Multiple sequence alignment - TraesCS5D01G508100

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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 TraesCS5D01G508100 chr5D 100.000 2549 0 0 1 2549 533166212 533163664 0.000000e+00 4708.0
1 TraesCS5D01G508100 chr5D 86.695 233 19 11 1 225 52572848 52572620 5.450000e-62 248.0
2 TraesCS5D01G508100 chr5D 90.435 115 6 5 1697 1809 555661765 555661654 2.040000e-31 147.0
3 TraesCS5D01G508100 chr5B 90.904 1627 74 35 677 2241 673106757 673105143 0.000000e+00 2117.0
4 TraesCS5D01G508100 chr5B 82.213 506 64 16 1143 1632 673102919 673102424 1.820000e-111 412.0
5 TraesCS5D01G508100 chr5B 89.894 188 19 0 2227 2414 673104940 673104753 2.530000e-60 243.0
6 TraesCS5D01G508100 chr5B 91.667 96 6 2 549 643 673108155 673108061 5.720000e-27 132.0
7 TraesCS5D01G508100 chr4A 93.023 1161 55 9 553 1696 638802095 638803246 0.000000e+00 1672.0
8 TraesCS5D01G508100 chr4A 90.794 630 50 2 1912 2533 638803327 638803956 0.000000e+00 835.0
9 TraesCS5D01G508100 chr4A 90.265 113 11 0 1697 1809 412274691 412274579 5.680000e-32 148.0
10 TraesCS5D01G508100 chr4A 90.265 113 11 0 1697 1809 412299035 412298923 5.680000e-32 148.0
11 TraesCS5D01G508100 chr7D 83.447 441 34 19 52 463 26866971 26866541 8.610000e-100 374.0
12 TraesCS5D01G508100 chr7D 78.175 252 37 13 9 247 554488916 554489162 7.350000e-31 145.0
13 TraesCS5D01G508100 chr7D 81.068 206 16 8 281 463 29563089 29563294 2.640000e-30 143.0
14 TraesCS5D01G508100 chr7D 85.714 98 5 4 205 296 38194032 38193938 7.510000e-16 95.3
15 TraesCS5D01G508100 chr7A 89.256 242 21 4 9 246 112781809 112781569 5.330000e-77 298.0
16 TraesCS5D01G508100 chr7A 88.525 244 21 6 9 246 112804540 112804298 3.210000e-74 289.0
17 TraesCS5D01G508100 chrUn 84.305 223 31 4 46 266 19266279 19266499 5.520000e-52 215.0
18 TraesCS5D01G508100 chr3B 82.258 248 26 13 9 240 738104112 738104357 5.560000e-47 198.0
19 TraesCS5D01G508100 chr3B 88.889 117 10 3 1697 1812 65154649 65154763 9.510000e-30 141.0
20 TraesCS5D01G508100 chr3B 88.136 118 11 3 1696 1812 186749125 186749010 1.230000e-28 137.0
21 TraesCS5D01G508100 chr6A 79.934 304 29 20 1 289 562274898 562274612 7.200000e-46 195.0
22 TraesCS5D01G508100 chr5A 81.102 254 36 7 46 289 599292345 599292596 2.590000e-45 193.0
23 TraesCS5D01G508100 chr7B 79.221 308 36 17 1 296 70091615 70091324 3.350000e-44 189.0
24 TraesCS5D01G508100 chr7B 79.221 308 36 17 1 296 70270865 70270574 3.350000e-44 189.0
25 TraesCS5D01G508100 chr2D 77.341 331 31 19 153 463 586581758 586581452 3.400000e-34 156.0
26 TraesCS5D01G508100 chr4D 78.740 254 34 14 9 247 398879230 398878982 4.390000e-33 152.0
27 TraesCS5D01G508100 chr4D 89.474 114 10 2 1697 1809 151932946 151933058 2.640000e-30 143.0
28 TraesCS5D01G508100 chr4D 86.735 98 4 3 205 296 356265294 356265200 1.610000e-17 100.0
29 TraesCS5D01G508100 chr3D 90.265 113 11 0 1697 1809 105443859 105443747 5.680000e-32 148.0
30 TraesCS5D01G508100 chr6B 88.596 114 11 2 1697 1809 17110518 17110630 1.230000e-28 137.0
31 TraesCS5D01G508100 chr2B 76.190 252 43 12 9 247 47461473 47461226 1.600000e-22 117.0
32 TraesCS5D01G508100 chr2B 97.101 69 2 0 9 77 719432346 719432414 1.600000e-22 117.0
33 TraesCS5D01G508100 chr2B 87.500 72 7 2 568 638 740390548 740390618 5.840000e-12 82.4
34 TraesCS5D01G508100 chr1D 91.765 85 4 1 382 463 376275656 376275572 5.760000e-22 115.0
35 TraesCS5D01G508100 chr2A 85.714 70 7 3 572 639 229917467 229917399 1.270000e-08 71.3


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 TraesCS5D01G508100 chr5D 533163664 533166212 2548 True 4708.0 4708 100.0000 1 2549 1 chr5D.!!$R2 2548
1 TraesCS5D01G508100 chr5B 673102424 673108155 5731 True 726.0 2117 88.6695 549 2414 4 chr5B.!!$R1 1865
2 TraesCS5D01G508100 chr4A 638802095 638803956 1861 False 1253.5 1672 91.9085 553 2533 2 chr4A.!!$F1 1980

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
348 349 0.109919 GATTTGTCGGCCCGTTTGAC 60.11 55.0 1.63 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 3528 0.039618 ATGAAACCGGCTGTGGGATT 59.96 50.0 0.0 0.0 0.0 3.01 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
46 47 9.942850 TTGAGTATGTTTAGATGATGAACTTGA 57.057 29.630 0.00 0.00 0.00 3.02
52 53 9.623000 ATGTTTAGATGATGAACTTGATCATGA 57.377 29.630 15.03 0.00 40.03 3.07
53 54 9.623000 TGTTTAGATGATGAACTTGATCATGAT 57.377 29.630 8.25 8.25 40.03 2.45
57 58 7.731882 GATGATGAACTTGATCATGATCTGT 57.268 36.000 30.65 25.39 43.13 3.41
58 59 7.731882 ATGATGAACTTGATCATGATCTGTC 57.268 36.000 30.65 22.12 40.08 3.51
59 60 6.646267 TGATGAACTTGATCATGATCTGTCA 58.354 36.000 30.65 25.68 40.08 3.58
60 61 7.280356 TGATGAACTTGATCATGATCTGTCAT 58.720 34.615 30.65 28.09 45.87 3.06
61 62 8.426489 TGATGAACTTGATCATGATCTGTCATA 58.574 33.333 30.65 19.15 43.14 2.15
62 63 9.438228 GATGAACTTGATCATGATCTGTCATAT 57.562 33.333 30.65 21.72 43.14 1.78
63 64 9.794719 ATGAACTTGATCATGATCTGTCATATT 57.205 29.630 30.65 17.19 43.14 1.28
64 65 9.623000 TGAACTTGATCATGATCTGTCATATTT 57.377 29.630 30.65 15.73 43.14 1.40
66 67 9.848710 AACTTGATCATGATCTGTCATATTTCT 57.151 29.630 30.65 12.70 43.14 2.52
67 68 9.274206 ACTTGATCATGATCTGTCATATTTCTG 57.726 33.333 30.65 11.42 43.14 3.02
68 69 9.274206 CTTGATCATGATCTGTCATATTTCTGT 57.726 33.333 30.65 0.00 43.14 3.41
69 70 8.603242 TGATCATGATCTGTCATATTTCTGTG 57.397 34.615 30.65 0.00 43.14 3.66
70 71 8.208903 TGATCATGATCTGTCATATTTCTGTGT 58.791 33.333 30.65 0.00 43.14 3.72
