Multiple sequence alignment - TraesCS2B01G459800

Loading Multiple Alignment...

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 TraesCS2B01G459800 chr2B 100.000 4086 0 0 1 4086 653917476 653913391 0.000000e+00 7546
1 TraesCS2B01G459800 chr2A 83.784 2220 172 77 1 2091 691235029 691237189 0.000000e+00 1932
2 TraesCS2B01G459800 chr2A 92.474 970 54 6 2219 3175 691237187 691238150 0.000000e+00 1369
3 TraesCS2B01G459800 chr2A 85.252 556 40 10 3561 4086 691244481 691245024 6.010000e-148 534
4 TraesCS2B01G459800 chr2A 86.413 184 7 8 3168 3336 691244308 691244488 6.970000e-43 185
5 TraesCS2B01G459800 chr2D 91.179 1281 75 20 2219 3480 547611458 547610197 0.000000e+00 1705
6 TraesCS2B01G459800 chr2D 83.993 1693 165 53 225 1859 547613372 547611728 0.000000e+00 1528
7 TraesCS2B01G459800 chr2D 81.693 579 37 20 3548 4086 547609948 547609399 6.320000e-113 418
8 TraesCS2B01G459800 chr6A 84.485 709 64 24 937 1613 54666093 54666787 0.000000e+00 658
9 TraesCS2B01G459800 chr1D 91.640 311 18 3 1292 1594 480516460 480516770 1.360000e-114 424
10 TraesCS2B01G459800 chr1D 95.973 149 3 3 2081 2228 407699389 407699535 5.280000e-59 239
11 TraesCS2B01G459800 chr1D 98.496 133 2 0 2089 2221 179435227 179435095 6.830000e-58 235
12 TraesCS2B01G459800 chr1D 95.726 117 3 2 1121 1236 480516213 480516328 1.940000e-43 187
13 TraesCS2B01G459800 chr3B 98.540 137 2 0 2083 2219 809457832 809457968 4.080000e-60 243
14 TraesCS2B01G459800 chr3B 97.727 132 3 0 2088 2219 153653432 153653563 1.140000e-55 228
15 TraesCS2B01G459800 chr6B 97.080 137 4 0 2085 2221 117838460 117838596 8.830000e-57 231
16 TraesCS2B01G459800 chr5A 97.761 134 3 0 2091 2224 590920329 590920462 8.830000e-57 231
17 TraesCS2B01G459800 chr1B 97.037 135 3 1 2086 2219 50990216 50990082 4.110000e-55 226
18 TraesCS2B01G459800 chr5B 95.588 136 6 0 2089 2224 645552938 645553073 6.880000e-53 219
19 TraesCS2B01G459800 chr5D 94.366 142 7 1 2091 2231 23153859 23154000 2.470000e-52 217


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 TraesCS2B01G459800 chr2B 653913391 653917476 4085 True 7546.0 7546 100.000000 1 4086 1 chr2B.!!$R1 4085
1 TraesCS2B01G459800 chr2A 691235029 691238150 3121 False 1650.5 1932 88.129000 1 3175 2 chr2A.!!$F1 3174
2 TraesCS2B01G459800 chr2A 691244308 691245024 716 False 359.5 534 85.832500 3168 4086 2 chr2A.!!$F2 918
3 TraesCS2B01G459800 chr2D 547609399 547613372 3973 True 1217.0 1705 85.621667 225 4086 3 chr2D.!!$R1 3861
4 TraesCS2B01G459800 chr6A 54666093 54666787 694 False 658.0 658 84.485000 937 1613 1 chr6A.!!$F1 676
5 TraesCS2B01G459800 chr1D 480516213 480516770 557 False 305.5 424 93.683000 1121 1594 2 chr1D.!!$F2 473

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
162 164 0.098200 GGACGACGATGATGACACGA 59.902 55.0 0.0 0.0 0.00 4.35 F
166 168 0.179171 GACGATGATGACACGACGGT 60.179 55.0 0.0 0.0 0.00 4.83 F
2143 2395 0.106469 TACGAGGAGCTGGAGCATCT 60.106 55.0 0.0 0.0 45.16 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2376 0.106469 AGATGCTCCAGCTCCTCGTA 60.106 55.0 0.0 0.0 42.66 3.43 R
2153 2405 0.250295 TGGAGTCAAAAGGCACGGAG 60.250 55.0 0.0 0.0 0.00 4.63 R
3760 4267 0.250901 GGTTGGATCTGTGGCTGTGT 60.251 55.0 0.0 0.0 0.00 3.72 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
64 65 1.226974 CATCGCACGGTGTAGGAGG 60.227 63.158 10.24 3.46 0.00 4.30
66 67 1.384989 ATCGCACGGTGTAGGAGGAG 61.385 60.000 10.24 0.00 0.00 3.69
67 68 2.184579 GCACGGTGTAGGAGGAGC 59.815 66.667 10.24 0.00 0.00 4.70
68 69 2.646175 GCACGGTGTAGGAGGAGCA 61.646 63.158 10.24 0.00 0.00 4.26
69 70 1.215647 CACGGTGTAGGAGGAGCAC 59.784 63.158 0.00 0.00 0.00 4.40
114 116 3.423154 CGGCCGAGCAAGGTTGTC 61.423 66.667 24.07 0.00 0.00 3.18
116 118 4.090057 GCCGAGCAAGGTTGTCGC 62.090 66.667 8.34 0.00 33.52 5.19
143 145 2.125512 CCCTTCGGTCGCTGGAAG 60.126 66.667 3.20 3.20 39.44 3.46
146 148 1.446272 CTTCGGTCGCTGGAAGGAC 60.446 63.158 2.45 0.00 36.78 3.85
152 154 2.044555 TCGCTGGAAGGACGACGAT 61.045 57.895 0.00 0.00 0.00 3.73
157 159 1.405463 CTGGAAGGACGACGATGATGA 59.595 52.381 0.00 0.00 0.00 2.92
160 162 2.186076 GAAGGACGACGATGATGACAC 58.814 52.381 0.00 0.00 0.00 3.67
161 163 0.098905 AGGACGACGATGATGACACG 59.901 55.000 0.00 0.00 0.00 4.49
162 164 0.098200 GGACGACGATGATGACACGA 59.902 55.000 0.00 0.00 0.00 4.35
163 165 1.181001 GACGACGATGATGACACGAC 58.819 55.000 0.00 0.00 0.00 4.34
164 166 0.520619 ACGACGATGATGACACGACG 60.521 55.000 0.00 0.00 45.94 5.12
166 168 0.179171 GACGATGATGACACGACGGT 60.179 55.000 0.00 0.00 0.00 4.83
206 218 1.792941 GCGTAGAAGGTCGTCGTCT 59.207 57.895 0.00 0.00 37.87 4.18
214 226 0.240411 AGGTCGTCGTCTGCTACAAC 59.760 55.000 0.00 0.00 0.00 3.32
219 231 1.912110 CGTCGTCTGCTACAACTTAGC 59.088 52.381 0.00 0.00 40.76 3.09
222 234 2.094700 TCGTCTGCTACAACTTAGCCTG 60.095 50.000 0.96 0.00 39.69 4.85
223 235 2.003301 GTCTGCTACAACTTAGCCTGC 58.997 52.381 0.96 0.00 39.69 4.85
225 237 3.096852 TCTGCTACAACTTAGCCTGCTA 58.903 45.455 0.00 0.00 39.69 3.49
226 238 3.131223 TCTGCTACAACTTAGCCTGCTAG 59.869 47.826 0.00 0.00 39.69 3.42
227 239 2.168521 TGCTACAACTTAGCCTGCTAGG 59.831 50.000 6.73 6.73 39.69 3.02
228 240 2.168728 GCTACAACTTAGCCTGCTAGGT 59.831 50.000 7.99 7.99 39.95 3.08
