3.66
65 66 2.484062 CCTGGCGCTTTAGCATGGG 61.484 63.158 7.64 0.00 42.21 4.00
66 67 1.451927 CTGGCGCTTTAGCATGGGA 60.452 57.895 7.64 0.00 42.21 4.37
67 68 1.718757 CTGGCGCTTTAGCATGGGAC 61.719 60.000 7.64 0.00 42.21 4.46
68 69 2.481471 GGCGCTTTAGCATGGGACC 61.481 63.158 7.64 0.00 42.21 4.46
69 70 2.481471 GCGCTTTAGCATGGGACCC 61.481 63.158 2.45 2.45 42.21 4.46
70 71 1.823899 CGCTTTAGCATGGGACCCC 60.824 63.158 8.45 2.69 42.21 4.95
71 72 1.823899 GCTTTAGCATGGGACCCCG 60.824 63.158 8.45 0.00 41.59 5.73
72 73 1.823899 CTTTAGCATGGGACCCCGC 60.824 63.158 8.45 11.18 39.42 6.13
73 74 3.352990 TTTAGCATGGGACCCCGCC 62.353 63.158 16.52 1.30 39.42 6.13
77 78 3.807839 CATGGGACCCCGCCATCA 61.808 66.667 8.45 0.00 39.42 3.07
78 79 3.492353 ATGGGACCCCGCCATCAG 61.492 66.667 8.45 0.00 39.42 2.90
79 80 4.731853 TGGGACCCCGCCATCAGA 62.732 66.667 8.45 0.00 39.42 3.27
80 81 4.176752 GGGACCCCGCCATCAGAC 62.177 72.222 0.00 0.00 0.00 3.51
81 82 4.176752 GGACCCCGCCATCAGACC 62.177 72.222 0.00 0.00 0.00 3.85
82 83 4.530857 GACCCCGCCATCAGACCG 62.531 72.222 0.00 0.00 0.00 4.79
84 85 4.530857 CCCCGCCATCAGACCGAC 62.531 72.222 0.00 0.00 0.00 4.79
85 86 4.873129 CCCGCCATCAGACCGACG 62.873 72.222 0.00 0.00 0.00 5.12
86 87 4.129737 CCGCCATCAGACCGACGT 62.130 66.667 0.00 0.00 0.00 4.34
87 88 2.880879 CGCCATCAGACCGACGTG 60.881 66.667 0.00 0.00 0.00 4.49
88 89 2.571757 GCCATCAGACCGACGTGA 59.428 61.111 0.00 0.00 0.00 4.35
89 90 1.805945 GCCATCAGACCGACGTGAC 60.806 63.158 0.00 0.00 0.00 3.67
90 91 1.514228 CCATCAGACCGACGTGACG 60.514 63.158 2.24 2.24 0.00 4.35
110 111 4.100084 CATGCCCTGACGCCTCCA 62.100 66.667 0.00 0.00 0.00 3.86
111 112 3.092511 ATGCCCTGACGCCTCCAT 61.093 61.111 0.00 0.00 0.00 3.41
112 113 1.766059 ATGCCCTGACGCCTCCATA 60.766 57.895 0.00 0.00 0.00 2.74
113 114 1.130054 ATGCCCTGACGCCTCCATAT 61.130 55.000 0.00 0.00 0.00 1.78
114 115 1.344953 TGCCCTGACGCCTCCATATT 61.345 55.000 0.00 0.00 0.00 1.28
115 116 0.603975 GCCCTGACGCCTCCATATTC 60.604 60.000 0.00 0.00 0.00 1.75
116 117 0.319900 CCCTGACGCCTCCATATTCG 60.320 60.000 0.00 0.00 0.00 3.34
117 118 0.946221 CCTGACGCCTCCATATTCGC 60.946 60.000 0.00 0.00 0.00 4.70
118 119 0.946221 CTGACGCCTCCATATTCGCC 60.946 60.000 0.00 0.00 0.00 5.54
119 120 1.668151 GACGCCTCCATATTCGCCC 60.668 63.158 0.00 0.00 0.00 6.13
120 121 2.358737 CGCCTCCATATTCGCCCC 60.359 66.667 0.00 0.00 0.00 5.80
121 122 2.836154 GCCTCCATATTCGCCCCA 59.164 61.111 0.00 0.00 0.00 4.96
122 123 1.380302 GCCTCCATATTCGCCCCAT 59.620 57.895 0.00 0.00 0.00 4.00
123 124 0.618458 GCCTCCATATTCGCCCCATA 59.382 55.000 0.00 0.00 0.00 2.74
124 125 1.212935 GCCTCCATATTCGCCCCATAT 59.787 52.381 0.00 0.00 0.00 1.78
125 126 2.357154 GCCTCCATATTCGCCCCATATT 60.357 50.000 0.00 0.00 0.00 1.28
126 127 3.877735 GCCTCCATATTCGCCCCATATTT 60.878 47.826 0.00 0.00 0.00 1.40
127 128 3.696051 CCTCCATATTCGCCCCATATTTG 59.304 47.826 0.00 0.00 0.00 2.32
128 129 3.696045 TCCATATTCGCCCCATATTTGG 58.304 45.455 0.00 0.00 43.23 3.28
140 141 3.368248 CCATATTTGGGCTGGATATGGG 58.632 50.000 17.88 6.92 44.56 4.00
141 142 3.368248 CATATTTGGGCTGGATATGGGG 58.632 50.000 0.00 0.00 32.63 4.96
142 143 1.244366 ATTTGGGCTGGATATGGGGT 58.756 50.000 0.00 0.00 0.00 4.95
143 144 0.261402 TTTGGGCTGGATATGGGGTG 59.739 55.000 0.00 0.00 0.00 4.61
144 145 2.116125 GGGCTGGATATGGGGTGC 59.884 66.667 0.00 0.00 0.00 5.01
145 146 2.116125 GGCTGGATATGGGGTGCC 59.884 66.667 0.00 0.00 0.00 5.01
146 147 2.281761 GCTGGATATGGGGTGCCG 60.282 66.667 0.00 0.00 0.00 5.69
147 148 2.431683 CTGGATATGGGGTGCCGG 59.568 66.667 0.00 0.00 0.00 6.13
148 149 2.367648 TGGATATGGGGTGCCGGT 60.368 61.111 1.90 0.00 0.00 5.28
149 150 2.397413 CTGGATATGGGGTGCCGGTC 62.397 65.000 1.90 0.00 0.00 4.79
150 151 2.448582 GGATATGGGGTGCCGGTCA 61.449 63.158 1.90 0.00 0.00 4.02
151 152 1.071471 GATATGGGGTGCCGGTCAG 59.929 63.158 1.90 0.00 0.00 3.51
152 153 1.692749 ATATGGGGTGCCGGTCAGT 60.693 57.895 1.90 0.00 0.00 3.41
153 154 1.696097 ATATGGGGTGCCGGTCAGTC 61.696 60.000 1.90 0.00 0.00 3.51
163 164 3.047877 GGTCAGTCCGGGCGTTTG 61.048 66.667 0.00 0.00 0.00 2.93
164 165 2.029964 GTCAGTCCGGGCGTTTGA 59.970 61.111 0.00 0.00 0.00 2.69
165 166 2.027625 GTCAGTCCGGGCGTTTGAG 61.028 63.158 0.00 0.00 0.00 3.02
166 167 2.742372 CAGTCCGGGCGTTTGAGG 60.742 66.667 0.00 0.00 0.00 3.86
167 168 4.699522 AGTCCGGGCGTTTGAGGC 62.700 66.667 0.00 0.00 0.00 4.70
173 174 3.292159 GGCGTTTGAGGCCCGTTT 61.292 61.111 0.00 0.00 42.98 3.60
174 175 1.967494 GGCGTTTGAGGCCCGTTTA 60.967 57.895 0.00 0.00 42.98 2.01
175 176 1.517210 GGCGTTTGAGGCCCGTTTAA 61.517 55.000 0.00 0.00 42.98 1.52
176 177 0.109919 GCGTTTGAGGCCCGTTTAAG 60.110 55.000 0.00 0.00 0.00 1.85
177 178 0.519961 CGTTTGAGGCCCGTTTAAGG 59.480 55.000 0.00 0.00 0.00 2.69
178 179 1.878948 CGTTTGAGGCCCGTTTAAGGA 60.879 52.381 0.00 0.00 0.00 3.36