71 72 9.702494 GATCATGATCTGTCATATTTCTGTGTA 57.298 33.333 25.47 0.00 43.14 2.90
99 100 9.807649 ATATATTTTCTGGTTTGAAATGCTGTC 57.192 29.630 0.00 0.00 36.07 3.51
100 101 3.624326 TTCTGGTTTGAAATGCTGTCG 57.376 42.857 0.00 0.00 0.00 4.35
101 102 2.844946 TCTGGTTTGAAATGCTGTCGA 58.155 42.857 0.00 0.00 0.00 4.20
102 103 3.210227 TCTGGTTTGAAATGCTGTCGAA 58.790 40.909 0.00 0.00 0.00 3.71
103 104 3.629855 TCTGGTTTGAAATGCTGTCGAAA 59.370 39.130 0.00 0.00 0.00 3.46
104 105 4.278170 TCTGGTTTGAAATGCTGTCGAAAT 59.722 37.500 0.00 0.00 0.00 2.17
105 106 4.297510 TGGTTTGAAATGCTGTCGAAATG 58.702 39.130 0.00 0.00 0.00 2.32
106 107 4.037327 TGGTTTGAAATGCTGTCGAAATGA 59.963 37.500 0.00 0.00 0.00 2.57
107 108 4.618489 GGTTTGAAATGCTGTCGAAATGAG 59.382 41.667 0.00 0.00 0.00 2.90
108 109 5.215160 GTTTGAAATGCTGTCGAAATGAGT 58.785 37.500 0.00 0.00 0.00 3.41
109 110 5.437289 TTGAAATGCTGTCGAAATGAGTT 57.563 34.783 0.00 0.00 0.00 3.01
110 111 4.786507 TGAAATGCTGTCGAAATGAGTTG 58.213 39.130 0.00 0.00 0.00 3.16
111 112 4.514816 TGAAATGCTGTCGAAATGAGTTGA 59.485 37.500 0.00 0.00 0.00 3.18
112 113 5.008514 TGAAATGCTGTCGAAATGAGTTGAA 59.991 36.000 0.00 0.00 0.00 2.69
113 114 5.437289 AATGCTGTCGAAATGAGTTGAAA 57.563 34.783 0.00 0.00 0.00 2.69
114 115 4.209452 TGCTGTCGAAATGAGTTGAAAC 57.791 40.909 0.00 0.00 0.00 2.78
115 116 3.625313 TGCTGTCGAAATGAGTTGAAACA 59.375 39.130 0.00 0.00 0.00 2.83
116 117 4.214437 GCTGTCGAAATGAGTTGAAACAG 58.786 43.478 0.00 0.00 36.75 3.16
117 118 4.024893 GCTGTCGAAATGAGTTGAAACAGA 60.025 41.667 0.00 0.00 35.95 3.41
118 119 5.657470 TGTCGAAATGAGTTGAAACAGAG 57.343 39.130 0.00 0.00 0.00 3.35
119 120 5.356426 TGTCGAAATGAGTTGAAACAGAGA 58.644 37.500 0.00 0.00 0.00 3.10
120 121 5.815222 TGTCGAAATGAGTTGAAACAGAGAA 59.185 36.000 0.00 0.00 0.00 2.87
121 122 6.315144 TGTCGAAATGAGTTGAAACAGAGAAA 59.685 34.615 0.00 0.00 0.00 2.52
122 123 7.148323 TGTCGAAATGAGTTGAAACAGAGAAAA 60.148 33.333 0.00 0.00 0.00 2.29
123 124 7.164335 GTCGAAATGAGTTGAAACAGAGAAAAC 59.836 37.037 0.00 0.00 0.00 2.43
124 125 6.966632 CGAAATGAGTTGAAACAGAGAAAACA 59.033 34.615 0.00 0.00 0.00 2.83
125 126 7.484641 CGAAATGAGTTGAAACAGAGAAAACAA 59.515 33.333 0.00 0.00 0.00 2.83
126 127 9.139174 GAAATGAGTTGAAACAGAGAAAACAAA 57.861 29.630 0.00 0.00 0.00 2.83
127 128 9.487790 AAATGAGTTGAAACAGAGAAAACAAAA 57.512 25.926 0.00 0.00 0.00 2.44
128 129 9.657419 AATGAGTTGAAACAGAGAAAACAAAAT 57.343 25.926 0.00 0.00 0.00 1.82
158 159 4.685169 AAAACAACACAGATCTATGCCG 57.315 40.909 0.00 0.00 0.00 5.69
159 160 3.610040 AACAACACAGATCTATGCCGA 57.390 42.857 0.00 0.00 0.00 5.54
160 161 2.893637 ACAACACAGATCTATGCCGAC 58.106 47.619 0.00 0.00 0.00 4.79
161 162 1.854743 CAACACAGATCTATGCCGACG 59.145 52.381 0.00 0.00 0.00 5.12
162 163 0.385751 ACACAGATCTATGCCGACGG 59.614 55.000 10.29 10.29 0.00 4.79
194 195 2.469274 CATAGCTATGCCCAGGAGTG 57.531 55.000 20.37 0.00 0.00 3.51
195 196 0.689623 ATAGCTATGCCCAGGAGTGC 59.310 55.000 5.15 0.00 0.00 4.40
196 197 1.748329 TAGCTATGCCCAGGAGTGCG 61.748 60.000 0.00 0.00 0.00 5.34
197 198 3.094062 GCTATGCCCAGGAGTGCGA 62.094 63.158 0.00 0.00 0.00 5.10
198 199 1.068753 CTATGCCCAGGAGTGCGAG 59.931 63.158 0.00 0.00 0.00 5.03
199 200 2.985512 CTATGCCCAGGAGTGCGAGC 62.986 65.000 0.00 0.00 0.00 5.03
202 203 3.842923 CCCAGGAGTGCGAGCGAT 61.843 66.667 0.00 0.00 0.00 4.58
203 204 2.185350 CCAGGAGTGCGAGCGATT 59.815 61.111 0.00 0.00 0.00 3.34
204 205 2.169789 CCAGGAGTGCGAGCGATTG 61.170 63.158 0.00 0.00 0.00 2.67
205 206 2.510238 AGGAGTGCGAGCGATTGC 60.510 61.111 5.79 5.79 43.24 3.56
206 207 3.567797 GGAGTGCGAGCGATTGCC 61.568 66.667 11.00 1.68 44.31 4.52
207 208 2.815211 GAGTGCGAGCGATTGCCA 60.815 61.111 11.00 0.00 44.31 4.92
208 209 3.088500 GAGTGCGAGCGATTGCCAC 62.089 63.158 11.00 8.74 44.31 5.01
209 210 4.505217 GTGCGAGCGATTGCCACG 62.505 66.667 11.00 15.02 44.31 4.94
211 212 4.505217 GCGAGCGATTGCCACGTG 62.505 66.667 9.08 9.08 44.31 4.49
212 213 3.853330 CGAGCGATTGCCACGTGG 61.853 66.667 30.66 30.66 44.31 4.94
222 223 4.521075 CCACGTGGCAGAGGTATG 57.479 61.111 24.02 0.00 0.00 2.39
223 224 1.815421 CCACGTGGCAGAGGTATGC 60.815 63.158 24.02 0.00 45.74 3.14
229 230 2.279517 GCAGAGGTATGCCGACGG 60.280 66.667 10.29 10.29 40.43 4.79
246 247 3.996825 GGCTTTGCCGTCAACATAG 57.003 52.632 0.00 0.00 39.62 2.23
247 248 1.448985 GGCTTTGCCGTCAACATAGA 58.551 50.000 0.00 0.00 39.62 1.98
248 249 2.017049 GGCTTTGCCGTCAACATAGAT 58.983 47.619 0.00 0.00 39.62 1.98
249 250 2.223340 GGCTTTGCCGTCAACATAGATG 60.223 50.000 0.00 0.00 39.62 2.90
250 251 2.677836 GCTTTGCCGTCAACATAGATGA 59.322 45.455 0.00 0.00 30.75 2.92
251 252 3.126858 GCTTTGCCGTCAACATAGATGAA 59.873 43.478 0.00 0.00 30.75 2.57
252 253 4.379394 GCTTTGCCGTCAACATAGATGAAA 60.379 41.667 0.00 0.00 30.75 2.69
253 254 5.697473 TTTGCCGTCAACATAGATGAAAA 57.303 34.783 0.00 0.00 30.75 2.29
254 255 5.895636 TTGCCGTCAACATAGATGAAAAT 57.104 34.783 0.00 0.00 0.00 1.82
255 256 5.484173 TGCCGTCAACATAGATGAAAATC 57.516 39.130 0.00 0.00 0.00 2.17
256 257 5.185454 TGCCGTCAACATAGATGAAAATCT 58.815 37.500 0.00 0.00 34.80 2.40
257 258 6.345298 TGCCGTCAACATAGATGAAAATCTA 58.655 36.000 0.00 0.00 37.53 1.98
258 259 6.992123 TGCCGTCAACATAGATGAAAATCTAT 59.008 34.615 2.99 2.99 42.78 1.98
266 267 2.802816 AGATGAAAATCTATGCCGACGC 59.197 45.455 0.00 0.00 0.00 5.19
267 268 1.295792 TGAAAATCTATGCCGACGCC 58.704 50.000 0.00 0.00 0.00 5.68
268 269 0.232303 GAAAATCTATGCCGACGCCG 59.768 55.000 0.00 0.00 0.00 6.46
269 270 0.461339 AAAATCTATGCCGACGCCGT 60.461 50.000 0.00 0.00 0.00 5.68