260 275 9.558648 TGAACAATCGAAATATCATCTGTTTTG 57.441 29.630 0.00 0.00 0.00 2.44
293 308 5.000591 TGTTCAAACTATGCTGAAATCCGA 58.999 37.500 0.00 0.00 33.52 4.55
303 318 2.661979 GCTGAAATCCGACGTGTTTGAC 60.662 50.000 0.00 0.00 0.00 3.18
350 376 5.776519 TTATTTTGAAATGCGTTGGATGC 57.223 34.783 0.00 0.00 0.00 3.91
351 377 2.077413 TTTGAAATGCGTTGGATGCC 57.923 45.000 0.00 0.00 0.00 4.40
352 378 1.255882 TTGAAATGCGTTGGATGCCT 58.744 45.000 0.00 0.00 0.00 4.75
358 384 2.270205 CGTTGGATGCCTGGCTCT 59.730 61.111 21.03 7.17 0.00 4.09
362 388 3.859414 GGATGCCTGGCTCTCGCT 61.859 66.667 21.03 0.00 36.09 4.93
370 396 1.074752 CTGGCTCTCGCTTCACTTTC 58.925 55.000 0.00 0.00 36.09 2.62
372 398 1.355066 GGCTCTCGCTTCACTTTCCG 61.355 60.000 0.00 0.00 36.09 4.30
386 413 2.093973 ACTTTCCGCGAACTGATCTCAT 60.094 45.455 8.23 0.00 0.00 2.90
394 421 3.192799 ACTGATCTCATCGGTCCGT 57.807 52.632 11.88 0.00 45.46 4.69
397 424 3.071123 ACTGATCTCATCGGTCCGTAGG 61.071 54.545 11.88 2.22 45.46 3.18
414 441 3.253677 CGTAGGCAGATAAGGTGTCCTAG 59.746 52.174 0.00 0.00 31.13 3.02
415 442 2.683768 AGGCAGATAAGGTGTCCTAGG 58.316 52.381 0.82 0.82 31.13 3.02
416 443 1.694696 GGCAGATAAGGTGTCCTAGGG 59.305 57.143 9.46 0.00 31.13 3.53
417 444 1.070914 GCAGATAAGGTGTCCTAGGGC 59.929 57.143 6.37 6.37 31.13 5.19
418 445 2.398588 CAGATAAGGTGTCCTAGGGCA 58.601 52.381 13.40 13.40 31.13 5.36
419 446 2.103263 CAGATAAGGTGTCCTAGGGCAC 59.897 54.545 34.22 34.22 31.13 5.01
450 481 2.821366 CCATGAGTGGTGAGCGGC 60.821 66.667 0.00 0.00 40.83 6.53
452 483 2.104859 CATGAGTGGTGAGCGGCAG 61.105 63.158 1.45 0.00 0.00 4.85
453 484 2.587247 ATGAGTGGTGAGCGGCAGT 61.587 57.895 1.45 0.00 0.00 4.40
455 486 3.521529 GAGTGGTGAGCGGCAGTGT 62.522 63.158 1.45 0.00 0.00 3.55
487 524 3.025262 TGTATGGGATGTGCTACGTACA 58.975 45.455 0.00 0.00 34.11 2.90
510 547 2.657960 CATGTGTGCAGCGTCATATC 57.342 50.000 0.00 0.00 0.00 1.63
548 585 1.371183 GCAGCCACAGACCACAGTA 59.629 57.895 0.00 0.00 0.00 2.74
563 600 2.580597 GTAGGTTACCGTCGGCGC 60.581 66.667 12.28 0.00 36.67 6.53
610 647 2.118404 CACAGTTGGTTGGGCGTGT 61.118 57.895 0.00 0.00 0.00 4.49
646 683 3.774959 GATGCTCGGCGTCGTCCAT 62.775 63.158 10.18 13.24 34.82 3.41
794 838 2.499205 CGCCACCATCTCCGCTAA 59.501 61.111 0.00 0.00 0.00 3.09
929 975 2.100087 TCAGCAAGACCGCGTTATATGA 59.900 45.455 4.92 0.00 36.85 2.15
939 988 7.102346 AGACCGCGTTATATGATACTACTAGT 58.898 38.462 4.92 0.00 0.00 2.57
954 1003 3.306472 ACTAGTAAGGGAGGAGCTCAG 57.694 52.381 17.19 2.33 31.08 3.35
982 1031 0.622665 ATCTTGCAAGGACAGGGGAG 59.377 55.000 25.73 0.00 0.00 4.30
1035 1084 3.224324 GGGATGAGCTACGGCGGA 61.224 66.667 13.24 0.00 44.37 5.54
1093 1166 2.044946 GGGATCCAAAGCAGCGGT 60.045 61.111 15.23 0.00 0.00 5.68
1172 1248 0.969894 CCCGACAGTGAGTCCTCTTT 59.030 55.000 0.00 0.00 44.66 2.52
1184 1261 4.080863 TGAGTCCTCTTTATTGCTCCTTCC 60.081 45.833 0.00 0.00 0.00 3.46
1248 1354 3.005155 GTGCCTGATCAAACTTTGCTTCT 59.995 43.478 0.00 0.00 0.00 2.85
1254 1360 6.199719 CCTGATCAAACTTTGCTTCTTTTGAC 59.800 38.462 0.00 3.43 39.96 3.18
1276 1431 7.661968 TGACCATCAGCTTAACTATACTGATC 58.338 38.462 1.52 0.00 45.64 2.92
1390 1559 3.781079 TCAGGTTTTGCTCAACAACTG 57.219 42.857 7.33 7.33 38.23 3.16
1398 1567 2.616639 TGCTCAACAACTGTGCACCAG 61.617 52.381 15.69 13.95 46.77 4.00
1422 1592 3.366273 CCTGCTCTTCGCTCATATCTCTC 60.366 52.174 0.00 0.00 40.11 3.20
1451 1626 0.819259 TTTGCAGTCCAGTCCAGTGC 60.819 55.000 0.00 0.00 40.16 4.40
1464 1639 3.377485 AGTCCAGTGCTGTACTACGTATG 59.623 47.826 0.00 0.00 37.60 2.39
1589 1778 1.068333 CACATACACCTTGCAACTGCC 60.068 52.381 0.00 0.00 41.18 4.85
1629 1818 1.104577 GTCAAGCCAACGTTTCCCCA 61.105 55.000 0.00 0.00 0.00 4.96
1642 1831 3.439129 CGTTTCCCCATCTAAACTCCAAC 59.561 47.826 0.00 0.00 34.21 3.77
1709 1898 2.753966 CCAAATCGGTGCGCCTCTG 61.754 63.158 15.69 3.24 0.00 3.35
1712 1901 2.748058 AAATCGGTGCGCCTCTGGTT 62.748 55.000 15.69 2.76 0.00 3.67
1782 1971 0.636647 TCCCTCTGGACCTATCTGCA 59.363 55.000 0.00 0.00 35.03 4.41
2018 2266 7.936847 ACTGTGAAAGTATGGATAGAACAAACA 59.063 33.333 0.00 0.00 37.36 2.83
2020 2268 7.095397 TGTGAAAGTATGGATAGAACAAACACG 60.095 37.037 0.00 0.00 0.00 4.49
2078 2330 7.319646 ACTGAAAAGTGAGATCTGATCAGTAC 58.680 38.462 21.92 16.09 39.79 2.73
2082 2334 6.849085 AAGTGAGATCTGATCAGTACTTGT 57.151 37.500 21.92 5.06 32.03 3.16
2098 2350 3.418684 CTTGTACAAGTTAGGCCCTGT 57.581 47.619 24.70 0.00 33.87 4.00
2099 2351 3.751518 CTTGTACAAGTTAGGCCCTGTT 58.248 45.455 24.70 0.00 33.87 3.16
2100 2352 3.868619 TGTACAAGTTAGGCCCTGTTT 57.131 42.857 0.00 0.00 0.00 2.83
2101 2353 3.482436 TGTACAAGTTAGGCCCTGTTTG 58.518 45.455 0.00 2.32 0.00 2.93
2102 2354 1.995376 ACAAGTTAGGCCCTGTTTGG 58.005 50.000 0.00 0.00 0.00 3.28
2103 2355 1.497286 ACAAGTTAGGCCCTGTTTGGA 59.503 47.619 0.00 0.00 38.35 3.53
2104 2356 2.162681 CAAGTTAGGCCCTGTTTGGAG 58.837 52.381 0.00 0.00 38.35 3.86
2105 2357 1.446016 AGTTAGGCCCTGTTTGGAGT 58.554 50.000 0.00 0.00 38.35 3.85
2106 2358 1.351350 AGTTAGGCCCTGTTTGGAGTC 59.649 52.381 0.00 0.00 38.35 3.36
2107 2359 1.073284 GTTAGGCCCTGTTTGGAGTCA 59.927 52.381 0.00 0.00 38.35 3.41
2108 2360 0.690762 TAGGCCCTGTTTGGAGTCAC 59.309 55.000 0.00 0.00 38.35 3.67
2109 2361 1.062488 AGGCCCTGTTTGGAGTCACT 61.062 55.000 0.00 0.00 38.35 3.41