179 180 1.810755 GTTTGAGGCCCGTTTAAGGAG 59.189 52.381 0.00 0.00 0.00 3.69
180 181 0.322187 TTGAGGCCCGTTTAAGGAGC 60.322 55.000 0.00 0.00 0.00 4.70
181 182 1.451567 GAGGCCCGTTTAAGGAGCC 60.452 63.158 0.00 1.91 43.50 4.70
182 183 2.439701 GGCCCGTTTAAGGAGCCC 60.440 66.667 0.00 0.00 39.90 5.19
183 184 2.822701 GCCCGTTTAAGGAGCCCG 60.823 66.667 0.00 0.00 0.00 6.13
184 185 2.666812 CCCGTTTAAGGAGCCCGT 59.333 61.111 0.00 0.00 0.00 5.28
185 186 1.449070 CCCGTTTAAGGAGCCCGTC 60.449 63.158 0.00 0.00 0.00 4.79
186 187 1.595357 CCGTTTAAGGAGCCCGTCT 59.405 57.895 0.00 0.00 0.00 4.18
187 188 0.739813 CCGTTTAAGGAGCCCGTCTG 60.740 60.000 0.00 0.00 0.00 3.51
188 189 0.739813 CGTTTAAGGAGCCCGTCTGG 60.740 60.000 0.00 0.00 37.09 3.86
212 213 3.464207 AAAAACGTGACCGGACAGT 57.536 47.368 9.46 5.79 38.78 3.55
213 214 1.011333 AAAAACGTGACCGGACAGTG 58.989 50.000 9.46 6.49 38.78 3.66
214 215 0.176219 AAAACGTGACCGGACAGTGA 59.824 50.000 9.46 0.00 38.78 3.41
215 216 0.529119 AAACGTGACCGGACAGTGAC 60.529 55.000 9.46 0.00 38.78 3.67
216 217 2.049433 CGTGACCGGACAGTGACC 60.049 66.667 9.46 0.00 0.00 4.02
223 224 2.737376 GGACAGTGACCGAACGGC 60.737 66.667 13.32 6.91 39.32 5.68
224 225 2.737376 GACAGTGACCGAACGGCC 60.737 66.667 13.32 2.56 39.32 6.13
225 226 4.309950 ACAGTGACCGAACGGCCC 62.310 66.667 13.32 6.26 39.32 5.80
254 255 4.732672 GTATGAGACGGGTTTAAGAGGT 57.267 45.455 0.00 0.00 0.00 3.85
255 256 3.889520 ATGAGACGGGTTTAAGAGGTC 57.110 47.619 0.00 0.00 0.00 3.85
256 257 1.897802 TGAGACGGGTTTAAGAGGTCC 59.102 52.381 0.00 0.00 0.00 4.46
257 258 0.893447 AGACGGGTTTAAGAGGTCCG 59.107 55.000 0.00 0.00 45.42 4.79
258 259 0.108472 GACGGGTTTAAGAGGTCCGG 60.108 60.000 0.00 0.00 44.36 5.14
259 260 1.449070 CGGGTTTAAGAGGTCCGGC 60.449 63.158 0.00 0.00 37.35 6.13
260 261 1.896122 CGGGTTTAAGAGGTCCGGCT 61.896 60.000 0.00 0.00 37.35 5.52
261 262 0.392595 GGGTTTAAGAGGTCCGGCTG 60.393 60.000 0.00 0.00 0.00 4.85
262 263 0.323957 GGTTTAAGAGGTCCGGCTGT 59.676 55.000 0.00 0.00 0.00 4.40
263 264 1.551883 GGTTTAAGAGGTCCGGCTGTA 59.448 52.381 0.00 0.00 0.00 2.74
264 265 2.418334 GGTTTAAGAGGTCCGGCTGTAG 60.418 54.545 0.00 0.00 0.00 2.74
265 266 2.494870 GTTTAAGAGGTCCGGCTGTAGA 59.505 50.000 0.00 0.00 0.00 2.59
266 267 2.750141 TAAGAGGTCCGGCTGTAGAT 57.250 50.000 0.00 0.00 0.00 1.98
267 268 1.115467 AAGAGGTCCGGCTGTAGATG 58.885 55.000 0.00 0.00 0.00 2.90
268 269 1.068250 GAGGTCCGGCTGTAGATGC 59.932 63.158 0.00 0.00 0.00 3.91
269 270 1.381872 AGGTCCGGCTGTAGATGCT 60.382 57.895 0.00 0.00 0.00 3.79
270 271 1.068250 GGTCCGGCTGTAGATGCTC 59.932 63.158 0.00 0.00 0.00 4.26
271 272 1.395826 GGTCCGGCTGTAGATGCTCT 61.396 60.000 0.00 0.00 0.00 4.09
297 298 4.340617 AGGCGAATAAAAACAAGGGATGA 58.659 39.130 0.00 0.00 0.00 2.92
347 348 3.882013 CCACGCACACGCACCAAA 61.882 61.111 0.00 0.00 45.53 3.28
349 350 1.515088 CACGCACACGCACCAAAAA 60.515 52.632 0.00 0.00 45.53 1.94
382 395 0.179153 GAAAGAATTGGCTGCCGCTC 60.179 55.000 14.98 10.07 36.09 5.03
465 484 2.435586 CCGCAGCCTCAACCTCAG 60.436 66.667 0.00 0.00 0.00 3.35
472 654 2.581354 CTCAACCTCAGCCTCGGG 59.419 66.667 0.00 0.00 0.00 5.14
476 658 1.686110 AACCTCAGCCTCGGGGTAG 60.686 63.158 1.62 0.00 34.45 3.18
477 659 2.840102 CCTCAGCCTCGGGGTAGG 60.840 72.222 1.62 3.90 39.87 3.18
478 660 2.840102 CTCAGCCTCGGGGTAGGG 60.840 72.222 1.62 0.00 37.11 3.53
481 663 4.798682 AGCCTCGGGGTAGGGTGG 62.799 72.222 1.62 0.00 45.57 4.61
483 665 2.691732 CCTCGGGGTAGGGTGGTA 59.308 66.667 0.00 0.00 32.55 3.25
484 666 1.002017 CCTCGGGGTAGGGTGGTAA 59.998 63.158 0.00 0.00 32.55 2.85
485 667 0.618393 CCTCGGGGTAGGGTGGTAAA 60.618 60.000 0.00 0.00 32.55 2.01
486 668 0.828677 CTCGGGGTAGGGTGGTAAAG 59.171 60.000 0.00 0.00 0.00 1.85
487 669 1.222661 CGGGGTAGGGTGGTAAAGC 59.777 63.158 0.00 0.00 0.00 3.51
488 670 1.555477 CGGGGTAGGGTGGTAAAGCA 61.555 60.000 0.00 0.00 0.00 3.91
489 671 0.699981 GGGGTAGGGTGGTAAAGCAA 59.300 55.000 0.00 0.00 0.00 3.91
490 672 1.340697 GGGGTAGGGTGGTAAAGCAAG 60.341 57.143 0.00 0.00 0.00 4.01
491 673 1.460504 GGTAGGGTGGTAAAGCAAGC 58.539 55.000 0.00 0.00 0.00 4.01
492 674 1.084289 GTAGGGTGGTAAAGCAAGCG 58.916 55.000 0.00 0.00 0.00 4.68
493 675 0.978151 TAGGGTGGTAAAGCAAGCGA 59.022 50.000 0.00 0.00 0.00 4.93
494 676 0.321653 AGGGTGGTAAAGCAAGCGAG 60.322 55.000 0.00 0.00 0.00 5.03
495 677 1.502190 GGTGGTAAAGCAAGCGAGC 59.498 57.895 0.00 0.00 0.00 5.03
497 679 0.166814 GTGGTAAAGCAAGCGAGCTG 59.833 55.000 6.71 0.00 45.89 4.24
498 680 0.955428 TGGTAAAGCAAGCGAGCTGG 60.955 55.000 6.71 0.00 45.89 4.85
499 681 1.135523 GTAAAGCAAGCGAGCTGGC 59.864 57.895 16.19 16.19 45.89 4.85
515 697 3.945434 GCTGGCGCGGTGATCATG 61.945 66.667 8.83 0.00 0.00 3.07
516 698 2.202919 CTGGCGCGGTGATCATGA 60.203 61.111 8.83 0.00 0.00 3.07