270 271 0.874607 AAATCTATGCCGACGCCGTC 60.875 55.000 7.29 7.29 0.00 4.79
283 284 2.279517 CCGTCGGCATACCTCTGC 60.280 66.667 0.00 0.00 41.53 4.26
284 285 2.786495 CCGTCGGCATACCTCTGCT 61.786 63.158 0.00 0.00 41.95 4.24
286 287 1.884926 GTCGGCATACCTCTGCTGC 60.885 63.158 0.00 0.00 46.10 5.25
289 290 3.819188 GCATACCTCTGCTGCCAC 58.181 61.111 0.00 0.00 39.12 5.01
290 291 2.176273 GCATACCTCTGCTGCCACG 61.176 63.158 0.00 0.00 39.12 4.94
291 292 1.219124 CATACCTCTGCTGCCACGT 59.781 57.895 0.00 0.00 0.00 4.49
292 293 1.086067 CATACCTCTGCTGCCACGTG 61.086 60.000 9.08 9.08 0.00 4.49
293 294 2.244117 ATACCTCTGCTGCCACGTGG 62.244 60.000 30.66 30.66 38.53 4.94
304 305 1.506262 CCACGTGGCAAAGGTATGC 59.494 57.895 24.02 0.00 45.67 3.14
305 306 0.960364 CCACGTGGCAAAGGTATGCT 60.960 55.000 24.02 0.00 45.68 3.79
306 307 1.677518 CCACGTGGCAAAGGTATGCTA 60.678 52.381 24.02 0.00 45.68 3.49
317 318 2.122783 GGTATGCTACCTTTGCCACA 57.877 50.000 5.42 0.00 45.52 4.17
318 319 1.743394 GGTATGCTACCTTTGCCACAC 59.257 52.381 5.42 0.00 45.52 3.82
319 320 1.396996 GTATGCTACCTTTGCCACACG 59.603 52.381 0.00 0.00 0.00 4.49
320 321 0.960364 ATGCTACCTTTGCCACACGG 60.960 55.000 0.00 0.00 0.00 4.94
336 337 2.877691 GGCAGCCCGTGATTTGTC 59.122 61.111 0.00 0.00 0.00 3.18
337 338 2.480555 GCAGCCCGTGATTTGTCG 59.519 61.111 0.00 0.00 0.00 4.35
338 339 3.039202 GCAGCCCGTGATTTGTCGG 62.039 63.158 0.00 0.00 45.42 4.79
339 340 2.746277 AGCCCGTGATTTGTCGGC 60.746 61.111 0.00 0.00 44.63 5.54
340 341 3.810896 GCCCGTGATTTGTCGGCC 61.811 66.667 0.00 0.00 44.63 6.13
341 342 3.131478 CCCGTGATTTGTCGGCCC 61.131 66.667 0.00 0.00 44.63 5.80
342 343 3.496131 CCGTGATTTGTCGGCCCG 61.496 66.667 0.00 0.00 40.28 6.13
343 344 2.740826 CGTGATTTGTCGGCCCGT 60.741 61.111 1.63 0.00 0.00 5.28
344 345 2.322081 CGTGATTTGTCGGCCCGTT 61.322 57.895 1.63 0.00 0.00 4.44
345 346 1.847890 CGTGATTTGTCGGCCCGTTT 61.848 55.000 1.63 0.00 0.00 3.60
346 347 0.386731 GTGATTTGTCGGCCCGTTTG 60.387 55.000 1.63 0.00 0.00 2.93
347 348 0.535328 TGATTTGTCGGCCCGTTTGA 60.535 50.000 1.63 0.00 0.00 2.69
348 349 0.109919 GATTTGTCGGCCCGTTTGAC 60.110 55.000 1.63 0.00 0.00 3.18
349 350 1.847890 ATTTGTCGGCCCGTTTGACG 61.848 55.000 1.63 0.00 42.11 4.35
358 359 4.499023 CGTTTGACGGCGCCATCG 62.499 66.667 28.98 15.56 38.08 3.84
359 360 3.115892 GTTTGACGGCGCCATCGA 61.116 61.111 28.98 19.47 38.10 3.59
360 361 3.115892 TTTGACGGCGCCATCGAC 61.116 61.111 28.98 13.50 41.23 4.20
368 369 4.429212 CGCCATCGACCACCGTCA 62.429 66.667 0.00 0.00 39.11 4.35
369 370 2.509336 GCCATCGACCACCGTCAG 60.509 66.667 0.00 0.00 39.11 3.51
370 371 2.509336 CCATCGACCACCGTCAGC 60.509 66.667 0.00 0.00 39.11 4.26
371 372 2.573869 CATCGACCACCGTCAGCT 59.426 61.111 0.00 0.00 39.11 4.24
372 373 1.663379 CCATCGACCACCGTCAGCTA 61.663 60.000 0.00 0.00 39.11 3.32
373 374 0.172578 CATCGACCACCGTCAGCTAA 59.827 55.000 0.00 0.00 39.11 3.09
374 375 0.892755 ATCGACCACCGTCAGCTAAA 59.107 50.000 0.00 0.00 39.11 1.85
375 376 0.675083 TCGACCACCGTCAGCTAAAA 59.325 50.000 0.00 0.00 39.11 1.52
376 377 1.068895 TCGACCACCGTCAGCTAAAAA 59.931 47.619 0.00 0.00 39.11 1.94
377 378 2.073816 CGACCACCGTCAGCTAAAAAT 58.926 47.619 0.00 0.00 39.11 1.82
378 379 2.093783 CGACCACCGTCAGCTAAAAATC 59.906 50.000 0.00 0.00 39.11 2.17
379 380 3.071479 GACCACCGTCAGCTAAAAATCA 58.929 45.455 0.00 0.00 38.99 2.57
380 381 3.686016 ACCACCGTCAGCTAAAAATCAT 58.314 40.909 0.00 0.00 0.00 2.45
381 382 4.079253 ACCACCGTCAGCTAAAAATCATT 58.921 39.130 0.00 0.00 0.00 2.57
382 383 4.082787 ACCACCGTCAGCTAAAAATCATTG 60.083 41.667 0.00 0.00 0.00 2.82
383 384 3.853671 CACCGTCAGCTAAAAATCATTGC 59.146 43.478 0.00 0.00 0.00 3.56
384 385 3.119495 ACCGTCAGCTAAAAATCATTGCC 60.119 43.478 0.00 0.00 0.00 4.52
385 386 3.100817 CGTCAGCTAAAAATCATTGCCG 58.899 45.455 0.00 0.00 0.00 5.69
386 387 3.181511 CGTCAGCTAAAAATCATTGCCGA 60.182 43.478 0.00 0.00 0.00 5.54
387 388 4.098416 GTCAGCTAAAAATCATTGCCGAC 58.902 43.478 0.00 0.00 0.00 4.79
388 389 3.100817 CAGCTAAAAATCATTGCCGACG 58.899 45.455 0.00 0.00 0.00 5.12
389 390 2.097466 AGCTAAAAATCATTGCCGACGG 59.903 45.455 10.29 10.29 0.00 4.79
401 402 4.527157 CGACGGCCGTACGGAGAC 62.527 72.222 37.62 25.74 38.39 3.36
402 403 4.185059 GACGGCCGTACGGAGACC 62.185 72.222 37.62 26.28 38.39 3.85
412 413 3.039988 CGGAGACCGTCGGCATAT 58.960 61.111 12.28 0.00 42.73 1.78
413 414 2.250646 CGGAGACCGTCGGCATATA 58.749 57.895 12.28 0.00 42.73 0.86
414 415 0.809385 CGGAGACCGTCGGCATATAT 59.191 55.000 12.28 0.00 42.73 0.86
415 416 2.011947 CGGAGACCGTCGGCATATATA 58.988 52.381 12.28 0.00 42.73 0.86
416 417 2.223203 CGGAGACCGTCGGCATATATAC 60.223 54.545 12.28 0.00 42.73 1.47
417 418 2.098770 GGAGACCGTCGGCATATATACC 59.901 54.545 12.28 0.37 0.00 2.73
418 419 3.015327 GAGACCGTCGGCATATATACCT 58.985 50.000 12.28 0.00 0.00 3.08
419 420 4.194640 GAGACCGTCGGCATATATACCTA 58.805 47.826 12.28 0.00 0.00 3.08
420 421 4.789807 AGACCGTCGGCATATATACCTAT 58.210 43.478 12.28 0.00 0.00 2.57
421 422 4.579340 AGACCGTCGGCATATATACCTATG 59.421 45.833 12.28 0.00 33.15 2.23
428 429 3.639538 GCATATATACCTATGCCGACGG 58.360 50.000 10.29 10.29 45.35 4.79
438 439 2.884207 GCCGACGGCTTTCCTACG 60.884 66.667 31.30 0.00 46.69 3.51
439 440 2.884207 CCGACGGCTTTCCTACGC 60.884 66.667 0.00 0.00 0.00 4.42
440 441 3.245315 CGACGGCTTTCCTACGCG 61.245 66.667 3.53 3.53 0.00 6.01
441 442 2.884207 GACGGCTTTCCTACGCGG 60.884 66.667 12.47 0.00 0.00 6.46
442 443 3.346631 GACGGCTTTCCTACGCGGA 62.347 63.158 12.47 0.00 41.06 5.54
