Multiple sequence alignment - TraesCS1B01G100100

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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 TraesCS1B01G100100 chr1B 100.000 2330 0 0 1 2330 108211663 108209334 0.000000e+00 4303.0
1 TraesCS1B01G100100 chr1B 87.179 117 11 3 2195 2308 34513177 34513292 1.880000e-26 130.0
2 TraesCS1B01G100100 chr1B 86.047 129 8 7 2164 2289 59498943 59499064 1.880000e-26 130.0
3 TraesCS1B01G100100 chr1B 86.047 129 8 7 2164 2289 59518645 59518766 1.880000e-26 130.0
4 TraesCS1B01G100100 chr1D 87.037 1674 107 49 581 2204 66988257 66986644 0.000000e+00 1788.0
5 TraesCS1B01G100100 chr1D 78.203 523 65 26 10 512 66988753 66988260 2.930000e-74 289.0
6 TraesCS1B01G100100 chr1D 95.833 48 2 0 2283 2330 66986649 66986602 6.900000e-11 78.7
7 TraesCS1B01G100100 chr1D 100.000 29 0 0 231 259 3423056 3423028 1.000000e-03 54.7
8 TraesCS1B01G100100 chr1A 87.500 688 49 25 857 1534 65759695 65759035 0.000000e+00 760.0
9 TraesCS1B01G100100 chr1A 87.467 383 28 11 336 703 65761502 65761125 7.700000e-115 424.0
10 TraesCS1B01G100100 chr1A 86.029 408 17 6 1594 1988 65758702 65758322 3.610000e-108 401.0
11 TraesCS1B01G100100 chr1A 94.783 115 6 0 716 830 65759805 65759691 1.840000e-41 180.0
12 TraesCS1B01G100100 chr5A 80.408 245 39 8 2061 2298 623008876 623008634 6.620000e-41 178.0
13 TraesCS1B01G100100 chr5A 79.412 136 24 4 2077 2208 562429769 562429634 2.470000e-15 93.5
14 TraesCS1B01G100100 chr6B 85.616 146 18 3 2061 2204 15042420 15042276 1.440000e-32 150.0
15 TraesCS1B01G100100 chr6B 90.909 99 9 0 2200 2298 156139196 156139294 1.450000e-27 134.0
16 TraesCS1B01G100100 chr7A 85.926 135 17 2 2061 2193 24692775 24692909 2.410000e-30 143.0
17 TraesCS1B01G100100 chr7A 84.615 143 20 2 2061 2201 24673526 24673668 8.680000e-30 141.0
18 TraesCS1B01G100100 chr7A 91.579 95 6 2 2193 2286 203530346 203530439 1.880000e-26 130.0
19 TraesCS1B01G100100 chr2B 85.714 133 19 0 2166 2298 245476519 245476387 8.680000e-30 141.0
20 TraesCS1B01G100100 chr2B 91.667 84 7 0 1006 1089 152175954 152175871 1.460000e-22 117.0
21 TraesCS1B01G100100 chr5D 91.089 101 8 1 2194 2293 413056269 413056169 4.040000e-28 135.0
22 TraesCS1B01G100100 chr5D 79.470 151 22 7 2061 2204 503190725 503190577 5.300000e-17 99.0
23 TraesCS1B01G100100 chrUn 86.047 129 8 7 2164 2289 303192096 303191975 1.880000e-26 130.0
24 TraesCS1B01G100100 chrUn 79.114 158 23 7 2057 2205 429803204 429803048 1.470000e-17 100.0
25 TraesCS1B01G100100 chr2D 92.941 85 6 0 1006 1090 100318439 100318355 8.740000e-25 124.0
26 TraesCS1B01G100100 chr2D 82.270 141 24 1 2064 2204 643327727 643327588 1.130000e-23 121.0
27 TraesCS1B01G100100 chr2D 91.358 81 7 0 1006 1086 54392651 54392731 6.810000e-21 111.0
28 TraesCS1B01G100100 chr2D 92.308 78 6 0 1012 1089 397962807 397962730 6.810000e-21 111.0
29 TraesCS1B01G100100 chr2A 92.857 84 6 0 1006 1089 100129663 100129580 3.140000e-24 122.0
30 TraesCS1B01G100100 chr3D 91.765 85 7 0 1006 1090 284206151 284206067 4.070000e-23 119.0
31 TraesCS1B01G100100 chr3B 91.765 85 7 0 1006 1090 245922878 245922794 4.070000e-23 119.0


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 TraesCS1B01G100100 chr1B 108209334 108211663 2329 True 4303.000000 4303 100.000000 1 2330 1 chr1B.!!$R1 2329
1 TraesCS1B01G100100 chr1D 66986602 66988753 2151 True 718.566667 1788 87.024333 10 2330 3 chr1D.!!$R2 2320
2 TraesCS1B01G100100 chr1A 65758322 65761502 3180 True 441.250000 760 88.944750 336 1988 4 chr1A.!!$R1 1652

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
126 127 0.108615 AATGTCACGCCTCCTTCTCG 60.109 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 2786 0.525761 CCCACACAAGCAATAACCCG 59.474 55.0 0.0 0.0 0.0 5.28 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
28 29 2.145397 CCACACTCTAGGCTACCTCA 57.855 55.000 0.00 0.00 34.61 3.86
34 35 3.511934 CACTCTAGGCTACCTCAACACTT 59.488 47.826 0.00 0.00 34.61 3.16
36 37 2.233922 TCTAGGCTACCTCAACACTTGC 59.766 50.000 0.00 0.00 34.61 4.01
45 46 2.035066 CCTCAACACTTGCAGAAAAGGG 59.965 50.000 0.00 0.00 36.59 3.95
56 57 2.555199 CAGAAAAGGGCTACCATCTCG 58.445 52.381 0.00 0.00 40.13 4.04
57 58 2.093447 CAGAAAAGGGCTACCATCTCGT 60.093 50.000 0.00 0.00 40.13 4.18
61 62 1.633774 AGGGCTACCATCTCGTATGG 58.366 55.000 15.21 15.21 44.54 2.74
90 91 6.060028 TCATCGTTTTCTTCAAAAGTCAGG 57.940 37.500 0.00 0.00 31.92 3.86
91 92 5.820423 TCATCGTTTTCTTCAAAAGTCAGGA 59.180 36.000 0.00 0.00 31.92 3.86
93 94 6.060028 TCGTTTTCTTCAAAAGTCAGGATG 57.940 37.500 0.00 0.00 31.92 3.51
95 96 6.094881 TCGTTTTCTTCAAAAGTCAGGATGTT 59.905 34.615 0.00 0.00 32.43 2.71
97 98 7.253750 CGTTTTCTTCAAAAGTCAGGATGTTTG 60.254 37.037 0.00 0.00 32.43 2.93
99 100 6.135290 TCTTCAAAAGTCAGGATGTTTGTG 57.865 37.500 0.00 0.00 37.40 3.33
100 101 5.652014 TCTTCAAAAGTCAGGATGTTTGTGT 59.348 36.000 0.00 0.00 37.40 3.72
101 102 5.499139 TCAAAAGTCAGGATGTTTGTGTC 57.501 39.130 0.00 0.00 37.40 3.67
102 103 4.946772 TCAAAAGTCAGGATGTTTGTGTCA 59.053 37.500 0.00 0.00 37.40 3.58
103 104 4.900635 AAAGTCAGGATGTTTGTGTCAC 57.099 40.909 0.00 0.00 37.40 3.67
