Multiple sequence alignment - TraesCS7B01G261700

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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 TraesCS7B01G261700 chr7B 100.000 3422 0 0 1 3422 482177163 482173742 0.000000e+00 6320.0
1 TraesCS7B01G261700 chr7D 96.517 2814 78 12 478 3281 459874267 459871464 0.000000e+00 4636.0
2 TraesCS7B01G261700 chr7D 75.749 367 73 13 2063 2421 47910871 47911229 1.630000e-38 171.0
3 TraesCS7B01G261700 chr7A 95.083 2298 72 17 527 2795 539651323 539653608 0.000000e+00 3579.0
4 TraesCS7B01G261700 chr7A 90.935 353 23 5 1 345 724305810 724306161 1.860000e-127 466.0
5 TraesCS7B01G261700 chr7A 96.154 78 3 0 393 470 724306150 724306227 9.970000e-26 128.0
6 TraesCS7B01G261700 chr7A 94.872 78 4 0 393 470 724300721 724300798 4.640000e-24 122.0
7 TraesCS7B01G261700 chr3B 88.338 343 36 4 4 345 696782371 696782032 3.180000e-110 409.0
8 TraesCS7B01G261700 chr3B 87.683 341 35 7 4 341 786049280 786049616 1.150000e-104 390.0
9 TraesCS7B01G261700 chr3B 92.806 139 8 1 3281 3417 611133438 611133576 2.080000e-47 200.0
10 TraesCS7B01G261700 chr3B 96.429 84 3 0 387 470 808953398 808953315 4.600000e-29 139.0
11 TraesCS7B01G261700 chr3B 95.000 80 2 1 393 470 741882302 741882223 1.290000e-24 124.0
12 TraesCS7B01G261700 chr2B 88.235 340 33 5 7 345 260642163 260641830 1.910000e-107 399.0
13 TraesCS7B01G261700 chr2B 86.957 345 37 8 4 345 646647 646986 6.930000e-102 381.0
14 TraesCS7B01G261700 chr2B 96.154 78 3 0 393 470 106078895 106078972 9.970000e-26 128.0
15 TraesCS7B01G261700 chr6D 76.397 716 148 17 1267 1971 157167882 157167177 1.940000e-97 366.0
16 TraesCS7B01G261700 chr6B 85.838 346 45 4 1 345 65762930 65763272 6.980000e-97 364.0
17 TraesCS7B01G261700 chr6B 85.131 343 47 4 1 341 33118898 33118558 7.030000e-92 348.0
18 TraesCS7B01G261700 chr6B 75.453 717 153 18 1267 1971 280049696 280048991 9.160000e-86 327.0
19 TraesCS7B01G261700 chr6B 95.062 81 4 0 393 473 33118566 33118486 9.970000e-26 128.0
20 TraesCS7B01G261700 chr6B 81.928 83 10 3 3028 3105 132123583 132123501 7.930000e-07 65.8
21 TraesCS7B01G261700 chr1B 85.920 348 37 10 4 345 689281336 689280995 9.030000e-96 361.0
22 TraesCS7B01G261700 chr1B 85.714 343 45 4 4 345 106770926 106770587 3.250000e-95 359.0
23 TraesCS7B01G261700 chr1B 95.062 81 2 1 393 471 689281006 689280926 3.590000e-25 126.0
24 TraesCS7B01G261700 chr6A 75.838 716 152 18 1267 1971 215528184 215528889 9.090000e-91 344.0
25 TraesCS7B01G261700 chr5B 93.706 143 7 1 3282 3422 573410933 573410791 2.680000e-51 213.0
26 TraesCS7B01G261700 chr5B 93.007 143 8 1 3282 3422 662945332 662945190 1.240000e-49 207.0
27 TraesCS7B01G261700 chr5B 96.154 78 3 0 393 470 669168784 669168861 9.970000e-26 128.0
28 TraesCS7B01G261700 chr5B 95.000 80 2 1 393 470 255403580 255403501 1.290000e-24 124.0
29 TraesCS7B01G261700 chr4A 91.667 144 10 1 3281 3422 660691200 660691343 7.490000e-47 198.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G261700 chr7B 482173742 482177163 3421 True 6320 6320 100.000 1 3422 1 chr7B.!!$R1 3421
1 TraesCS7B01G261700 chr7D 459871464 459874267 2803 True 4636 4636 96.517 478 3281 1 chr7D.!!$R1 2803
2 TraesCS7B01G261700 chr7A 539651323 539653608 2285 False 3579 3579 95.083 527 2795 1 chr7A.!!$F1 2268
3 TraesCS7B01G261700 chr6D 157167177 157167882 705 True 366 366 76.397 1267 1971 1 chr6D.!!$R1 704
4 TraesCS7B01G261700 chr6B 280048991 280049696 705 True 327 327 75.453 1267 1971 1 chr6B.!!$R2 704
5 TraesCS7B01G261700 chr6A 215528184 215528889 705 False 344 344 75.838 1267 1971 1 chr6A.!!$F1 704

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
306 307 0.335019 ATAGGTTTGGGGGAACTGGC 59.665 55.0 0.0 0.0 0.00 4.85 F
310 311 0.469144 GTTTGGGGGAACTGGCTCAA 60.469 55.0 0.0 0.0 0.00 3.02 F
1659 1670 0.391597 ACATCCACGTGAACGACCTT 59.608 50.0 19.3 0.0 43.02 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1238 0.108424 CCAGCAACTTCCTCCTCGAG 60.108 60.0 5.13 5.13 0.00 4.04 R
2229 2248 0.393077 ACACCCAGTTCTTCCACTCG 59.607 55.0 0.00 0.00 0.00 4.18 R
3382 3419 0.259647 TGTAGCCCGGCCTACTAAGA 59.740 55.0 22.08 0.20 38.75 2.10 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.276091 TGAACCACCAGCGCGTTG 61.276 61.111 16.72 16.72 0.00 4.10
18 19 4.683334 GAACCACCAGCGCGTTGC 62.683 66.667 18.28 0.00 46.98 4.17
31 32 4.467084 GTTGCCCGGCATCGAGGA 62.467 66.667 14.30 0.00 38.76 3.71
32 33 4.161295 TTGCCCGGCATCGAGGAG 62.161 66.667 14.30 0.00 38.76 3.69
34 35 3.849951 GCCCGGCATCGAGGAGAA 61.850 66.667 3.91 0.00 39.00 2.87
35 36 2.900273 CCCGGCATCGAGGAGAAA 59.100 61.111 0.00 0.00 39.00 2.52
36 37 1.220749 CCCGGCATCGAGGAGAAAA 59.779 57.895 0.00 0.00 39.00 2.29
37 38 0.392461 CCCGGCATCGAGGAGAAAAA 60.392 55.000 0.00 0.00 39.00 1.94
38 39 1.009829 CCGGCATCGAGGAGAAAAAG 58.990 55.000 0.00 0.00 39.00 2.27
39 40 1.009829 CGGCATCGAGGAGAAAAAGG 58.990 55.000 0.00 0.00 39.00 3.11
40 41 1.405526 CGGCATCGAGGAGAAAAAGGA 60.406 52.381 0.00 0.00 39.00 3.36
41 42 2.284190 GGCATCGAGGAGAAAAAGGAG 58.716 52.381 0.00 0.00 0.00 3.69
42 43 1.668237 GCATCGAGGAGAAAAAGGAGC 59.332 52.381 0.00 0.00 0.00 4.70
43 44 2.679349 GCATCGAGGAGAAAAAGGAGCT 60.679 50.000 0.00 0.00 0.00 4.09
44 45 2.751166 TCGAGGAGAAAAAGGAGCTG 57.249 50.000 0.00 0.00 0.00 4.24
45 46 2.248248 TCGAGGAGAAAAAGGAGCTGA 58.752 47.619 0.00 0.00 0.00 4.26
46 47 2.028930 TCGAGGAGAAAAAGGAGCTGAC 60.029 50.000 0.00 0.00 0.00 3.51