517 699 2.511373 TGGCGCGGTGATCATGAC 60.511 61.111 8.83 0.00 0.00 3.06
518 700 3.630148 GGCGCGGTGATCATGACG 61.630 66.667 8.83 5.86 0.00 4.35
519 701 3.630148 GCGCGGTGATCATGACGG 61.630 66.667 8.83 9.23 0.00 4.79
520 702 2.961721 CGCGGTGATCATGACGGG 60.962 66.667 15.84 15.84 0.00 5.28
521 703 2.499205 GCGGTGATCATGACGGGA 59.501 61.111 15.82 0.00 0.00 5.14
522 704 1.153449 GCGGTGATCATGACGGGAA 60.153 57.895 15.82 0.00 0.00 3.97
523 705 0.532862 GCGGTGATCATGACGGGAAT 60.533 55.000 15.82 0.00 0.00 3.01
524 706 1.220529 CGGTGATCATGACGGGAATG 58.779 55.000 0.00 0.00 0.00 2.67
525 707 1.202521 CGGTGATCATGACGGGAATGA 60.203 52.381 0.00 0.29 38.37 2.57
526 708 2.213499 GGTGATCATGACGGGAATGAC 58.787 52.381 0.00 0.00 36.89 3.06
527 709 2.419990 GGTGATCATGACGGGAATGACA 60.420 50.000 0.00 0.00 36.89 3.58
528 710 2.609459 GTGATCATGACGGGAATGACAC 59.391 50.000 0.00 6.63 36.89 3.67
529 711 2.501316 TGATCATGACGGGAATGACACT 59.499 45.455 0.00 0.00 36.89 3.55
530 712 3.704061 TGATCATGACGGGAATGACACTA 59.296 43.478 0.00 0.00 36.89 2.74
531 713 3.520290 TCATGACGGGAATGACACTAC 57.480 47.619 0.00 0.00 0.00 2.73
532 714 3.096852 TCATGACGGGAATGACACTACT 58.903 45.455 0.00 0.00 0.00 2.57
533 715 3.119137 TCATGACGGGAATGACACTACTG 60.119 47.826 0.00 0.00 0.00 2.74
534 716 1.067142 TGACGGGAATGACACTACTGC 60.067 52.381 0.00 0.00 0.00 4.40
535 717 0.249398 ACGGGAATGACACTACTGCC 59.751 55.000 0.00 0.00 0.00 4.85
536 718 0.249120 CGGGAATGACACTACTGCCA 59.751 55.000 0.00 0.00 0.00 4.92
537 719 1.740380 CGGGAATGACACTACTGCCAG 60.740 57.143 0.00 0.00 0.00 4.85
538 720 1.279271 GGGAATGACACTACTGCCAGT 59.721 52.381 1.54 1.54 0.00 4.00
539 721 2.622436 GGAATGACACTACTGCCAGTC 58.378 52.381 0.00 0.00 0.00 3.51
540 722 2.263077 GAATGACACTACTGCCAGTCG 58.737 52.381 0.00 0.00 33.83 4.18
541 723 1.257743 ATGACACTACTGCCAGTCGT 58.742 50.000 0.00 0.00 33.83 4.34
542 724 1.900245 TGACACTACTGCCAGTCGTA 58.100 50.000 0.00 0.00 33.83 3.43
543 725 1.538512 TGACACTACTGCCAGTCGTAC 59.461 52.381 0.00 0.00 33.83 3.67
544 726 1.811359 GACACTACTGCCAGTCGTACT 59.189 52.381 0.00 0.00 0.00 2.73
545 727 2.228343 GACACTACTGCCAGTCGTACTT 59.772 50.000 0.00 0.00 0.00 2.24
546 728 3.415212 ACACTACTGCCAGTCGTACTTA 58.585 45.455 0.00 0.00 0.00 2.24
547 729 3.439476 ACACTACTGCCAGTCGTACTTAG 59.561 47.826 0.00 0.00 0.00 2.18
548 730 3.015327 ACTACTGCCAGTCGTACTTAGG 58.985 50.000 0.00 0.00 0.00 2.69
549 731 2.211250 ACTGCCAGTCGTACTTAGGA 57.789 50.000 0.00 0.00 0.00 2.94
550 732 2.093106 ACTGCCAGTCGTACTTAGGAG 58.907 52.381 0.00 0.00 0.00 3.69
561 743 9.798994 CAGTCGTACTTAGGAGTAATTAAACAT 57.201 33.333 0.00 0.00 39.95 2.71
562 744 9.798994 AGTCGTACTTAGGAGTAATTAAACATG 57.201 33.333 0.00 0.00 39.95 3.21
696 885 5.049818 CACAAGAGACACTGATCAAAACCTC 60.050 44.000 0.00 2.09 0.00 3.85
697 886 5.163258 ACAAGAGACACTGATCAAAACCTCT 60.163 40.000 0.00 4.39 0.00 3.69
698 887 5.146010 AGAGACACTGATCAAAACCTCTC 57.854 43.478 0.00 2.60 0.00 3.20
699 888 4.020662 AGAGACACTGATCAAAACCTCTCC 60.021 45.833 0.00 0.00 0.00 3.71
719 908 0.698818 TCCCTGCTTTTTCCTCTCCC 59.301 55.000 0.00 0.00 0.00 4.30
819 1008 3.578716 CCACTCCTCCTTGTTCTTCTACA 59.421 47.826 0.00 0.00 0.00 2.74
877 1071 1.873591 CACCAAGGAGAGAAAACACCG 59.126 52.381 0.00 0.00 0.00 4.94
887 1081 1.844544 GAAAACACCGCCTCCCCCTA 61.845 60.000 0.00 0.00 0.00 3.53
1069 1266 6.255020 GCATTCTGCAACCATTCTTTTATCAG 59.745 38.462 0.00 0.00 44.26 2.90
1070 1267 5.314923 TCTGCAACCATTCTTTTATCAGC 57.685 39.130 0.00 0.00 0.00 4.26
1071 1268 4.158394 TCTGCAACCATTCTTTTATCAGCC 59.842 41.667 0.00 0.00 0.00 4.85
1075 1272 5.105595 GCAACCATTCTTTTATCAGCCTTCT 60.106 40.000 0.00 0.00 0.00 2.85
1098 1295 0.114168 TTTTGGAGTGATGGGTGGGG 59.886 55.000 0.00 0.00 0.00 4.96
1112 1309 4.864334 GGGGATGGGCACGCAGAG 62.864 72.222 0.00 0.00 0.00 3.35
1125 1322 1.230635 CGCAGAGGTGGTTCTTGGTG 61.231 60.000 0.00 0.00 0.00 4.17
1128 1325 1.966451 GAGGTGGTTCTTGGTGGCG 60.966 63.158 0.00 0.00 0.00 5.69
1188 1385 0.323451 GGATCTTGGTGGTTGGGGAC 60.323 60.000 0.00 0.00 0.00 4.46
1200 1397 4.344865 GGGGACGGAGCTGCCAAA 62.345 66.667 0.00 0.00 35.94 3.28
1213 1410 4.279145 AGCTGCCAAATTCTTGATCTGAT 58.721 39.130 0.00 0.00 34.14 2.90
1619 1825 5.805728 AGTGGAATCTTAGTAGTGGTTTGG 58.194 41.667 0.00 0.00 0.00 3.28
1774 1980 1.747444 AGGAGGAAGAGAAGGGCAAA 58.253 50.000 0.00 0.00 0.00 3.68
1789 1995 1.447945 GCAAAGTTCTGGAGGAGCTC 58.552 55.000 4.71 4.71 34.39 4.09
1881 2087 2.901975 TGGAGATCCAGAAGGTCCG 58.098 57.895 0.00 0.00 42.01 4.79
1902 2108 2.825836 CATGGAACCGGAGCAGGC 60.826 66.667 9.46 0.00 33.69 4.85
2041 2247 3.833304 GCAAGGTATGAGCTGGCC 58.167 61.111 0.00 0.00 36.68 5.36
2116 2322 2.555199 GCTTGCGAGGTGAATACTCAT 58.445 47.619 2.37 0.00 34.66 2.90
2122 2328 7.624360 TTGCGAGGTGAATACTCATAAAATT 57.376 32.000 0.00 0.00 34.66 1.82