443 444 2.106332 CGGCTTTCCTACGCGGAT 59.894 61.111 12.47 0.00 42.70 4.18
444 445 2.237751 CGGCTTTCCTACGCGGATG 61.238 63.158 12.47 0.00 42.70 3.51
445 446 1.887707 GGCTTTCCTACGCGGATGG 60.888 63.158 12.47 9.65 42.70 3.51
446 447 1.153429 GCTTTCCTACGCGGATGGT 60.153 57.895 12.47 0.00 42.70 3.55
447 448 1.152383 GCTTTCCTACGCGGATGGTC 61.152 60.000 12.47 0.00 42.70 4.02
448 449 0.460311 CTTTCCTACGCGGATGGTCT 59.540 55.000 12.47 0.00 42.70 3.85
449 450 0.174845 TTTCCTACGCGGATGGTCTG 59.825 55.000 12.47 0.00 42.70 3.51
450 451 0.681887 TTCCTACGCGGATGGTCTGA 60.682 55.000 12.47 0.00 42.70 3.27
451 452 1.065928 CCTACGCGGATGGTCTGAC 59.934 63.158 12.47 0.00 33.16 3.51
452 453 1.663379 CCTACGCGGATGGTCTGACA 61.663 60.000 12.47 0.00 33.16 3.58
453 454 0.525668 CTACGCGGATGGTCTGACAC 60.526 60.000 12.47 0.00 0.00 3.67
454 455 1.245376 TACGCGGATGGTCTGACACA 61.245 55.000 12.47 5.83 0.00 3.72
455 456 1.153568 CGCGGATGGTCTGACACAT 60.154 57.895 10.38 10.33 0.00 3.21
456 457 1.148157 CGCGGATGGTCTGACACATC 61.148 60.000 21.23 21.23 42.05 3.06
457 458 0.176680 GCGGATGGTCTGACACATCT 59.823 55.000 24.97 5.95 42.34 2.90
458 459 1.409064 GCGGATGGTCTGACACATCTA 59.591 52.381 24.97 3.98 42.34 1.98
459 460 2.799917 GCGGATGGTCTGACACATCTAC 60.800 54.545 24.97 18.19 42.34 2.59
460 461 2.541794 CGGATGGTCTGACACATCTACG 60.542 54.545 24.97 20.16 42.34 3.51
461 462 2.464865 GATGGTCTGACACATCTACGC 58.535 52.381 21.70 5.94 40.17 4.42
462 463 1.545841 TGGTCTGACACATCTACGCT 58.454 50.000 10.38 0.00 0.00 5.07
463 464 2.718563 TGGTCTGACACATCTACGCTA 58.281 47.619 10.38 0.00 0.00 4.26
464 465 2.683362 TGGTCTGACACATCTACGCTAG 59.317 50.000 10.38 0.00 0.00 3.42
465 466 2.033550 GGTCTGACACATCTACGCTAGG 59.966 54.545 10.38 0.00 0.00 3.02
466 467 1.676529 TCTGACACATCTACGCTAGGC 59.323 52.381 0.00 0.00 0.00 3.93
467 468 0.744874 TGACACATCTACGCTAGGCC 59.255 55.000 0.00 0.00 0.00 5.19
468 469 0.317938 GACACATCTACGCTAGGCCG 60.318 60.000 0.00 0.00 0.00 6.13
469 470 1.035932 ACACATCTACGCTAGGCCGT 61.036 55.000 0.00 1.09 44.62 5.68
470 471 0.317938 CACATCTACGCTAGGCCGTC 60.318 60.000 0.00 0.00 42.20 4.79
471 472 1.082038 CATCTACGCTAGGCCGTCG 60.082 63.158 11.73 11.73 42.20 5.12
472 473 2.259439 ATCTACGCTAGGCCGTCGG 61.259 63.158 6.99 6.99 42.20 4.79
492 493 1.197721 GCATACATCTATGCCAACGGC 59.802 52.381 1.74 0.00 46.80 5.68
508 509 3.372730 GCATTGGTGCCTTGCCGA 61.373 61.111 5.73 0.00 45.76 5.54
509 510 2.568090 CATTGGTGCCTTGCCGAC 59.432 61.111 0.00 0.00 0.00 4.79
510 511 3.055719 ATTGGTGCCTTGCCGACG 61.056 61.111 0.00 0.00 0.00 5.12
540 541 4.767255 CGGCACAGAGGGGCAGTC 62.767 72.222 0.00 0.00 0.00 3.51
541 542 4.416738 GGCACAGAGGGGCAGTCC 62.417 72.222 0.00 0.00 0.00 3.85
542 543 4.767255 GCACAGAGGGGCAGTCCG 62.767 72.222 0.00 0.00 36.01 4.79
543 544 4.087892 CACAGAGGGGCAGTCCGG 62.088 72.222 0.00 0.00 36.01 5.14
544 545 4.640690 ACAGAGGGGCAGTCCGGT 62.641 66.667 0.00 0.00 36.01 5.28
545 546 2.363795 CAGAGGGGCAGTCCGGTA 60.364 66.667 0.00 0.00 36.01 4.02
546 547 2.042843 AGAGGGGCAGTCCGGTAG 60.043 66.667 0.00 0.00 36.01 3.18
547 548 2.363925 GAGGGGCAGTCCGGTAGT 60.364 66.667 0.00 0.00 36.01 2.73
568 569 3.311871 GTGATGCATCAGTGAGCCTTAAG 59.688 47.826 29.38 0.00 37.51 1.85
634 635 5.503357 CGACATCGAACCTGAAAAGAACAAA 60.503 40.000 0.00 0.00 43.02 2.83
640 641 9.810545 ATCGAACCTGAAAAGAACAAATTTTTA 57.189 25.926 0.00 0.00 30.22 1.52
694 1966 2.923020 GCTACGGTCGGTTCGAATTTAA 59.077 45.455 0.00 0.00 37.72 1.52
743 2020 4.417506 CGAATATACGTCAGGACACAACA 58.582 43.478 0.00 0.00 0.00 3.33
771 2048 3.549150 CGAGCTTCTTCCGCGCTG 61.549 66.667 5.56 0.00 33.47 5.18
792 2073 0.391130 TTAGCGTGCATGAGGTCCAC 60.391 55.000 10.93 0.00 0.00 4.02
900 2181 1.679305 GACGTGGCTCCTCTCCTCA 60.679 63.158 0.00 0.00 0.00 3.86
937 2218 3.364441 TGCATGCAACGGCCTCAC 61.364 61.111 20.30 0.00 40.13 3.51
938 2219 3.364441 GCATGCAACGGCCTCACA 61.364 61.111 14.21 0.00 40.13 3.58
980 2261 2.594541 GAATGATCGACGGGACAGC 58.405 57.895 0.00 0.00 0.00 4.40
981 2262 0.179111 GAATGATCGACGGGACAGCA 60.179 55.000 0.00 0.00 0.00 4.41
985 2266 0.526524 GATCGACGGGACAGCAAGAG 60.527 60.000 0.00 0.00 0.00 2.85
1207 2496 3.699894 CTGAGCTGGCGGTGACCT 61.700 66.667 0.00 0.00 0.00 3.85
1215 2504 4.830765 GCGGTGACCTATGCGGCA 62.831 66.667 4.58 4.58 35.61 5.69
1359 2648 1.819632 GAACAGGGCGGCGATCATT 60.820 57.895 12.98 0.00 0.00 2.57
1399 2688 1.185618 CGTGAAGAGGTGGGTGAGGA 61.186 60.000 0.00 0.00 0.00 3.71
1400 2689 1.280457 GTGAAGAGGTGGGTGAGGAT 58.720 55.000 0.00 0.00 0.00 3.24
1591 2880 7.859325 TTACCAGCTTAATTTATGTCTCACC 57.141 36.000 0.00 0.00 0.00 4.02
1632 2933 6.259743 CAGTGCACTGTTGAATTTGTAAAC 57.740 37.500 34.04 0.00 39.09 2.01
1749 3053 7.743116 TTGGTAGTCTAGGATTTGTAATCCA 57.257 36.000 18.02 6.02 40.61 3.41
1847 3182 0.106918 TTTCCTTCCGCACCAACTGT 60.107 50.000 0.00 0.00 0.00 3.55
1903 3258 6.294564 GGATGAACATTCCGCATAGACTACTA 60.295 42.308 0.00 0.00 0.00 1.82
1910 3265 2.095668 CCGCATAGACTACTAAGGCTCG 60.096 54.545 0.00 0.00 35.55 5.03
1922 3281 4.789807 ACTAAGGCTCGTATCTTGTCCTA 58.210 43.478 0.00 0.00 0.00 2.94
1928 3287 4.329256 GGCTCGTATCTTGTCCTAAACAAC 59.671 45.833 0.00 0.00 42.95 3.32
1956 3315 1.603802 CACACCAACTGCGTCTGATTT 59.396 47.619 0.00 0.00 0.00 2.17
1964 3323 5.106555 CCAACTGCGTCTGATTTAACTTGAT 60.107 40.000 0.00 0.00 0.00 2.57
1969 3328 7.094634 ACTGCGTCTGATTTAACTTGATTTGAT 60.095 33.333 0.00 0.00 0.00 2.57
2055 3414 0.909623 CCGAAACATGGGGGAGTAGT 59.090 55.000 0.00 0.00 0.00 2.73