47 48 2.342179 GAGGAGAAAAAGGAGCTGACG 58.658 52.381 0.00 0.00 0.00 4.35
48 49 0.799393 GGAGAAAAAGGAGCTGACGC 59.201 55.000 0.00 0.00 0.00 5.19
63 64 4.315122 CGCTCCTCGTCCCGATCG 62.315 72.222 8.51 8.51 34.61 3.69
64 65 3.967335 GCTCCTCGTCCCGATCGG 61.967 72.222 27.65 27.65 34.61 4.18
74 75 3.822192 CCGATCGGGAGTGTCGCA 61.822 66.667 26.95 0.00 38.47 5.10
75 76 2.278206 CGATCGGGAGTGTCGCAG 60.278 66.667 7.38 0.00 33.96 5.18
76 77 2.583593 GATCGGGAGTGTCGCAGC 60.584 66.667 0.00 0.00 0.00 5.25
77 78 4.148825 ATCGGGAGTGTCGCAGCC 62.149 66.667 0.00 0.00 0.00 4.85
101 102 3.787001 GAGTTGAGGGGCCGGGAG 61.787 72.222 2.18 0.00 0.00 4.30
102 103 4.332543 AGTTGAGGGGCCGGGAGA 62.333 66.667 2.18 0.00 0.00 3.71
103 104 3.787001 GTTGAGGGGCCGGGAGAG 61.787 72.222 2.18 0.00 0.00 3.20
112 113 3.151022 CCGGGAGAGGAGAGCCAC 61.151 72.222 0.00 0.00 36.29 5.01
113 114 3.522731 CGGGAGAGGAGAGCCACG 61.523 72.222 0.00 0.00 36.29 4.94
114 115 2.043852 GGGAGAGGAGAGCCACGA 60.044 66.667 0.00 0.00 36.29 4.35
115 116 2.124693 GGGAGAGGAGAGCCACGAG 61.125 68.421 0.00 0.00 36.29 4.18
116 117 2.124693 GGAGAGGAGAGCCACGAGG 61.125 68.421 0.00 0.00 36.29 4.63
117 118 2.043450 AGAGGAGAGCCACGAGGG 60.043 66.667 0.00 0.00 40.85 4.30
118 119 2.043852 GAGGAGAGCCACGAGGGA 60.044 66.667 0.00 0.00 40.01 4.20
119 120 2.043450 AGGAGAGCCACGAGGGAG 60.043 66.667 0.00 0.00 40.01 4.30
120 121 3.151022 GGAGAGCCACGAGGGAGG 61.151 72.222 0.00 0.00 40.01 4.30
130 131 2.524394 GAGGGAGGCCGGCAGATA 60.524 66.667 30.85 0.00 0.00 1.98
131 132 2.525381 AGGGAGGCCGGCAGATAG 60.525 66.667 30.85 0.00 0.00 2.08
132 133 4.321966 GGGAGGCCGGCAGATAGC 62.322 72.222 30.85 9.73 44.65 2.97
133 134 3.237741 GGAGGCCGGCAGATAGCT 61.238 66.667 30.85 15.26 44.79 3.32
141 142 2.590007 GCAGATAGCTGGCCGTGG 60.590 66.667 10.52 0.00 42.53 4.94
142 143 3.094062 GCAGATAGCTGGCCGTGGA 62.094 63.158 10.52 0.00 42.53 4.02
143 144 1.068753 CAGATAGCTGGCCGTGGAG 59.931 63.158 0.00 0.00 38.51 3.86
144 145 2.136878 AGATAGCTGGCCGTGGAGG 61.137 63.158 0.00 0.00 44.97 4.30
145 146 2.041922 ATAGCTGGCCGTGGAGGA 60.042 61.111 0.00 0.00 45.00 3.71
146 147 2.093537 GATAGCTGGCCGTGGAGGAG 62.094 65.000 0.00 0.00 45.00 3.69
153 154 4.227134 CCGTGGAGGAGCCGGATG 62.227 72.222 5.05 0.00 44.41 3.51
154 155 4.899239 CGTGGAGGAGCCGGATGC 62.899 72.222 5.05 3.22 40.66 3.91
193 194 4.520846 GGCGGCGCGATCAACAAG 62.521 66.667 26.95 0.00 0.00 3.16
194 195 4.520846 GCGGCGCGATCAACAAGG 62.521 66.667 19.09 0.00 0.00 3.61
195 196 2.813474 CGGCGCGATCAACAAGGA 60.813 61.111 12.10 0.00 0.00 3.36
196 197 2.785258 GGCGCGATCAACAAGGAC 59.215 61.111 12.10 0.00 0.00 3.85
197 198 2.395690 GCGCGATCAACAAGGACG 59.604 61.111 12.10 0.00 0.00 4.79
198 199 3.081133 CGCGATCAACAAGGACGG 58.919 61.111 0.00 0.00 0.00 4.79
199 200 2.785258 GCGATCAACAAGGACGGC 59.215 61.111 0.00 0.00 0.00 5.68
200 201 3.081133 CGATCAACAAGGACGGCG 58.919 61.111 4.80 4.80 0.00 6.46
201 202 2.452813 CGATCAACAAGGACGGCGG 61.453 63.158 13.24 0.00 0.00 6.13
202 203 2.746277 ATCAACAAGGACGGCGGC 60.746 61.111 13.24 8.60 0.00 6.53
225 226 2.328639 GACGCGATCGAGGAGGAC 59.671 66.667 21.57 3.10 39.41 3.85
226 227 3.509296 GACGCGATCGAGGAGGACG 62.509 68.421 21.57 13.29 39.41 4.79
227 228 4.315122 CGCGATCGAGGAGGACGG 62.315 72.222 21.57 0.00 38.10 4.79
228 229 4.632458 GCGATCGAGGAGGACGGC 62.632 72.222 21.57 0.00 0.00 5.68
229 230 4.315122 CGATCGAGGAGGACGGCG 62.315 72.222 10.26 4.80 0.00 6.46
230 231 2.900838 GATCGAGGAGGACGGCGA 60.901 66.667 16.62 0.00 35.79 5.54
231 232 3.183776 GATCGAGGAGGACGGCGAC 62.184 68.421 16.62 7.58 34.57 5.19
246 247 4.747529 GACGGCGGCGTAGGGTTT 62.748 66.667 37.57 13.25 0.00 3.27
247 248 3.355203 GACGGCGGCGTAGGGTTTA 62.355 63.158 37.57 0.00 0.00 2.01
248 249 2.584143 CGGCGGCGTAGGGTTTAG 60.584 66.667 24.74 0.00 0.00 1.85
249 250 2.202974 GGCGGCGTAGGGTTTAGG 60.203 66.667 9.37 0.00 0.00 2.69
250 251 2.893895 GCGGCGTAGGGTTTAGGC 60.894 66.667 9.37 0.00 0.00 3.93
251 252 2.584143 CGGCGTAGGGTTTAGGCG 60.584 66.667 0.00 0.00 45.35 5.52
252 253 2.202974 GGCGTAGGGTTTAGGCGG 60.203 66.667 0.00 0.00 0.00 6.13
253 254 2.724273 GGCGTAGGGTTTAGGCGGA 61.724 63.158 0.00 0.00 0.00 5.54
254 255 1.218854 GCGTAGGGTTTAGGCGGAA 59.781 57.895 0.00 0.00 0.00 4.30
255 256 0.808847 GCGTAGGGTTTAGGCGGAAG 60.809 60.000 0.00 0.00 0.00 3.46
269 270 1.841450 CGGAAGCGATTGACCTAGTC 58.159 55.000 0.00 0.00 0.00 2.59
270 271 1.405821 CGGAAGCGATTGACCTAGTCT 59.594 52.381 0.00 0.00 33.15 3.24
271 272 2.796383 CGGAAGCGATTGACCTAGTCTG 60.796 54.545 0.00 0.00 33.15 3.51
272 273 2.427453 GGAAGCGATTGACCTAGTCTGA 59.573 50.000 0.00 0.00 33.15 3.27
273 274 3.068873 GGAAGCGATTGACCTAGTCTGAT 59.931 47.826 0.00 0.00 33.15 2.90
274 275 4.278669 GGAAGCGATTGACCTAGTCTGATA 59.721 45.833 0.00 0.00 33.15 2.15
275 276 4.839668 AGCGATTGACCTAGTCTGATAC 57.160 45.455 0.00 0.00 33.15 2.24
276 277 3.570550 AGCGATTGACCTAGTCTGATACC 59.429 47.826 0.00 0.00 33.15 2.73
277 278 3.318275 GCGATTGACCTAGTCTGATACCA 59.682 47.826 0.00 0.00 33.15 3.25
278 279 4.021894 GCGATTGACCTAGTCTGATACCAT 60.022 45.833 0.00 0.00 33.15 3.55
279 280 5.465051 CGATTGACCTAGTCTGATACCATG 58.535 45.833 0.00 0.00 33.15 3.66
280 281 5.010112 CGATTGACCTAGTCTGATACCATGT 59.990 44.000 0.00 0.00 33.15 3.21
281 282 6.206829 CGATTGACCTAGTCTGATACCATGTA 59.793 42.308 0.00 0.00 33.15 2.29
282 283 7.255486 CGATTGACCTAGTCTGATACCATGTAA 60.255 40.741 0.00 0.00 33.15 2.41