2171 2377 0.323725 GAAGGGGCTGCTTGATTCCA 60.324 55.000 0.00 0.00 0.00 3.53
2534 2740 2.090658 GCTGTACTTCATGACAACGTCG 59.909 50.000 0.00 0.00 34.95 5.12
2620 2826 2.864114 TGCAGAGAAAGATGCAGCC 58.136 52.632 0.00 0.00 46.97 4.85
2681 2887 5.083533 ACAGGCAGTAGAAGATGAGAAAG 57.916 43.478 0.00 0.00 0.00 2.62
2785 2991 5.584251 GCTAGAAGCTAGCAAAGATGAAGTT 59.416 40.000 18.83 0.00 38.45 2.66
2896 3102 3.196469 TCAAACAGGAAGAGATCGAGCAT 59.804 43.478 2.38 0.00 0.00 3.79
3106 3312 3.487879 GGAAGTCGGAAGAAGAGATCGTC 60.488 52.174 0.00 0.00 45.01 4.20
3107 3313 2.712709 AGTCGGAAGAAGAGATCGTCA 58.287 47.619 0.00 0.00 45.01 4.35
3176 3382 2.770164 AGCTGAAAATACCGAGCTGT 57.230 45.000 0.00 0.00 40.31 4.40
3257 3463 3.236003 AAGGCCGAGACCCGTCAAC 62.236 63.158 0.00 0.00 36.31 3.18
3313 3519 9.606631 GAATTACAGAACATACAAGAGGAGAAT 57.393 33.333 0.00 0.00 0.00 2.40
3427 3633 5.941555 AGGAAGAAGATAACGAGAATGGT 57.058 39.130 0.00 0.00 0.00 3.55
3502 3708 0.035881 AGGTCACCGACTACGACTCA 59.964 55.000 0.00 0.00 42.66 3.41
3566 3772 1.056660 GTCCAACAAGGGAGACTCCA 58.943 55.000 23.06 0.00 38.64 3.86
3584 3790 4.003788 CCCTCGACAGCAACGGGT 62.004 66.667 0.00 0.00 0.00 5.28
3708 3914 5.675575 GCTCAAATTAGCACAAGATCACCAG 60.676 44.000 0.00 0.00 42.30 4.00
3725 3932 5.305585 TCACCAGTCTTATGTTGTTCCTTC 58.694 41.667 0.00 0.00 0.00 3.46
4035 4242 6.409524 TGTTGAAGGAAATTCTTTGAGCAT 57.590 33.333 0.00 0.00 38.83 3.79
4036 4243 6.218019 TGTTGAAGGAAATTCTTTGAGCATG 58.782 36.000 0.00 0.00 38.83 4.06
4038 4245 4.834496 TGAAGGAAATTCTTTGAGCATGGT 59.166 37.500 0.00 0.00 38.83 3.55
4039 4246 4.796038 AGGAAATTCTTTGAGCATGGTG 57.204 40.909 0.00 0.00 0.00 4.17
4040 4247 3.056322 AGGAAATTCTTTGAGCATGGTGC 60.056 43.478 0.00 0.00 45.46 5.01
4041 4248 8.460759 GAAGGAAATTCTTTGAGCATGGTGCT 62.461 42.308 0.00 3.79 45.05 4.40
4049 4256 3.731728 GCATGGTGCTCCCTCCCA 61.732 66.667 1.59 0.00 40.96 4.37
4051 4258 1.152819 CATGGTGCTCCCTCCCATG 60.153 63.158 1.59 3.72 46.86 3.66
4059 4294 0.549950 CTCCCTCCCATGCATGTTCT 59.450 55.000 24.58 0.00 0.00 3.01
4101 4336 1.751349 GATGATGGTGGCAATGGGGC 61.751 60.000 0.00 0.00 43.73 5.80
4159 4399 2.046507 GTGAGCCAGCCAGGAGTG 60.047 66.667 0.00 0.00 41.22 3.51
4224 4464 2.619074 GGTTTGCTCCACTCCAGCTAAT 60.619 50.000 0.00 0.00 37.79 1.73
4393 4638 0.034059 GTCCTATGGTGGAGCGATGG 59.966 60.000 0.00 0.00 36.69 3.51
4630 4881 0.546122 TGTGTGCCAAAGGAGTGACT 59.454 50.000 0.00 0.00 0.00 3.41
4670 4921 2.653890 GTGTTGTACATGCAGCACAAG 58.346 47.619 12.99 0.00 45.65 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.108992 TCCATCGCTACGGTGTGAAC 60.109 55.000 0.00 0.00 36.10 3.18
1 2 0.108992 GTCCATCGCTACGGTGTGAA 60.109 55.000 0.00 0.00 36.10 3.18
2 3 1.245376 TGTCCATCGCTACGGTGTGA 61.245 55.000 0.00 0.00 36.10 3.58
3 4 1.076533 GTGTCCATCGCTACGGTGTG 61.077 60.000 0.00 0.00 36.10 3.82
4 5 1.214589 GTGTCCATCGCTACGGTGT 59.785 57.895 0.00 0.00 36.10 4.16
5 6 1.872234 CGTGTCCATCGCTACGGTG 60.872 63.158 0.00 0.00 37.76 4.94
6 7 2.042259 TCGTGTCCATCGCTACGGT 61.042 57.895 0.00 0.00 37.18 4.83
7 8 1.585521 GTCGTGTCCATCGCTACGG 60.586 63.158 0.00 0.00 37.18 4.02
8 9 1.933041 CGTCGTGTCCATCGCTACG 60.933 63.158 0.00 0.00 38.80 3.51
9 10 0.860618 GACGTCGTGTCCATCGCTAC 60.861 60.000 0.63 0.00 42.04 3.58
10 11 1.426621 GACGTCGTGTCCATCGCTA 59.573 57.895 0.63 0.00 42.04 4.26
11 12 2.178521 GACGTCGTGTCCATCGCT 59.821 61.111 0.63 0.00 42.04 4.93
41 42 0.960861 GCTAAAGCGCCAGGAAACCT 60.961 55.000 2.29 0.00 0.00 3.50
42 43 1.241315 TGCTAAAGCGCCAGGAAACC 61.241 55.000 2.29 0.00 45.83 3.27
43 44 0.811281 ATGCTAAAGCGCCAGGAAAC 59.189 50.000 2.29 0.00 45.83 2.78
44 45 0.810648 CATGCTAAAGCGCCAGGAAA 59.189 50.000 2.29 0.00 45.83 3.13
45 46 1.031571 CCATGCTAAAGCGCCAGGAA 61.032 55.000 2.29 0.00 45.83 3.36
46 47 1.451927 CCATGCTAAAGCGCCAGGA 60.452 57.895 2.29 0.00 45.83 3.86
47 48 2.484062 CCCATGCTAAAGCGCCAGG 61.484 63.158 2.29 0.00 45.83 4.45
48 49 1.451927 TCCCATGCTAAAGCGCCAG 60.452 57.895 2.29 0.00 45.83 4.85
49 50 1.748879 GTCCCATGCTAAAGCGCCA 60.749 57.895 2.29 0.00 45.83 5.69
50 51 2.481471 GGTCCCATGCTAAAGCGCC 61.481 63.158 2.29 0.00 45.83 6.53
51 52 2.481471 GGGTCCCATGCTAAAGCGC 61.481 63.158 1.78 0.00 45.83 5.92
52 53 1.823899 GGGGTCCCATGCTAAAGCG 60.824 63.158 10.98 0.00 38.97 4.68
53 54 1.823899 CGGGGTCCCATGCTAAAGC 60.824 63.158 10.98 0.00 37.50 3.51
54 55 1.823899 GCGGGGTCCCATGCTAAAG 60.824 63.158 10.98 0.00 35.37 1.85
55 56 2.274104 GCGGGGTCCCATGCTAAA 59.726 61.111 10.98 0.00 35.37 1.85
56 57 3.804329 GGCGGGGTCCCATGCTAA 61.804 66.667 20.34 0.00 35.37 3.09
60 61 3.779850 CTGATGGCGGGGTCCCATG 62.780 68.421 10.98 2.22 42.94 3.66
61 62 3.492353 CTGATGGCGGGGTCCCAT 61.492 66.667 10.98 0.00 45.47 4.00
62 63 4.731853 TCTGATGGCGGGGTCCCA 62.732 66.667 10.98 0.00 36.66 4.37