104 105 2.483876 AGTCAGGATGTTTGTGTCACG 58.516 47.619 0.00 0.00 37.40 4.35
105 106 2.102420 AGTCAGGATGTTTGTGTCACGA 59.898 45.455 0.00 0.00 37.40 4.35
106 107 2.221055 GTCAGGATGTTTGTGTCACGAC 59.779 50.000 0.00 0.62 37.40 4.34
107 108 2.159028 TCAGGATGTTTGTGTCACGACA 60.159 45.455 12.62 12.62 36.71 4.35
110 111 3.250762 AGGATGTTTGTGTCACGACAATG 59.749 43.478 13.82 0.00 43.77 2.82
111 112 3.003275 GGATGTTTGTGTCACGACAATGT 59.997 43.478 13.82 0.00 43.77 2.71
112 113 3.666883 TGTTTGTGTCACGACAATGTC 57.333 42.857 2.75 2.75 43.77 3.06
113 114 3.003480 TGTTTGTGTCACGACAATGTCA 58.997 40.909 14.24 0.00 43.77 3.58
114 115 3.181515 TGTTTGTGTCACGACAATGTCAC 60.182 43.478 14.24 4.87 43.77 3.67
115 116 1.204792 TGTGTCACGACAATGTCACG 58.795 50.000 14.24 3.50 43.77 4.35
117 118 1.218875 TGTCACGACAATGTCACGCC 61.219 55.000 14.24 0.00 38.56 5.68
118 119 0.944311 GTCACGACAATGTCACGCCT 60.944 55.000 14.24 0.00 32.09 5.52
119 120 0.666274 TCACGACAATGTCACGCCTC 60.666 55.000 14.24 0.00 32.09 4.70
121 122 1.079819 CGACAATGTCACGCCTCCT 60.080 57.895 14.24 0.00 32.09 3.69
123 124 1.079503 GACAATGTCACGCCTCCTTC 58.920 55.000 8.74 0.00 32.09 3.46
125 126 1.338200 ACAATGTCACGCCTCCTTCTC 60.338 52.381 0.00 0.00 0.00 2.87
126 127 0.108615 AATGTCACGCCTCCTTCTCG 60.109 55.000 0.00 0.00 0.00 4.04
127 128 1.949847 ATGTCACGCCTCCTTCTCGG 61.950 60.000 0.00 0.00 0.00 4.63
128 129 3.068691 TCACGCCTCCTTCTCGGG 61.069 66.667 0.00 0.00 0.00 5.14
129 130 3.382832 CACGCCTCCTTCTCGGGT 61.383 66.667 0.00 0.00 0.00 5.28
130 131 3.069318 ACGCCTCCTTCTCGGGTC 61.069 66.667 0.00 0.00 0.00 4.46
133 134 3.066233 GCCTCCTTCTCGGGTCGTC 62.066 68.421 0.00 0.00 0.00 4.20
150 151 0.598158 GTCCGTGACGCTACCACAAA 60.598 55.000 0.00 0.00 34.36 2.83
157 158 2.225491 TGACGCTACCACAAAGATTTGC 59.775 45.455 5.23 0.00 41.79 3.68
160 161 1.810151 GCTACCACAAAGATTTGCGGA 59.190 47.619 17.03 0.00 41.68 5.54
163 164 0.527565 CCACAAAGATTTGCGGAGGG 59.472 55.000 6.52 0.00 41.68 4.30
171 172 3.230976 AGATTTGCGGAGGGAAGTTTTT 58.769 40.909 0.00 0.00 0.00 1.94
172 173 4.403734 AGATTTGCGGAGGGAAGTTTTTA 58.596 39.130 0.00 0.00 0.00 1.52
173 174 4.459337 AGATTTGCGGAGGGAAGTTTTTAG 59.541 41.667 0.00 0.00 0.00 1.85
174 175 1.530323 TGCGGAGGGAAGTTTTTAGC 58.470 50.000 0.00 0.00 0.00 3.09
175 176 0.446616 GCGGAGGGAAGTTTTTAGCG 59.553 55.000 0.00 0.00 0.00 4.26
176 177 1.804601 CGGAGGGAAGTTTTTAGCGT 58.195 50.000 0.00 0.00 0.00 5.07
177 178 2.932187 GCGGAGGGAAGTTTTTAGCGTA 60.932 50.000 0.00 0.00 0.00 4.42
179 180 3.937079 CGGAGGGAAGTTTTTAGCGTATT 59.063 43.478 0.00 0.00 0.00 1.89
180 181 4.201783 CGGAGGGAAGTTTTTAGCGTATTG 60.202 45.833 0.00 0.00 0.00 1.90
181 182 4.939439 GGAGGGAAGTTTTTAGCGTATTGA 59.061 41.667 0.00 0.00 0.00 2.57
186 187 6.349033 GGGAAGTTTTTAGCGTATTGACACAT 60.349 38.462 0.00 0.00 0.00 3.21
187 188 6.741358 GGAAGTTTTTAGCGTATTGACACATC 59.259 38.462 0.00 0.00 0.00 3.06
205 210 3.206150 CATCTGTATTTGTCCCTTCGGG 58.794 50.000 0.00 0.00 46.11 5.14
231 236 6.484643 GGCATCTGACATATCTTTGTACATGT 59.515 38.462 2.69 2.69 34.41 3.21
272 277 7.507733 TCCATCTCCTATTTTACGTCTAGAC 57.492 40.000 13.18 13.18 0.00 2.59
273 278 7.288560 TCCATCTCCTATTTTACGTCTAGACT 58.711 38.462 20.34 10.13 0.00 3.24
278 283 8.566260 TCTCCTATTTTACGTCTAGACTAATGC 58.434 37.037 20.34 0.00 0.00 3.56
279 284 8.461249 TCCTATTTTACGTCTAGACTAATGCT 57.539 34.615 20.34 4.52 0.00 3.79
293 298 6.064717 AGACTAATGCTCTTCAAACCTTGTT 58.935 36.000 0.00 0.00 0.00 2.83
294 299 6.205658 AGACTAATGCTCTTCAAACCTTGTTC 59.794 38.462 0.00 0.00 0.00 3.18
296 301 7.224297 ACTAATGCTCTTCAAACCTTGTTCTA 58.776 34.615 0.00 0.00 0.00 2.10
297 302 6.959639 AATGCTCTTCAAACCTTGTTCTAA 57.040 33.333 0.00 0.00 0.00 2.10
299 304 6.767524 TGCTCTTCAAACCTTGTTCTAAAA 57.232 33.333 0.00 0.00 0.00 1.52
300 305 6.560711 TGCTCTTCAAACCTTGTTCTAAAAC 58.439 36.000 0.00 0.00 35.85 2.43
301 306 6.151985 TGCTCTTCAAACCTTGTTCTAAAACA 59.848 34.615 0.00 0.00 43.58 2.83
302 307 6.472486 GCTCTTCAAACCTTGTTCTAAAACAC 59.528 38.462 0.00 0.00 44.90 3.32
303 308 6.859017 TCTTCAAACCTTGTTCTAAAACACC 58.141 36.000 0.00 0.00 44.90 4.16
304 309 5.238006 TCAAACCTTGTTCTAAAACACCG 57.762 39.130 0.00 0.00 44.90 4.94
313 324 4.992319 TGTTCTAAAACACCGGTCATACAG 59.008 41.667 2.59 0.00 40.45 2.74
317 328 1.808411 AACACCGGTCATACAGCAAG 58.192 50.000 2.59 0.00 0.00 4.01
321 332 0.391661 CCGGTCATACAGCAAGCACT 60.392 55.000 0.00 0.00 0.00 4.40
327 338 4.635765 GGTCATACAGCAAGCACTGAATTA 59.364 41.667 8.23 0.00 40.25 1.40
329 340 5.352569 GTCATACAGCAAGCACTGAATTACT 59.647 40.000 8.23 0.00 40.25 2.24
330 341 5.939883 TCATACAGCAAGCACTGAATTACTT 59.060 36.000 8.23 0.00 40.25 2.24
331 342 4.756084 ACAGCAAGCACTGAATTACTTC 57.244 40.909 8.23 0.00 40.25 3.01
332 343 4.136796 ACAGCAAGCACTGAATTACTTCA 58.863 39.130 8.23 0.00 40.25 3.02
342 353 6.347725 GCACTGAATTACTTCACGTCTCATTT 60.348 38.462 0.00 0.00 36.46 2.32
345 356 7.657761 ACTGAATTACTTCACGTCTCATTTCTT 59.342 33.333 0.00 0.00 36.46 2.52
346 357 8.378172 TGAATTACTTCACGTCTCATTTCTTT 57.622 30.769 0.00 0.00 36.46 2.52