283 284 6.961360 TGACCTAGTCTGATACCATGTAAG 57.039 41.667 0.00 0.00 33.15 2.34
284 285 6.669631 TGACCTAGTCTGATACCATGTAAGA 58.330 40.000 0.00 0.00 33.15 2.10
285 286 6.546403 TGACCTAGTCTGATACCATGTAAGAC 59.454 42.308 0.00 0.00 38.01 3.01
286 287 6.432581 ACCTAGTCTGATACCATGTAAGACA 58.567 40.000 4.16 0.00 39.77 3.41
287 288 6.895756 ACCTAGTCTGATACCATGTAAGACAA 59.104 38.462 4.16 0.00 39.77 3.18
288 289 7.565398 ACCTAGTCTGATACCATGTAAGACAAT 59.435 37.037 4.16 0.00 39.77 2.71
289 290 9.078990 CCTAGTCTGATACCATGTAAGACAATA 57.921 37.037 4.16 0.00 39.77 1.90
291 292 7.957002 AGTCTGATACCATGTAAGACAATAGG 58.043 38.462 4.16 0.00 39.77 2.57
292 293 7.565398 AGTCTGATACCATGTAAGACAATAGGT 59.435 37.037 4.16 0.00 39.77 3.08
293 294 8.204836 GTCTGATACCATGTAAGACAATAGGTT 58.795 37.037 6.95 0.00 37.72 3.50
294 295 8.768397 TCTGATACCATGTAAGACAATAGGTTT 58.232 33.333 6.95 1.38 34.89 3.27
295 296 8.731275 TGATACCATGTAAGACAATAGGTTTG 57.269 34.615 6.95 0.00 34.89 2.93
296 297 7.773224 TGATACCATGTAAGACAATAGGTTTGG 59.227 37.037 6.95 0.84 34.89 3.28
297 298 5.261216 ACCATGTAAGACAATAGGTTTGGG 58.739 41.667 0.00 0.00 30.92 4.12
298 299 4.644685 CCATGTAAGACAATAGGTTTGGGG 59.355 45.833 0.00 0.00 0.00 4.96
299 300 4.310022 TGTAAGACAATAGGTTTGGGGG 57.690 45.455 0.00 0.00 0.00 5.40
300 301 3.917629 TGTAAGACAATAGGTTTGGGGGA 59.082 43.478 0.00 0.00 0.00 4.81
301 302 4.354387 TGTAAGACAATAGGTTTGGGGGAA 59.646 41.667 0.00 0.00 0.00 3.97
302 303 3.451402 AGACAATAGGTTTGGGGGAAC 57.549 47.619 0.00 0.00 0.00 3.62
303 304 2.993863 AGACAATAGGTTTGGGGGAACT 59.006 45.455 0.00 0.00 0.00 3.01
304 305 3.089284 GACAATAGGTTTGGGGGAACTG 58.911 50.000 0.00 0.00 0.00 3.16
305 306 2.225267 ACAATAGGTTTGGGGGAACTGG 60.225 50.000 0.00 0.00 0.00 4.00
306 307 0.335019 ATAGGTTTGGGGGAACTGGC 59.665 55.000 0.00 0.00 0.00 4.85
307 308 0.774491 TAGGTTTGGGGGAACTGGCT 60.774 55.000 0.00 0.00 0.00 4.75
308 309 1.606601 GGTTTGGGGGAACTGGCTC 60.607 63.158 0.00 0.00 0.00 4.70
309 310 1.152830 GTTTGGGGGAACTGGCTCA 59.847 57.895 0.00 0.00 0.00 4.26
310 311 0.469144 GTTTGGGGGAACTGGCTCAA 60.469 55.000 0.00 0.00 0.00 3.02
311 312 0.469144 TTTGGGGGAACTGGCTCAAC 60.469 55.000 0.00 0.00 0.00 3.18
312 313 2.035783 GGGGGAACTGGCTCAACC 59.964 66.667 0.00 0.00 39.84 3.77
313 314 2.035783 GGGGAACTGGCTCAACCC 59.964 66.667 0.00 0.00 37.83 4.11
314 315 2.539081 GGGGAACTGGCTCAACCCT 61.539 63.158 0.00 0.00 40.31 4.34
315 316 1.002011 GGGAACTGGCTCAACCCTC 60.002 63.158 0.00 0.00 37.83 4.30
316 317 1.492993 GGGAACTGGCTCAACCCTCT 61.493 60.000 0.00 0.00 37.83 3.69
317 318 1.276622 GGAACTGGCTCAACCCTCTA 58.723 55.000 0.00 0.00 37.83 2.43
318 319 1.208293 GGAACTGGCTCAACCCTCTAG 59.792 57.143 0.00 0.00 37.83 2.43
319 320 2.180276 GAACTGGCTCAACCCTCTAGA 58.820 52.381 0.00 0.00 37.83 2.43
320 321 1.859302 ACTGGCTCAACCCTCTAGAG 58.141 55.000 13.18 13.18 37.83 2.43
423 424 6.963049 AATGAAGAGGTACAACGTTACATC 57.037 37.500 0.00 3.91 0.00 3.06
424 425 5.456548 TGAAGAGGTACAACGTTACATCA 57.543 39.130 15.78 6.45 30.33 3.07
425 426 6.032956 TGAAGAGGTACAACGTTACATCAT 57.967 37.500 15.78 6.07 30.33 2.45
426 427 7.160547 TGAAGAGGTACAACGTTACATCATA 57.839 36.000 15.78 2.08 30.33 2.15
427 428 7.031372 TGAAGAGGTACAACGTTACATCATAC 58.969 38.462 15.78 8.47 30.33 2.39
428 429 5.575957 AGAGGTACAACGTTACATCATACG 58.424 41.667 15.78 0.00 43.08 3.06
454 455 9.378597 GTACACATACGTACACATATACAGAAG 57.621 37.037 0.00 0.00 41.20 2.85
455 456 6.916387 ACACATACGTACACATATACAGAAGC 59.084 38.462 0.00 0.00 0.00 3.86
456 457 7.139392 CACATACGTACACATATACAGAAGCT 58.861 38.462 0.00 0.00 0.00 3.74
457 458 8.287503 CACATACGTACACATATACAGAAGCTA 58.712 37.037 0.00 0.00 0.00 3.32
458 459 9.011095 ACATACGTACACATATACAGAAGCTAT 57.989 33.333 0.00 0.00 0.00 2.97
461 462 8.387190 ACGTACACATATACAGAAGCTATACA 57.613 34.615 0.00 0.00 0.00 2.29
462 463 8.504815 ACGTACACATATACAGAAGCTATACAG 58.495 37.037 0.00 0.00 0.00 2.74
463 464 8.504815 CGTACACATATACAGAAGCTATACAGT 58.495 37.037 0.00 0.00 0.00 3.55
499 500 7.285629 TGTGATTATGTTTTGAGGTGGTTTGTA 59.714 33.333 0.00 0.00 0.00 2.41
652 663 5.940617 TGCATAGCAACCCAAGAATAGTAT 58.059 37.500 0.00 0.00 34.76 2.12
970 981 1.871676 TCGATCGATCCTAACGGTGAG 59.128 52.381 19.51 1.80 0.00 3.51
987 998 6.968250 ACGGTGAGTAATAATCTACTACAGC 58.032 40.000 0.00 0.00 32.14 4.40
1039 1050 4.070552 GGCCCGTCTCGTTGCTCT 62.071 66.667 0.00 0.00 0.00 4.09
1227 1238 4.516195 GTTCGGGAGGAGAGCGGC 62.516 72.222 0.00 0.00 0.00 6.53
1401 1412 4.129148 GGGCTGGGCGGGAAGATT 62.129 66.667 0.00 0.00 0.00 2.40
1659 1670 0.391597 ACATCCACGTGAACGACCTT 59.608 50.000 19.30 0.00 43.02 3.50
1884 1895 1.154016 CGACGTCATGCTCTTCGGT 60.154 57.895 17.16 0.00 0.00 4.69
1985 1996 5.072736 AGAGAATGCCAAGGTCATCATCATA 59.927 40.000 0.00 0.00 0.00 2.15
1988 1999 5.977489 ATGCCAAGGTCATCATCATAATG 57.023 39.130 0.00 0.00 0.00 1.90
2229 2248 4.208686 CTGTACGCGGAGGAGGCC 62.209 72.222 12.47 0.00 0.00 5.19
2477 2496 4.770795 TCCCTTCCGAATCTTCAATTCTC 58.229 43.478 0.00 0.00 0.00 2.87
2478 2497 4.471386 TCCCTTCCGAATCTTCAATTCTCT 59.529 41.667 0.00 0.00 0.00 3.10
2479 2498 5.661312 TCCCTTCCGAATCTTCAATTCTCTA 59.339 40.000 0.00 0.00 0.00 2.43
2587 2613 4.345859 CCCTGTAGGTTGTTCTTGTACA 57.654 45.455 0.00 0.00 0.00 2.90
2742 2773 3.063045 GGGCCGAGACTAATTTGTTAACG 59.937 47.826 0.00 1.67 0.00 3.18
2748 2780 7.413328 GCCGAGACTAATTTGTTAACGGTTATT 60.413 37.037 22.19 0.00 39.95 1.40