2110 2362 0.606673 GGCCCTGTTTGGAGTCACTC 60.607 60.000 0.00 0.00 38.35 3.51
2126 2378 7.598189 GAGTCACTCCAACTCCTAAAAATAC 57.402 40.000 0.00 0.00 37.72 1.89
2127 2379 6.164176 AGTCACTCCAACTCCTAAAAATACG 58.836 40.000 0.00 0.00 0.00 3.06
2128 2380 6.014840 AGTCACTCCAACTCCTAAAAATACGA 60.015 38.462 0.00 0.00 0.00 3.43
2129 2381 6.310711 GTCACTCCAACTCCTAAAAATACGAG 59.689 42.308 0.00 0.00 0.00 4.18
2130 2382 5.581085 CACTCCAACTCCTAAAAATACGAGG 59.419 44.000 0.00 0.00 0.00 4.63
2131 2383 5.482878 ACTCCAACTCCTAAAAATACGAGGA 59.517 40.000 0.00 0.00 37.02 3.71
2136 2388 4.402056 TCCTAAAAATACGAGGAGCTGG 57.598 45.455 0.00 0.00 34.36 4.85
2137 2389 4.028131 TCCTAAAAATACGAGGAGCTGGA 58.972 43.478 0.00 0.00 34.36 3.86
2138 2390 4.099573 TCCTAAAAATACGAGGAGCTGGAG 59.900 45.833 0.00 0.00 34.36 3.86
2139 2391 2.317530 AAAATACGAGGAGCTGGAGC 57.682 50.000 0.00 0.00 42.49 4.70
2140 2392 1.195115 AAATACGAGGAGCTGGAGCA 58.805 50.000 0.00 0.00 45.16 4.26
2141 2393 1.418334 AATACGAGGAGCTGGAGCAT 58.582 50.000 0.00 0.00 45.16 3.79
2142 2394 0.965439 ATACGAGGAGCTGGAGCATC 59.035 55.000 0.00 0.00 45.16 3.91
2143 2395 0.106469 TACGAGGAGCTGGAGCATCT 60.106 55.000 0.00 0.00 45.16 2.90
2144 2396 1.363443 CGAGGAGCTGGAGCATCTC 59.637 63.158 0.00 6.34 45.16 2.75
2145 2397 1.108727 CGAGGAGCTGGAGCATCTCT 61.109 60.000 14.87 2.67 45.16 3.10
2146 2398 1.122227 GAGGAGCTGGAGCATCTCTT 58.878 55.000 0.00 0.00 45.16 2.85
2147 2399 1.485895 GAGGAGCTGGAGCATCTCTTT 59.514 52.381 0.00 0.00 45.16 2.52
2148 2400 1.485895 AGGAGCTGGAGCATCTCTTTC 59.514 52.381 0.00 0.00 45.16 2.62
2149 2401 1.474855 GGAGCTGGAGCATCTCTTTCC 60.475 57.143 0.00 0.00 45.16 3.13
2150 2402 0.545646 AGCTGGAGCATCTCTTTCCC 59.454 55.000 0.65 0.00 45.16 3.97
2151 2403 0.254178 GCTGGAGCATCTCTTTCCCA 59.746 55.000 0.00 0.00 41.59 4.37
2152 2404 1.746516 GCTGGAGCATCTCTTTCCCAG 60.747 57.143 0.00 0.00 42.88 4.45
2153 2405 0.254178 TGGAGCATCTCTTTCCCAGC 59.746 55.000 0.00 0.00 33.73 4.85
2154 2406 0.545646 GGAGCATCTCTTTCCCAGCT 59.454 55.000 0.00 0.00 33.73 4.24
2155 2407 1.474855 GGAGCATCTCTTTCCCAGCTC 60.475 57.143 0.00 0.00 45.65 4.09
2156 2408 0.545646 AGCATCTCTTTCCCAGCTCC 59.454 55.000 0.00 0.00 0.00 4.70
2157 2409 0.813210 GCATCTCTTTCCCAGCTCCG 60.813 60.000 0.00 0.00 0.00 4.63
2158 2410 0.539051 CATCTCTTTCCCAGCTCCGT 59.461 55.000 0.00 0.00 0.00 4.69
2159 2411 0.539051 ATCTCTTTCCCAGCTCCGTG 59.461 55.000 0.00 0.00 0.00 4.94
2160 2412 1.743252 CTCTTTCCCAGCTCCGTGC 60.743 63.158 0.00 0.00 43.29 5.34
2161 2413 2.747855 CTTTCCCAGCTCCGTGCC 60.748 66.667 0.00 0.00 44.23 5.01
2162 2414 3.249189 TTTCCCAGCTCCGTGCCT 61.249 61.111 0.00 0.00 44.23 4.75
2163 2415 2.754664 CTTTCCCAGCTCCGTGCCTT 62.755 60.000 0.00 0.00 44.23 4.35
2164 2416 2.351924 TTTCCCAGCTCCGTGCCTTT 62.352 55.000 0.00 0.00 44.23 3.11
2165 2417 2.282462 CCCAGCTCCGTGCCTTTT 60.282 61.111 0.00 0.00 44.23 2.27
2166 2418 2.629656 CCCAGCTCCGTGCCTTTTG 61.630 63.158 0.00 0.00 44.23 2.44
2167 2419 1.600636 CCAGCTCCGTGCCTTTTGA 60.601 57.895 0.00 0.00 44.23 2.69
2168 2420 1.576421 CAGCTCCGTGCCTTTTGAC 59.424 57.895 0.00 0.00 44.23 3.18
2169 2421 0.886490 CAGCTCCGTGCCTTTTGACT 60.886 55.000 0.00 0.00 44.23 3.41
2170 2422 0.603975 AGCTCCGTGCCTTTTGACTC 60.604 55.000 0.00 0.00 44.23 3.36
2171 2423 1.578206 GCTCCGTGCCTTTTGACTCC 61.578 60.000 0.00 0.00 35.15 3.85
2172 2424 0.250295 CTCCGTGCCTTTTGACTCCA 60.250 55.000 0.00 0.00 0.00 3.86
2173 2425 0.250295 TCCGTGCCTTTTGACTCCAG 60.250 55.000 0.00 0.00 0.00 3.86
2174 2426 1.576421 CGTGCCTTTTGACTCCAGC 59.424 57.895 0.00 0.00 0.00 4.85
2175 2427 0.886490 CGTGCCTTTTGACTCCAGCT 60.886 55.000 0.00 0.00 0.00 4.24
2176 2428 0.877743 GTGCCTTTTGACTCCAGCTC 59.122 55.000 0.00 0.00 0.00 4.09
2177 2429 0.250901 TGCCTTTTGACTCCAGCTCC 60.251 55.000 0.00 0.00 0.00 4.70
2178 2430 1.301677 GCCTTTTGACTCCAGCTCCG 61.302 60.000 0.00 0.00 0.00 4.63
2179 2431 0.674895 CCTTTTGACTCCAGCTCCGG 60.675 60.000 0.00 0.00 0.00 5.14
2180 2432 0.674895 CTTTTGACTCCAGCTCCGGG 60.675 60.000 0.00 0.00 0.00 5.73
2181 2433 1.125093 TTTTGACTCCAGCTCCGGGA 61.125 55.000 0.00 0.00 0.00 5.14
2195 2447 3.775654 GGGAGCGGAGTGGTGGAG 61.776 72.222 0.00 0.00 0.00 3.86
2196 2448 2.997897 GGAGCGGAGTGGTGGAGT 60.998 66.667 0.00 0.00 0.00 3.85
2197 2449 2.262915 GAGCGGAGTGGTGGAGTG 59.737 66.667 0.00 0.00 0.00 3.51
2198 2450 3.302347 GAGCGGAGTGGTGGAGTGG 62.302 68.421 0.00 0.00 0.00 4.00
2200 2452 4.742201 CGGAGTGGTGGAGTGGCG 62.742 72.222 0.00 0.00 0.00 5.69
2201 2453 4.394712 GGAGTGGTGGAGTGGCGG 62.395 72.222 0.00 0.00 0.00 6.13
2202 2454 4.394712 GAGTGGTGGAGTGGCGGG 62.395 72.222 0.00 0.00 0.00 6.13
2204 2456 4.699522 GTGGTGGAGTGGCGGGTC 62.700 72.222 0.00 0.00 0.00 4.46
2205 2457 4.954118 TGGTGGAGTGGCGGGTCT 62.954 66.667 0.00 0.00 0.00 3.85
2206 2458 4.083862 GGTGGAGTGGCGGGTCTC 62.084 72.222 0.00 0.00 0.00 3.36
2217 2469 4.097361 GGGTCTCCGAACAGGGCC 62.097 72.222 0.00 0.00 41.52 5.80
2218 2470 3.003763 GGTCTCCGAACAGGGCCT 61.004 66.667 0.00 0.00 41.52 5.19
2219 2471 2.593956 GGTCTCCGAACAGGGCCTT 61.594 63.158 1.32 0.00 41.52 4.35
2284 2537 8.766994 ACTTGCCATTCCAAAAGTATATATGT 57.233 30.769 0.00 0.00 31.26 2.29
2307 2560 6.821665 TGTAAAGTTTCATATACAGAGGCACC 59.178 38.462 0.00 0.00 0.00 5.01