351 362 5.006746 ACTTCACGTCTCATTTCTTTCACAC 59.993 40.000 0.00 0.00 0.00 3.82
355 366 4.816385 ACGTCTCATTTCTTTCACACATGT 59.184 37.500 0.00 0.00 0.00 3.21
356 367 5.142265 CGTCTCATTTCTTTCACACATGTG 58.858 41.667 24.25 24.25 46.91 3.21
357 368 5.455392 GTCTCATTTCTTTCACACATGTGG 58.545 41.667 28.64 17.57 45.65 4.17
358 369 5.239306 GTCTCATTTCTTTCACACATGTGGA 59.761 40.000 28.64 19.45 45.65 4.02
359 370 5.239306 TCTCATTTCTTTCACACATGTGGAC 59.761 40.000 28.64 0.00 45.65 4.02
360 371 3.961477 TTTCTTTCACACATGTGGACG 57.039 42.857 28.64 16.72 45.65 4.79
363 376 3.536570 TCTTTCACACATGTGGACGAAA 58.463 40.909 28.64 26.83 45.65 3.46
373 386 4.387862 ACATGTGGACGAAACGATAGAAAC 59.612 41.667 0.00 0.00 41.38 2.78
374 387 3.319755 TGTGGACGAAACGATAGAAACC 58.680 45.455 0.00 0.00 41.38 3.27
375 388 3.243805 TGTGGACGAAACGATAGAAACCA 60.244 43.478 0.00 0.00 41.38 3.67
391 404 2.534019 CCACACACACGACCACAGC 61.534 63.158 0.00 0.00 0.00 4.40
392 405 1.813337 CACACACACGACCACAGCA 60.813 57.895 0.00 0.00 0.00 4.41
396 409 1.521457 CACACGACCACAGCACACT 60.521 57.895 0.00 0.00 0.00 3.55
410 423 4.893424 AGCACACTGAAATAACAAACGT 57.107 36.364 0.00 0.00 0.00 3.99
417 430 3.281601 TGAAATAACAAACGTTGACGCG 58.718 40.909 3.53 3.53 44.43 6.01
419 432 2.565367 ATAACAAACGTTGACGCGAC 57.435 45.000 15.93 7.62 44.43 5.19
420 433 0.226734 TAACAAACGTTGACGCGACG 59.773 50.000 15.93 16.02 45.61 5.12
453 475 1.293498 CAAGGAGCACGCCACTACT 59.707 57.895 0.00 0.00 0.00 2.57
454 476 0.530744 CAAGGAGCACGCCACTACTA 59.469 55.000 0.00 0.00 0.00 1.82
515 537 4.314522 TGCAATCCTACAAAATCCCAGA 57.685 40.909 0.00 0.00 0.00 3.86
519 541 6.101997 GCAATCCTACAAAATCCCAGAAAAG 58.898 40.000 0.00 0.00 0.00 2.27
528 550 7.267857 ACAAAATCCCAGAAAAGTTCAAAGAG 58.732 34.615 0.00 0.00 0.00 2.85
556 578 0.248094 CGCGCAGTGAGTCGATTCTA 60.248 55.000 8.75 0.00 43.07 2.10
609 636 9.439537 GCTTAACAGCTAAGTAATTAAATCAGC 57.560 33.333 0.00 0.00 43.51 4.26
620 647 9.807649 AAGTAATTAAATCAGCCAAATTGCTAG 57.192 29.630 0.00 0.00 40.32 3.42
621 648 8.971073 AGTAATTAAATCAGCCAAATTGCTAGT 58.029 29.630 0.00 0.00 40.32 2.57
708 2036 4.189639 AGCTCGAACGAGTTTTTATCCT 57.810 40.909 22.03 8.10 43.70 3.24
813 2147 1.452833 GCCTTGGCCTCCATCTCAC 60.453 63.158 3.32 0.00 31.53 3.51
814 2148 1.225704 CCTTGGCCTCCATCTCACC 59.774 63.158 3.32 0.00 31.53 4.02
815 2149 1.277580 CCTTGGCCTCCATCTCACCT 61.278 60.000 3.32 0.00 31.53 4.00
816 2150 0.179936 CTTGGCCTCCATCTCACCTC 59.820 60.000 3.32 0.00 31.53 3.85
817 2151 0.547471 TTGGCCTCCATCTCACCTCA 60.547 55.000 3.32 0.00 31.53 3.86
818 2152 1.267574 TGGCCTCCATCTCACCTCAC 61.268 60.000 3.32 0.00 0.00 3.51
852 2186 1.263356 CCGTCCACCCTTGACTTCTA 58.737 55.000 0.00 0.00 0.00 2.10
916 2250 1.165782 ACCCCTTCCTTCCCATCCA 59.834 57.895 0.00 0.00 0.00 3.41
917 2251 1.214992 ACCCCTTCCTTCCCATCCAC 61.215 60.000 0.00 0.00 0.00 4.02
1147 2486 0.321653 TCTTCCCTTTTCTGGCTCGC 60.322 55.000 0.00 0.00 0.00 5.03
1331 2699 4.481368 TCTACGCCATCACCAAGTAAAT 57.519 40.909 0.00 0.00 0.00 1.40
1332 2700 4.439057 TCTACGCCATCACCAAGTAAATC 58.561 43.478 0.00 0.00 0.00 2.17
1334 2702 3.417101 ACGCCATCACCAAGTAAATCAA 58.583 40.909 0.00 0.00 0.00 2.57
1335 2703 3.440173 ACGCCATCACCAAGTAAATCAAG 59.560 43.478 0.00 0.00 0.00 3.02
1336 2704 3.181497 CGCCATCACCAAGTAAATCAAGG 60.181 47.826 0.00 0.00 0.00 3.61
1337 2705 3.429410 GCCATCACCAAGTAAATCAAGGC 60.429 47.826 0.00 0.00 0.00 4.35
1343 2714 0.811281 AAGTAAATCAAGGCAGCCGC 59.189 50.000 5.55 0.00 37.44 6.53
1362 2733 4.367023 CCGAGTGTTCCGGCGGAA 62.367 66.667 35.71 35.71 46.29 4.30
1363 2734 2.125673 CGAGTGTTCCGGCGGAAT 60.126 61.111 40.18 27.03 44.04 3.01
1364 2735 1.140161 CGAGTGTTCCGGCGGAATA 59.860 57.895 40.18 35.35 44.04 1.75
1365 2736 0.870307 CGAGTGTTCCGGCGGAATAG 60.870 60.000 40.18 23.58 44.04 1.73
1366 2737 0.175073 GAGTGTTCCGGCGGAATAGT 59.825 55.000 40.18 37.90 44.04 2.12
1367 2738 1.406539 GAGTGTTCCGGCGGAATAGTA 59.593 52.381 40.18 24.73 44.04 1.82
1368 2739 1.407979 AGTGTTCCGGCGGAATAGTAG 59.592 52.381 40.18 6.93 44.04 2.57
1369 2740 1.135721 GTGTTCCGGCGGAATAGTAGT 59.864 52.381 40.18 0.00 44.04 2.73
1376 2747 6.199937 TCCGGCGGAATAGTAGTATATTTC 57.800 41.667 29.11 0.00 0.00 2.17
1379 2750 6.406624 CCGGCGGAATAGTAGTATATTTCCAT 60.407 42.308 24.41 0.00 0.00 3.41
1390 2761 8.194104 AGTAGTATATTTCCATGATGATCTCGC 58.806 37.037 0.00 0.00 0.00 5.03
1398 2773 3.195182 CCATGATGATCTCGCCTGTCTAT 59.805 47.826 0.00 0.00 0.00 1.98
1402 2777 2.950781 TGATCTCGCCTGTCTATTCCT 58.049 47.619 0.00 0.00 0.00 3.36
1403 2778 4.100279 TGATCTCGCCTGTCTATTCCTA 57.900 45.455 0.00 0.00 0.00 2.94
1404 2779 4.075682 TGATCTCGCCTGTCTATTCCTAG 58.924 47.826 0.00 0.00 0.00 3.02
1406 2781 0.952280 TCGCCTGTCTATTCCTAGCG 59.048 55.000 0.00 0.00 43.20 4.26
1407 2782 0.669077 CGCCTGTCTATTCCTAGCGT 59.331 55.000 0.00 0.00 37.47 5.07
1408 2783 1.600663 CGCCTGTCTATTCCTAGCGTG 60.601 57.143 0.00 0.00 37.47 5.34
1409 2784 1.870167 GCCTGTCTATTCCTAGCGTGC 60.870 57.143 0.00 0.00 0.00 5.34
1410 2785 1.683917 CCTGTCTATTCCTAGCGTGCT 59.316 52.381 0.00 0.00 0.00 4.40