63 64 4.176752 GTCTGATGGCGGGGTCCC 62.177 72.222 0.00 0.00 0.00 4.46
64 65 4.176752 GGTCTGATGGCGGGGTCC 62.177 72.222 0.00 0.00 0.00 4.46
65 66 4.530857 CGGTCTGATGGCGGGGTC 62.531 72.222 0.00 0.00 0.00 4.46
67 68 4.530857 GTCGGTCTGATGGCGGGG 62.531 72.222 0.00 0.00 0.00 5.73
68 69 4.873129 CGTCGGTCTGATGGCGGG 62.873 72.222 0.00 0.00 0.00 6.13
69 70 4.129737 ACGTCGGTCTGATGGCGG 62.130 66.667 10.74 0.00 37.96 6.13
70 71 2.880879 CACGTCGGTCTGATGGCG 60.881 66.667 5.86 5.51 37.96 5.69
71 72 1.805945 GTCACGTCGGTCTGATGGC 60.806 63.158 5.86 0.00 37.96 4.40
72 73 1.514228 CGTCACGTCGGTCTGATGG 60.514 63.158 5.86 0.00 37.96 3.51
73 74 1.514228 CCGTCACGTCGGTCTGATG 60.514 63.158 7.49 0.00 44.77 3.07
74 75 2.875485 CCGTCACGTCGGTCTGAT 59.125 61.111 7.49 0.00 44.77 2.90
93 94 2.043604 TATGGAGGCGTCAGGGCATG 62.044 60.000 8.91 0.00 45.36 4.06
94 95 1.130054 ATATGGAGGCGTCAGGGCAT 61.130 55.000 8.91 5.08 45.36 4.40
95 96 1.344953 AATATGGAGGCGTCAGGGCA 61.345 55.000 8.91 0.00 45.36 5.36
96 97 0.603975 GAATATGGAGGCGTCAGGGC 60.604 60.000 8.91 0.00 42.69 5.19
97 98 0.319900 CGAATATGGAGGCGTCAGGG 60.320 60.000 8.91 0.00 0.00 4.45
98 99 0.946221 GCGAATATGGAGGCGTCAGG 60.946 60.000 8.91 0.00 0.00 3.86
99 100 0.946221 GGCGAATATGGAGGCGTCAG 60.946 60.000 8.91 0.00 0.00 3.51
100 101 1.069090 GGCGAATATGGAGGCGTCA 59.931 57.895 8.91 0.00 0.00 4.35
101 102 1.668151 GGGCGAATATGGAGGCGTC 60.668 63.158 0.00 0.00 0.00 5.19
102 103 2.426023 GGGCGAATATGGAGGCGT 59.574 61.111 0.00 0.00 0.00 5.68
103 104 2.358737 GGGGCGAATATGGAGGCG 60.359 66.667 0.00 0.00 0.00 5.52
104 105 0.618458 TATGGGGCGAATATGGAGGC 59.382 55.000 0.00 0.00 0.00 4.70
105 106 3.652057 AATATGGGGCGAATATGGAGG 57.348 47.619 0.00 0.00 0.00 4.30
106 107 3.696051 CCAAATATGGGGCGAATATGGAG 59.304 47.826 0.00 0.00 43.51 3.86
107 108 3.696045 CCAAATATGGGGCGAATATGGA 58.304 45.455 0.00 0.00 43.51 3.41
119 120 3.368248 CCCATATCCAGCCCAAATATGG 58.632 50.000 11.86 11.86 46.37 2.74
120 121 3.245730 ACCCCATATCCAGCCCAAATATG 60.246 47.826 0.00 0.00 34.55 1.78
121 122 3.003270 ACCCCATATCCAGCCCAAATAT 58.997 45.455 0.00 0.00 0.00 1.28
122 123 2.109834 CACCCCATATCCAGCCCAAATA 59.890 50.000 0.00 0.00 0.00 1.40
123 124 1.133072 CACCCCATATCCAGCCCAAAT 60.133 52.381 0.00 0.00 0.00 2.32
124 125 0.261402 CACCCCATATCCAGCCCAAA 59.739 55.000 0.00 0.00 0.00 3.28
125 126 1.929745 CACCCCATATCCAGCCCAA 59.070 57.895 0.00 0.00 0.00 4.12
126 127 2.766925 GCACCCCATATCCAGCCCA 61.767 63.158 0.00 0.00 0.00 5.36
127 128 2.116125 GCACCCCATATCCAGCCC 59.884 66.667 0.00 0.00 0.00 5.19
128 129 2.116125 GGCACCCCATATCCAGCC 59.884 66.667 0.00 0.00 34.71 4.85
129 130 2.281761 CGGCACCCCATATCCAGC 60.282 66.667 0.00 0.00 0.00 4.85
130 131 2.397413 GACCGGCACCCCATATCCAG 62.397 65.000 0.00 0.00 0.00 3.86
131 132 2.367648 ACCGGCACCCCATATCCA 60.368 61.111 0.00 0.00 0.00 3.41
132 133 2.397413 CTGACCGGCACCCCATATCC 62.397 65.000 0.00 0.00 0.00 2.59
133 134 1.071471 CTGACCGGCACCCCATATC 59.929 63.158 0.00 0.00 0.00 1.63
134 135 1.692749 ACTGACCGGCACCCCATAT 60.693 57.895 0.00 0.00 0.00 1.78
135 136 2.285069 ACTGACCGGCACCCCATA 60.285 61.111 0.00 0.00 0.00 2.74
136 137 3.717294 GACTGACCGGCACCCCAT 61.717 66.667 0.00 0.00 0.00 4.00
146 147 3.047877 CAAACGCCCGGACTGACC 61.048 66.667 0.73 0.00 0.00 4.02
147 148 2.027625 CTCAAACGCCCGGACTGAC 61.028 63.158 0.73 0.00 0.00 3.51
148 149 2.342279 CTCAAACGCCCGGACTGA 59.658 61.111 0.73 0.00 0.00 3.41
149 150 2.742372 CCTCAAACGCCCGGACTG 60.742 66.667 0.73 0.00 0.00 3.51
150 151 4.699522 GCCTCAAACGCCCGGACT 62.700 66.667 0.73 0.00 0.00 3.85
156 157 1.517210 TTAAACGGGCCTCAAACGCC 61.517 55.000 0.84 0.00 46.29 5.68
157 158 0.109919 CTTAAACGGGCCTCAAACGC 60.110 55.000 0.84 0.00 0.00 4.84
158 159 0.519961 CCTTAAACGGGCCTCAAACG 59.480 55.000 0.84 0.00 0.00 3.60
159 160 1.810755 CTCCTTAAACGGGCCTCAAAC 59.189 52.381 0.84 0.00 0.00 2.93
160 161 1.884928 GCTCCTTAAACGGGCCTCAAA 60.885 52.381 0.84 0.00 0.00 2.69
161 162 0.322187 GCTCCTTAAACGGGCCTCAA 60.322 55.000 0.84 0.00 0.00 3.02
162 163 1.298667 GCTCCTTAAACGGGCCTCA 59.701 57.895 0.84 0.00 0.00 3.86
163 164 1.451567 GGCTCCTTAAACGGGCCTC 60.452 63.158 0.84 0.00 37.40 4.70
164 165 2.675371 GGCTCCTTAAACGGGCCT 59.325 61.111 0.84 0.00 37.40 5.19
165 166 2.439701 GGGCTCCTTAAACGGGCC 60.440 66.667 4.76 4.76 38.75 5.80
166 167 2.822701 CGGGCTCCTTAAACGGGC 60.823 66.667 0.00 0.00 0.00 6.13
167 168 1.449070 GACGGGCTCCTTAAACGGG 60.449 63.158 0.00 0.00 0.00 5.28
168 169 0.739813 CAGACGGGCTCCTTAAACGG 60.740 60.000 0.00 0.00 0.00 4.44
169 170 0.739813 CCAGACGGGCTCCTTAAACG 60.740 60.000 0.00 0.00 0.00 3.60
170 171 3.154589 CCAGACGGGCTCCTTAAAC 57.845 57.895 0.00 0.00 0.00 2.01
194 195 1.011333 CACTGTCCGGTCACGTTTTT 58.989 50.000 0.00 0.00 38.78 1.94