2848 2883 2.196925 TGTGCAATTTTCCCCGCGT 61.197 52.632 4.92 0.00 0.00 6.01
2899 2934 1.560505 ATTGTTGGGGCTGGACAATC 58.439 50.000 6.95 0.00 39.14 2.67
2917 2952 3.933861 ATCACCCACTTCCTACAATCC 57.066 47.619 0.00 0.00 0.00 3.01
2921 2956 0.251916 CCACTTCCTACAATCCGGCA 59.748 55.000 0.00 0.00 0.00 5.69
2948 2983 1.440618 TTGGGCCAGGTTGTCTCTTA 58.559 50.000 6.23 0.00 0.00 2.10
2959 2994 3.055819 GGTTGTCTCTTACCTGCTCATGA 60.056 47.826 0.00 0.00 0.00 3.07
2961 2996 4.462508 TGTCTCTTACCTGCTCATGAAG 57.537 45.455 0.00 0.00 0.00 3.02
2967 3002 0.689055 ACCTGCTCATGAAGTCAGCA 59.311 50.000 6.43 6.43 31.61 4.41
2984 3019 5.008415 AGTCAGCAGTCAGTTCAAAAGATTG 59.992 40.000 0.00 0.00 37.92 2.67
3006 3041 7.645058 TTGACCTATTTGAAATGGAATCTCC 57.355 36.000 2.62 0.00 36.96 3.71
3011 3046 6.491403 CCTATTTGAAATGGAATCTCCGGATT 59.509 38.462 3.57 0.00 43.99 3.01
3124 3159 7.100458 ACCAATTAGTTAGCAATGTTCCATC 57.900 36.000 0.00 0.00 0.00 3.51
3129 3165 9.995003 AATTAGTTAGCAATGTTCCATCAAAAA 57.005 25.926 0.00 0.00 0.00 1.94
3152 3188 7.930513 AAAACTAGCAAGCAACAGAATAAAC 57.069 32.000 0.00 0.00 0.00 2.01
3164 3200 8.629158 AGCAACAGAATAAACTCAAACAACATA 58.371 29.630 0.00 0.00 0.00 2.29
3165 3201 9.410556 GCAACAGAATAAACTCAAACAACATAT 57.589 29.630 0.00 0.00 0.00 1.78
3197 3233 8.242053 TGACACTTAATTTAACGTGGAAAAACA 58.758 29.630 16.26 0.00 0.00 2.83
3198 3234 8.397215 ACACTTAATTTAACGTGGAAAAACAC 57.603 30.769 16.26 0.00 37.99 3.32
3199 3235 7.488792 ACACTTAATTTAACGTGGAAAAACACC 59.511 33.333 16.26 0.00 38.11 4.16
3200 3236 7.488471 CACTTAATTTAACGTGGAAAAACACCA 59.512 33.333 0.00 0.00 38.11 4.17
3232 3269 3.758554 ACACAACTTCACCATTAGGATGC 59.241 43.478 0.00 0.00 38.69 3.91
3234 3271 5.185454 CACAACTTCACCATTAGGATGCTA 58.815 41.667 0.00 0.00 38.69 3.49
3288 3325 3.118454 CCAACCGGCACAGTAGCG 61.118 66.667 0.00 0.00 34.64 4.26
3289 3326 3.118454 CAACCGGCACAGTAGCGG 61.118 66.667 0.00 0.00 35.37 5.52
3290 3327 3.307906 AACCGGCACAGTAGCGGA 61.308 61.111 0.00 0.00 37.03 5.54
3291 3328 3.296709 AACCGGCACAGTAGCGGAG 62.297 63.158 0.00 0.00 37.03 4.63
3306 3343 1.216122 CGGAGCTAGAAGCAGATTGC 58.784 55.000 1.22 0.00 45.56 3.56
3326 3363 2.409948 GCCTGGGGCTAAGCTATATG 57.590 55.000 0.80 0.00 46.69 1.78
3327 3364 1.909302 GCCTGGGGCTAAGCTATATGA 59.091 52.381 0.80 0.00 46.69 2.15
3328 3365 2.093235 GCCTGGGGCTAAGCTATATGAG 60.093 54.545 0.80 0.00 46.69 2.90
3329 3366 3.177228 CCTGGGGCTAAGCTATATGAGT 58.823 50.000 0.00 0.00 0.00 3.41
3330 3367 3.055530 CCTGGGGCTAAGCTATATGAGTG 60.056 52.174 0.00 0.00 0.00 3.51
3331 3368 3.834813 CTGGGGCTAAGCTATATGAGTGA 59.165 47.826 0.00 0.00 0.00 3.41
3332 3369 4.231273 TGGGGCTAAGCTATATGAGTGAA 58.769 43.478 0.00 0.00 0.00 3.18
3333 3370 4.658435 TGGGGCTAAGCTATATGAGTGAAA 59.342 41.667 0.00 0.00 0.00 2.69
3334 3371 5.131977 TGGGGCTAAGCTATATGAGTGAAAA 59.868 40.000 0.00 0.00 0.00 2.29
3335 3372 6.062095 GGGGCTAAGCTATATGAGTGAAAAA 58.938 40.000 0.00 0.00 0.00 1.94
3336 3373 6.717084 GGGGCTAAGCTATATGAGTGAAAAAT 59.283 38.462 0.00 0.00 0.00 1.82
3337 3374 7.231519 GGGGCTAAGCTATATGAGTGAAAAATT 59.768 37.037 0.00 0.00 0.00 1.82
3338 3375 8.633561 GGGCTAAGCTATATGAGTGAAAAATTT 58.366 33.333 0.00 0.00 0.00 1.82
3339 3376 9.670719 GGCTAAGCTATATGAGTGAAAAATTTC 57.329 33.333 0.00 0.00 37.69 2.17
3344 3381 9.817809 AGCTATATGAGTGAAAAATTTCTACGA 57.182 29.630 7.36 0.00 38.02 3.43
3361 3398 9.606631 ATTTCTACGATTTTCTATGCTTTCTCT 57.393 29.630 0.00 0.00 0.00 3.10
3366 3403 8.202745 ACGATTTTCTATGCTTTCTCTAAAGG 57.797 34.615 0.00 0.00 42.07 3.11
3367 3404 8.041323 ACGATTTTCTATGCTTTCTCTAAAGGA 58.959 33.333 0.00 0.00 45.62 3.36
3368 3405 8.883731 CGATTTTCTATGCTTTCTCTAAAGGAA 58.116 33.333 0.00 0.00 44.85 3.36
3376 3413 7.687941 TGCTTTCTCTAAAGGAATTACAAGG 57.312 36.000 0.00 0.00 39.75 3.61
3377 3414 6.659242 TGCTTTCTCTAAAGGAATTACAAGGG 59.341 38.462 0.00 0.00 39.75 3.95
3378 3415 6.884836 GCTTTCTCTAAAGGAATTACAAGGGA 59.115 38.462 0.00 0.00 42.07 4.20
3379 3416 7.393515 GCTTTCTCTAAAGGAATTACAAGGGAA 59.606 37.037 0.00 0.00 42.07 3.97
3380 3417 9.467796 CTTTCTCTAAAGGAATTACAAGGGAAT 57.532 33.333 2.00 0.00 38.77 3.01
3381 3418 9.822727 TTTCTCTAAAGGAATTACAAGGGAATT 57.177 29.630 2.00 0.00 0.00 2.17
3382 3419 9.822727 TTCTCTAAAGGAATTACAAGGGAATTT 57.177 29.630 0.00 0.00 0.00 1.82
3383 3420 9.462606 TCTCTAAAGGAATTACAAGGGAATTTC 57.537 33.333 0.00 0.00 0.00 2.17
3384 3421 9.467796 CTCTAAAGGAATTACAAGGGAATTTCT 57.532 33.333 0.00 0.00 34.20 2.52
3385 3422 9.822727 TCTAAAGGAATTACAAGGGAATTTCTT 57.177 29.630 2.25 2.25 41.77 2.52
3388 3425 9.601810 AAAGGAATTACAAGGGAATTTCTTAGT 57.398 29.630 7.67 0.00 39.96 2.24
3390 3427 9.907229 AGGAATTACAAGGGAATTTCTTAGTAG 57.093 33.333 0.00 0.00 29.32 2.57
3391 3428 9.121658 GGAATTACAAGGGAATTTCTTAGTAGG 57.878 37.037 0.00 0.00 0.00 3.18
3392 3429 8.521170 AATTACAAGGGAATTTCTTAGTAGGC 57.479 34.615 0.00 0.00 0.00 3.93
3393 3430 4.856509 ACAAGGGAATTTCTTAGTAGGCC 58.143 43.478 0.00 0.00 0.00 5.19
3394 3431 3.840124 AGGGAATTTCTTAGTAGGCCG 57.160 47.619 0.00 0.00 0.00 6.13
3395 3432 2.438392 AGGGAATTTCTTAGTAGGCCGG 59.562 50.000 0.00 0.00 0.00 6.13
3396 3433 2.486727 GGGAATTTCTTAGTAGGCCGGG 60.487 54.545 2.18 0.00 0.00 5.73
3397 3434 2.219458 GAATTTCTTAGTAGGCCGGGC 58.781 52.381 22.67 22.67 0.00 6.13
3398 3435 1.508256 ATTTCTTAGTAGGCCGGGCT 58.492 50.000 34.70 34.70 0.00 5.19
3399 3436 2.163810 TTTCTTAGTAGGCCGGGCTA 57.836 50.000 32.25 32.25 0.00 3.93