2086 3445 1.138859 CAGCGAGGAATACACCATGGA 59.861 52.381 21.47 0.00 0.00 3.41
2095 3454 2.988010 TACACCATGGATGTCTCTGC 57.012 50.000 21.47 0.00 0.00 4.26
2122 3489 2.049627 GCCTGTAGAGCCATCCCCTG 62.050 65.000 0.00 0.00 0.00 4.45
2138 3505 2.028112 CCCCTGTCTCGACATGAAAAGA 60.028 50.000 0.00 0.00 41.01 2.52
2141 3508 4.310769 CCTGTCTCGACATGAAAAGAAGT 58.689 43.478 0.00 0.00 41.01 3.01
2167 3534 5.357314 TCAACGTTAACTTTGACAAATCCCA 59.643 36.000 20.15 0.00 30.57 4.37
2185 3552 1.238439 CACAGCCGGTTTCATTCACT 58.762 50.000 1.90 0.00 0.00 3.41
2206 3573 2.291365 GAACACCCACACGGTTAACTT 58.709 47.619 5.42 0.00 45.36 2.66
2248 3833 4.822026 ACTTCTCTGATAGTTCAAACGGG 58.178 43.478 0.00 0.00 0.00 5.28
2307 3892 0.827089 TTTGGCCATGGTGTGTCTGG 60.827 55.000 14.67 0.00 0.00 3.86
2310 3895 2.629656 GCCATGGTGTGTCTGGTGC 61.630 63.158 14.67 0.00 32.42 5.01
2331 3916 1.301874 CCGCGTCCACCAAAGGTAA 60.302 57.895 4.92 0.00 32.11 2.85
2358 3943 3.745799 TGTCGTTGCAATTCCTTCCTTA 58.254 40.909 0.59 0.00 0.00 2.69
2365 3950 4.464008 TGCAATTCCTTCCTTATAGCCAG 58.536 43.478 0.00 0.00 0.00 4.85
2385 3970 3.445805 CAGCCGTGGGTAAATTTGGTAAT 59.554 43.478 0.00 0.00 0.00 1.89
2417 4002 3.738282 GGCATTCGCAGTAGATGTTCTAG 59.262 47.826 0.00 0.00 41.24 2.43
2424 4009 5.646793 TCGCAGTAGATGTTCTAGTACAACT 59.353 40.000 14.96 14.96 35.62 3.16
2429 4014 8.132362 CAGTAGATGTTCTAGTACAACTGATCC 58.868 40.741 20.00 8.62 36.90 3.36
2457 6222 2.733671 CTGTGTCACTGCATCCGCG 61.734 63.158 0.00 0.00 42.97 6.46
2466 6231 0.877649 CTGCATCCGCGATTAGCTGT 60.878 55.000 8.23 0.00 45.59 4.40
2507 6272 2.048222 TTCGGCTGCTCTTCCACG 60.048 61.111 0.00 0.00 0.00 4.94
2533 6298 5.907207 TGAATAGCAGATACAGGACACTTC 58.093 41.667 0.00 0.00 0.00 3.01
2534 6299 4.946478 ATAGCAGATACAGGACACTTCC 57.054 45.455 0.00 0.00 43.22 3.46
2542 6307 4.150994 GGACACTTCCGGCAACAA 57.849 55.556 0.00 0.00 29.98 2.83
2543 6308 1.652563 GGACACTTCCGGCAACAAC 59.347 57.895 0.00 0.00 29.98 3.32
2544 6309 1.098712 GGACACTTCCGGCAACAACA 61.099 55.000 0.00 0.00 29.98 3.33
2545 6310 0.736053 GACACTTCCGGCAACAACAA 59.264 50.000 0.00 0.00 0.00 2.83
2546 6311 0.454196 ACACTTCCGGCAACAACAAC 59.546 50.000 0.00 0.00 0.00 3.32
2547 6312 0.453793 CACTTCCGGCAACAACAACA 59.546 50.000 0.00 0.00 0.00 3.33
2548 6313 1.135257 CACTTCCGGCAACAACAACAA 60.135 47.619 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.942850 TCAAGTTCATCATCTAAACATACTCAA 57.057 29.630 0.00 0.00 0.00 3.02
26 27 9.623000 TCATGATCAAGTTCATCATCTAAACAT 57.377 29.630 0.00 0.00 38.67 2.71
27 28 9.623000 ATCATGATCAAGTTCATCATCTAAACA 57.377 29.630 1.18 0.00 38.67 2.83
30 31 9.490379 CAGATCATGATCAAGTTCATCATCTAA 57.510 33.333 31.99 0.00 40.63 2.10
31 32 8.648693 ACAGATCATGATCAAGTTCATCATCTA 58.351 33.333 31.99 0.00 40.63 1.98
32 33 7.510407 ACAGATCATGATCAAGTTCATCATCT 58.490 34.615 31.99 9.31 42.54 2.90
33 34 7.441458 TGACAGATCATGATCAAGTTCATCATC 59.559 37.037 31.99 17.61 38.67 2.92
34 35 7.280356 TGACAGATCATGATCAAGTTCATCAT 58.720 34.615 31.99 9.31 40.92 2.45
35 36 6.646267 TGACAGATCATGATCAAGTTCATCA 58.354 36.000 31.99 20.76 40.22 3.07
36 37 7.731882 ATGACAGATCATGATCAAGTTCATC 57.268 36.000 31.99 18.97 44.26 2.92
37 38 9.794719 AATATGACAGATCATGATCAAGTTCAT 57.205 29.630 31.99 28.96 45.54 2.57
38 39 9.623000 AAATATGACAGATCATGATCAAGTTCA 57.377 29.630 31.99 25.81 45.54 3.18
40 41 9.848710 AGAAATATGACAGATCATGATCAAGTT 57.151 29.630 31.99 19.27 45.54 2.66
41 42 9.274206 CAGAAATATGACAGATCATGATCAAGT 57.726 33.333 31.99 28.23 45.54 3.16
42 43 9.274206 ACAGAAATATGACAGATCATGATCAAG 57.726 33.333 31.99 25.73 45.54 3.02
43 44 9.052759 CACAGAAATATGACAGATCATGATCAA 57.947 33.333 31.99 17.55 45.54 2.57
44 45 8.208903 ACACAGAAATATGACAGATCATGATCA 58.791 33.333 31.99 17.30 45.54 2.92
45 46 8.604640 ACACAGAAATATGACAGATCATGATC 57.395 34.615 25.42 25.42 45.54 2.92
73 74 9.807649 GACAGCATTTCAAACCAGAAAATATAT 57.192 29.630 0.00 0.00 40.54 0.86
74 75 7.967854 CGACAGCATTTCAAACCAGAAAATATA 59.032 33.333 0.00 0.00 40.54 0.86
75 76 6.808212 CGACAGCATTTCAAACCAGAAAATAT 59.192 34.615 0.00 0.00 40.54 1.28
76 77 6.016693 TCGACAGCATTTCAAACCAGAAAATA 60.017 34.615 0.00 0.00 40.54 1.40
77 78 4.984161 CGACAGCATTTCAAACCAGAAAAT 59.016 37.500 0.00 0.00 40.54 1.82
78 79 4.097135 TCGACAGCATTTCAAACCAGAAAA 59.903 37.500 0.00 0.00 40.54 2.29
79 80 3.629855 TCGACAGCATTTCAAACCAGAAA 59.370 39.130 0.00 0.00 41.31 2.52
80 81 3.210227 TCGACAGCATTTCAAACCAGAA 58.790 40.909 0.00 0.00 0.00 3.02
81 82 2.844946 TCGACAGCATTTCAAACCAGA 58.155 42.857 0.00 0.00 0.00 3.86
82 83 3.624326 TTCGACAGCATTTCAAACCAG 57.376 42.857 0.00 0.00 0.00 4.00
83 84 4.037327 TCATTTCGACAGCATTTCAAACCA 59.963 37.500 0.00 0.00 0.00 3.67
84 85 4.545610 TCATTTCGACAGCATTTCAAACC 58.454 39.130 0.00 0.00 0.00 3.27
85 86 5.215160 ACTCATTTCGACAGCATTTCAAAC 58.785 37.500 0.00 0.00 0.00 2.93
86 87 5.437289 ACTCATTTCGACAGCATTTCAAA 57.563 34.783 0.00 0.00 0.00 2.69
87 88 5.008514 TCAACTCATTTCGACAGCATTTCAA 59.991 36.000 0.00 0.00 0.00 2.69
88 89 4.514816 TCAACTCATTTCGACAGCATTTCA 59.485 37.500 0.00 0.00 0.00 2.69
89 90 5.034554 TCAACTCATTTCGACAGCATTTC 57.965 39.130 0.00 0.00 0.00 2.17
90 91 5.437289 TTCAACTCATTTCGACAGCATTT 57.563 34.783 0.00 0.00 0.00 2.32
91 92 5.215160 GTTTCAACTCATTTCGACAGCATT 58.785 37.500 0.00 0.00 0.00 3.56
92 93 4.275689 TGTTTCAACTCATTTCGACAGCAT 59.724 37.500 0.00 0.00 0.00 3.79
93 94 3.625313 TGTTTCAACTCATTTCGACAGCA 59.375 39.130 0.00 0.00 0.00 4.41
94 95 4.024893 TCTGTTTCAACTCATTTCGACAGC 60.025 41.667 0.00 0.00 34.72 4.40