1411 2786 2.287909 CCTGTCTATTCCTAGCGTGCTC 60.288 54.545 0.00 0.00 0.00 4.26
1412 2787 1.333931 TGTCTATTCCTAGCGTGCTCG 59.666 52.381 3.31 3.31 40.37 5.03
1413 2788 0.952280 TCTATTCCTAGCGTGCTCGG 59.048 55.000 10.52 6.09 37.56 4.63
1414 2789 0.039074 CTATTCCTAGCGTGCTCGGG 60.039 60.000 11.96 9.45 37.56 5.14
1415 2790 0.754217 TATTCCTAGCGTGCTCGGGT 60.754 55.000 11.96 4.92 37.56 5.28
1416 2791 1.614241 ATTCCTAGCGTGCTCGGGTT 61.614 55.000 11.96 0.00 37.56 4.11
1417 2792 0.966875 TTCCTAGCGTGCTCGGGTTA 60.967 55.000 11.96 0.00 37.56 2.85
1437 2812 2.957491 TTGCTTGTGTGGGTTCTTTG 57.043 45.000 0.00 0.00 0.00 2.77
1453 2828 6.238814 GGGTTCTTTGAATTCTTTTCCGTGTA 60.239 38.462 7.05 0.00 0.00 2.90
1460 2835 4.720530 ATTCTTTTCCGTGTACGTTGAC 57.279 40.909 0.00 0.00 37.74 3.18
1471 2846 2.732500 TGTACGTTGACGATGCGAATTT 59.267 40.909 10.87 0.00 43.02 1.82
1502 2877 0.608130 CCATGGACCGTGTGAAGAGA 59.392 55.000 5.56 0.00 0.00 3.10
1503 2878 1.208052 CCATGGACCGTGTGAAGAGAT 59.792 52.381 5.56 0.00 0.00 2.75
1504 2879 2.355108 CCATGGACCGTGTGAAGAGATT 60.355 50.000 5.56 0.00 0.00 2.40
1515 2890 5.049818 CGTGTGAAGAGATTTCAGCTTCTTT 60.050 40.000 0.00 0.00 38.96 2.52
1516 2891 6.146184 CGTGTGAAGAGATTTCAGCTTCTTTA 59.854 38.462 0.00 0.00 38.96 1.85
1517 2892 7.148507 CGTGTGAAGAGATTTCAGCTTCTTTAT 60.149 37.037 0.00 0.00 38.96 1.40
1518 2893 9.155975 GTGTGAAGAGATTTCAGCTTCTTTATA 57.844 33.333 0.00 0.00 38.96 0.98
1519 2894 9.896645 TGTGAAGAGATTTCAGCTTCTTTATAT 57.103 29.630 0.00 0.00 38.96 0.86
1521 2896 9.896645 TGAAGAGATTTCAGCTTCTTTATATGT 57.103 29.630 0.00 0.00 38.96 2.29
1560 2935 9.645059 CACTAGTATCATGTATGGGAGTTTATG 57.355 37.037 0.00 0.00 0.00 1.90
1561 2936 8.314751 ACTAGTATCATGTATGGGAGTTTATGC 58.685 37.037 0.00 0.00 0.00 3.14
1564 2939 8.825774 AGTATCATGTATGGGAGTTTATGCATA 58.174 33.333 1.16 1.16 30.17 3.14
1566 2941 6.836242 TCATGTATGGGAGTTTATGCATACA 58.164 36.000 5.74 0.00 39.05 2.29
1567 2942 6.936335 TCATGTATGGGAGTTTATGCATACAG 59.064 38.462 5.74 0.00 38.41 2.74
1573 2960 7.426606 TGGGAGTTTATGCATACAGTACTTA 57.573 36.000 5.74 0.00 0.00 2.24
1626 3291 1.134580 AGTCTGGAATCGGCAGTGATG 60.135 52.381 0.00 0.00 0.00 3.07
1656 3328 6.488683 TGTAGTCGGGTTTCTCATTTGATTTT 59.511 34.615 0.00 0.00 0.00 1.82
1657 3329 6.405278 AGTCGGGTTTCTCATTTGATTTTT 57.595 33.333 0.00 0.00 0.00 1.94
1658 3330 6.447162 AGTCGGGTTTCTCATTTGATTTTTC 58.553 36.000 0.00 0.00 0.00 2.29
1659 3331 6.040391 AGTCGGGTTTCTCATTTGATTTTTCA 59.960 34.615 0.00 0.00 0.00 2.69
1660 3332 6.363357 GTCGGGTTTCTCATTTGATTTTTCAG 59.637 38.462 0.00 0.00 0.00 3.02
1661 3333 6.040391 TCGGGTTTCTCATTTGATTTTTCAGT 59.960 34.615 0.00 0.00 0.00 3.41
1662 3334 6.701400 CGGGTTTCTCATTTGATTTTTCAGTT 59.299 34.615 0.00 0.00 0.00 3.16
1663 3335 7.224557 CGGGTTTCTCATTTGATTTTTCAGTTT 59.775 33.333 0.00 0.00 0.00 2.66
1664 3336 8.892723 GGGTTTCTCATTTGATTTTTCAGTTTT 58.107 29.630 0.00 0.00 0.00 2.43
1736 3412 6.083098 TGTAGTGCTGTTATGCAAATTTGT 57.917 33.333 19.03 3.40 45.12 2.83
1737 3413 6.511416 TGTAGTGCTGTTATGCAAATTTGTT 58.489 32.000 19.03 9.96 45.12 2.83
1738 3414 7.652727 TGTAGTGCTGTTATGCAAATTTGTTA 58.347 30.769 19.03 9.50 45.12 2.41
1822 3498 5.316167 AGGAACAAAAGCTGTGTCATCATA 58.684 37.500 3.90 0.00 38.67 2.15
1823 3499 5.948162 AGGAACAAAAGCTGTGTCATCATAT 59.052 36.000 3.90 0.00 38.67 1.78
1903 3583 0.524862 GCCTGTCAAGTGGATGCAAG 59.475 55.000 0.00 0.00 0.00 4.01
1905 3585 2.875672 GCCTGTCAAGTGGATGCAAGTA 60.876 50.000 0.00 0.00 0.00 2.24
1906 3586 3.614092 CCTGTCAAGTGGATGCAAGTAT 58.386 45.455 0.00 0.00 0.00 2.12
1959 3639 2.035321 GTCAGAAAATGGGGACGCAAAA 59.965 45.455 0.00 0.00 0.00 2.44
1973 3653 4.088496 GGACGCAAAACTTCGAAAATGATG 59.912 41.667 0.00 0.00 0.00 3.07
2017 3697 2.357327 TGCTATGCGTACGACACTTT 57.643 45.000 21.65 4.64 0.00 2.66
2024 3704 0.233848 CGTACGACACTTTTGCACCC 59.766 55.000 10.44 0.00 0.00 4.61
2036 3716 5.354234 CACTTTTGCACCCGATTTACTATCT 59.646 40.000 0.00 0.00 0.00 1.98
2038 3718 4.481368 TTGCACCCGATTTACTATCTGT 57.519 40.909 0.00 0.00 0.00 3.41
2039 3719 4.054780 TGCACCCGATTTACTATCTGTC 57.945 45.455 0.00 0.00 0.00 3.51
2040 3720 3.181469 TGCACCCGATTTACTATCTGTCC 60.181 47.826 0.00 0.00 0.00 4.02
2041 3721 3.181469 GCACCCGATTTACTATCTGTCCA 60.181 47.826 0.00 0.00 0.00 4.02
2042 3722 4.682320 GCACCCGATTTACTATCTGTCCAA 60.682 45.833 0.00 0.00 0.00 3.53
2066 3746 6.746120 ACAATCGTTGGATCATACTACTACC 58.254 40.000 0.00 0.00 34.12 3.18
2067 3747 6.322969 ACAATCGTTGGATCATACTACTACCA 59.677 38.462 0.00 0.00 34.12 3.25
2069 3749 4.581824 TCGTTGGATCATACTACTACCACC 59.418 45.833 0.00 0.00 0.00 4.61
2081 3761 3.236632 ACTACCACCGTTCCGAAATAC 57.763 47.619 0.00 0.00 0.00 1.89
2086 3766 2.414138 CCACCGTTCCGAAATACAAGTC 59.586 50.000 0.00 0.00 0.00 3.01
2090 3770 4.450080 ACCGTTCCGAAATACAAGTCTTTC 59.550 41.667 2.12 2.12 0.00 2.62
2213 3895 7.646548 AAAAAGCTTATACTTCCTCCATTCC 57.353 36.000 0.00 0.00 0.00 3.01
2214 3896 5.975988 AAGCTTATACTTCCTCCATTCCA 57.024 39.130 0.00 0.00 0.00 3.53
2215 3897 5.975988 AGCTTATACTTCCTCCATTCCAA 57.024 39.130 0.00 0.00 0.00 3.53
2216 3898 6.327386 AGCTTATACTTCCTCCATTCCAAA 57.673 37.500 0.00 0.00 0.00 3.28