2311 2564 5.189736 AGTTTCATATACAGAGGCACCAAGA 59.810 40.000 0.00 0.00 0.00 3.02
2365 2618 2.860735 GTCATGCGTCTTCTATGTGTCC 59.139 50.000 0.00 0.00 0.00 4.02
2375 2628 6.157211 GTCTTCTATGTGTCCTTTTCTTCGA 58.843 40.000 0.00 0.00 0.00 3.71
2422 2675 8.661352 ACTAACCATTTCCAAAACATTTCTTG 57.339 30.769 0.00 0.00 0.00 3.02
2496 2749 2.354510 CCAAAGAGAACTGTGCGAACAA 59.645 45.455 0.00 0.00 30.46 2.83
2552 2805 2.305927 ACTCCCAAACTCTGTACCATGG 59.694 50.000 11.19 11.19 0.00 3.66
2575 2842 8.905660 TGGCGTAGGTTAAAAATGCTTATATA 57.094 30.769 0.00 0.00 0.00 0.86
2726 2993 0.463204 CCAGATCACAGCTCACGGAT 59.537 55.000 0.00 0.00 0.00 4.18
2747 3014 0.252103 TCAACCTAGCTCTTCCGGGT 60.252 55.000 0.00 0.00 0.00 5.28
2748 3015 0.175989 CAACCTAGCTCTTCCGGGTC 59.824 60.000 0.00 0.00 0.00 4.46
2750 3017 0.396001 ACCTAGCTCTTCCGGGTCTC 60.396 60.000 0.00 0.00 0.00 3.36
2751 3018 0.395862 CCTAGCTCTTCCGGGTCTCA 60.396 60.000 0.00 0.00 0.00 3.27
2764 3031 1.134670 GGGTCTCACGGAGAATGGAAG 60.135 57.143 5.34 0.00 40.59 3.46
2802 3069 1.268539 GCGGTGAACAGTTGGTGAAAG 60.269 52.381 0.00 0.00 0.00 2.62
2913 3180 1.001406 CGAAAACTGAGGACCTGCTCT 59.999 52.381 0.00 0.00 0.00 4.09
3048 3316 5.502079 TGACAGTTTTTGGGAGTTTCACTA 58.498 37.500 0.00 0.00 0.00 2.74
3052 3320 7.847096 ACAGTTTTTGGGAGTTTCACTATTTT 58.153 30.769 0.00 0.00 0.00 1.82
3055 3323 8.197439 AGTTTTTGGGAGTTTCACTATTTTCTG 58.803 33.333 0.00 0.00 0.00 3.02
3120 3390 5.354234 CACAAGTTTGACTTACTCTGTGGTT 59.646 40.000 0.00 0.00 36.03 3.67
3204 3475 1.004044 AGAGTGCACATGGGAAAGGAG 59.996 52.381 21.04 0.00 0.00 3.69
3205 3476 1.003580 GAGTGCACATGGGAAAGGAGA 59.996 52.381 21.04 0.00 0.00 3.71
3207 3478 1.815003 GTGCACATGGGAAAGGAGAAG 59.185 52.381 13.17 0.00 0.00 2.85
3298 3582 3.949754 CAGAGCCACATAACATGTTCCAT 59.050 43.478 15.85 0.53 42.70 3.41
3299 3583 4.400251 CAGAGCCACATAACATGTTCCATT 59.600 41.667 15.85 0.00 42.70 3.16
3344 3629 4.423625 AGCAGAATAAACCCGATTAGCT 57.576 40.909 0.00 0.00 0.00 3.32
3350 3635 7.571428 GCAGAATAAACCCGATTAGCTTGATAC 60.571 40.741 0.00 0.00 0.00 2.24
3354 3639 4.602340 ACCCGATTAGCTTGATACGAAT 57.398 40.909 0.00 0.00 0.00 3.34
3356 3641 6.282199 ACCCGATTAGCTTGATACGAATAT 57.718 37.500 0.00 0.00 0.00 1.28
3357 3642 6.698380 ACCCGATTAGCTTGATACGAATATT 58.302 36.000 0.00 0.00 0.00 1.28
3453 3739 6.509418 ACTTCGCTAAATCCTAAATGCAAA 57.491 33.333 0.00 0.00 0.00 3.68
3455 3741 7.029563 ACTTCGCTAAATCCTAAATGCAAAAG 58.970 34.615 0.00 0.00 0.00 2.27
3461 3747 7.489435 GCTAAATCCTAAATGCAAAAGTCCTTC 59.511 37.037 0.00 0.00 0.00 3.46
3480 3766 8.027189 AGTCCTTCAAAGTTTAAACAAAGACAC 58.973 33.333 20.06 14.54 0.00 3.67
3481 3767 7.810759 GTCCTTCAAAGTTTAAACAAAGACACA 59.189 33.333 20.06 0.31 0.00 3.72
3482 3768 8.026607 TCCTTCAAAGTTTAAACAAAGACACAG 58.973 33.333 20.06 8.47 0.00 3.66
3483 3769 8.026607 CCTTCAAAGTTTAAACAAAGACACAGA 58.973 33.333 20.06 2.74 0.00 3.41
3484 3770 9.405587 CTTCAAAGTTTAAACAAAGACACAGAA 57.594 29.630 20.06 9.23 0.00 3.02
3485 3771 9.751542 TTCAAAGTTTAAACAAAGACACAGAAA 57.248 25.926 20.06 0.00 0.00 2.52
3486 3772 9.751542 TCAAAGTTTAAACAAAGACACAGAAAA 57.248 25.926 20.06 0.00 0.00 2.29
3488 3774 9.758651 AAAGTTTAAACAAAGACACAGAAAAGT 57.241 25.926 20.06 0.00 0.00 2.66
3489 3775 8.742554 AGTTTAAACAAAGACACAGAAAAGTG 57.257 30.769 20.06 0.00 44.93 3.16
3490 3776 7.812669 AGTTTAAACAAAGACACAGAAAAGTGG 59.187 33.333 20.06 0.00 43.72 4.00
3491 3777 5.975693 AAACAAAGACACAGAAAAGTGGA 57.024 34.783 0.00 0.00 43.72 4.02
3492 3778 5.567138 AACAAAGACACAGAAAAGTGGAG 57.433 39.130 0.00 0.00 43.72 3.86
3493 3779 4.843728 ACAAAGACACAGAAAAGTGGAGA 58.156 39.130 0.00 0.00 43.72 3.71
3501 3787 5.888161 ACACAGAAAAGTGGAGAGTGAATTT 59.112 36.000 0.00 0.00 43.72 1.82
3506 3792 7.857885 CAGAAAAGTGGAGAGTGAATTTGTTAC 59.142 37.037 0.00 0.00 0.00 2.50
3510 3796 4.757149 GTGGAGAGTGAATTTGTTACTGCT 59.243 41.667 0.00 0.00 0.00 4.24
3523 3809 3.253188 TGTTACTGCTCAATTGCAAGGAC 59.747 43.478 4.94 1.69 42.83 3.85
3540 3826 4.590850 AGGACAATTTTCCTTGCTCAAC 57.409 40.909 7.37 0.00 44.22 3.18
3542 3828 4.038402 AGGACAATTTTCCTTGCTCAACAG 59.962 41.667 7.37 0.00 44.22 3.16
3545 3831 5.351458 ACAATTTTCCTTGCTCAACAGAAC 58.649 37.500 0.00 0.00 0.00 3.01
3546 3832 5.127682 ACAATTTTCCTTGCTCAACAGAACT 59.872 36.000 0.00 0.00 0.00 3.01
3553 4034 4.260784 CCTTGCTCAACAGAACTTGTACAC 60.261 45.833 0.00 0.00 39.73 2.90
3556 4037 3.308866 GCTCAACAGAACTTGTACACGTT 59.691 43.478 16.79 16.79 39.73 3.99
3578 4059 4.787551 TGTCAATTAACCACCTGACACTT 58.212 39.130 0.00 0.00 42.36 3.16
3597 4078 4.218417 CACTTATGTGTCCTTGGAAAAGGG 59.782 45.833 4.73 0.00 39.24 3.95
3620 4101 5.393461 GGCAAGGAACATAAGATTTGTGAGG 60.393 44.000 0.00 0.00 0.00 3.86
3622 4103 4.922206 AGGAACATAAGATTTGTGAGGCA 58.078 39.130 0.00 0.00 0.00 4.75
3633 4114 4.647424 TTTGTGAGGCAAACTAAACTGG 57.353 40.909 0.00 0.00 41.68 4.00
3643 4124 2.694616 ACTAAACTGGCCCATTTGGT 57.305 45.000 10.84 10.84 36.04 3.67
3647 4128 0.678950 AACTGGCCCATTTGGTTTCG 59.321 50.000 0.00 0.00 36.04 3.46
3677 4158 6.096141 TCAGACAACTCATGGTTAAAGCAAAA 59.904 34.615 0.00 0.00 36.23 2.44
3704 4208 4.227864 ACCATCTTGGGATTGACTCTTC 57.772 45.455 0.00 0.00 43.37 2.87
3760 4267 5.181245 GGAAACTAGCAACTGTGAAGCATAA 59.819 40.000 0.00 0.00 0.00 1.90