3400 3437 1.406903 TTCTTAGTAGGCCGGGCTAC 58.593 55.000 44.99 44.99 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.276091 CAACGCGCTGGTGGTTCA 61.276 61.111 5.73 0.00 0.00 3.18
14 15 4.467084 TCCTCGATGCCGGGCAAC 62.467 66.667 27.70 22.67 43.62 4.17
15 16 4.161295 CTCCTCGATGCCGGGCAA 62.161 66.667 27.70 8.95 43.62 4.52
17 18 2.869503 TTTTCTCCTCGATGCCGGGC 62.870 60.000 13.32 13.32 34.24 6.13
18 19 0.392461 TTTTTCTCCTCGATGCCGGG 60.392 55.000 2.18 0.00 36.24 5.73
19 20 1.009829 CTTTTTCTCCTCGATGCCGG 58.990 55.000 0.00 0.00 36.24 6.13
20 21 1.009829 CCTTTTTCTCCTCGATGCCG 58.990 55.000 0.00 0.00 37.07 5.69
21 22 2.284190 CTCCTTTTTCTCCTCGATGCC 58.716 52.381 0.00 0.00 0.00 4.40
22 23 1.668237 GCTCCTTTTTCTCCTCGATGC 59.332 52.381 0.00 0.00 0.00 3.91
23 24 2.935201 CAGCTCCTTTTTCTCCTCGATG 59.065 50.000 0.00 0.00 0.00 3.84
24 25 2.834549 TCAGCTCCTTTTTCTCCTCGAT 59.165 45.455 0.00 0.00 0.00 3.59
25 26 2.028930 GTCAGCTCCTTTTTCTCCTCGA 60.029 50.000 0.00 0.00 0.00 4.04
26 27 2.342179 GTCAGCTCCTTTTTCTCCTCG 58.658 52.381 0.00 0.00 0.00 4.63
27 28 2.342179 CGTCAGCTCCTTTTTCTCCTC 58.658 52.381 0.00 0.00 0.00 3.71
28 29 1.609320 GCGTCAGCTCCTTTTTCTCCT 60.609 52.381 0.00 0.00 41.01 3.69
29 30 0.799393 GCGTCAGCTCCTTTTTCTCC 59.201 55.000 0.00 0.00 41.01 3.71
57 58 3.758088 CTGCGACACTCCCGATCGG 62.758 68.421 27.65 27.65 36.37 4.18
58 59 2.278206 CTGCGACACTCCCGATCG 60.278 66.667 8.51 8.51 38.87 3.69
59 60 2.583593 GCTGCGACACTCCCGATC 60.584 66.667 0.00 0.00 0.00 3.69
60 61 4.148825 GGCTGCGACACTCCCGAT 62.149 66.667 0.00 0.00 0.00 4.18
84 85 3.787001 CTCCCGGCCCCTCAACTC 61.787 72.222 0.00 0.00 0.00 3.01
85 86 4.332543 TCTCCCGGCCCCTCAACT 62.333 66.667 0.00 0.00 0.00 3.16
86 87 3.787001 CTCTCCCGGCCCCTCAAC 61.787 72.222 0.00 0.00 0.00 3.18
95 96 3.151022 GTGGCTCTCCTCTCCCGG 61.151 72.222 0.00 0.00 0.00 5.73
96 97 3.522731 CGTGGCTCTCCTCTCCCG 61.523 72.222 0.00 0.00 0.00 5.14
97 98 2.043852 TCGTGGCTCTCCTCTCCC 60.044 66.667 0.00 0.00 0.00 4.30
98 99 2.124693 CCTCGTGGCTCTCCTCTCC 61.125 68.421 0.00 0.00 0.00 3.71
99 100 2.124693 CCCTCGTGGCTCTCCTCTC 61.125 68.421 0.00 0.00 0.00 3.20
100 101 2.043450 CCCTCGTGGCTCTCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
101 102 2.043852 TCCCTCGTGGCTCTCCTC 60.044 66.667 0.00 0.00 0.00 3.71
102 103 2.043450 CTCCCTCGTGGCTCTCCT 60.043 66.667 0.00 0.00 0.00 3.69
103 104 3.151022 CCTCCCTCGTGGCTCTCC 61.151 72.222 0.00 0.00 0.00 3.71
104 105 3.844090 GCCTCCCTCGTGGCTCTC 61.844 72.222 0.00 0.00 43.90 3.20
113 114 2.524394 TATCTGCCGGCCTCCCTC 60.524 66.667 26.77 0.00 0.00 4.30
114 115 2.525381 CTATCTGCCGGCCTCCCT 60.525 66.667 26.77 6.65 0.00 4.20
115 116 4.321966 GCTATCTGCCGGCCTCCC 62.322 72.222 26.77 3.33 35.15 4.30
116 117 3.237741 AGCTATCTGCCGGCCTCC 61.238 66.667 26.77 6.24 44.23 4.30
117 118 2.030262 CAGCTATCTGCCGGCCTC 59.970 66.667 26.77 6.27 44.23 4.70
118 119 3.554342 CCAGCTATCTGCCGGCCT 61.554 66.667 26.77 9.76 44.23 5.19
121 122 4.976925 CGGCCAGCTATCTGCCGG 62.977 72.222 23.00 0.00 46.45 6.13
123 124 2.590007 CACGGCCAGCTATCTGCC 60.590 66.667 2.24 5.84 44.23 4.85
124 125 2.590007 CCACGGCCAGCTATCTGC 60.590 66.667 2.24 0.00 39.00 4.26
125 126 1.068753 CTCCACGGCCAGCTATCTG 59.931 63.158 2.24 0.00 40.02 2.90
126 127 2.136878 CCTCCACGGCCAGCTATCT 61.137 63.158 2.24 0.00 0.00 1.98
127 128 2.093537 CTCCTCCACGGCCAGCTATC 62.094 65.000 2.24 0.00 0.00 2.08
128 129 2.041922 TCCTCCACGGCCAGCTAT 60.042 61.111 2.24 0.00 0.00 2.97
129 130 2.759973 CTCCTCCACGGCCAGCTA 60.760 66.667 2.24 0.00 0.00 3.32
137 138 4.899239 GCATCCGGCTCCTCCACG 62.899 72.222 0.00 0.00 40.25 4.94
138 139 4.899239 CGCATCCGGCTCCTCCAC 62.899 72.222 0.00 0.00 41.67 4.02
176 177 4.520846 CTTGTTGATCGCGCCGCC 62.521 66.667 2.28 0.00 0.00 6.13
177 178 4.520846 CCTTGTTGATCGCGCCGC 62.521 66.667 0.00 0.00 0.00 6.53
178 179 2.813474 TCCTTGTTGATCGCGCCG 60.813 61.111 0.00 0.00 0.00 6.46
179 180 2.785258 GTCCTTGTTGATCGCGCC 59.215 61.111 0.00 0.00 0.00 6.53
180 181 2.395690 CGTCCTTGTTGATCGCGC 59.604 61.111 0.00 0.00 0.00 6.86
181 182 3.081133 CCGTCCTTGTTGATCGCG 58.919 61.111 0.00 0.00 0.00 5.87
182 183 2.785258 GCCGTCCTTGTTGATCGC 59.215 61.111 0.00 0.00 0.00 4.58
183 184 2.452813 CCGCCGTCCTTGTTGATCG 61.453 63.158 0.00 0.00 0.00 3.69
184 185 2.750888 GCCGCCGTCCTTGTTGATC 61.751 63.158 0.00 0.00 0.00 2.92
185 186 2.746277 GCCGCCGTCCTTGTTGAT 60.746 61.111 0.00 0.00 0.00 2.57
208 209 2.328639 GTCCTCCTCGATCGCGTC 59.671 66.667 11.09 1.94 38.98 5.19
209 210 3.574445 CGTCCTCCTCGATCGCGT 61.574 66.667 11.09 0.00 38.98 6.01
210 211 4.315122 CCGTCCTCCTCGATCGCG 62.315 72.222 11.09 3.62 39.35 5.87
211 212 4.632458 GCCGTCCTCCTCGATCGC 62.632 72.222 11.09 0.00 0.00 4.58
212 213 4.315122 CGCCGTCCTCCTCGATCG 62.315 72.222 9.36 9.36 0.00 3.69
213 214 2.900838 TCGCCGTCCTCCTCGATC 60.901 66.667 0.00 0.00 0.00 3.69
214 215 3.210528 GTCGCCGTCCTCCTCGAT 61.211 66.667 0.00 0.00 33.37 3.59
229 230 3.355203 TAAACCCTACGCCGCCGTC 62.355 63.158 0.00 0.00 46.39 4.79
231 232 2.584143 CTAAACCCTACGCCGCCG 60.584 66.667 0.00 0.00 41.14 6.46
232 233 2.202974 CCTAAACCCTACGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
233 234 2.893895 GCCTAAACCCTACGCCGC 60.894 66.667 0.00 0.00 0.00 6.53
234 235 2.584143 CGCCTAAACCCTACGCCG 60.584 66.667 0.00 0.00 0.00 6.46
235 236 2.202974 CCGCCTAAACCCTACGCC 60.203 66.667 0.00 0.00 0.00 5.68
236 237 0.808847 CTTCCGCCTAAACCCTACGC 60.809 60.000 0.00 0.00 0.00 4.42