195 196 0.176219 TCACTGTCCGGTCACGTTTT 59.824 50.000 0.00 0.00 38.78 2.43
196 197 0.529119 GTCACTGTCCGGTCACGTTT 60.529 55.000 0.00 0.00 38.78 3.60
197 198 1.066918 GTCACTGTCCGGTCACGTT 59.933 57.895 0.00 0.00 38.78 3.99
198 199 2.726274 GTCACTGTCCGGTCACGT 59.274 61.111 0.00 0.00 38.78 4.49
199 200 2.049433 GGTCACTGTCCGGTCACG 60.049 66.667 0.00 0.00 40.55 4.35
200 201 2.049433 CGGTCACTGTCCGGTCAC 60.049 66.667 0.00 0.00 43.68 3.67
201 202 1.829096 TTCGGTCACTGTCCGGTCA 60.829 57.895 13.73 0.00 46.82 4.02
202 203 1.372623 GTTCGGTCACTGTCCGGTC 60.373 63.158 13.73 0.00 46.82 4.79
203 204 2.732658 GTTCGGTCACTGTCCGGT 59.267 61.111 13.73 0.00 46.82 5.28
204 205 2.430244 CGTTCGGTCACTGTCCGG 60.430 66.667 13.73 0.00 46.82 5.14
206 207 2.737376 GCCGTTCGGTCACTGTCC 60.737 66.667 12.81 0.00 0.00 4.02
207 208 2.737376 GGCCGTTCGGTCACTGTC 60.737 66.667 11.06 0.00 0.00 3.51
208 209 4.309950 GGGCCGTTCGGTCACTGT 62.310 66.667 17.39 0.00 0.00 3.55
233 234 4.441217 GGACCTCTTAAACCCGTCTCATAC 60.441 50.000 0.00 0.00 0.00 2.39
234 235 3.703052 GGACCTCTTAAACCCGTCTCATA 59.297 47.826 0.00 0.00 0.00 2.15
235 236 2.500504 GGACCTCTTAAACCCGTCTCAT 59.499 50.000 0.00 0.00 0.00 2.90
236 237 1.897802 GGACCTCTTAAACCCGTCTCA 59.102 52.381 0.00 0.00 0.00 3.27
237 238 1.135170 CGGACCTCTTAAACCCGTCTC 60.135 57.143 0.00 0.00 35.83 3.36
238 239 0.893447 CGGACCTCTTAAACCCGTCT 59.107 55.000 0.00 0.00 35.83 4.18
239 240 0.108472 CCGGACCTCTTAAACCCGTC 60.108 60.000 0.00 0.00 38.61 4.79
240 241 1.977685 CCGGACCTCTTAAACCCGT 59.022 57.895 0.00 0.00 38.61 5.28
241 242 1.449070 GCCGGACCTCTTAAACCCG 60.449 63.158 5.05 0.00 39.85 5.28
242 243 0.392595 CAGCCGGACCTCTTAAACCC 60.393 60.000 5.05 0.00 0.00 4.11
243 244 0.323957 ACAGCCGGACCTCTTAAACC 59.676 55.000 5.05 0.00 0.00 3.27
244 245 2.494870 TCTACAGCCGGACCTCTTAAAC 59.505 50.000 5.05 0.00 0.00 2.01
245 246 2.811410 TCTACAGCCGGACCTCTTAAA 58.189 47.619 5.05 0.00 0.00 1.52
246 247 2.519771 TCTACAGCCGGACCTCTTAA 57.480 50.000 5.05 0.00 0.00 1.85
247 248 2.307768 CATCTACAGCCGGACCTCTTA 58.692 52.381 5.05 0.00 0.00 2.10
248 249 1.115467 CATCTACAGCCGGACCTCTT 58.885 55.000 5.05 0.00 0.00 2.85
249 250 1.395826 GCATCTACAGCCGGACCTCT 61.396 60.000 5.05 0.00 0.00 3.69
250 251 1.068250 GCATCTACAGCCGGACCTC 59.932 63.158 5.05 0.00 0.00 3.85
251 252 1.381872 AGCATCTACAGCCGGACCT 60.382 57.895 5.05 0.00 0.00 3.85
252 253 1.068250 GAGCATCTACAGCCGGACC 59.932 63.158 5.05 0.00 0.00 4.46
253 254 4.740235 GAGCATCTACAGCCGGAC 57.260 61.111 5.05 0.00 0.00 4.79
264 265 7.861630 TGTTTTTATTCGCCTATTAGAGCATC 58.138 34.615 0.00 0.00 0.00 3.91
265 266 7.801716 TGTTTTTATTCGCCTATTAGAGCAT 57.198 32.000 0.00 0.00 0.00 3.79
266 267 7.201696 CCTTGTTTTTATTCGCCTATTAGAGCA 60.202 37.037 0.00 0.00 0.00 4.26
267 268 7.132863 CCTTGTTTTTATTCGCCTATTAGAGC 58.867 38.462 0.00 0.00 0.00 4.09
268 269 7.497909 TCCCTTGTTTTTATTCGCCTATTAGAG 59.502 37.037 0.00 0.00 0.00 2.43
269 270 7.340256 TCCCTTGTTTTTATTCGCCTATTAGA 58.660 34.615 0.00 0.00 0.00 2.10
270 271 7.562454 TCCCTTGTTTTTATTCGCCTATTAG 57.438 36.000 0.00 0.00 0.00 1.73
271 272 7.776030 TCATCCCTTGTTTTTATTCGCCTATTA 59.224 33.333 0.00 0.00 0.00 0.98
297 298 6.127479 TGAGGAAAATAAAGCCGCATAAATGT 60.127 34.615 0.00 0.00 0.00 2.71
357 358 2.038952 GGCAGCCAATTCTTTCCCTTTT 59.961 45.455 6.55 0.00 0.00 2.27
358 359 1.625315 GGCAGCCAATTCTTTCCCTTT 59.375 47.619 6.55 0.00 0.00 3.11
382 395 2.009774 CTGTGGAACCTCATAAAGCGG 58.990 52.381 0.00 0.00 34.36 5.52
456 475 2.449967 TACCCCGAGGCTGAGGTTGA 62.450 60.000 5.14 0.00 36.11 3.18
465 484 3.684369 TACCACCCTACCCCGAGGC 62.684 68.421 0.00 0.00 35.00 4.70
472 654 1.460504 GCTTGCTTTACCACCCTACC 58.539 55.000 0.00 0.00 0.00 3.18
476 658 1.923227 GCTCGCTTGCTTTACCACCC 61.923 60.000 0.00 0.00 0.00 4.61
477 659 0.955919 AGCTCGCTTGCTTTACCACC 60.956 55.000 0.00 0.00 40.93 4.61
478 660 0.166814 CAGCTCGCTTGCTTTACCAC 59.833 55.000 0.00 0.00 41.98 4.16
479 661 0.955428 CCAGCTCGCTTGCTTTACCA 60.955 55.000 0.00 0.00 41.98 3.25
480 662 1.796796 CCAGCTCGCTTGCTTTACC 59.203 57.895 0.00 0.00 41.98 2.85
481 663 1.135523 GCCAGCTCGCTTGCTTTAC 59.864 57.895 7.63 0.00 41.98 2.01
482 664 1.003355 AGCCAGCTCGCTTGCTTTA 60.003 52.632 11.25 0.00 41.44 1.85
483 665 2.282040 AGCCAGCTCGCTTGCTTT 60.282 55.556 11.25 0.00 41.44 3.51
484 666 3.054503 CAGCCAGCTCGCTTGCTT 61.055 61.111 14.01 0.00 41.44 3.91
498 680 3.945434 CATGATCACCGCGCCAGC 61.945 66.667 0.00 0.00 40.74 4.85
499 681 2.202919 TCATGATCACCGCGCCAG 60.203 61.111 0.00 0.00 0.00 4.85
500 682 2.511373 GTCATGATCACCGCGCCA 60.511 61.111 0.00 0.00 0.00 5.69
501 683 3.630148 CGTCATGATCACCGCGCC 61.630 66.667 0.00 0.00 0.00 6.53
502 684 3.630148 CCGTCATGATCACCGCGC 61.630 66.667 0.00 0.00 0.00 6.86
503 685 2.899345 TTCCCGTCATGATCACCGCG 62.899 60.000 0.00 0.00 0.00 6.46