95 96 5.463392 TCTCTGTTTCAACTCATTTCGACAG 59.537 40.000 0.00 0.00 35.73 3.51
96 97 5.356426 TCTCTGTTTCAACTCATTTCGACA 58.644 37.500 0.00 0.00 0.00 4.35
97 98 5.907197 TCTCTGTTTCAACTCATTTCGAC 57.093 39.130 0.00 0.00 0.00 4.20
98 99 6.918892 TTTCTCTGTTTCAACTCATTTCGA 57.081 33.333 0.00 0.00 0.00 3.71
99 100 6.966632 TGTTTTCTCTGTTTCAACTCATTTCG 59.033 34.615 0.00 0.00 0.00 3.46
100 101 8.687824 TTGTTTTCTCTGTTTCAACTCATTTC 57.312 30.769 0.00 0.00 0.00 2.17
101 102 9.487790 TTTTGTTTTCTCTGTTTCAACTCATTT 57.512 25.926 0.00 0.00 0.00 2.32
102 103 9.657419 ATTTTGTTTTCTCTGTTTCAACTCATT 57.343 25.926 0.00 0.00 0.00 2.57
136 137 4.759693 TCGGCATAGATCTGTGTTGTTTTT 59.240 37.500 19.28 0.00 0.00 1.94
137 138 4.154195 GTCGGCATAGATCTGTGTTGTTTT 59.846 41.667 19.28 0.00 0.00 2.43
138 139 3.684788 GTCGGCATAGATCTGTGTTGTTT 59.315 43.478 19.28 0.00 0.00 2.83
139 140 3.262420 GTCGGCATAGATCTGTGTTGTT 58.738 45.455 19.28 0.00 0.00 2.83
140 141 2.735444 CGTCGGCATAGATCTGTGTTGT 60.735 50.000 19.28 0.00 0.00 3.32
141 142 1.854743 CGTCGGCATAGATCTGTGTTG 59.145 52.381 19.28 12.55 0.00 3.33
142 143 1.202417 CCGTCGGCATAGATCTGTGTT 60.202 52.381 19.28 0.00 0.00 3.32
143 144 0.385751 CCGTCGGCATAGATCTGTGT 59.614 55.000 19.28 0.00 0.00 3.72
144 145 3.185651 CCGTCGGCATAGATCTGTG 57.814 57.895 14.69 14.69 0.00 3.66
175 176 1.610102 GCACTCCTGGGCATAGCTATG 60.610 57.143 26.42 26.42 36.78 2.23
176 177 0.689623 GCACTCCTGGGCATAGCTAT 59.310 55.000 0.00 0.00 0.00 2.97
177 178 1.748329 CGCACTCCTGGGCATAGCTA 61.748 60.000 0.00 0.00 0.00 3.32
178 179 2.914289 GCACTCCTGGGCATAGCT 59.086 61.111 0.00 0.00 0.00 3.32
179 180 2.590007 CGCACTCCTGGGCATAGC 60.590 66.667 0.00 0.00 0.00 2.97
180 181 1.068753 CTCGCACTCCTGGGCATAG 59.931 63.158 0.00 0.00 0.00 2.23
181 182 3.094062 GCTCGCACTCCTGGGCATA 62.094 63.158 0.00 0.00 0.00 3.14
182 183 4.479993 GCTCGCACTCCTGGGCAT 62.480 66.667 0.00 0.00 0.00 4.40
185 186 3.376935 AATCGCTCGCACTCCTGGG 62.377 63.158 0.00 0.00 0.00 4.45
186 187 2.169789 CAATCGCTCGCACTCCTGG 61.170 63.158 0.00 0.00 0.00 4.45
187 188 2.806856 GCAATCGCTCGCACTCCTG 61.807 63.158 0.00 0.00 34.30 3.86
188 189 2.510238 GCAATCGCTCGCACTCCT 60.510 61.111 0.00 0.00 34.30 3.69
189 190 3.567797 GGCAATCGCTCGCACTCC 61.568 66.667 0.00 0.00 38.60 3.85
190 191 2.815211 TGGCAATCGCTCGCACTC 60.815 61.111 0.00 0.00 38.60 3.51
191 192 3.121030 GTGGCAATCGCTCGCACT 61.121 61.111 0.00 0.00 38.60 4.40
192 193 4.505217 CGTGGCAATCGCTCGCAC 62.505 66.667 0.00 0.00 38.60 5.34
194 195 4.505217 CACGTGGCAATCGCTCGC 62.505 66.667 7.95 0.00 38.35 5.03
195 196 3.853330 CCACGTGGCAATCGCTCG 61.853 66.667 24.02 0.00 39.74 5.03
205 206 1.815421 GCATACCTCTGCCACGTGG 60.815 63.158 30.66 30.66 36.10 4.94
206 207 3.799753 GCATACCTCTGCCACGTG 58.200 61.111 9.08 9.08 36.10 4.49
212 213 2.279517 CCGTCGGCATACCTCTGC 60.280 66.667 0.00 0.00 41.53 4.26
228 229 1.448985 TCTATGTTGACGGCAAAGCC 58.551 50.000 4.55 0.00 46.75 4.35
229 230 2.677836 TCATCTATGTTGACGGCAAAGC 59.322 45.455 4.55 0.00 35.42 3.51
230 231 4.944962 TTCATCTATGTTGACGGCAAAG 57.055 40.909 4.55 0.00 35.42 2.77
231 232 5.697473 TTTTCATCTATGTTGACGGCAAA 57.303 34.783 4.55 0.00 35.42 3.68
232 233 5.647658 AGATTTTCATCTATGTTGACGGCAA 59.352 36.000 0.00 0.00 38.06 4.52
233 234 5.185454 AGATTTTCATCTATGTTGACGGCA 58.815 37.500 0.00 0.00 38.06 5.69
234 235 5.741388 AGATTTTCATCTATGTTGACGGC 57.259 39.130 0.00 0.00 38.06 5.68
244 245 3.987868 GCGTCGGCATAGATTTTCATCTA 59.012 43.478 0.00 0.00 44.61 1.98
245 246 2.802816 GCGTCGGCATAGATTTTCATCT 59.197 45.455 0.00 0.00 40.16 2.90
246 247 2.096218 GGCGTCGGCATAGATTTTCATC 60.096 50.000 14.73 0.00 42.47 2.92
247 248 1.873591 GGCGTCGGCATAGATTTTCAT 59.126 47.619 14.73 0.00 42.47 2.57
248 249 1.295792 GGCGTCGGCATAGATTTTCA 58.704 50.000 14.73 0.00 42.47 2.69
249 250 0.232303 CGGCGTCGGCATAGATTTTC 59.768 55.000 19.59 0.00 42.47 2.29
250 251 0.461339 ACGGCGTCGGCATAGATTTT 60.461 50.000 16.39 0.00 42.47 1.82
251 252 0.874607 GACGGCGTCGGCATAGATTT 60.875 55.000 25.42 0.00 45.37 2.17
252 253 1.299926 GACGGCGTCGGCATAGATT 60.300 57.895 25.42 0.00 45.37 2.40
253 254 2.335369 GACGGCGTCGGCATAGAT 59.665 61.111 25.42 0.00 45.37 1.98
266 267 2.279517 GCAGAGGTATGCCGACGG 60.280 66.667 10.29 10.29 40.43 4.79
272 273 2.176273 CGTGGCAGCAGAGGTATGC 61.176 63.158 0.00 0.00 46.88 3.14
273 274 1.086067 CACGTGGCAGCAGAGGTATG 61.086 60.000 7.95 0.00 0.00 2.39
274 275 1.219124 CACGTGGCAGCAGAGGTAT 59.781 57.895 7.95 0.00 0.00 2.73
275 276 2.656646 CACGTGGCAGCAGAGGTA 59.343 61.111 7.95 0.00 0.00 3.08
276 277 4.320456 CCACGTGGCAGCAGAGGT 62.320 66.667 24.02 0.00 0.00 3.85
286 287 0.960364 AGCATACCTTTGCCACGTGG 60.960 55.000 30.66 30.66 43.83 4.94
287 288 1.396996 GTAGCATACCTTTGCCACGTG 59.603 52.381 9.08 9.08 43.83 4.49
288 289 1.734163 GTAGCATACCTTTGCCACGT 58.266 50.000 0.00 0.00 43.83 4.49
299 300 1.396996 CGTGTGGCAAAGGTAGCATAC 59.603 52.381 0.00 0.00 42.04 2.39
300 301 1.677518 CCGTGTGGCAAAGGTAGCATA 60.678 52.381 0.00 0.00 0.00 3.14
301 302 0.960364 CCGTGTGGCAAAGGTAGCAT 60.960 55.000 0.00 0.00 0.00 3.79
302 303 1.599518 CCGTGTGGCAAAGGTAGCA 60.600 57.895 0.00 0.00 0.00 3.49
303 304 3.263941 CCGTGTGGCAAAGGTAGC 58.736 61.111 0.00 0.00 0.00 3.58
318 319 3.039202 GACAAATCACGGGCTGCCG 62.039 63.158 13.40 10.64 39.31 5.69
319 320 2.877691 GACAAATCACGGGCTGCC 59.122 61.111 11.05 11.05 0.00 4.85
320 321 2.480555 CGACAAATCACGGGCTGC 59.519 61.111 0.00 0.00 0.00 5.25
321 322 3.177600 CCGACAAATCACGGGCTG 58.822 61.111 0.00 0.00 44.59 4.85