2217 3899 6.731467 AGCTTATACTTCCTCCATTCCAAAA 58.269 36.000 0.00 0.00 0.00 2.44
2218 3900 7.357471 AGCTTATACTTCCTCCATTCCAAAAT 58.643 34.615 0.00 0.00 0.00 1.82
2219 3901 8.502738 AGCTTATACTTCCTCCATTCCAAAATA 58.497 33.333 0.00 0.00 0.00 1.40
2220 3902 8.787852 GCTTATACTTCCTCCATTCCAAAATAG 58.212 37.037 0.00 0.00 0.00 1.73
2223 3905 8.930846 ATACTTCCTCCATTCCAAAATAGATG 57.069 34.615 0.00 0.00 0.00 2.90
2224 3906 6.973642 ACTTCCTCCATTCCAAAATAGATGA 58.026 36.000 0.00 0.00 0.00 2.92
2225 3907 7.589993 ACTTCCTCCATTCCAAAATAGATGAT 58.410 34.615 0.00 0.00 0.00 2.45
2226 3908 7.723172 ACTTCCTCCATTCCAAAATAGATGATC 59.277 37.037 0.00 0.00 0.00 2.92
2227 3909 6.546484 TCCTCCATTCCAAAATAGATGATCC 58.454 40.000 0.00 0.00 0.00 3.36
2228 3910 6.103057 TCCTCCATTCCAAAATAGATGATCCA 59.897 38.462 0.00 0.00 0.00 3.41
2229 3911 6.779049 CCTCCATTCCAAAATAGATGATCCAA 59.221 38.462 0.00 0.00 0.00 3.53
2230 3912 7.453752 CCTCCATTCCAAAATAGATGATCCAAT 59.546 37.037 0.00 0.00 0.00 3.16
2231 3913 8.786710 TCCATTCCAAAATAGATGATCCAATT 57.213 30.769 0.00 0.00 0.00 2.32
2232 3914 9.216148 TCCATTCCAAAATAGATGATCCAATTT 57.784 29.630 0.00 0.00 0.00 1.82
2233 3915 9.841295 CCATTCCAAAATAGATGATCCAATTTT 57.159 29.630 9.17 9.17 33.07 1.82
2260 3942 7.920908 ACTAACGTTAGTACAAAGTTGAGTC 57.079 36.000 33.80 0.00 41.92 3.36
2261 3943 7.483307 ACTAACGTTAGTACAAAGTTGAGTCA 58.517 34.615 33.80 0.00 41.92 3.41
2262 3944 8.139989 ACTAACGTTAGTACAAAGTTGAGTCAT 58.860 33.333 33.80 8.05 41.92 3.06
2263 3945 7.404139 AACGTTAGTACAAAGTTGAGTCATC 57.596 36.000 0.00 0.00 0.00 2.92
2264 3946 6.746120 ACGTTAGTACAAAGTTGAGTCATCT 58.254 36.000 0.00 0.00 0.00 2.90
2265 3947 7.879070 ACGTTAGTACAAAGTTGAGTCATCTA 58.121 34.615 4.14 0.00 0.00 1.98
2266 3948 8.521176 ACGTTAGTACAAAGTTGAGTCATCTAT 58.479 33.333 4.14 0.00 0.00 1.98
2267 3949 9.355215 CGTTAGTACAAAGTTGAGTCATCTATT 57.645 33.333 4.14 0.00 0.00 1.73
2271 3953 9.778741 AGTACAAAGTTGAGTCATCTATTTTGA 57.221 29.630 15.99 3.46 38.91 2.69
2274 3956 9.736023 ACAAAGTTGAGTCATCTATTTTGAAAC 57.264 29.630 15.99 0.00 38.91 2.78
2275 3957 8.895845 CAAAGTTGAGTCATCTATTTTGAAACG 58.104 33.333 4.14 0.00 38.91 3.60
2276 3958 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
2277 3959 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
2278 3960 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
2279 3961 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
2280 3962 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
2281 3963 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
2282 3964 5.646360 GTCATCTATTTTGAAACGGAGGGAA 59.354 40.000 0.00 0.00 0.00 3.97
2283 3965 6.318900 GTCATCTATTTTGAAACGGAGGGAAT 59.681 38.462 0.00 0.00 0.00 3.01
2284 3966 7.497909 GTCATCTATTTTGAAACGGAGGGAATA 59.502 37.037 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.667487 CTAGAGTGTGGCACGTGTGG 60.667 60.000 18.38 0.00 39.64 4.17
1 2 0.667487 CCTAGAGTGTGGCACGTGTG 60.667 60.000 18.38 0.00 39.64 3.82
2 3 1.666011 CCTAGAGTGTGGCACGTGT 59.334 57.895 18.38 3.89 39.64 4.49
3 4 4.578913 CCTAGAGTGTGGCACGTG 57.421 61.111 12.28 12.28 39.64 4.49
13 14 3.459710 AGTGTTGAGGTAGCCTAGAGT 57.540 47.619 0.00 0.00 31.76 3.24
28 29 1.780503 AGCCCTTTTCTGCAAGTGTT 58.219 45.000 0.00 0.00 33.76 3.32
34 35 1.635487 AGATGGTAGCCCTTTTCTGCA 59.365 47.619 0.00 0.00 0.00 4.41
36 37 2.093447 ACGAGATGGTAGCCCTTTTCTG 60.093 50.000 0.00 0.00 0.00 3.02
45 46 0.679505 TGCCCATACGAGATGGTAGC 59.320 55.000 16.46 14.15 37.48 3.58
56 57 2.038387 AAACGATGAGGTGCCCATAC 57.962 50.000 0.00 0.00 0.00 2.39
57 58 2.238646 AGAAAACGATGAGGTGCCCATA 59.761 45.455 0.00 0.00 0.00 2.74
61 62 2.151202 TGAAGAAAACGATGAGGTGCC 58.849 47.619 0.00 0.00 0.00 5.01
70 71 5.588648 ACATCCTGACTTTTGAAGAAAACGA 59.411 36.000 0.00 0.00 0.00 3.85
73 74 7.545265 CACAAACATCCTGACTTTTGAAGAAAA 59.455 33.333 8.53 0.00 33.90 2.29
75 76 6.152661 ACACAAACATCCTGACTTTTGAAGAA 59.847 34.615 8.53 0.00 33.90 2.52
76 77 5.652014 ACACAAACATCCTGACTTTTGAAGA 59.348 36.000 8.53 0.00 33.90 2.87
90 91 4.209452 ACATTGTCGTGACACAAACATC 57.791 40.909 6.37 0.00 41.67 3.06
91 92 3.625313 TGACATTGTCGTGACACAAACAT 59.375 39.130 11.97 0.00 41.67 2.71
93 94 3.350912 GTGACATTGTCGTGACACAAAC 58.649 45.455 11.97 3.88 41.94 2.93
95 96 1.590698 CGTGACATTGTCGTGACACAA 59.409 47.619 11.97 3.75 42.28 3.33
97 98 0.111266 GCGTGACATTGTCGTGACAC 60.111 55.000 11.97 4.22 41.67 3.67
99 100 0.944311 AGGCGTGACATTGTCGTGAC 60.944 55.000 11.97 8.80 34.95 3.67
100 101 0.666274 GAGGCGTGACATTGTCGTGA 60.666 55.000 11.97 0.00 34.95 4.35
101 102 1.626654 GGAGGCGTGACATTGTCGTG 61.627 60.000 11.97 7.84 34.95 4.35
102 103 1.374252 GGAGGCGTGACATTGTCGT 60.374 57.895 11.97 0.00 34.95 4.34
103 104 0.670546 AAGGAGGCGTGACATTGTCG 60.671 55.000 11.97 3.11 34.95 4.35
104 105 1.079503 GAAGGAGGCGTGACATTGTC 58.920 55.000 9.93 9.93 0.00 3.18
105 106 0.687354 AGAAGGAGGCGTGACATTGT 59.313 50.000 0.00 0.00 0.00 2.71
106 107 1.363744 GAGAAGGAGGCGTGACATTG 58.636 55.000 0.00 0.00 0.00 2.82
107 108 0.108615 CGAGAAGGAGGCGTGACATT 60.109 55.000 0.00 0.00 0.00 2.71