237 238 0.808847 GCTTCCGCCTAAACCCTACG 60.809 60.000 0.00 0.00 0.00 3.51
238 239 0.808847 CGCTTCCGCCTAAACCCTAC 60.809 60.000 0.00 0.00 0.00 3.18
239 240 0.971959 TCGCTTCCGCCTAAACCCTA 60.972 55.000 0.00 0.00 0.00 3.53
240 241 1.623542 ATCGCTTCCGCCTAAACCCT 61.624 55.000 0.00 0.00 0.00 4.34
241 242 0.746923 AATCGCTTCCGCCTAAACCC 60.747 55.000 0.00 0.00 0.00 4.11
242 243 0.377203 CAATCGCTTCCGCCTAAACC 59.623 55.000 0.00 0.00 0.00 3.27
243 244 1.062148 GTCAATCGCTTCCGCCTAAAC 59.938 52.381 0.00 0.00 0.00 2.01
244 245 1.365699 GTCAATCGCTTCCGCCTAAA 58.634 50.000 0.00 0.00 0.00 1.85
245 246 0.461339 GGTCAATCGCTTCCGCCTAA 60.461 55.000 0.00 0.00 0.00 2.69
246 247 1.143183 GGTCAATCGCTTCCGCCTA 59.857 57.895 0.00 0.00 0.00 3.93
247 248 1.327690 TAGGTCAATCGCTTCCGCCT 61.328 55.000 0.00 0.00 0.00 5.52
248 249 0.876342 CTAGGTCAATCGCTTCCGCC 60.876 60.000 0.00 0.00 0.00 6.13
249 250 0.179108 ACTAGGTCAATCGCTTCCGC 60.179 55.000 0.00 0.00 0.00 5.54
250 251 1.405821 AGACTAGGTCAATCGCTTCCG 59.594 52.381 0.00 0.00 34.60 4.30
251 252 2.427453 TCAGACTAGGTCAATCGCTTCC 59.573 50.000 0.00 0.00 34.60 3.46
252 253 3.784701 TCAGACTAGGTCAATCGCTTC 57.215 47.619 0.00 0.00 34.60 3.86
253 254 4.038162 GGTATCAGACTAGGTCAATCGCTT 59.962 45.833 0.00 0.00 34.60 4.68
254 255 3.570550 GGTATCAGACTAGGTCAATCGCT 59.429 47.826 0.00 0.00 34.60 4.93
255 256 3.318275 TGGTATCAGACTAGGTCAATCGC 59.682 47.826 0.00 0.00 34.60 4.58
256 257 5.010112 ACATGGTATCAGACTAGGTCAATCG 59.990 44.000 0.00 0.00 34.60 3.34
257 258 6.412362 ACATGGTATCAGACTAGGTCAATC 57.588 41.667 0.00 0.00 34.60 2.67
258 259 7.785028 TCTTACATGGTATCAGACTAGGTCAAT 59.215 37.037 0.00 0.00 35.05 2.57
259 260 7.068348 GTCTTACATGGTATCAGACTAGGTCAA 59.932 40.741 0.00 0.00 35.05 3.18
260 261 6.546403 GTCTTACATGGTATCAGACTAGGTCA 59.454 42.308 0.00 0.00 35.05 4.02
261 262 6.546403 TGTCTTACATGGTATCAGACTAGGTC 59.454 42.308 0.00 0.00 35.05 3.85
262 263 6.432581 TGTCTTACATGGTATCAGACTAGGT 58.567 40.000 0.00 0.00 37.34 3.08
263 264 6.961360 TGTCTTACATGGTATCAGACTAGG 57.039 41.667 0.00 0.00 35.80 3.02
265 266 9.078990 CCTATTGTCTTACATGGTATCAGACTA 57.921 37.037 0.00 0.00 35.80 2.59
266 267 7.565398 ACCTATTGTCTTACATGGTATCAGACT 59.435 37.037 0.00 0.00 35.80 3.24
267 268 7.727181 ACCTATTGTCTTACATGGTATCAGAC 58.273 38.462 0.00 1.66 35.42 3.51
268 269 7.914427 ACCTATTGTCTTACATGGTATCAGA 57.086 36.000 0.00 0.00 29.37 3.27
269 270 8.830580 CAAACCTATTGTCTTACATGGTATCAG 58.169 37.037 0.00 0.00 30.40 2.90
270 271 7.773224 CCAAACCTATTGTCTTACATGGTATCA 59.227 37.037 0.00 0.00 30.40 2.15
271 272 7.228706 CCCAAACCTATTGTCTTACATGGTATC 59.771 40.741 0.00 0.00 30.40 2.24
272 273 7.060421 CCCAAACCTATTGTCTTACATGGTAT 58.940 38.462 0.00 0.00 30.40 2.73
273 274 6.419791 CCCAAACCTATTGTCTTACATGGTA 58.580 40.000 0.00 0.00 30.40 3.25
274 275 5.261216 CCCAAACCTATTGTCTTACATGGT 58.739 41.667 0.00 0.00 31.33 3.55
275 276 4.644685 CCCCAAACCTATTGTCTTACATGG 59.355 45.833 0.00 0.00 0.00 3.66
276 277 4.644685 CCCCCAAACCTATTGTCTTACATG 59.355 45.833 0.00 0.00 0.00 3.21
277 278 4.542525 TCCCCCAAACCTATTGTCTTACAT 59.457 41.667 0.00 0.00 0.00 2.29
278 279 3.917629 TCCCCCAAACCTATTGTCTTACA 59.082 43.478 0.00 0.00 0.00 2.41
279 280 4.579647 TCCCCCAAACCTATTGTCTTAC 57.420 45.455 0.00 0.00 0.00 2.34
280 281 4.604490 AGTTCCCCCAAACCTATTGTCTTA 59.396 41.667 0.00 0.00 0.00 2.10
281 282 3.401342 AGTTCCCCCAAACCTATTGTCTT 59.599 43.478 0.00 0.00 0.00 3.01
282 283 2.993863 AGTTCCCCCAAACCTATTGTCT 59.006 45.455 0.00 0.00 0.00 3.41
283 284 3.089284 CAGTTCCCCCAAACCTATTGTC 58.911 50.000 0.00 0.00 0.00 3.18
284 285 2.225267 CCAGTTCCCCCAAACCTATTGT 60.225 50.000 0.00 0.00 0.00 2.71
285 286 2.456577 CCAGTTCCCCCAAACCTATTG 58.543 52.381 0.00 0.00 0.00 1.90
286 287 1.273041 GCCAGTTCCCCCAAACCTATT 60.273 52.381 0.00 0.00 0.00 1.73
287 288 0.335019 GCCAGTTCCCCCAAACCTAT 59.665 55.000 0.00 0.00 0.00 2.57
288 289 0.774491 AGCCAGTTCCCCCAAACCTA 60.774 55.000 0.00 0.00 0.00 3.08
289 290 2.081585 GAGCCAGTTCCCCCAAACCT 62.082 60.000 0.00 0.00 0.00 3.50
290 291 1.606601 GAGCCAGTTCCCCCAAACC 60.607 63.158 0.00 0.00 0.00 3.27
291 292 0.469144 TTGAGCCAGTTCCCCCAAAC 60.469 55.000 0.00 0.00 0.00 2.93
292 293 0.469144 GTTGAGCCAGTTCCCCCAAA 60.469 55.000 0.00 0.00 0.00 3.28
293 294 1.152830 GTTGAGCCAGTTCCCCCAA 59.847 57.895 0.00 0.00 0.00 4.12
294 295 2.840753 GGTTGAGCCAGTTCCCCCA 61.841 63.158 0.00 0.00 37.17 4.96
295 296 2.035783 GGTTGAGCCAGTTCCCCC 59.964 66.667 0.00 0.00 37.17 5.40
296 297 2.035783 GGGTTGAGCCAGTTCCCC 59.964 66.667 0.00 0.00 39.65 4.81
297 298 1.002011 GAGGGTTGAGCCAGTTCCC 60.002 63.158 1.66 0.00 39.65 3.97
298 299 1.208293 CTAGAGGGTTGAGCCAGTTCC 59.792 57.143 1.66 0.00 39.65 3.62
299 300 2.167487 CTCTAGAGGGTTGAGCCAGTTC 59.833 54.545 12.27 0.00 39.65 3.01
300 301 2.183679 CTCTAGAGGGTTGAGCCAGTT 58.816 52.381 12.27 0.00 39.65 3.16
301 302 1.621072 CCTCTAGAGGGTTGAGCCAGT 60.621 57.143 28.68 0.00 44.87 4.00
302 303 1.118838 CCTCTAGAGGGTTGAGCCAG 58.881 60.000 28.68 1.06 44.87 4.85
303 304 3.306902 CCTCTAGAGGGTTGAGCCA 57.693 57.895 28.68 0.00 44.87 4.75
397 398 9.740239 GATGTAACGTTGTACCTCTTCATTATA 57.260 33.333 11.99 0.00 0.00 0.98
398 399 8.255206 TGATGTAACGTTGTACCTCTTCATTAT 58.745 33.333 11.99 0.00 0.00 1.28
399 400 7.604549 TGATGTAACGTTGTACCTCTTCATTA 58.395 34.615 11.99 0.00 0.00 1.90
400 401 6.460781 TGATGTAACGTTGTACCTCTTCATT 58.539 36.000 11.99 0.00 0.00 2.57