326 327 1.847890 AAACGGGCCGACAAATCACG 61.848 55.000 35.78 1.17 0.00 4.35
327 328 0.386731 CAAACGGGCCGACAAATCAC 60.387 55.000 35.78 0.00 0.00 3.06
328 329 0.535328 TCAAACGGGCCGACAAATCA 60.535 50.000 35.78 6.23 0.00 2.57
329 330 0.109919 GTCAAACGGGCCGACAAATC 60.110 55.000 35.78 13.94 0.00 2.17
330 331 1.847890 CGTCAAACGGGCCGACAAAT 61.848 55.000 35.78 6.54 38.08 2.32
331 332 2.535788 CGTCAAACGGGCCGACAAA 61.536 57.895 35.78 12.47 38.08 2.83
332 333 2.968156 CGTCAAACGGGCCGACAA 60.968 61.111 35.78 12.07 38.08 3.18
341 342 4.499023 CGATGGCGCCGTCAAACG 62.499 66.667 39.79 26.99 42.11 3.60
342 343 3.115892 TCGATGGCGCCGTCAAAC 61.116 61.111 39.79 20.29 37.46 2.93
343 344 3.115892 GTCGATGGCGCCGTCAAA 61.116 61.111 39.79 27.81 37.46 2.69
351 352 4.429212 TGACGGTGGTCGATGGCG 62.429 66.667 0.00 0.00 46.49 5.69
352 353 2.509336 CTGACGGTGGTCGATGGC 60.509 66.667 0.00 0.00 46.49 4.40
353 354 1.663379 TAGCTGACGGTGGTCGATGG 61.663 60.000 0.00 0.00 46.49 3.51
354 355 0.172578 TTAGCTGACGGTGGTCGATG 59.827 55.000 0.00 0.00 46.49 3.84
355 356 0.892755 TTTAGCTGACGGTGGTCGAT 59.107 50.000 0.00 0.00 46.49 3.59
356 357 0.675083 TTTTAGCTGACGGTGGTCGA 59.325 50.000 0.00 0.00 46.49 4.20
357 358 1.504359 TTTTTAGCTGACGGTGGTCG 58.496 50.000 0.00 0.00 46.49 4.79
358 359 3.071479 TGATTTTTAGCTGACGGTGGTC 58.929 45.455 0.00 0.00 43.71 4.02
359 360 3.134574 TGATTTTTAGCTGACGGTGGT 57.865 42.857 0.00 0.00 0.00 4.16
360 361 4.414852 CAATGATTTTTAGCTGACGGTGG 58.585 43.478 0.00 0.00 0.00 4.61
361 362 3.853671 GCAATGATTTTTAGCTGACGGTG 59.146 43.478 0.00 0.00 0.00 4.94
362 363 3.119495 GGCAATGATTTTTAGCTGACGGT 60.119 43.478 0.00 0.00 0.00 4.83
363 364 3.438360 GGCAATGATTTTTAGCTGACGG 58.562 45.455 0.00 0.00 0.00 4.79
364 365 3.100817 CGGCAATGATTTTTAGCTGACG 58.899 45.455 0.00 0.00 33.54 4.35
365 366 4.355543 TCGGCAATGATTTTTAGCTGAC 57.644 40.909 0.00 0.00 35.82 3.51
366 367 3.181511 CGTCGGCAATGATTTTTAGCTGA 60.182 43.478 0.00 0.00 38.19 4.26
367 368 3.100817 CGTCGGCAATGATTTTTAGCTG 58.899 45.455 0.00 0.00 0.00 4.24
368 369 2.097466 CCGTCGGCAATGATTTTTAGCT 59.903 45.455 0.00 0.00 0.00 3.32
369 370 2.450160 CCGTCGGCAATGATTTTTAGC 58.550 47.619 0.00 0.00 0.00 3.09
384 385 4.527157 GTCTCCGTACGGCCGTCG 62.527 72.222 38.01 33.17 45.88 5.12
385 386 4.185059 GGTCTCCGTACGGCCGTC 62.185 72.222 38.01 24.37 34.68 4.79
396 397 2.098770 GGTATATATGCCGACGGTCTCC 59.901 54.545 16.73 0.00 0.00 3.71
397 398 3.015327 AGGTATATATGCCGACGGTCTC 58.985 50.000 16.73 0.00 37.65 3.36
398 399 3.083122 AGGTATATATGCCGACGGTCT 57.917 47.619 16.73 5.65 37.65 3.85
399 400 4.856664 CATAGGTATATATGCCGACGGTC 58.143 47.826 16.73 8.54 37.65 4.79
400 401 4.913335 CATAGGTATATATGCCGACGGT 57.087 45.455 16.73 0.00 37.65 4.83
422 423 2.884207 GCGTAGGAAAGCCGTCGG 60.884 66.667 6.99 6.99 39.96 4.79
423 424 3.245315 CGCGTAGGAAAGCCGTCG 61.245 66.667 0.00 0.00 39.96 5.12
424 425 2.884207 CCGCGTAGGAAAGCCGTC 60.884 66.667 4.92 0.00 45.00 4.79
433 434 1.065928 GTCAGACCATCCGCGTAGG 59.934 63.158 4.92 6.24 42.97 3.18
434 435 0.525668 GTGTCAGACCATCCGCGTAG 60.526 60.000 4.92 0.00 0.00 3.51
435 436 1.245376 TGTGTCAGACCATCCGCGTA 61.245 55.000 4.92 0.00 0.00 4.42
436 437 1.888436 ATGTGTCAGACCATCCGCGT 61.888 55.000 4.92 0.00 0.00 6.01
437 438 1.148157 GATGTGTCAGACCATCCGCG 61.148 60.000 15.91 0.00 33.00 6.46
438 439 0.176680 AGATGTGTCAGACCATCCGC 59.823 55.000 20.18 5.36 38.57 5.54
439 440 2.541794 CGTAGATGTGTCAGACCATCCG 60.542 54.545 20.18 15.91 38.57 4.18
440 441 2.799917 GCGTAGATGTGTCAGACCATCC 60.800 54.545 20.18 10.73 38.57 3.51
441 442 2.099921 AGCGTAGATGTGTCAGACCATC 59.900 50.000 17.82 17.82 38.17 3.51
442 443 2.103373 AGCGTAGATGTGTCAGACCAT 58.897 47.619 0.00 1.18 0.00 3.55
443 444 1.545841 AGCGTAGATGTGTCAGACCA 58.454 50.000 0.00 0.00 0.00 4.02
444 445 2.033550 CCTAGCGTAGATGTGTCAGACC 59.966 54.545 0.00 0.00 0.00 3.85
445 446 2.541999 GCCTAGCGTAGATGTGTCAGAC 60.542 54.545 0.00 0.00 0.00 3.51
446 447 1.676529 GCCTAGCGTAGATGTGTCAGA 59.323 52.381 0.00 0.00 0.00 3.27
447 448 1.269309 GGCCTAGCGTAGATGTGTCAG 60.269 57.143 0.00 0.00 0.00 3.51
448 449 0.744874 GGCCTAGCGTAGATGTGTCA 59.255 55.000 0.00 0.00 0.00 3.58
449 450 0.317938 CGGCCTAGCGTAGATGTGTC 60.318 60.000 0.00 0.00 0.00 3.67
450 451 1.035932 ACGGCCTAGCGTAGATGTGT 61.036 55.000 0.00 0.00 0.00 3.72
451 452 0.317938 GACGGCCTAGCGTAGATGTG 60.318 60.000 0.00 0.00 0.00 3.21
452 453 1.783031 CGACGGCCTAGCGTAGATGT 61.783 60.000 0.00 0.00 0.00 3.06
453 454 1.082038 CGACGGCCTAGCGTAGATG 60.082 63.158 0.00 0.00 0.00 2.90
454 455 2.259439 CCGACGGCCTAGCGTAGAT 61.259 63.158 0.00 0.00 0.00 1.98
455 456 2.898840 CCGACGGCCTAGCGTAGA 60.899 66.667 0.00 0.00 0.00 2.59
456 457 4.625781 GCCGACGGCCTAGCGTAG 62.626 72.222 28.74 0.00 44.06 3.51
492 493 2.568090 GTCGGCAAGGCACCAATG 59.432 61.111 0.00 0.00 0.00 2.82
493 494 3.055719 CGTCGGCAAGGCACCAAT 61.056 61.111 0.00 0.00 0.00 3.16
523 524 4.767255 GACTGCCCCTCTGTGCCG 62.767 72.222 0.00 0.00 0.00 5.69
524 525 4.416738 GGACTGCCCCTCTGTGCC 62.417 72.222 0.00 0.00 0.00 5.01
525 526 4.767255 CGGACTGCCCCTCTGTGC 62.767 72.222 0.00 0.00 0.00 4.57
526 527 4.087892 CCGGACTGCCCCTCTGTG 62.088 72.222 0.00 0.00 0.00 3.66
527 528 3.233919 TACCGGACTGCCCCTCTGT 62.234 63.158 9.46 0.00 0.00 3.41
528 529 2.363795 TACCGGACTGCCCCTCTG 60.364 66.667 9.46 0.00 0.00 3.35
529 530 2.042843 CTACCGGACTGCCCCTCT 60.043 66.667 9.46 0.00 0.00 3.69
530 531 2.363925 ACTACCGGACTGCCCCTC 60.364 66.667 9.46 0.00 0.00 4.30