504 686 0.532862 ATTCCCGTCATGATCACCGC 60.533 55.000 0.00 0.00 0.00 5.68
505 687 1.202521 TCATTCCCGTCATGATCACCG 60.203 52.381 0.00 0.46 0.00 4.94
506 688 2.213499 GTCATTCCCGTCATGATCACC 58.787 52.381 0.00 0.00 33.22 4.02
507 689 2.609459 GTGTCATTCCCGTCATGATCAC 59.391 50.000 0.00 0.00 33.22 3.06
508 690 2.501316 AGTGTCATTCCCGTCATGATCA 59.499 45.455 0.00 0.00 33.22 2.92
509 691 3.185246 AGTGTCATTCCCGTCATGATC 57.815 47.619 0.00 0.00 33.22 2.92
510 692 3.706594 AGTAGTGTCATTCCCGTCATGAT 59.293 43.478 0.00 0.00 33.22 2.45
511 693 3.096852 AGTAGTGTCATTCCCGTCATGA 58.903 45.455 0.00 0.00 0.00 3.07
512 694 3.190079 CAGTAGTGTCATTCCCGTCATG 58.810 50.000 0.00 0.00 0.00 3.07
513 695 2.418746 GCAGTAGTGTCATTCCCGTCAT 60.419 50.000 0.00 0.00 0.00 3.06
514 696 1.067142 GCAGTAGTGTCATTCCCGTCA 60.067 52.381 0.00 0.00 0.00 4.35
515 697 1.641577 GCAGTAGTGTCATTCCCGTC 58.358 55.000 0.00 0.00 0.00 4.79
516 698 0.249398 GGCAGTAGTGTCATTCCCGT 59.751 55.000 0.00 0.00 0.00 5.28
517 699 0.249120 TGGCAGTAGTGTCATTCCCG 59.751 55.000 0.00 0.00 31.64 5.14
518 700 1.279271 ACTGGCAGTAGTGTCATTCCC 59.721 52.381 20.61 0.00 37.75 3.97
519 701 2.622436 GACTGGCAGTAGTGTCATTCC 58.378 52.381 22.11 0.00 37.75 3.01
520 702 2.263077 CGACTGGCAGTAGTGTCATTC 58.737 52.381 22.11 8.81 37.75 2.67
521 703 1.618837 ACGACTGGCAGTAGTGTCATT 59.381 47.619 28.82 6.54 37.75 2.57
522 704 1.257743 ACGACTGGCAGTAGTGTCAT 58.742 50.000 28.82 7.25 37.75 3.06
523 705 1.538512 GTACGACTGGCAGTAGTGTCA 59.461 52.381 34.27 18.10 34.91 3.58
524 706 1.811359 AGTACGACTGGCAGTAGTGTC 59.189 52.381 34.27 26.74 34.91 3.67
525 707 1.906990 AGTACGACTGGCAGTAGTGT 58.093 50.000 34.27 26.56 34.91 3.55
526 708 3.181499 CCTAAGTACGACTGGCAGTAGTG 60.181 52.174 34.27 23.04 34.91 2.74
527 709 3.015327 CCTAAGTACGACTGGCAGTAGT 58.985 50.000 31.07 31.07 37.76 2.73
528 710 3.276857 TCCTAAGTACGACTGGCAGTAG 58.723 50.000 22.11 23.01 0.00 2.57
529 711 3.276857 CTCCTAAGTACGACTGGCAGTA 58.723 50.000 22.11 1.49 0.00 2.74
530 712 2.093106 CTCCTAAGTACGACTGGCAGT 58.907 52.381 22.26 22.26 0.00 4.40
531 713 2.093106 ACTCCTAAGTACGACTGGCAG 58.907 52.381 14.16 14.16 32.59 4.85
532 714 2.211250 ACTCCTAAGTACGACTGGCA 57.789 50.000 0.00 0.00 32.59 4.92
533 715 4.915158 ATTACTCCTAAGTACGACTGGC 57.085 45.455 0.00 0.00 37.72 4.85
534 716 8.246180 TGTTTAATTACTCCTAAGTACGACTGG 58.754 37.037 0.00 0.00 37.72 4.00
535 717 9.798994 ATGTTTAATTACTCCTAAGTACGACTG 57.201 33.333 0.00 0.00 37.72 3.51
536 718 9.798994 CATGTTTAATTACTCCTAAGTACGACT 57.201 33.333 0.00 0.00 37.72 4.18
537 719 8.538039 GCATGTTTAATTACTCCTAAGTACGAC 58.462 37.037 0.00 0.00 37.72 4.34
538 720 7.433131 CGCATGTTTAATTACTCCTAAGTACGA 59.567 37.037 0.00 0.00 37.72 3.43
539 721 7.306399 CCGCATGTTTAATTACTCCTAAGTACG 60.306 40.741 0.00 0.00 37.72 3.67
540 722 7.707893 TCCGCATGTTTAATTACTCCTAAGTAC 59.292 37.037 0.00 0.00 37.72 2.73
541 723 7.784037 TCCGCATGTTTAATTACTCCTAAGTA 58.216 34.615 0.00 0.00 36.92 2.24
542 724 6.646267 TCCGCATGTTTAATTACTCCTAAGT 58.354 36.000 0.00 0.00 39.66 2.24
543 725 7.730364 ATCCGCATGTTTAATTACTCCTAAG 57.270 36.000 0.00 0.00 0.00 2.18
544 726 9.616156 TTAATCCGCATGTTTAATTACTCCTAA 57.384 29.630 0.00 0.00 0.00 2.69
545 727 9.048446 GTTAATCCGCATGTTTAATTACTCCTA 57.952 33.333 0.00 0.00 0.00 2.94
546 728 7.012989 GGTTAATCCGCATGTTTAATTACTCCT 59.987 37.037 0.00 0.00 0.00 3.69
547 729 7.136772 GGTTAATCCGCATGTTTAATTACTCC 58.863 38.462 0.00 0.00 0.00 3.85
548 730 7.136772 GGGTTAATCCGCATGTTTAATTACTC 58.863 38.462 0.00 0.00 37.00 2.59
549 731 6.238538 CGGGTTAATCCGCATGTTTAATTACT 60.239 38.462 15.43 0.00 43.71 2.24
550 732 5.910723 CGGGTTAATCCGCATGTTTAATTAC 59.089 40.000 15.43 0.00 43.71 1.89
696 885 1.632920 AGAGGAAAAAGCAGGGAGGAG 59.367 52.381 0.00 0.00 0.00 3.69
697 886 1.630878 GAGAGGAAAAAGCAGGGAGGA 59.369 52.381 0.00 0.00 0.00 3.71
698 887 1.340502 GGAGAGGAAAAAGCAGGGAGG 60.341 57.143 0.00 0.00 0.00 4.30
699 888 1.340502 GGGAGAGGAAAAAGCAGGGAG 60.341 57.143 0.00 0.00 0.00 4.30
807 996 2.143122 CTGCGGCTTGTAGAAGAACAA 58.857 47.619 3.33 0.00 37.75 2.83
877 1071 2.040606 TGAGTGGTAGGGGGAGGC 59.959 66.667 0.00 0.00 0.00 4.70
887 1081 2.147387 GGAGTGGTGGGTGAGTGGT 61.147 63.158 0.00 0.00 0.00 4.16
890 1084 0.544595 GGTAGGAGTGGTGGGTGAGT 60.545 60.000 0.00 0.00 0.00 3.41
1069 1266 5.394553 CCCATCACTCCAAAATAAAGAAGGC 60.395 44.000 0.00 0.00 0.00 4.35
1070 1267 5.716703 ACCCATCACTCCAAAATAAAGAAGG 59.283 40.000 0.00 0.00 0.00 3.46
1071 1268 6.350445 CCACCCATCACTCCAAAATAAAGAAG 60.350 42.308 0.00 0.00 0.00 2.85
1075 1272 4.093011 CCCACCCATCACTCCAAAATAAA 58.907 43.478 0.00 0.00 0.00 1.40
1098 1295 2.821366 CACCTCTGCGTGCCCATC 60.821 66.667 0.00 0.00 0.00 3.51
1108 1305 0.890996 GCCACCAAGAACCACCTCTG 60.891 60.000 0.00 0.00 0.00 3.35
1109 1306 1.456287 GCCACCAAGAACCACCTCT 59.544 57.895 0.00 0.00 0.00 3.69