3821 4335 4.906618 TCTGGCTCGGAAGATTAAGTTTT 58.093 39.130 0.00 0.00 40.84 2.43
3828 4342 6.094186 GCTCGGAAGATTAAGTTTTTCCTGAT 59.906 38.462 1.21 0.00 40.84 2.90
3841 4355 4.733077 TTTCCTGATTACCCTTCAACCA 57.267 40.909 0.00 0.00 0.00 3.67
3958 4483 4.550076 AGAAAACAGAGGAGGATCAGTG 57.450 45.455 0.00 0.00 36.25 3.66
3968 4493 1.208293 GAGGATCAGTGTTGGGAGTCC 59.792 57.143 0.00 0.00 33.17 3.85
3969 4494 0.984230 GGATCAGTGTTGGGAGTCCA 59.016 55.000 12.30 0.00 42.25 4.02
3983 4508 5.205056 TGGGAGTCCAACTGTTTTACATTT 58.795 37.500 12.30 0.00 40.73 2.32
3984 4509 5.068460 TGGGAGTCCAACTGTTTTACATTTG 59.932 40.000 12.30 3.69 40.73 2.32
3985 4510 4.982295 GGAGTCCAACTGTTTTACATTTGC 59.018 41.667 3.60 0.00 37.41 3.68
3986 4511 5.451242 GGAGTCCAACTGTTTTACATTTGCA 60.451 40.000 3.60 0.00 37.41 4.08
3987 4512 5.348164 AGTCCAACTGTTTTACATTTGCAC 58.652 37.500 4.85 1.40 37.41 4.57
3988 4513 5.105554 AGTCCAACTGTTTTACATTTGCACA 60.106 36.000 6.70 0.00 37.41 4.57
3989 4514 5.005299 GTCCAACTGTTTTACATTTGCACAC 59.995 40.000 4.85 0.00 37.41 3.82
4015 4540 5.957798 ACAGACAAACATGCTCCATATTTG 58.042 37.500 7.25 7.25 42.00 2.32
4016 4541 4.802039 CAGACAAACATGCTCCATATTTGC 59.198 41.667 8.41 3.32 40.56 3.68
4017 4542 4.463539 AGACAAACATGCTCCATATTTGCA 59.536 37.500 8.41 0.00 40.56 4.08
4018 4543 4.751060 ACAAACATGCTCCATATTTGCAG 58.249 39.130 8.41 0.00 40.56 4.41
4019 4544 4.463539 ACAAACATGCTCCATATTTGCAGA 59.536 37.500 8.41 0.00 40.56 4.26
4020 4545 5.128171 ACAAACATGCTCCATATTTGCAGAT 59.872 36.000 8.41 0.00 40.56 2.90
4021 4546 5.864418 AACATGCTCCATATTTGCAGATT 57.136 34.783 0.00 0.00 40.18 2.40
4022 4547 5.864418 ACATGCTCCATATTTGCAGATTT 57.136 34.783 0.00 0.00 40.18 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.202878 CCTACACCGTGCGATGGG 60.203 66.667 0.00 0.00 0.00 4.00
46 47 1.226974 CCTCCTACACCGTGCGATG 60.227 63.158 0.00 0.00 0.00 3.84
47 48 1.379443 TCCTCCTACACCGTGCGAT 60.379 57.895 0.00 0.00 0.00 4.58
48 49 2.034532 TCCTCCTACACCGTGCGA 59.965 61.111 0.00 0.00 0.00 5.10
50 51 2.184579 GCTCCTCCTACACCGTGC 59.815 66.667 0.00 0.00 0.00 5.34
56 57 0.253044 GCCATTGTGCTCCTCCTACA 59.747 55.000 0.00 0.00 0.00 2.74
57 58 0.543749 AGCCATTGTGCTCCTCCTAC 59.456 55.000 0.00 0.00 36.75 3.18
58 59 3.012153 AGCCATTGTGCTCCTCCTA 57.988 52.632 0.00 0.00 36.75 2.94
96 98 4.250305 ACAACCTTGCTCGGCCGT 62.250 61.111 27.15 0.00 0.00 5.68
130 132 3.744719 CGTCCTTCCAGCGACCGA 61.745 66.667 0.00 0.00 0.00 4.69
134 136 2.044555 ATCGTCGTCCTTCCAGCGA 61.045 57.895 0.00 0.00 0.00 4.93
137 139 1.405463 TCATCATCGTCGTCCTTCCAG 59.595 52.381 0.00 0.00 0.00 3.86
143 145 0.098200 TCGTGTCATCATCGTCGTCC 59.902 55.000 0.00 0.00 0.00 4.79
146 148 1.194280 CCGTCGTGTCATCATCGTCG 61.194 60.000 0.00 0.00 36.37 5.12
185 197 1.862147 CGACGACCTTCTACGCGTG 60.862 63.158 24.59 12.26 37.07 5.34
189 201 0.520827 GCAGACGACGACCTTCTACG 60.521 60.000 0.00 0.00 0.00 3.51
193 205 0.520404 TGTAGCAGACGACGACCTTC 59.480 55.000 0.00 0.00 0.00 3.46
194 206 0.956633 TTGTAGCAGACGACGACCTT 59.043 50.000 0.00 0.00 0.00 3.50
206 218 2.168521 CCTAGCAGGCTAAGTTGTAGCA 59.831 50.000 7.59 0.00 42.06 3.49
341 356 1.817099 GAGAGCCAGGCATCCAACG 60.817 63.158 15.80 0.00 0.00 4.10
362 388 2.066262 GATCAGTTCGCGGAAAGTGAA 58.934 47.619 18.45 6.21 46.05 3.18
370 396 0.936764 CCGATGAGATCAGTTCGCGG 60.937 60.000 6.13 0.00 29.73 6.46
372 398 1.482278 GACCGATGAGATCAGTTCGC 58.518 55.000 0.00 0.00 29.73 4.70
386 413 1.315690 CTTATCTGCCTACGGACCGA 58.684 55.000 23.38 3.17 32.77 4.69
394 421 3.438078 CCCTAGGACACCTTATCTGCCTA 60.438 52.174 11.48 0.00 34.61 3.93
397 424 1.070914 GCCCTAGGACACCTTATCTGC 59.929 57.143 11.48 0.00 34.61 4.26
404 431 1.982938 GTCGTGCCCTAGGACACCT 60.983 63.158 21.14 0.00 42.34 4.00
414 441 2.100631 CATCTCCAACGTCGTGCCC 61.101 63.158 0.00 0.00 0.00 5.36
415 442 2.740714 GCATCTCCAACGTCGTGCC 61.741 63.158 0.00 0.00 0.00 5.01
416 443 2.740714 GGCATCTCCAACGTCGTGC 61.741 63.158 0.00 0.00 34.01 5.34
417 444 1.374125 TGGCATCTCCAACGTCGTG 60.374 57.895 0.00 0.00 43.21 4.35
418 445 3.056458 TGGCATCTCCAACGTCGT 58.944 55.556 0.00 0.00 43.21 4.34
450 481 6.003326 TCCCATACATATTTGGCATACACTG 58.997 40.000 0.00 0.00 0.00 3.66
452 483 6.434028 ACATCCCATACATATTTGGCATACAC 59.566 38.462 0.00 0.00 0.00 2.90
453 484 6.433716 CACATCCCATACATATTTGGCATACA 59.566 38.462 0.00 0.00 0.00 2.29
455 486 5.418524 GCACATCCCATACATATTTGGCATA 59.581 40.000 0.00 0.00 0.00 3.14
644 681 1.148310 AACAAGACGACAAGCCGATG 58.852 50.000 0.00 0.00 0.00 3.84
646 683 1.202486 AGAAACAAGACGACAAGCCGA 60.202 47.619 0.00 0.00 0.00 5.54
716 753 3.269520 GGAACGGAATCTACTCGGC 57.730 57.895 0.00 0.00 0.00 5.54
771 815 4.899239 GAGATGGTGGCGCGGGAG 62.899 72.222 8.83 0.00 0.00 4.30
794 838 1.877367 GCAAGACGACGAGAGGAGT 59.123 57.895 0.00 0.00 0.00 3.85
873 919 2.096013 GCTGGGAGAAAAGATACGTTGC 59.904 50.000 0.00 0.00 0.00 4.17
917 963 8.333908 CCTTACTAGTAGTATCATATAACGCGG 58.666 40.741 12.47 0.00 29.64 6.46
918 964 8.333908 CCCTTACTAGTAGTATCATATAACGCG 58.666 40.741 10.82 3.53 29.64 6.01
929 975 5.611835 TGAGCTCCTCCCTTACTAGTAGTAT 59.388 44.000 12.15 0.00 29.64 2.12
939 988 1.198713 CAAGCTGAGCTCCTCCCTTA 58.801 55.000 7.72 0.00 38.25 2.69
982 1031 2.650813 ATCTTGACCCGATCGGCTGC 62.651 60.000 29.12 18.75 33.26 5.25