110 111 2.182030 CCGAGAAGGAGGCGTGAC 59.818 66.667 0.00 0.00 45.00 3.67
111 112 3.068691 CCCGAGAAGGAGGCGTGA 61.069 66.667 0.00 0.00 45.00 4.35
112 113 3.358076 GACCCGAGAAGGAGGCGTG 62.358 68.421 0.00 0.00 45.00 5.34
113 114 3.069318 GACCCGAGAAGGAGGCGT 61.069 66.667 0.00 0.00 45.00 5.68
114 115 4.194720 CGACCCGAGAAGGAGGCG 62.195 72.222 0.00 0.00 45.00 5.52
115 116 3.066233 GACGACCCGAGAAGGAGGC 62.066 68.421 0.00 0.00 45.00 4.70
117 118 3.198582 GGACGACCCGAGAAGGAG 58.801 66.667 0.00 0.00 45.00 3.69
133 134 0.319211 TCTTTGTGGTAGCGTCACGG 60.319 55.000 0.00 0.00 37.91 4.94
136 137 2.225491 GCAAATCTTTGTGGTAGCGTCA 59.775 45.455 4.71 0.00 40.24 4.35
150 151 2.586648 AAACTTCCCTCCGCAAATCT 57.413 45.000 0.00 0.00 0.00 2.40
157 158 1.804601 ACGCTAAAAACTTCCCTCCG 58.195 50.000 0.00 0.00 0.00 4.63
160 161 5.180680 GTGTCAATACGCTAAAAACTTCCCT 59.819 40.000 0.00 0.00 33.16 4.20
163 164 7.478667 CAGATGTGTCAATACGCTAAAAACTTC 59.521 37.037 0.00 0.00 37.03 3.01
171 172 7.039270 ACAAATACAGATGTGTCAATACGCTA 58.961 34.615 0.00 0.00 38.19 4.26
172 173 5.874810 ACAAATACAGATGTGTCAATACGCT 59.125 36.000 0.00 0.00 38.19 5.07
173 174 6.106877 ACAAATACAGATGTGTCAATACGC 57.893 37.500 0.00 0.00 38.19 4.42
180 181 4.330074 CGAAGGGACAAATACAGATGTGTC 59.670 45.833 0.00 0.36 46.09 3.67
181 182 4.253685 CGAAGGGACAAATACAGATGTGT 58.746 43.478 0.00 0.00 36.11 3.72
205 210 5.368145 TGTACAAAGATATGTCAGATGCCC 58.632 41.667 0.00 0.00 34.75 5.36
207 212 7.488187 ACATGTACAAAGATATGTCAGATGC 57.512 36.000 0.00 0.00 34.75 3.91
246 251 8.578151 GTCTAGACGTAAAATAGGAGATGGATT 58.422 37.037 7.22 0.00 0.00 3.01
262 267 6.997239 TTGAAGAGCATTAGTCTAGACGTA 57.003 37.500 17.07 9.57 36.20 3.57
265 270 6.635755 AGGTTTGAAGAGCATTAGTCTAGAC 58.364 40.000 15.41 15.41 0.00 2.59
272 277 6.566197 AGAACAAGGTTTGAAGAGCATTAG 57.434 37.500 0.00 0.00 0.00 1.73
273 278 8.458573 TTTAGAACAAGGTTTGAAGAGCATTA 57.541 30.769 0.00 0.00 0.00 1.90
276 281 6.151985 TGTTTTAGAACAAGGTTTGAAGAGCA 59.848 34.615 0.00 0.00 42.54 4.26
278 283 6.972901 GGTGTTTTAGAACAAGGTTTGAAGAG 59.027 38.462 0.00 0.00 46.62 2.85
279 284 6.403855 CGGTGTTTTAGAACAAGGTTTGAAGA 60.404 38.462 0.00 0.00 46.62 2.87
293 298 3.007074 TGCTGTATGACCGGTGTTTTAGA 59.993 43.478 14.63 0.00 0.00 2.10
294 299 3.331150 TGCTGTATGACCGGTGTTTTAG 58.669 45.455 14.63 6.07 0.00 1.85
296 301 2.264005 TGCTGTATGACCGGTGTTTT 57.736 45.000 14.63 0.00 0.00 2.43
297 302 2.151202 CTTGCTGTATGACCGGTGTTT 58.849 47.619 14.63 0.00 0.00 2.83
299 304 0.673644 GCTTGCTGTATGACCGGTGT 60.674 55.000 14.63 2.27 0.00 4.16
300 305 0.673333 TGCTTGCTGTATGACCGGTG 60.673 55.000 14.63 0.00 0.00 4.94
301 306 0.673644 GTGCTTGCTGTATGACCGGT 60.674 55.000 6.92 6.92 0.00 5.28
302 307 0.391661 AGTGCTTGCTGTATGACCGG 60.392 55.000 0.00 0.00 0.00 5.28
303 308 0.723414 CAGTGCTTGCTGTATGACCG 59.277 55.000 0.00 0.00 0.00 4.79
304 309 2.099141 TCAGTGCTTGCTGTATGACC 57.901 50.000 0.00 0.00 37.70 4.02
313 324 3.058914 ACGTGAAGTAATTCAGTGCTTGC 60.059 43.478 5.73 0.00 0.00 4.01
317 328 3.987868 TGAGACGTGAAGTAATTCAGTGC 59.012 43.478 5.73 0.00 0.00 4.40
321 332 7.962964 AAGAAATGAGACGTGAAGTAATTCA 57.037 32.000 0.56 0.56 0.00 2.57
327 338 5.006746 GTGTGAAAGAAATGAGACGTGAAGT 59.993 40.000 0.00 0.00 0.00 3.01
329 340 4.873259 TGTGTGAAAGAAATGAGACGTGAA 59.127 37.500 0.00 0.00 0.00 3.18
330 341 4.438148 TGTGTGAAAGAAATGAGACGTGA 58.562 39.130 0.00 0.00 0.00 4.35
331 342 4.794248 TGTGTGAAAGAAATGAGACGTG 57.206 40.909 0.00 0.00 0.00 4.49
332 343 4.816385 ACATGTGTGAAAGAAATGAGACGT 59.184 37.500 0.00 0.00 0.00 4.34
351 362 4.201685 GGTTTCTATCGTTTCGTCCACATG 60.202 45.833 0.00 0.00 0.00 3.21
355 366 3.243805 TGTGGTTTCTATCGTTTCGTCCA 60.244 43.478 0.00 0.00 0.00 4.02
356 367 3.122445 GTGTGGTTTCTATCGTTTCGTCC 59.878 47.826 0.00 0.00 0.00 4.79
357 368 3.737266 TGTGTGGTTTCTATCGTTTCGTC 59.263 43.478 0.00 0.00 0.00 4.20
358 369 3.492011 GTGTGTGGTTTCTATCGTTTCGT 59.508 43.478 0.00 0.00 0.00 3.85
359 370 3.491639 TGTGTGTGGTTTCTATCGTTTCG 59.508 43.478 0.00 0.00 0.00 3.46
360 371 4.607557 CGTGTGTGTGGTTTCTATCGTTTC 60.608 45.833 0.00 0.00 0.00 2.78
363 376 2.034939 TCGTGTGTGTGGTTTCTATCGT 59.965 45.455 0.00 0.00 0.00 3.73
373 386 2.534019 GCTGTGGTCGTGTGTGTGG 61.534 63.158 0.00 0.00 0.00 4.17
374 387 1.813337 TGCTGTGGTCGTGTGTGTG 60.813 57.895 0.00 0.00 0.00 3.82
375 388 1.813753 GTGCTGTGGTCGTGTGTGT 60.814 57.895 0.00 0.00 0.00 3.72
391 404 5.168856 CGTCAACGTTTGTTATTTCAGTGTG 59.831 40.000 0.00 0.00 36.28 3.82
392 405 5.260140 CGTCAACGTTTGTTATTTCAGTGT 58.740 37.500 0.00 0.00 36.28 3.55
396 409 3.001026 TCGCGTCAACGTTTGTTATTTCA 59.999 39.130 5.77 0.00 42.22 2.69
401 414 0.226734 CGTCGCGTCAACGTTTGTTA 59.773 50.000 5.77 0.00 42.22 2.41
417 430 0.179111 TGGATTCGAGGATGCACGTC 60.179 55.000 3.77 0.00 0.00 4.34
419 432 0.933097 CTTGGATTCGAGGATGCACG 59.067 55.000 0.00 0.00 0.00 5.34
420 433 1.134401 TCCTTGGATTCGAGGATGCAC 60.134 52.381 5.78 0.00 46.14 4.57
453 475 1.468565 GGCGATGACTGCGTTGTACTA 60.469 52.381 0.00 0.00 0.00 1.82
454 476 0.736325 GGCGATGACTGCGTTGTACT 60.736 55.000 0.00 0.00 0.00 2.73