531 532 2.531483 ATCACTACCGGACTGCCCCT 62.531 60.000 9.46 0.00 0.00 4.79
532 533 2.064581 ATCACTACCGGACTGCCCC 61.065 63.158 9.46 0.00 0.00 5.80
533 534 1.144057 CATCACTACCGGACTGCCC 59.856 63.158 9.46 0.00 0.00 5.36
534 535 1.521681 GCATCACTACCGGACTGCC 60.522 63.158 9.46 0.00 0.00 4.85
535 536 0.179073 ATGCATCACTACCGGACTGC 60.179 55.000 9.46 8.04 0.00 4.40
536 537 1.136891 TGATGCATCACTACCGGACTG 59.863 52.381 25.42 0.00 0.00 3.51
537 538 1.410517 CTGATGCATCACTACCGGACT 59.589 52.381 25.42 0.00 32.50 3.85
538 539 1.137086 ACTGATGCATCACTACCGGAC 59.863 52.381 25.42 0.00 32.50 4.79
539 540 1.136891 CACTGATGCATCACTACCGGA 59.863 52.381 25.42 2.00 32.50 5.14
540 541 1.136891 TCACTGATGCATCACTACCGG 59.863 52.381 25.42 16.41 32.50 5.28
541 542 2.467838 CTCACTGATGCATCACTACCG 58.532 52.381 25.42 17.12 32.50 4.02
542 543 2.208431 GCTCACTGATGCATCACTACC 58.792 52.381 25.42 9.20 32.50 3.18
543 544 2.158986 AGGCTCACTGATGCATCACTAC 60.159 50.000 25.42 12.54 32.50 2.73
544 545 2.113807 AGGCTCACTGATGCATCACTA 58.886 47.619 25.42 12.22 32.50 2.74
545 546 0.910338 AGGCTCACTGATGCATCACT 59.090 50.000 25.42 16.32 32.50 3.41
546 547 1.747709 AAGGCTCACTGATGCATCAC 58.252 50.000 25.42 14.78 32.50 3.06
547 548 3.538591 CTTAAGGCTCACTGATGCATCA 58.461 45.455 27.10 27.10 35.16 3.07
568 569 2.153034 TTTTATGCCCACCCTAAGCC 57.847 50.000 0.00 0.00 0.00 4.35
572 573 1.634459 TCGGTTTTTATGCCCACCCTA 59.366 47.619 0.00 0.00 0.00 3.53
657 1799 3.512680 CGTAGCAGAGAAGAAATTCGGT 58.487 45.455 0.00 0.00 0.00 4.69
658 1800 2.860735 CCGTAGCAGAGAAGAAATTCGG 59.139 50.000 0.00 0.00 0.00 4.30
667 1809 0.524862 GAACCGACCGTAGCAGAGAA 59.475 55.000 0.00 0.00 0.00 2.87
694 1966 9.051679 GTTTTCTTTTTGGTTAACCATGCTAAT 57.948 29.630 27.57 0.00 46.97 1.73
743 2020 1.093159 AGAAGCTCGTTCGGTCGTAT 58.907 50.000 0.00 0.00 40.49 3.06
771 2048 1.090052 GGACCTCATGCACGCTAACC 61.090 60.000 0.00 0.00 0.00 2.85
792 2073 7.430992 AATCTGTTGCATATATAGCACACAG 57.569 36.000 23.64 23.64 43.84 3.66
891 2172 1.716826 GAGCGTACGGTGAGGAGAGG 61.717 65.000 26.54 0.00 0.00 3.69
900 2181 4.125695 GGAAGGCGAGCGTACGGT 62.126 66.667 21.51 21.51 0.00 4.83
937 2218 2.344441 CGTGGTGTTGTTATAGAGCGTG 59.656 50.000 0.00 0.00 0.00 5.34
938 2219 2.602878 CGTGGTGTTGTTATAGAGCGT 58.397 47.619 0.00 0.00 0.00 5.07
997 2283 1.599518 TTGAAGCGGACGCCATGTT 60.600 52.632 13.63 0.48 43.17 2.71
1191 2480 1.685765 ATAGGTCACCGCCAGCTCA 60.686 57.895 0.00 0.00 0.00 4.26
1359 2648 4.314440 GCCACGTCCCTGTGCTCA 62.314 66.667 0.00 0.00 38.55 4.26
1536 2825 4.557296 CGCAAAGATTATTAGCCATGGGTG 60.557 45.833 26.70 6.46 0.00 4.61
1584 2873 5.548406 AGTACAAACATAACCAGGTGAGAC 58.452 41.667 0.00 0.00 0.00 3.36
1591 2880 5.699001 TGCACTGTAGTACAAACATAACCAG 59.301 40.000 4.21 0.00 0.00 4.00
1677 2981 8.615878 TCTAACACAATTTATGCACTGTAACT 57.384 30.769 0.00 0.00 0.00 2.24
1723 3027 8.778059 TGGATTACAAATCCTAGACTACCAAAT 58.222 33.333 17.27 0.00 38.95 2.32
1724 3028 8.153221 TGGATTACAAATCCTAGACTACCAAA 57.847 34.615 17.27 0.00 38.95 3.28
1746 3050 6.099139 TCCTAGAGATAAGGTAGGAGATGGA 58.901 44.000 0.00 0.00 37.92 3.41
1811 3146 7.106239 GGAAGGAAATAGAGACAAGATTGACA 58.894 38.462 0.00 0.00 0.00 3.58
1830 3165 1.227823 CACAGTTGGTGCGGAAGGA 60.228 57.895 0.00 0.00 41.36 3.36
1903 3258 4.222145 TGTTTAGGACAAGATACGAGCCTT 59.778 41.667 0.00 0.00 34.69 4.35
1922 3281 4.405358 AGTTGGTGTGATTGATGGTTGTTT 59.595 37.500 0.00 0.00 0.00 2.83
1928 3287 1.135603 CGCAGTTGGTGTGATTGATGG 60.136 52.381 0.00 0.00 39.20 3.51
1956 3315 8.869109 AGATGGGTTTTCAATCAAATCAAGTTA 58.131 29.630 0.00 0.00 0.00 2.24
1964 3323 6.427547 GCAAATGAGATGGGTTTTCAATCAAA 59.572 34.615 0.00 0.00 0.00 2.69
1969 3328 4.800249 GCAGCAAATGAGATGGGTTTTCAA 60.800 41.667 0.00 0.00 0.00 2.69
1977 3336 3.793797 TTGATGCAGCAAATGAGATGG 57.206 42.857 16.30 0.00 0.00 3.51
2034 3393 0.906775 TACTCCCCCATGTTTCGGAC 59.093 55.000 0.00 0.00 0.00 4.79
2038 3397 2.681097 GCTCACTACTCCCCCATGTTTC 60.681 54.545 0.00 0.00 0.00 2.78
2055 3414 2.186125 CTCGCTGGCTCATGCTCA 59.814 61.111 0.00 0.00 39.59 4.26
2086 3445 1.276421 AGGCGTTGTTAGCAGAGACAT 59.724 47.619 0.00 0.00 36.08 3.06
2095 3454 1.641577 GGCTCTACAGGCGTTGTTAG 58.358 55.000 0.17 1.40 41.29 2.34
2122 3489 4.745125 TGACACTTCTTTTCATGTCGAGAC 59.255 41.667 0.00 0.00 43.58 3.36
2161 3528 0.039618 ATGAAACCGGCTGTGGGATT 59.960 50.000 0.00 0.00 0.00 3.01
2167 3534 1.202758 TCAGTGAATGAAACCGGCTGT 60.203 47.619 0.00 0.00 34.02 4.40
2206 3573 8.062065 AGAAGTTTAAACACAAGAAATGACCA 57.938 30.769 20.06 0.00 0.00 4.02
2248 3833 1.687494 GCGATGTCCGTGAGAGCAAC 61.687 60.000 0.00 0.00 41.15 4.17
2317 3902 3.634910 ACATGTTGTTACCTTTGGTGGAC 59.365 43.478 0.00 0.00 36.19 4.02
2358 3943 0.843984 ATTTACCCACGGCTGGCTAT 59.156 50.000 0.00 0.00 36.00 2.97
2365 3950 4.459390 AATTACCAAATTTACCCACGGC 57.541 40.909 0.00 0.00 30.98 5.68
2417 4002 4.892934 AGGAGAGATCAGGATCAGTTGTAC 59.107 45.833 11.55 0.00 40.22 2.90
2424 4009 3.295093 GACACAGGAGAGATCAGGATCA 58.705 50.000 11.55 0.00 40.22 2.92
2429 4014 2.417107 GCAGTGACACAGGAGAGATCAG 60.417 54.545 8.59 0.00 0.00 2.90
2457 6222 4.414337 AATGGGACTCTCACAGCTAATC 57.586 45.455 0.00 0.00 30.64 1.75
2466 6231 2.061848 TGGAACCAAATGGGACTCTCA 58.938 47.619 4.17 0.00 41.15 3.27
2507 6272 3.070159 TGTCCTGTATCTGCTATTCAGGC 59.930 47.826 15.69 12.55 43.49 4.85
2522 6287 1.227853 GTTGCCGGAAGTGTCCTGT 60.228 57.895 5.05 0.00 42.44 4.00
2526 6291 0.736053 TTGTTGTTGCCGGAAGTGTC 59.264 50.000 5.05 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.