1076 1146 1.678970 AACCGCTGCTTTGGATCCC 60.679 57.895 9.90 0.00 0.00 3.85
1172 1248 1.846439 CAGGGGAAGGAAGGAGCAATA 59.154 52.381 0.00 0.00 0.00 1.90
1184 1261 2.125912 CGTGACGAGCAGGGGAAG 60.126 66.667 0.00 0.00 0.00 3.46
1236 1320 5.976458 TGATGGTCAAAAGAAGCAAAGTTT 58.024 33.333 0.00 0.00 0.00 2.66
1238 1322 4.500375 GCTGATGGTCAAAAGAAGCAAAGT 60.500 41.667 0.00 0.00 0.00 2.66
1248 1354 8.318412 TCAGTATAGTTAAGCTGATGGTCAAAA 58.682 33.333 0.00 0.00 33.62 2.44
1390 1559 0.952984 GAAGAGCAGGACTGGTGCAC 60.953 60.000 8.80 8.80 43.82 4.57
1422 1592 3.072944 CTGGACTGCAAAAGAGAAGAGG 58.927 50.000 0.00 0.00 0.00 3.69
1464 1639 7.241376 ACAAACATCGCTGTTAATTAGTAAGC 58.759 34.615 4.87 6.20 44.83 3.09
1589 1778 1.559149 GCATTTTGGCGTTGGCTGTG 61.559 55.000 0.00 0.00 39.81 3.66
1629 1818 6.567602 AGATAGCAAGGTTGGAGTTTAGAT 57.432 37.500 0.00 0.00 0.00 1.98
1642 1831 7.040409 ACTCTGGTAAAAACAAAGATAGCAAGG 60.040 37.037 0.00 0.00 0.00 3.61
2018 2266 2.504367 CAGTCCCAATTTCTGGTTCGT 58.496 47.619 0.00 0.00 44.76 3.85
2020 2268 3.154827 TCCAGTCCCAATTTCTGGTTC 57.845 47.619 9.71 0.00 46.04 3.62
2078 2330 3.418684 ACAGGGCCTAACTTGTACAAG 57.581 47.619 29.76 29.76 43.79 3.16
2082 2334 2.712087 TCCAAACAGGGCCTAACTTGTA 59.288 45.455 5.28 0.00 38.24 2.41
2090 2342 1.062488 AGTGACTCCAAACAGGGCCT 61.062 55.000 0.00 0.00 38.24 5.19
2091 2343 0.606673 GAGTGACTCCAAACAGGGCC 60.607 60.000 0.00 0.00 38.24 5.80
2092 2344 2.934083 GAGTGACTCCAAACAGGGC 58.066 57.895 0.00 0.00 38.24 5.19
2102 2354 6.310711 CGTATTTTTAGGAGTTGGAGTGACTC 59.689 42.308 3.47 3.47 42.16 3.36
2103 2355 6.014840 TCGTATTTTTAGGAGTTGGAGTGACT 60.015 38.462 0.00 0.00 0.00 3.41
2104 2356 6.161381 TCGTATTTTTAGGAGTTGGAGTGAC 58.839 40.000 0.00 0.00 0.00 3.67
2105 2357 6.349243 TCGTATTTTTAGGAGTTGGAGTGA 57.651 37.500 0.00 0.00 0.00 3.41
2106 2358 5.581085 CCTCGTATTTTTAGGAGTTGGAGTG 59.419 44.000 0.00 0.00 31.94 3.51
2107 2359 5.482878 TCCTCGTATTTTTAGGAGTTGGAGT 59.517 40.000 0.00 0.00 34.46 3.85
2108 2360 5.974108 TCCTCGTATTTTTAGGAGTTGGAG 58.026 41.667 0.00 0.00 34.46 3.86
2115 2367 4.028131 TCCAGCTCCTCGTATTTTTAGGA 58.972 43.478 0.00 0.00 37.07 2.94
2116 2368 4.372656 CTCCAGCTCCTCGTATTTTTAGG 58.627 47.826 0.00 0.00 0.00 2.69
2117 2369 3.804873 GCTCCAGCTCCTCGTATTTTTAG 59.195 47.826 0.00 0.00 38.21 1.85
2118 2370 3.196901 TGCTCCAGCTCCTCGTATTTTTA 59.803 43.478 0.00 0.00 42.66 1.52
2119 2371 2.027192 TGCTCCAGCTCCTCGTATTTTT 60.027 45.455 0.00 0.00 42.66 1.94
2120 2372 1.555075 TGCTCCAGCTCCTCGTATTTT 59.445 47.619 0.00 0.00 42.66 1.82
2121 2373 1.195115 TGCTCCAGCTCCTCGTATTT 58.805 50.000 0.00 0.00 42.66 1.40
2122 2374 1.342819 GATGCTCCAGCTCCTCGTATT 59.657 52.381 0.00 0.00 42.66 1.89
2123 2375 0.965439 GATGCTCCAGCTCCTCGTAT 59.035 55.000 0.00 0.00 42.66 3.06
2124 2376 0.106469 AGATGCTCCAGCTCCTCGTA 60.106 55.000 0.00 0.00 42.66 3.43
2125 2377 1.381056 AGATGCTCCAGCTCCTCGT 60.381 57.895 0.00 0.00 42.66 4.18
2126 2378 1.108727 AGAGATGCTCCAGCTCCTCG 61.109 60.000 6.85 0.00 46.56 4.63
2127 2379 1.122227 AAGAGATGCTCCAGCTCCTC 58.878 55.000 6.85 10.76 46.56 3.71
2128 2380 1.485895 GAAAGAGATGCTCCAGCTCCT 59.514 52.381 6.85 0.00 46.56 3.69
2129 2381 1.474855 GGAAAGAGATGCTCCAGCTCC 60.475 57.143 6.85 0.00 46.56 4.70
2130 2382 1.474855 GGGAAAGAGATGCTCCAGCTC 60.475 57.143 2.47 2.47 45.85 4.09
2131 2383 0.545646 GGGAAAGAGATGCTCCAGCT 59.454 55.000 0.00 0.00 42.66 4.24
2132 2384 0.254178 TGGGAAAGAGATGCTCCAGC 59.746 55.000 0.00 0.00 42.50 4.85
2133 2385 1.746516 GCTGGGAAAGAGATGCTCCAG 60.747 57.143 0.00 0.00 43.20 3.86
2134 2386 0.254178 GCTGGGAAAGAGATGCTCCA 59.746 55.000 0.00 0.00 0.00 3.86
2135 2387 0.545646 AGCTGGGAAAGAGATGCTCC 59.454 55.000 0.00 0.00 0.00 4.70
2136 2388 1.474855 GGAGCTGGGAAAGAGATGCTC 60.475 57.143 0.00 0.00 44.08 4.26
2137 2389 0.545646 GGAGCTGGGAAAGAGATGCT 59.454 55.000 0.00 0.00 0.00 3.79
2138 2390 0.813210 CGGAGCTGGGAAAGAGATGC 60.813 60.000 0.00 0.00 0.00 3.91
2139 2391 0.539051 ACGGAGCTGGGAAAGAGATG 59.461 55.000 0.00 0.00 0.00 2.90
2140 2392 0.539051 CACGGAGCTGGGAAAGAGAT 59.461 55.000 0.00 0.00 0.00 2.75
2141 2393 1.975327 CACGGAGCTGGGAAAGAGA 59.025 57.895 0.00 0.00 0.00 3.10
2142 2394 1.743252 GCACGGAGCTGGGAAAGAG 60.743 63.158 0.00 0.00 41.15 2.85
2143 2395 2.347490 GCACGGAGCTGGGAAAGA 59.653 61.111 0.00 0.00 41.15 2.52
2144 2396 2.747855 GGCACGGAGCTGGGAAAG 60.748 66.667 0.00 0.00 44.79 2.62
2145 2397 2.351924 AAAGGCACGGAGCTGGGAAA 62.352 55.000 0.00 0.00 44.79 3.13
2146 2398 2.351924 AAAAGGCACGGAGCTGGGAA 62.352 55.000 0.00 0.00 44.79 3.97
2147 2399 2.829384 AAAAGGCACGGAGCTGGGA 61.829 57.895 0.00 0.00 44.79 4.37
2148 2400 2.282462 AAAAGGCACGGAGCTGGG 60.282 61.111 0.00 0.00 44.79 4.45
2149 2401 1.600636 TCAAAAGGCACGGAGCTGG 60.601 57.895 0.00 0.00 44.79 4.85
2150 2402 0.886490 AGTCAAAAGGCACGGAGCTG 60.886 55.000 0.00 0.00 44.79 4.24
2151 2403 0.603975 GAGTCAAAAGGCACGGAGCT 60.604 55.000 0.00 0.00 44.79 4.09
2152 2404 1.578206 GGAGTCAAAAGGCACGGAGC 61.578 60.000 0.00 0.00 44.65 4.70
2153 2405 0.250295 TGGAGTCAAAAGGCACGGAG 60.250 55.000 0.00 0.00 0.00 4.63
2154 2406 0.250295 CTGGAGTCAAAAGGCACGGA 60.250 55.000 0.00 0.00 0.00 4.69
2155 2407 1.856265 GCTGGAGTCAAAAGGCACGG 61.856 60.000 0.00 0.00 0.00 4.94