515 537 5.163652 GCGTATATGCCCTCTTTGAACTTTT 60.164 40.000 5.56 0.00 0.00 2.27
519 541 2.221055 CGCGTATATGCCCTCTTTGAAC 59.779 50.000 11.33 0.00 0.00 3.18
528 550 1.284982 CTCACTGCGCGTATATGCCC 61.285 60.000 8.43 2.91 0.00 5.36
556 578 5.260424 TGTTAGTGGTATGAATTGCACCAT 58.740 37.500 5.86 0.00 43.88 3.55
605 632 5.887214 TCCTATACTAGCAATTTGGCTGA 57.113 39.130 0.68 0.00 45.44 4.26
609 636 6.238759 GCCAGTTTCCTATACTAGCAATTTGG 60.239 42.308 0.00 0.00 31.74 3.28
620 647 5.109210 GCCAAATTTGCCAGTTTCCTATAC 58.891 41.667 12.92 0.00 0.00 1.47
621 648 4.774726 TGCCAAATTTGCCAGTTTCCTATA 59.225 37.500 12.92 0.00 0.00 1.31
622 649 3.582208 TGCCAAATTTGCCAGTTTCCTAT 59.418 39.130 12.92 0.00 0.00 2.57
623 650 2.968574 TGCCAAATTTGCCAGTTTCCTA 59.031 40.909 12.92 0.00 0.00 2.94
813 2147 3.775654 GCGAGGGTGAGGGTGAGG 61.776 72.222 0.00 0.00 0.00 3.86
814 2148 3.775654 GGCGAGGGTGAGGGTGAG 61.776 72.222 0.00 0.00 0.00 3.51
852 2186 5.105837 GCTCTCGTTATATAGACGGGGAAAT 60.106 44.000 13.67 0.00 41.20 2.17
916 2250 1.606885 GAGCTGAGCAGAGCAGAGGT 61.607 60.000 7.39 0.00 41.83 3.85
917 2251 1.142314 GAGCTGAGCAGAGCAGAGG 59.858 63.158 7.39 0.00 41.83 3.69
989 2324 2.961721 CCGCCATGGTCGTCGATG 60.962 66.667 21.61 0.00 0.00 3.84
1147 2486 2.159043 ACGCATCTATCAACCTGTGGAG 60.159 50.000 0.00 0.00 0.00 3.86
1184 2527 9.325248 TCAGAATTCCATCCATATATGTCACTA 57.675 33.333 11.73 0.00 0.00 2.74
1222 2590 4.269183 TGCAAGAGAGAAACCAAGAAACA 58.731 39.130 0.00 0.00 0.00 2.83
1357 2728 9.035607 CATCATGGAAATATACTACTATTCCGC 57.964 37.037 0.00 0.00 0.00 5.54
1364 2735 8.194104 GCGAGATCATCATGGAAATATACTACT 58.806 37.037 0.00 0.00 0.00 2.57
1365 2736 7.436673 GGCGAGATCATCATGGAAATATACTAC 59.563 40.741 0.00 0.00 0.00 2.73
1366 2737 7.343057 AGGCGAGATCATCATGGAAATATACTA 59.657 37.037 0.00 0.00 0.00 1.82
1367 2738 6.155910 AGGCGAGATCATCATGGAAATATACT 59.844 38.462 0.00 0.00 0.00 2.12
1368 2739 6.257411 CAGGCGAGATCATCATGGAAATATAC 59.743 42.308 0.00 0.00 0.00 1.47
1369 2740 6.070596 ACAGGCGAGATCATCATGGAAATATA 60.071 38.462 0.00 0.00 0.00 0.86
1376 2747 1.343789 AGACAGGCGAGATCATCATGG 59.656 52.381 0.00 0.00 0.00 3.66
1379 2750 3.256879 GGAATAGACAGGCGAGATCATCA 59.743 47.826 0.00 0.00 0.00 3.07
1386 2757 1.068885 CGCTAGGAATAGACAGGCGAG 60.069 57.143 0.00 0.00 43.05 5.03
1388 2759 0.669077 ACGCTAGGAATAGACAGGCG 59.331 55.000 0.00 0.00 45.31 5.52
1389 2760 1.870167 GCACGCTAGGAATAGACAGGC 60.870 57.143 0.00 0.00 0.00 4.85
1390 2761 1.683917 AGCACGCTAGGAATAGACAGG 59.316 52.381 0.00 0.00 0.00 4.00
1398 2773 0.966875 TAACCCGAGCACGCTAGGAA 60.967 55.000 18.55 2.38 40.61 3.36
1402 2777 0.808453 GCAATAACCCGAGCACGCTA 60.808 55.000 0.00 0.00 38.29 4.26
1403 2778 2.106683 GCAATAACCCGAGCACGCT 61.107 57.895 0.00 0.00 38.29 5.07
1404 2779 1.644786 AAGCAATAACCCGAGCACGC 61.645 55.000 0.00 0.00 38.29 5.34
1406 2781 1.135689 CACAAGCAATAACCCGAGCAC 60.136 52.381 0.00 0.00 0.00 4.40
1407 2782 1.164411 CACAAGCAATAACCCGAGCA 58.836 50.000 0.00 0.00 0.00 4.26
1408 2783 1.135689 CACACAAGCAATAACCCGAGC 60.136 52.381 0.00 0.00 0.00 5.03
1409 2784 1.468520 CCACACAAGCAATAACCCGAG 59.531 52.381 0.00 0.00 0.00 4.63
1410 2785 1.529226 CCACACAAGCAATAACCCGA 58.471 50.000 0.00 0.00 0.00 5.14
1411 2786 0.525761 CCCACACAAGCAATAACCCG 59.474 55.000 0.00 0.00 0.00 5.28
1412 2787 1.627864 ACCCACACAAGCAATAACCC 58.372 50.000 0.00 0.00 0.00 4.11
1413 2788 2.890945 AGAACCCACACAAGCAATAACC 59.109 45.455 0.00 0.00 0.00 2.85
1414 2789 4.584327 AAGAACCCACACAAGCAATAAC 57.416 40.909 0.00 0.00 0.00 1.89
1415 2790 4.646945 TCAAAGAACCCACACAAGCAATAA 59.353 37.500 0.00 0.00 0.00 1.40
1416 2791 4.211125 TCAAAGAACCCACACAAGCAATA 58.789 39.130 0.00 0.00 0.00 1.90
1417 2792 3.030291 TCAAAGAACCCACACAAGCAAT 58.970 40.909 0.00 0.00 0.00 3.56
1437 2812 5.135330 GTCAACGTACACGGAAAAGAATTC 58.865 41.667 6.72 0.00 44.95 2.17
1453 2828 2.066262 AGAAATTCGCATCGTCAACGT 58.934 42.857 2.09 0.00 40.80 3.99
1460 2835 2.002586 ACCACAGAGAAATTCGCATCG 58.997 47.619 0.00 0.00 0.00 3.84
1471 2846 1.351017 GGTCCATGGAAACCACAGAGA 59.649 52.381 18.20 0.00 35.80 3.10
1534 2909 9.645059 CATAAACTCCCATACATGATACTAGTG 57.355 37.037 5.39 0.00 0.00 2.74
1543 2918 6.712095 ACTGTATGCATAAACTCCCATACATG 59.288 38.462 8.28 0.00 45.03 3.21
1546 2921 7.442656 AGTACTGTATGCATAAACTCCCATAC 58.557 38.462 8.28 6.23 40.07 2.39
1573 2960 5.497474 AGGCGGTAATCTAACTTCAACAAT 58.503 37.500 0.00 0.00 0.00 2.71
1579 2966 2.699321 AGGGAGGCGGTAATCTAACTTC 59.301 50.000 0.00 0.00 0.00 3.01
1591 3256 1.376037 GACTTGAACAGGGAGGCGG 60.376 63.158 0.00 0.00 0.00 6.13
1592 3257 0.671781 CAGACTTGAACAGGGAGGCG 60.672 60.000 0.00 0.00 0.00 5.52
1626 3291 4.445452 TGAGAAACCCGACTACATACAC 57.555 45.455 0.00 0.00 0.00 2.90
1822 3498 2.697751 GGCTAGGACACATCTGACAGAT 59.302 50.000 12.37 12.37 34.74 2.90
1823 3499 2.103373 GGCTAGGACACATCTGACAGA 58.897 52.381 7.80 7.80 0.00 3.41
1903 3583 1.664965 GATGACGAGGCCCGCATAC 60.665 63.158 12.78 8.24 43.32 2.39
1905 3585 1.832608 TAGATGACGAGGCCCGCAT 60.833 57.895 12.78 15.17 43.32 4.73
1906 3586 2.441348 TAGATGACGAGGCCCGCA 60.441 61.111 12.78 11.76 43.32 5.69