401 402 6.032956 TGATGTAACGTTGTACCTCTTCAT 57.967 37.500 11.99 1.99 0.00 2.57
402 403 5.456548 TGATGTAACGTTGTACCTCTTCA 57.543 39.130 11.99 5.71 0.00 3.02
403 404 6.195983 CGTATGATGTAACGTTGTACCTCTTC 59.804 42.308 11.99 3.48 34.48 2.87
404 405 6.032094 CGTATGATGTAACGTTGTACCTCTT 58.968 40.000 11.99 5.72 34.48 2.85
405 406 5.575957 CGTATGATGTAACGTTGTACCTCT 58.424 41.667 11.99 0.00 34.48 3.69
406 407 5.861491 CGTATGATGTAACGTTGTACCTC 57.139 43.478 11.99 5.35 34.48 3.85
415 416 6.340131 CGTATGTGTACGTATGATGTAACG 57.660 41.667 0.00 0.33 46.51 3.18
428 429 9.378597 CTTCTGTATATGTGTACGTATGTGTAC 57.621 37.037 0.00 3.16 43.95 2.90
429 430 8.071967 GCTTCTGTATATGTGTACGTATGTGTA 58.928 37.037 0.00 0.00 31.14 2.90
430 431 6.916387 GCTTCTGTATATGTGTACGTATGTGT 59.084 38.462 0.00 0.00 31.14 3.72
431 432 7.139392 AGCTTCTGTATATGTGTACGTATGTG 58.861 38.462 0.00 0.00 31.14 3.21
432 433 7.273320 AGCTTCTGTATATGTGTACGTATGT 57.727 36.000 0.00 0.00 31.14 2.29
435 436 9.492973 TGTATAGCTTCTGTATATGTGTACGTA 57.507 33.333 0.00 0.00 0.00 3.57
436 437 8.387190 TGTATAGCTTCTGTATATGTGTACGT 57.613 34.615 0.00 0.00 0.00 3.57
437 438 8.504815 ACTGTATAGCTTCTGTATATGTGTACG 58.495 37.037 0.00 0.00 0.00 3.67
466 467 9.044150 CACCTCAAAACATAATCACAATTTGTT 57.956 29.630 0.00 0.00 32.44 2.83
467 468 7.656948 CCACCTCAAAACATAATCACAATTTGT 59.343 33.333 0.00 0.00 0.00 2.83
468 469 7.656948 ACCACCTCAAAACATAATCACAATTTG 59.343 33.333 0.00 0.00 0.00 2.32
469 470 7.734942 ACCACCTCAAAACATAATCACAATTT 58.265 30.769 0.00 0.00 0.00 1.82
470 471 7.301868 ACCACCTCAAAACATAATCACAATT 57.698 32.000 0.00 0.00 0.00 2.32
471 472 6.916360 ACCACCTCAAAACATAATCACAAT 57.084 33.333 0.00 0.00 0.00 2.71
472 473 6.723298 AACCACCTCAAAACATAATCACAA 57.277 33.333 0.00 0.00 0.00 3.33
473 474 6.097554 ACAAACCACCTCAAAACATAATCACA 59.902 34.615 0.00 0.00 0.00 3.58
474 475 6.512297 ACAAACCACCTCAAAACATAATCAC 58.488 36.000 0.00 0.00 0.00 3.06
475 476 6.723298 ACAAACCACCTCAAAACATAATCA 57.277 33.333 0.00 0.00 0.00 2.57
476 477 7.882179 AGTACAAACCACCTCAAAACATAATC 58.118 34.615 0.00 0.00 0.00 1.75
477 478 7.833285 AGTACAAACCACCTCAAAACATAAT 57.167 32.000 0.00 0.00 0.00 1.28
478 479 7.558444 AGAAGTACAAACCACCTCAAAACATAA 59.442 33.333 0.00 0.00 0.00 1.90
479 480 7.057894 AGAAGTACAAACCACCTCAAAACATA 58.942 34.615 0.00 0.00 0.00 2.29
480 481 5.891551 AGAAGTACAAACCACCTCAAAACAT 59.108 36.000 0.00 0.00 0.00 2.71
481 482 5.258051 AGAAGTACAAACCACCTCAAAACA 58.742 37.500 0.00 0.00 0.00 2.83
482 483 5.830000 AGAAGTACAAACCACCTCAAAAC 57.170 39.130 0.00 0.00 0.00 2.43
483 484 8.528044 AATAAGAAGTACAAACCACCTCAAAA 57.472 30.769 0.00 0.00 0.00 2.44
589 600 2.128771 ACACCATAATGTGAGGGCAC 57.871 50.000 0.00 0.00 45.35 5.01
652 663 5.258841 TCCGGTGTTTAGAGTCTCTTATCA 58.741 41.667 7.89 1.57 0.00 2.15
987 998 3.299503 CCCCTCCATGGTTCCTTTATTG 58.700 50.000 12.58 0.00 0.00 1.90
1032 1043 0.666577 AGACGGCGTACAAGAGCAAC 60.667 55.000 14.74 0.00 34.54 4.17
1039 1050 0.963962 AGGAAGAAGACGGCGTACAA 59.036 50.000 14.74 0.00 0.00 2.41
1150 1161 0.254107 ATGGGGTTGGGATGGTAGGT 60.254 55.000 0.00 0.00 0.00 3.08
1206 1217 3.066233 GCTCTCCTCCCGAACGGTC 62.066 68.421 12.23 0.00 0.00 4.79
1207 1218 3.069318 GCTCTCCTCCCGAACGGT 61.069 66.667 12.23 0.00 0.00 4.83
1227 1238 0.108424 CCAGCAACTTCCTCCTCGAG 60.108 60.000 5.13 5.13 0.00 4.04
1659 1670 4.169696 CCGCCCTTGCCCACGATA 62.170 66.667 0.00 0.00 0.00 2.92
1884 1895 2.281484 GGGTTGCTGTCGCTGGAA 60.281 61.111 0.00 0.00 36.97 3.53
1985 1996 7.232118 ACCAGCTTAATTTTAGCTTGACATT 57.768 32.000 13.49 0.00 46.42 2.71
1988 1999 9.639601 AATTAACCAGCTTAATTTTAGCTTGAC 57.360 29.630 13.49 0.00 46.42 3.18
2229 2248 0.393077 ACACCCAGTTCTTCCACTCG 59.607 55.000 0.00 0.00 0.00 4.18
2313 2332 3.055747 GGTCATCCTTCTCGAACTTCCTT 60.056 47.826 0.00 0.00 0.00 3.36
2587 2613 2.753966 GCTGACACGGCGAATGCAT 61.754 57.895 16.62 0.00 45.35 3.96
2800 2835 2.651135 TGCGCATTTTGCATGTATGT 57.349 40.000 5.66 0.00 45.36 2.29
2815 2850 1.270777 GCACACATGTTCACTTGCGC 61.271 55.000 0.00 0.00 0.00 6.09
2848 2883 8.751335 GCTTGTTTCTAAAAATGTTTTCATCGA 58.249 29.630 0.00 0.00 39.94 3.59
2880 2915 1.203162 TGATTGTCCAGCCCCAACAAT 60.203 47.619 0.00 0.00 44.14 2.71
2886 2921 2.043953 GGGTGATTGTCCAGCCCC 60.044 66.667 0.00 0.00 46.12 5.80
2899 2934 1.406887 CCGGATTGTAGGAAGTGGGTG 60.407 57.143 0.00 0.00 0.00 4.61
2917 2952 2.573340 GCCCAAAGGTTCATGCCG 59.427 61.111 0.00 0.00 34.57 5.69
2921 2956 1.860696 ACCTGGCCCAAAGGTTCAT 59.139 52.632 7.44 0.00 46.14 2.57
2948 2983 0.689055 TGCTGACTTCATGAGCAGGT 59.311 50.000 18.18 7.94 37.81 4.00
2959 2994 4.517285 TCTTTTGAACTGACTGCTGACTT 58.483 39.130 0.00 0.00 0.00 3.01
2961 2996 5.008019 TCAATCTTTTGAACTGACTGCTGAC 59.992 40.000 0.00 0.00 38.90 3.51
2984 3019 5.239525 CCGGAGATTCCATTTCAAATAGGTC 59.760 44.000 0.00 0.00 35.91 3.85
3034 3069 6.230849 TGTATATTTGTTGTGTCGGTGAAC 57.769 37.500 0.00 0.00 0.00 3.18
3129 3165 7.013274 TGAGTTTATTCTGTTGCTTGCTAGTTT 59.987 33.333 0.00 0.00 0.00 2.66
3136 3172 7.275341 TGTTGTTTGAGTTTATTCTGTTGCTTG 59.725 33.333 0.00 0.00 0.00 4.01
3139 3175 7.698836 ATGTTGTTTGAGTTTATTCTGTTGC 57.301 32.000 0.00 0.00 0.00 4.17
3143 3179 8.969121 TGCATATGTTGTTTGAGTTTATTCTG 57.031 30.769 4.29 0.00 0.00 3.02
3152 3188 5.570206 GTGTCACATGCATATGTTGTTTGAG 59.430 40.000 4.61 0.00 45.01 3.02
3164 3200 6.801377 CACGTTAAATTAAGTGTCACATGCAT 59.199 34.615 5.62 0.00 0.00 3.96
3165 3201 6.139435 CACGTTAAATTAAGTGTCACATGCA 58.861 36.000 5.62 0.00 0.00 3.96