2156 2408 0.886490 AGCTGGAGTCAAAAGGCACG 60.886 55.000 0.00 0.00 0.00 5.34
2157 2409 0.877743 GAGCTGGAGTCAAAAGGCAC 59.122 55.000 0.00 0.00 0.00 5.01
2158 2410 0.250901 GGAGCTGGAGTCAAAAGGCA 60.251 55.000 0.00 0.00 0.00 4.75
2159 2411 1.301677 CGGAGCTGGAGTCAAAAGGC 61.302 60.000 0.00 0.00 0.00 4.35
2160 2412 0.674895 CCGGAGCTGGAGTCAAAAGG 60.675 60.000 0.00 0.00 0.00 3.11
2161 2413 0.674895 CCCGGAGCTGGAGTCAAAAG 60.675 60.000 0.73 0.00 0.00 2.27
2162 2414 1.125093 TCCCGGAGCTGGAGTCAAAA 61.125 55.000 0.73 0.00 0.00 2.44
2163 2415 1.535444 TCCCGGAGCTGGAGTCAAA 60.535 57.895 0.73 0.00 0.00 2.69
2164 2416 1.984570 CTCCCGGAGCTGGAGTCAA 60.985 63.158 0.73 0.00 43.68 3.18
2165 2417 2.363018 CTCCCGGAGCTGGAGTCA 60.363 66.667 0.73 0.00 43.68 3.41
2178 2430 3.775654 CTCCACCACTCCGCTCCC 61.776 72.222 0.00 0.00 0.00 4.30
2179 2431 2.997897 ACTCCACCACTCCGCTCC 60.998 66.667 0.00 0.00 0.00 4.70
2180 2432 2.262915 CACTCCACCACTCCGCTC 59.737 66.667 0.00 0.00 0.00 5.03
2181 2433 3.314331 CCACTCCACCACTCCGCT 61.314 66.667 0.00 0.00 0.00 5.52
2183 2435 4.742201 CGCCACTCCACCACTCCG 62.742 72.222 0.00 0.00 0.00 4.63
2184 2436 4.394712 CCGCCACTCCACCACTCC 62.395 72.222 0.00 0.00 0.00 3.85
2185 2437 4.394712 CCCGCCACTCCACCACTC 62.395 72.222 0.00 0.00 0.00 3.51
2187 2439 4.699522 GACCCGCCACTCCACCAC 62.700 72.222 0.00 0.00 0.00 4.16
2188 2440 4.954118 AGACCCGCCACTCCACCA 62.954 66.667 0.00 0.00 0.00 4.17
2189 2441 4.083862 GAGACCCGCCACTCCACC 62.084 72.222 0.00 0.00 0.00 4.61
2200 2452 4.097361 GGCCCTGTTCGGAGACCC 62.097 72.222 0.00 0.00 34.32 4.46
2201 2453 1.262640 TAAGGCCCTGTTCGGAGACC 61.263 60.000 0.00 0.00 34.32 3.85
2202 2454 0.611714 TTAAGGCCCTGTTCGGAGAC 59.388 55.000 0.00 0.00 34.32 3.36
2203 2455 1.580059 ATTAAGGCCCTGTTCGGAGA 58.420 50.000 0.00 0.00 33.16 3.71
2204 2456 2.807108 GCTATTAAGGCCCTGTTCGGAG 60.807 54.545 0.00 0.00 33.16 4.63
2205 2457 1.140252 GCTATTAAGGCCCTGTTCGGA 59.860 52.381 0.00 0.00 33.16 4.55
2206 2458 1.134220 TGCTATTAAGGCCCTGTTCGG 60.134 52.381 0.00 0.00 0.00 4.30
2207 2459 2.325583 TGCTATTAAGGCCCTGTTCG 57.674 50.000 0.00 0.00 0.00 3.95
2208 2460 3.621558 ACTTGCTATTAAGGCCCTGTTC 58.378 45.455 0.00 0.00 31.94 3.18
2209 2461 3.739401 ACTTGCTATTAAGGCCCTGTT 57.261 42.857 0.00 0.00 31.94 3.16
2210 2462 3.780850 AGTACTTGCTATTAAGGCCCTGT 59.219 43.478 0.00 0.00 31.94 4.00
2211 2463 4.423625 AGTACTTGCTATTAAGGCCCTG 57.576 45.455 0.00 0.00 31.94 4.45
2212 2464 4.040584 GCTAGTACTTGCTATTAAGGCCCT 59.959 45.833 20.15 0.00 31.94 5.19
2213 2465 4.040584 AGCTAGTACTTGCTATTAAGGCCC 59.959 45.833 27.05 0.00 39.72 5.80
2214 2466 5.216614 AGCTAGTACTTGCTATTAAGGCC 57.783 43.478 27.05 0.00 39.72 5.19
2215 2467 7.496263 AGAAAAGCTAGTACTTGCTATTAAGGC 59.504 37.037 28.11 14.90 40.57 4.35
2216 2468 8.950208 AGAAAAGCTAGTACTTGCTATTAAGG 57.050 34.615 28.11 0.00 40.57 2.69
2218 2470 9.162764 CCAAGAAAAGCTAGTACTTGCTATTAA 57.837 33.333 28.11 0.00 40.57 1.40
2219 2471 7.280205 GCCAAGAAAAGCTAGTACTTGCTATTA 59.720 37.037 28.11 0.00 40.57 0.98
2284 2537 6.953101 TGGTGCCTCTGTATATGAAACTTTA 58.047 36.000 0.00 0.00 0.00 1.85
2293 2546 5.894298 TTCATCTTGGTGCCTCTGTATAT 57.106 39.130 0.00 0.00 0.00 0.86
2307 2560 7.353414 TCAGTAGGAGTAGGATTTCATCTTG 57.647 40.000 0.00 0.00 0.00 3.02
2311 2564 9.440761 AAGTAATCAGTAGGAGTAGGATTTCAT 57.559 33.333 0.00 0.00 31.28 2.57
2339 2592 5.102313 CACATAGAAGACGCATGACAGTAA 58.898 41.667 0.00 0.00 0.00 2.24
2340 2593 4.157840 ACACATAGAAGACGCATGACAGTA 59.842 41.667 0.00 0.00 0.00 2.74
2341 2594 3.056536 ACACATAGAAGACGCATGACAGT 60.057 43.478 0.00 0.00 0.00 3.55
2365 2618 9.647679 CATCATACAATCTCAATCGAAGAAAAG 57.352 33.333 0.00 0.00 43.58 2.27
2409 2662 7.916977 TCTCTGATTCACACAAGAAATGTTTTG 59.083 33.333 0.00 0.00 41.46 2.44
2422 2675 2.476854 GCGGCATTTCTCTGATTCACAC 60.477 50.000 0.00 0.00 0.00 3.82
2580 2847 0.321346 TTCTTCTGCACCTGATCGCA 59.679 50.000 0.00 0.00 36.52 5.10
2581 2848 1.005340 CTTCTTCTGCACCTGATCGC 58.995 55.000 0.00 0.00 0.00 4.58
2726 2993 1.278127 CCCGGAAGAGCTAGGTTGAAA 59.722 52.381 0.73 0.00 0.00 2.69
2747 3014 2.493675 CTGTCTTCCATTCTCCGTGAGA 59.506 50.000 0.11 0.11 36.86 3.27
2748 3015 2.417924 CCTGTCTTCCATTCTCCGTGAG 60.418 54.545 0.00 0.00 0.00 3.51
2750 3017 1.276421 ACCTGTCTTCCATTCTCCGTG 59.724 52.381 0.00 0.00 0.00 4.94
2751 3018 1.276421 CACCTGTCTTCCATTCTCCGT 59.724 52.381 0.00 0.00 0.00 4.69
2764 3031 2.673368 CCGCTTTCTTCATACACCTGTC 59.327 50.000 0.00 0.00 0.00 3.51
2834 3101 3.372206 CACGGTAGAGCTGAAAATCCAAG 59.628 47.826 0.00 0.00 0.00 3.61
3048 3316 9.533253 CACAGGAAACAAATTCTAACAGAAAAT 57.467 29.630 0.00 0.00 37.82 1.82
3052 3320 5.009610 GCCACAGGAAACAAATTCTAACAGA 59.990 40.000 0.00 0.00 38.18 3.41
3055 3323 5.195001 TGCCACAGGAAACAAATTCTAAC 57.805 39.130 0.00 0.00 38.18 2.34
3110 3380 7.230510 TCAGCAAATTTAACATAACCACAGAGT 59.769 33.333 0.00 0.00 0.00 3.24
3204 3475 7.734924 TGATATCTGATTGTTACATGCCTTC 57.265 36.000 3.98 0.00 0.00 3.46
3205 3476 7.994911 TCTTGATATCTGATTGTTACATGCCTT 59.005 33.333 3.98 0.00 0.00 4.35
3207 3478 7.734924 TCTTGATATCTGATTGTTACATGCC 57.265 36.000 3.98 0.00 0.00 4.40
3268 3552 2.489329 GTTATGTGGCTCTGTGCACATT 59.511 45.455 22.00 0.92 45.15 2.71
3356 3641 8.325787 TGGACAGGCTAAATATAGTTCTGAAAA 58.674 33.333 7.00 0.00 36.71 2.29