1928 3608 6.149807 GTCCCCATTTTCTGACGTGTTAAATA 59.850 38.462 0.00 0.00 0.00 1.40
1943 3623 2.544903 CGAAGTTTTGCGTCCCCATTTT 60.545 45.455 0.00 0.00 0.00 1.82
1954 3634 4.090498 GCTCCATCATTTTCGAAGTTTTGC 59.910 41.667 0.00 0.00 0.00 3.68
1959 3639 2.416547 CGTGCTCCATCATTTTCGAAGT 59.583 45.455 0.00 0.00 0.00 3.01
1973 3653 0.924090 CAGAAAGATACGCGTGCTCC 59.076 55.000 24.59 13.68 0.00 4.70
2017 3697 4.439057 GACAGATAGTAAATCGGGTGCAA 58.561 43.478 0.00 0.00 0.00 4.08
2024 3704 6.475727 ACGATTGTTGGACAGATAGTAAATCG 59.524 38.462 11.19 11.19 45.55 3.34
2041 3721 7.147794 TGGTAGTAGTATGATCCAACGATTGTT 60.148 37.037 0.00 0.00 39.43 2.83
2042 3722 6.322969 TGGTAGTAGTATGATCCAACGATTGT 59.677 38.462 0.00 0.00 0.00 2.71
2109 3789 5.627499 TTCACTCATTTGCTCCAATGTAC 57.373 39.130 4.45 0.00 0.00 2.90
2115 3795 4.937620 GTGTAGATTCACTCATTTGCTCCA 59.062 41.667 0.00 0.00 35.68 3.86
2116 3796 5.181748 AGTGTAGATTCACTCATTTGCTCC 58.818 41.667 0.00 0.00 44.07 4.70
2148 3830 9.821662 TGAACTACATACGAATGAATATAGACG 57.178 33.333 0.00 0.00 36.54 4.18
2192 3874 5.975988 TGGAATGGAGGAAGTATAAGCTT 57.024 39.130 3.48 3.48 0.00 3.74
2194 3876 7.588497 ATTTTGGAATGGAGGAAGTATAAGC 57.412 36.000 0.00 0.00 0.00 3.09
2201 3883 7.176340 GGATCATCTATTTTGGAATGGAGGAAG 59.824 40.741 4.45 0.00 43.49 3.46
2202 3884 7.006509 GGATCATCTATTTTGGAATGGAGGAA 58.993 38.462 4.45 0.00 43.49 3.36
2203 3885 6.103057 TGGATCATCTATTTTGGAATGGAGGA 59.897 38.462 0.00 3.11 44.08 3.71
2204 3886 6.309357 TGGATCATCTATTTTGGAATGGAGG 58.691 40.000 0.00 0.00 36.39 4.30
2205 3887 7.828508 TTGGATCATCTATTTTGGAATGGAG 57.171 36.000 0.00 0.00 36.39 3.86
2206 3888 8.786710 AATTGGATCATCTATTTTGGAATGGA 57.213 30.769 0.00 0.00 37.20 3.41
2207 3889 9.841295 AAAATTGGATCATCTATTTTGGAATGG 57.159 29.630 9.05 0.00 31.14 3.16
2234 3916 9.617975 GACTCAACTTTGTACTAACGTTAGTAT 57.382 33.333 37.39 24.72 45.11 2.12
2235 3917 8.620416 TGACTCAACTTTGTACTAACGTTAGTA 58.380 33.333 33.82 33.82 43.36 1.82
2236 3918 7.483307 TGACTCAACTTTGTACTAACGTTAGT 58.517 34.615 35.71 35.71 45.39 2.24
2237 3919 7.919313 TGACTCAACTTTGTACTAACGTTAG 57.081 36.000 29.27 29.27 36.82 2.34
2238 3920 8.355169 AGATGACTCAACTTTGTACTAACGTTA 58.645 33.333 7.94 7.94 0.00 3.18
2239 3921 7.208080 AGATGACTCAACTTTGTACTAACGTT 58.792 34.615 5.88 5.88 0.00 3.99
2240 3922 6.746120 AGATGACTCAACTTTGTACTAACGT 58.254 36.000 0.00 0.00 0.00 3.99
2241 3923 8.912787 ATAGATGACTCAACTTTGTACTAACG 57.087 34.615 0.00 0.00 0.00 3.18
2245 3927 9.778741 TCAAAATAGATGACTCAACTTTGTACT 57.221 29.630 0.00 0.00 0.00 2.73
2248 3930 9.736023 GTTTCAAAATAGATGACTCAACTTTGT 57.264 29.630 0.00 0.00 0.00 2.83
2249 3931 8.895845 CGTTTCAAAATAGATGACTCAACTTTG 58.104 33.333 0.00 0.00 0.00 2.77
2250 3932 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
2251 3933 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
2252 3934 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
2253 3935 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
2254 3936 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
2255 3937 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
2256 3938 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
2257 3939 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
2258 3940 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
2259 3941 5.429681 TCCCTCCGTTTCAAAATAGATGA 57.570 39.130 0.00 0.00 0.00 2.92
2260 3942 6.699575 ATTCCCTCCGTTTCAAAATAGATG 57.300 37.500 0.00 0.00 0.00 2.90
2261 3943 7.574607 ACTATTCCCTCCGTTTCAAAATAGAT 58.425 34.615 0.00 0.00 32.32 1.98
2262 3944 6.954232 ACTATTCCCTCCGTTTCAAAATAGA 58.046 36.000 0.00 0.00 32.32 1.98
2263 3945 7.625828 AACTATTCCCTCCGTTTCAAAATAG 57.374 36.000 0.00 0.00 33.52 1.73
2264 3946 7.771826 CCTAACTATTCCCTCCGTTTCAAAATA 59.228 37.037 0.00 0.00 0.00 1.40
2265 3947 6.602009 CCTAACTATTCCCTCCGTTTCAAAAT 59.398 38.462 0.00 0.00 0.00 1.82
2266 3948 5.941647 CCTAACTATTCCCTCCGTTTCAAAA 59.058 40.000 0.00 0.00 0.00 2.44
2267 3949 5.248934 TCCTAACTATTCCCTCCGTTTCAAA 59.751 40.000 0.00 0.00 0.00 2.69
2268 3950 4.778958 TCCTAACTATTCCCTCCGTTTCAA 59.221 41.667 0.00 0.00 0.00 2.69
2269 3951 4.355549 TCCTAACTATTCCCTCCGTTTCA 58.644 43.478 0.00 0.00 0.00 2.69
2270 3952 5.114780 GTTCCTAACTATTCCCTCCGTTTC 58.885 45.833 0.00 0.00 0.00 2.78
2271 3953 4.382362 CGTTCCTAACTATTCCCTCCGTTT 60.382 45.833 0.00 0.00 0.00 3.60
2272 3954 3.131755 CGTTCCTAACTATTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
2273 3955 2.692041 CGTTCCTAACTATTCCCTCCGT 59.308 50.000 0.00 0.00 0.00 4.69
2274 3956 2.035576 CCGTTCCTAACTATTCCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
2275 3957 3.303049 TCCGTTCCTAACTATTCCCTCC 58.697 50.000 0.00 0.00 0.00 4.30
2276 3958 4.213513 TCTCCGTTCCTAACTATTCCCTC 58.786 47.826 0.00 0.00 0.00 4.30
2277 3959 4.261411 TCTCCGTTCCTAACTATTCCCT 57.739 45.455 0.00 0.00 0.00 4.20
2278 3960 5.349061 TTTCTCCGTTCCTAACTATTCCC 57.651 43.478 0.00 0.00 0.00 3.97
2284 3966 9.901172 AAACATATATTTTCTCCGTTCCTAACT 57.099 29.630 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.