3166 3202 5.567534 CCACGTTAAATTAAGTGTCACATGC 59.432 40.000 5.62 0.00 33.14 4.06
3214 3251 6.313519 TCTTAGCATCCTAATGGTGAAGTT 57.686 37.500 0.62 0.00 43.29 2.66
3232 3269 7.123547 AGGTCCTAGAGATGACTTTGTTCTTAG 59.876 40.741 0.00 0.00 0.00 2.18
3234 3271 5.782845 AGGTCCTAGAGATGACTTTGTTCTT 59.217 40.000 0.00 0.00 0.00 2.52
3281 3318 0.741326 TGCTTCTAGCTCCGCTACTG 59.259 55.000 0.00 0.00 42.97 2.74
3282 3319 1.028905 CTGCTTCTAGCTCCGCTACT 58.971 55.000 0.00 0.00 42.97 2.57
3283 3320 1.025812 TCTGCTTCTAGCTCCGCTAC 58.974 55.000 0.00 0.00 42.97 3.58
3284 3321 1.988293 ATCTGCTTCTAGCTCCGCTA 58.012 50.000 0.00 0.00 42.97 4.26
3285 3322 1.118838 AATCTGCTTCTAGCTCCGCT 58.881 50.000 0.00 0.00 42.97 5.52
3286 3323 1.216122 CAATCTGCTTCTAGCTCCGC 58.784 55.000 0.00 0.00 42.97 5.54
3287 3324 1.216122 GCAATCTGCTTCTAGCTCCG 58.784 55.000 0.00 0.00 42.97 4.63
3288 3325 1.216122 CGCAATCTGCTTCTAGCTCC 58.784 55.000 0.00 0.00 42.97 4.70
3289 3326 0.581053 GCGCAATCTGCTTCTAGCTC 59.419 55.000 0.30 0.00 42.97 4.09
3290 3327 0.813210 GGCGCAATCTGCTTCTAGCT 60.813 55.000 10.83 0.00 42.97 3.32
3291 3328 0.813210 AGGCGCAATCTGCTTCTAGC 60.813 55.000 10.83 0.00 42.25 3.42
3292 3329 0.935898 CAGGCGCAATCTGCTTCTAG 59.064 55.000 10.83 0.00 42.25 2.43
3293 3330 0.462581 CCAGGCGCAATCTGCTTCTA 60.463 55.000 10.83 0.00 42.25 2.10
3294 3331 1.748122 CCAGGCGCAATCTGCTTCT 60.748 57.895 10.83 0.00 42.25 2.85
3295 3332 2.768492 CCCAGGCGCAATCTGCTTC 61.768 63.158 10.83 0.00 42.25 3.86
3296 3333 2.753043 CCCAGGCGCAATCTGCTT 60.753 61.111 10.83 0.00 42.25 3.91
3297 3334 4.809496 CCCCAGGCGCAATCTGCT 62.809 66.667 10.83 0.00 42.25 4.24
3308 3345 3.055530 CACTCATATAGCTTAGCCCCAGG 60.056 52.174 0.00 0.00 0.00 4.45
3309 3346 3.834813 TCACTCATATAGCTTAGCCCCAG 59.165 47.826 0.00 0.00 0.00 4.45
3310 3347 3.856900 TCACTCATATAGCTTAGCCCCA 58.143 45.455 0.00 0.00 0.00 4.96
3311 3348 4.891992 TTCACTCATATAGCTTAGCCCC 57.108 45.455 0.00 0.00 0.00 5.80
3312 3349 7.751768 ATTTTTCACTCATATAGCTTAGCCC 57.248 36.000 0.00 0.00 0.00 5.19
3313 3350 9.670719 GAAATTTTTCACTCATATAGCTTAGCC 57.329 33.333 0.00 0.00 37.15 3.93
3318 3355 9.817809 TCGTAGAAATTTTTCACTCATATAGCT 57.182 29.630 5.88 0.00 39.61 3.32
3335 3372 9.606631 AGAGAAAGCATAGAAAATCGTAGAAAT 57.393 29.630 0.00 0.00 43.58 2.17
3340 3377 9.314321 CCTTTAGAGAAAGCATAGAAAATCGTA 57.686 33.333 0.00 0.00 40.76 3.43
3341 3378 8.041323 TCCTTTAGAGAAAGCATAGAAAATCGT 58.959 33.333 0.00 0.00 40.76 3.73
3342 3379 8.425577 TCCTTTAGAGAAAGCATAGAAAATCG 57.574 34.615 0.00 0.00 40.76 3.34
3350 3387 9.396022 CCTTGTAATTCCTTTAGAGAAAGCATA 57.604 33.333 0.00 0.00 40.76 3.14
3351 3388 7.340487 CCCTTGTAATTCCTTTAGAGAAAGCAT 59.660 37.037 0.00 0.00 40.76 3.79
3352 3389 6.659242 CCCTTGTAATTCCTTTAGAGAAAGCA 59.341 38.462 0.00 0.00 40.76 3.91
3353 3390 6.884836 TCCCTTGTAATTCCTTTAGAGAAAGC 59.115 38.462 0.00 0.00 40.76 3.51
3354 3391 8.863872 TTCCCTTGTAATTCCTTTAGAGAAAG 57.136 34.615 0.00 0.00 41.61 2.62
3355 3392 9.822727 AATTCCCTTGTAATTCCTTTAGAGAAA 57.177 29.630 0.00 0.00 0.00 2.52
3356 3393 9.822727 AAATTCCCTTGTAATTCCTTTAGAGAA 57.177 29.630 0.00 0.00 0.00 2.87
3357 3394 9.462606 GAAATTCCCTTGTAATTCCTTTAGAGA 57.537 33.333 0.00 0.00 0.00 3.10
3358 3395 9.467796 AGAAATTCCCTTGTAATTCCTTTAGAG 57.532 33.333 0.00 0.00 0.00 2.43
3359 3396 9.822727 AAGAAATTCCCTTGTAATTCCTTTAGA 57.177 29.630 0.00 0.00 0.00 2.10
3362 3399 9.601810 ACTAAGAAATTCCCTTGTAATTCCTTT 57.398 29.630 3.98 0.00 26.31 3.11
3364 3401 9.907229 CTACTAAGAAATTCCCTTGTAATTCCT 57.093 33.333 3.98 0.00 0.00 3.36
3365 3402 9.121658 CCTACTAAGAAATTCCCTTGTAATTCC 57.878 37.037 3.98 0.00 0.00 3.01
3366 3403 8.622157 GCCTACTAAGAAATTCCCTTGTAATTC 58.378 37.037 3.98 0.00 0.00 2.17
3367 3404 7.560262 GGCCTACTAAGAAATTCCCTTGTAATT 59.440 37.037 0.00 0.00 0.00 1.40
3368 3405 7.061054 GGCCTACTAAGAAATTCCCTTGTAAT 58.939 38.462 0.00 0.00 0.00 1.89
3369 3406 6.420638 GGCCTACTAAGAAATTCCCTTGTAA 58.579 40.000 0.00 0.00 0.00 2.41
3370 3407 5.395990 CGGCCTACTAAGAAATTCCCTTGTA 60.396 44.000 0.00 4.28 0.00 2.41
3371 3408 4.625564 CGGCCTACTAAGAAATTCCCTTGT 60.626 45.833 0.00 3.58 0.00 3.16
3372 3409 3.877508 CGGCCTACTAAGAAATTCCCTTG 59.122 47.826 0.00 0.00 0.00 3.61
3373 3410 3.118000 CCGGCCTACTAAGAAATTCCCTT 60.118 47.826 0.00 0.00 0.00 3.95
3374 3411 2.438392 CCGGCCTACTAAGAAATTCCCT 59.562 50.000 0.00 0.00 0.00 4.20
3375 3412 2.486727 CCCGGCCTACTAAGAAATTCCC 60.487 54.545 0.00 0.00 0.00 3.97
3376 3413 2.847441 CCCGGCCTACTAAGAAATTCC 58.153 52.381 0.00 0.00 0.00 3.01
3377 3414 2.158798 AGCCCGGCCTACTAAGAAATTC 60.159 50.000 5.55 0.00 0.00 2.17
3378 3415 1.844497 AGCCCGGCCTACTAAGAAATT 59.156 47.619 5.55 0.00 0.00 1.82
3379 3416 1.508256 AGCCCGGCCTACTAAGAAAT 58.492 50.000 5.55 0.00 0.00 2.17
3380 3417 1.758862 GTAGCCCGGCCTACTAAGAAA 59.241 52.381 15.20 0.00 35.82 2.52
3381 3418 1.342275 TGTAGCCCGGCCTACTAAGAA 60.342 52.381 22.08 0.00 38.75 2.52
3382 3419 0.259647 TGTAGCCCGGCCTACTAAGA 59.740 55.000 22.08 0.20 38.75 2.10
3383 3420 0.674534 CTGTAGCCCGGCCTACTAAG 59.325 60.000 22.08 9.51 38.75 2.18
3384 3421 1.397390 GCTGTAGCCCGGCCTACTAA 61.397 60.000 22.08 3.46 39.74 2.24
3385 3422 1.831286 GCTGTAGCCCGGCCTACTA 60.831 63.158 22.08 8.92 39.74 1.82
3386 3423 3.155167 GCTGTAGCCCGGCCTACT 61.155 66.667 22.08 6.93 39.74 2.57


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

AutoCloner maintained by Alex Coulton.