3357 3642 7.857456 TGGACAGGCTAAATATAGTTCTGAAA 58.143 34.615 7.00 0.00 36.71 2.69
3370 3656 4.525100 GGGTTTATTGTTGGACAGGCTAAA 59.475 41.667 0.00 0.00 0.00 1.85
3372 3658 3.332485 AGGGTTTATTGTTGGACAGGCTA 59.668 43.478 0.00 0.00 0.00 3.93
3376 3662 5.782893 TTCAAGGGTTTATTGTTGGACAG 57.217 39.130 0.00 0.00 0.00 3.51
3427 3713 7.618502 TGCATTTAGGATTTAGCGAAGTTTA 57.381 32.000 0.00 0.00 0.00 2.01
3453 3739 8.581578 TGTCTTTGTTTAAACTTTGAAGGACTT 58.418 29.630 21.40 0.00 0.00 3.01
3455 3741 7.810759 TGTGTCTTTGTTTAAACTTTGAAGGAC 59.189 33.333 18.72 17.92 0.00 3.85
3480 3766 6.382869 ACAAATTCACTCTCCACTTTTCTG 57.617 37.500 0.00 0.00 0.00 3.02
3481 3767 7.775561 AGTAACAAATTCACTCTCCACTTTTCT 59.224 33.333 0.00 0.00 0.00 2.52
3482 3768 7.857885 CAGTAACAAATTCACTCTCCACTTTTC 59.142 37.037 0.00 0.00 0.00 2.29
3483 3769 7.682021 GCAGTAACAAATTCACTCTCCACTTTT 60.682 37.037 0.00 0.00 0.00 2.27
3484 3770 6.238759 GCAGTAACAAATTCACTCTCCACTTT 60.239 38.462 0.00 0.00 0.00 2.66
3485 3771 5.239525 GCAGTAACAAATTCACTCTCCACTT 59.760 40.000 0.00 0.00 0.00 3.16
3486 3772 4.757149 GCAGTAACAAATTCACTCTCCACT 59.243 41.667 0.00 0.00 0.00 4.00
3487 3773 4.757149 AGCAGTAACAAATTCACTCTCCAC 59.243 41.667 0.00 0.00 0.00 4.02
3488 3774 4.973168 AGCAGTAACAAATTCACTCTCCA 58.027 39.130 0.00 0.00 0.00 3.86
3489 3775 4.997395 TGAGCAGTAACAAATTCACTCTCC 59.003 41.667 0.00 0.00 0.00 3.71
3490 3776 6.545504 TTGAGCAGTAACAAATTCACTCTC 57.454 37.500 0.00 0.00 0.00 3.20
3491 3777 7.365741 CAATTGAGCAGTAACAAATTCACTCT 58.634 34.615 0.00 0.00 0.00 3.24
3492 3778 6.088616 GCAATTGAGCAGTAACAAATTCACTC 59.911 38.462 10.34 0.00 0.00 3.51
3493 3779 5.922544 GCAATTGAGCAGTAACAAATTCACT 59.077 36.000 10.34 0.00 0.00 3.41
3501 3787 3.253188 GTCCTTGCAATTGAGCAGTAACA 59.747 43.478 10.34 0.00 46.54 2.41
3506 3792 3.587797 ATTGTCCTTGCAATTGAGCAG 57.412 42.857 10.34 0.77 46.54 4.24
3510 3796 5.549742 AGGAAAATTGTCCTTGCAATTGA 57.450 34.783 11.79 0.00 46.42 2.57
3523 3809 5.594926 AGTTCTGTTGAGCAAGGAAAATTG 58.405 37.500 0.00 0.00 0.00 2.32
3535 3821 4.328983 ACAACGTGTACAAGTTCTGTTGAG 59.671 41.667 22.01 12.69 39.64 3.02
3537 3823 4.092237 TGACAACGTGTACAAGTTCTGTTG 59.908 41.667 22.01 17.86 39.64 3.33
3538 3824 4.247258 TGACAACGTGTACAAGTTCTGTT 58.753 39.130 22.01 8.77 39.64 3.16
3539 3825 3.852286 TGACAACGTGTACAAGTTCTGT 58.148 40.909 22.01 18.81 42.47 3.41
3540 3826 4.850859 TTGACAACGTGTACAAGTTCTG 57.149 40.909 22.01 16.02 30.85 3.02
3542 3828 6.630045 GGTTAATTGACAACGTGTACAAGTTC 59.370 38.462 22.01 13.92 30.85 3.01
3545 3831 5.905181 GTGGTTAATTGACAACGTGTACAAG 59.095 40.000 7.29 7.29 0.00 3.16
3546 3832 5.220815 GGTGGTTAATTGACAACGTGTACAA 60.221 40.000 0.00 0.00 0.00 2.41
3553 4034 3.562141 TGTCAGGTGGTTAATTGACAACG 59.438 43.478 2.50 0.00 44.81 4.10
3556 4037 4.431416 AGTGTCAGGTGGTTAATTGACA 57.569 40.909 2.50 2.33 45.37 3.58
3597 4078 5.644644 CCTCACAAATCTTATGTTCCTTGC 58.355 41.667 0.00 0.00 0.00 4.01
3620 4101 3.066380 CAAATGGGCCAGTTTAGTTTGC 58.934 45.455 17.88 0.00 0.00 3.68
3622 4103 3.313791 ACCAAATGGGCCAGTTTAGTTT 58.686 40.909 17.88 5.53 42.05 2.66
3633 4114 2.494073 TGAATACCGAAACCAAATGGGC 59.506 45.455 4.17 0.00 42.05 5.36
3643 4124 4.935205 CCATGAGTTGTCTGAATACCGAAA 59.065 41.667 0.00 0.00 0.00 3.46
3647 4128 7.626452 GCTTTAACCATGAGTTGTCTGAATACC 60.626 40.741 9.13 0.00 39.67 2.73
3677 4158 5.892348 AGTCAATCCCAAGATGGTAAAGTT 58.108 37.500 0.00 0.00 35.17 2.66
3704 4208 8.422973 TCTCAAAATGTGGAAAGTGAAAATTG 57.577 30.769 0.00 0.00 0.00 2.32
3760 4267 0.250901 GGTTGGATCTGTGGCTGTGT 60.251 55.000 0.00 0.00 0.00 3.72
3821 4335 4.540099 AGATGGTTGAAGGGTAATCAGGAA 59.460 41.667 0.00 0.00 0.00 3.36
3828 4342 2.901192 TCGACAGATGGTTGAAGGGTAA 59.099 45.455 0.00 0.00 36.96 2.85
3841 4355 1.141881 GCACCGGTGATCGACAGAT 59.858 57.895 38.30 0.00 42.43 2.90
3936 4461 4.349342 ACACTGATCCTCCTCTGTTTTCTT 59.651 41.667 0.00 0.00 0.00 2.52
3969 4494 6.425114 TGTTTGTGTGCAAATGTAAAACAGTT 59.575 30.769 0.00 0.00 45.11 3.16
3983 4508 3.509740 CATGTTTGTCTGTTTGTGTGCA 58.490 40.909 0.00 0.00 0.00 4.57
3984 4509 2.282290 GCATGTTTGTCTGTTTGTGTGC 59.718 45.455 0.00 0.00 0.00 4.57
3985 4510 3.772932 AGCATGTTTGTCTGTTTGTGTG 58.227 40.909 0.00 0.00 0.00 3.82
3986 4511 3.181487 GGAGCATGTTTGTCTGTTTGTGT 60.181 43.478 0.00 0.00 0.00 3.72
3987 4512 3.181488 TGGAGCATGTTTGTCTGTTTGTG 60.181 43.478 0.00 0.00 0.00 3.33
3988 4513 3.023119 TGGAGCATGTTTGTCTGTTTGT 58.977 40.909 0.00 0.00 0.00 2.83
3989 4514 3.713858 TGGAGCATGTTTGTCTGTTTG 57.286 42.857 0.00 0.00 0.00 2.93
4016 4541 5.179045 ACTTGTTGAGAACAGCAAATCTG 57.821 39.130 0.00 0.00 44.06 2.90
4017 4542 5.841957 AACTTGTTGAGAACAGCAAATCT 57.158 34.783 0.00 0.00 44.06 2.40
4018 4543 9.118236 GTAATAACTTGTTGAGAACAGCAAATC 57.882 33.333 0.00 0.00 44.06 2.17
4019 4544 8.850156 AGTAATAACTTGTTGAGAACAGCAAAT 58.150 29.630 0.00 0.00 44.06 2.32
4020 4545 8.128582 CAGTAATAACTTGTTGAGAACAGCAAA 58.871 33.333 0.00 0.00 44.06 3.68
4021 4546 7.497579 TCAGTAATAACTTGTTGAGAACAGCAA 59.502 33.333 0.00 0.00 43.27 3.91
4022 4547 6.989759 TCAGTAATAACTTGTTGAGAACAGCA 59.010 34.615 0.00 0.00 43.27 4.41
4059 4584 4.888239 TCTAGAGCAACATCCTGTACTACC 59.112 45.833 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.