1110 1307 1.966451 CGCCACCAAGAACCACCTC 60.966 63.158 0.00 0.00 0.00 3.85
1111 1308 2.113139 CGCCACCAAGAACCACCT 59.887 61.111 0.00 0.00 0.00 4.00
1112 1309 2.203294 ACGCCACCAAGAACCACC 60.203 61.111 0.00 0.00 0.00 4.61
1125 1322 1.661509 GAAACCAAGCAAGCACGCC 60.662 57.895 0.00 0.00 0.00 5.68
1128 1325 0.032540 CCAGGAAACCAAGCAAGCAC 59.967 55.000 0.00 0.00 0.00 4.40
1188 1385 1.167851 TCAAGAATTTGGCAGCTCCG 58.832 50.000 0.00 0.00 37.80 4.63
1232 1429 1.077930 GGCCAGATCTGCTCAGCAA 60.078 57.895 17.76 0.00 38.41 3.91
1235 1432 1.146485 CCAGGCCAGATCTGCTCAG 59.854 63.158 17.76 4.77 0.00 3.35
1453 1650 2.345760 GGGAGACTTGTCGGCCGTA 61.346 63.158 27.15 13.22 0.00 4.02
1553 1750 1.205655 CACAAGCAGAGGAGGAATCGA 59.794 52.381 0.00 0.00 0.00 3.59
1774 1980 0.039035 ACTCGAGCTCCTCCAGAACT 59.961 55.000 13.61 0.00 0.00 3.01
1789 1995 2.357517 ACCTTCTTGGCGCACTCG 60.358 61.111 10.83 0.00 40.22 4.18
1902 2108 1.659491 GCGCAGAATCATCATTGCTCG 60.659 52.381 0.30 0.00 34.50 5.03
2122 2328 1.519246 CTCGGCATTGAGGAGCTCA 59.481 57.895 17.19 0.00 38.87 4.26
2137 2343 3.997064 CTTCAGGCGCTCCACCTCG 62.997 68.421 7.64 0.00 34.42 4.63
2171 2377 0.605589 CTCGACTTGCTCTCCACCTT 59.394 55.000 0.00 0.00 0.00 3.50
2620 2826 3.355626 TCGATCTCTGCAATTAGGTCG 57.644 47.619 16.08 16.08 0.00 4.79
2681 2887 1.136147 CATTGTTCAGCGCCTCTGC 59.864 57.895 2.29 0.00 42.56 4.26
2785 2991 4.042809 TCCATTGCCTTCTTAACCTTCTCA 59.957 41.667 0.00 0.00 0.00 3.27
3106 3312 5.885230 TGTCCATTTGAGCTTTGATAGTG 57.115 39.130 0.00 0.00 0.00 2.74
3107 3313 6.006449 ACTTGTCCATTTGAGCTTTGATAGT 58.994 36.000 0.00 0.00 0.00 2.12
3196 3402 1.919918 CTTCAACTAGCTGAGCCTCG 58.080 55.000 0.00 0.00 0.00 4.63
3226 3432 1.676967 GGCCTTGGCTTCCTCACTG 60.677 63.158 11.71 0.00 0.00 3.66
3229 3435 2.927856 TCGGCCTTGGCTTCCTCA 60.928 61.111 11.71 0.00 0.00 3.86
3253 3459 7.732025 TGTCTAATAGTTTGTCCTTCAGTTGA 58.268 34.615 0.00 0.00 0.00 3.18
3257 3463 8.833231 TCTTTGTCTAATAGTTTGTCCTTCAG 57.167 34.615 0.00 0.00 0.00 3.02
3313 3519 0.538057 CCTTTGCCTGCAAGTCCTCA 60.538 55.000 4.58 0.00 37.24 3.86
3388 3594 1.686052 TCCTTGTTGCCACCATTTGTC 59.314 47.619 0.00 0.00 0.00 3.18
3427 3633 2.873525 TTCGTCATCCACACCGCCA 61.874 57.895 0.00 0.00 0.00 5.69
3502 3708 2.498078 GTCGTTCTCCTTCTCCTTGGAT 59.502 50.000 0.00 0.00 0.00 3.41
3532 3738 2.215942 TGGACTCCAGATCGACTTCA 57.784 50.000 0.00 0.00 0.00 3.02
3566 3772 4.003788 CCCGTTGCTGTCGAGGGT 62.004 66.667 0.00 0.00 37.36 4.34
3599 3805 1.398041 CGATGTGATGCCGTTGTTCAT 59.602 47.619 0.00 0.00 0.00 2.57
3708 3914 5.668558 ACAACGAAGGAACAACATAAGAC 57.331 39.130 0.00 0.00 0.00 3.01
3725 3932 4.445718 GGAGATGTCACATAGCATACAACG 59.554 45.833 0.00 0.00 0.00 4.10
3777 3984 6.030548 TGATGACAGACTCAGAAAACTAGG 57.969 41.667 0.00 0.00 30.20 3.02
4005 4212 8.934825 TCAAAGAATTTCCTTCAACAAAAACAG 58.065 29.630 0.00 0.00 35.03 3.16
4035 4242 3.731728 GCATGGGAGGGAGCACCA 61.732 66.667 1.58 0.00 43.89 4.17
4036 4243 3.065787 ATGCATGGGAGGGAGCACC 62.066 63.158 0.00 0.00 40.14 5.01
4038 4245 1.866483 AACATGCATGGGAGGGAGCA 61.866 55.000 29.41 0.00 41.73 4.26
4039 4246 1.076485 AACATGCATGGGAGGGAGC 60.076 57.895 29.41 0.00 0.00 4.70
4040 4247 0.549950 AGAACATGCATGGGAGGGAG 59.450 55.000 29.41 3.17 0.00 4.30
4041 4248 1.002069 AAGAACATGCATGGGAGGGA 58.998 50.000 29.41 0.00 0.00 4.20
4042 4249 1.108776 CAAGAACATGCATGGGAGGG 58.891 55.000 29.41 12.75 0.00 4.30
4043 4250 1.843368 ACAAGAACATGCATGGGAGG 58.157 50.000 29.41 16.71 0.00 4.30
4044 4251 2.821378 TCAACAAGAACATGCATGGGAG 59.179 45.455 29.41 16.34 0.00 4.30
4045 4252 2.557924 GTCAACAAGAACATGCATGGGA 59.442 45.455 29.41 11.03 0.00 4.37
4046 4253 2.353011 GGTCAACAAGAACATGCATGGG 60.353 50.000 29.41 15.41 32.78 4.00
4047 4254 2.559668 AGGTCAACAAGAACATGCATGG 59.440 45.455 29.41 14.24 35.97 3.66
4048 4255 3.253921 TCAGGTCAACAAGAACATGCATG 59.746 43.478 25.09 25.09 35.97 4.06
4049 4256 3.489355 TCAGGTCAACAAGAACATGCAT 58.511 40.909 0.00 0.00 35.97 3.96
4051 4258 3.254166 ACATCAGGTCAACAAGAACATGC 59.746 43.478 0.00 0.00 35.97 4.06
4127 4367 1.612726 GCTCACATGCTTTGGTCCTCT 60.613 52.381 0.00 0.00 0.00 3.69
4159 4399 1.419387 AGCCTCATCAGAAGCCATACC 59.581 52.381 0.00 0.00 31.35 2.73
4168 4408 0.978907 TGAGCAACAGCCTCATCAGA 59.021 50.000 0.00 0.00 0.00 3.27
4224 4464 1.214175 TGTGGAGGAACAGCAAAAGGA 59.786 47.619 0.00 0.00 0.00 3.36
4275 4515 3.710722 AGCCTCCCCTCTTGTGCG 61.711 66.667 0.00 0.00 0.00 5.34
4393 4638 4.874970 AGTGCATTTTGTCATGGAAAGTC 58.125 39.130 0.00 0.00 0.00 3.01
4630 4881 0.320050 TCTGTCGCTGCCACATTACA 59.680 50.000 0.00 0.00 0.00 2.41
4670 4921 2.113860 TTGCAGTAGGCCTCATGTTC 57.886 50.000 9.68 0.00 43.89 3.18


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

AutoCloner maintained by Alex Coulton.