Multiple sequence alignment - TraesCS6D01G253000

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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 TraesCS6D01G253000 chr6D 100.000 3913 0 0 1 3913 357014754 357010842 0.000000e+00 7227.0
1 TraesCS6D01G253000 chr6D 88.506 174 16 2 2309 2482 450750190 450750359 1.420000e-49 207.0
2 TraesCS6D01G253000 chr6A 87.887 4037 279 88 1 3910 499408719 499404766 0.000000e+00 4553.0
3 TraesCS6D01G253000 chr6B 86.870 3511 259 103 368 3774 538377448 538374036 0.000000e+00 3744.0
4 TraesCS6D01G253000 chr6B 95.833 48 2 0 277 324 388333670 388333623 1.170000e-10 78.7
5 TraesCS6D01G253000 chr3B 80.813 443 41 26 888 1302 508758397 508757971 1.370000e-79 307.0
6 TraesCS6D01G253000 chr3B 92.308 39 3 0 1949 1987 10592017 10591979 5.460000e-04 56.5
7 TraesCS6D01G253000 chr5A 89.080 174 15 2 2309 2482 134749117 134748948 3.060000e-51 213.0
8 TraesCS6D01G253000 chr5A 87.931 174 17 2 2309 2482 505515324 505515155 6.630000e-48 202.0
9 TraesCS6D01G253000 chr4D 89.535 172 12 3 2313 2482 505656834 505657001 3.060000e-51 213.0
10 TraesCS6D01G253000 chr7B 88.506 174 16 2 2309 2482 707684051 707683882 1.420000e-49 207.0
11 TraesCS6D01G253000 chr7B 94.118 51 3 0 1937 1987 748599811 748599761 1.170000e-10 78.7
12 TraesCS6D01G253000 chr7B 94.872 39 1 1 1581 1618 541170888 541170850 4.220000e-05 60.2
13 TraesCS6D01G253000 chr1D 88.953 172 13 3 2313 2482 393126547 393126714 1.420000e-49 207.0
14 TraesCS6D01G253000 chr4A 87.931 174 17 2 2309 2482 502593297 502593128 6.630000e-48 202.0
15 TraesCS6D01G253000 chr2D 87.059 85 8 3 1758 1842 343557405 343557486 4.160000e-15 93.5
16 TraesCS6D01G253000 chr2D 92.157 51 4 0 1937 1987 609903109 609903159 5.420000e-09 73.1
17 TraesCS6D01G253000 chr2A 87.059 85 8 3 1758 1842 454692284 454692365 4.160000e-15 93.5
18 TraesCS6D01G253000 chr2B 85.882 85 9 3 1758 1842 408725946 408726027 1.940000e-13 87.9
19 TraesCS6D01G253000 chr2B 92.157 51 4 0 1937 1987 796475827 796475777 5.420000e-09 73.1
20 TraesCS6D01G253000 chrUn 95.000 40 2 0 1948 1987 142663073 142663034 3.260000e-06 63.9
21 TraesCS6D01G253000 chr7A 94.872 39 1 1 1581 1618 584387825 584387863 4.220000e-05 60.2
22 TraesCS6D01G253000 chr7D 100.000 29 0 0 869 897 236013500 236013528 2.000000e-03 54.7
23 TraesCS6D01G253000 chr4B 100.000 29 0 0 871 899 258832030 258832058 2.000000e-03 54.7


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 TraesCS6D01G253000 chr6D 357010842 357014754 3912 True 7227 7227 100.000 1 3913 1 chr6D.!!$R1 3912
1 TraesCS6D01G253000 chr6A 499404766 499408719 3953 True 4553 4553 87.887 1 3910 1 chr6A.!!$R1 3909
2 TraesCS6D01G253000 chr6B 538374036 538377448 3412 True 3744 3744 86.870 368 3774 1 chr6B.!!$R2 3406

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
297 298 0.035458 CCCGAGAGCTGAACCAAAGT 59.965 55.0 0.00 0.0 0.00 2.66 F
341 342 0.179048 TTGGCTGGTGTGTGTCTCTG 60.179 55.0 0.00 0.0 0.00 3.35 F
344 345 0.179073 GCTGGTGTGTGTCTCTGTGT 60.179 55.0 0.00 0.0 0.00 3.72 F
1933 2019 0.097674 CACGCTGCATGCTTCTTACC 59.902 55.0 20.33 0.0 40.11 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1929 0.240945 GGTTTGGTCTGGTTGATGCG 59.759 55.0 0.0 0.0 0.00 4.73 R
1853 1933 0.550914 AGCTGGTTTGGTCTGGTTGA 59.449 50.0 0.0 0.0 0.00 3.18 R
2280 2388 0.978146 AGGACGGTTCATCTCCTGGG 60.978 60.0 0.0 0.0 32.85 4.45 R
3862 4047 0.179073 GCGTCTGTGTATGCCCAGAT 60.179 55.0 0.0 0.0 39.70 2.90 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
27 28 4.262036 GCAGATATGTCAACTCATCGGGTA 60.262 45.833 0.00 0.00 0.00 3.69
28 29 5.223382 CAGATATGTCAACTCATCGGGTAC 58.777 45.833 0.00 0.00 0.00 3.34
53 54 1.114627 CTAGGGCCCAATTTGGAAGC 58.885 55.000 27.56 12.01 40.96 3.86
56 57 2.578664 GCCCAATTTGGAAGCCGG 59.421 61.111 17.24 0.00 40.96 6.13
58 59 1.540435 GCCCAATTTGGAAGCCGGAA 61.540 55.000 17.24 0.00 40.96 4.30
86 87 1.581954 CTTCGGAGAGCGTCTGTGT 59.418 57.895 0.00 0.00 38.43 3.72
87 88 0.039074 CTTCGGAGAGCGTCTGTGTT 60.039 55.000 0.00 0.00 38.43 3.32
99 100 1.338973 GTCTGTGTTGTAGGGTGTCGA 59.661 52.381 0.00 0.00 0.00 4.20
122 123 2.666272 TGGTAACATGGGTTGCAGAA 57.334 45.000 0.00 0.00 46.17 3.02
137 138 0.994995 CAGAATCGTTGGCTCGTCTG 59.005 55.000 8.06 8.06 31.45 3.51
155 156 2.516225 GTATGCAACCTCGGGGCC 60.516 66.667 0.00 0.00 35.63 5.80
173 174 0.746563 CCGGTGTGTGTTGTTGAGGT 60.747 55.000 0.00 0.00 0.00 3.85
183 184 4.142491 TGTGTTGTTGAGGTTTGTAAGCTG 60.142 41.667 0.00 0.00 39.77 4.24
186 187 3.476552 TGTTGAGGTTTGTAAGCTGGAG 58.523 45.455 0.00 0.00 39.77 3.86
187 188 2.814336 GTTGAGGTTTGTAAGCTGGAGG 59.186 50.000 0.00 0.00 39.77 4.30
188 189 1.271379 TGAGGTTTGTAAGCTGGAGGC 60.271 52.381 0.00 0.00 39.77 4.70
189 190 0.038310 AGGTTTGTAAGCTGGAGGCC 59.962 55.000 0.00 0.00 43.05 5.19
190 191 0.038310 GGTTTGTAAGCTGGAGGCCT 59.962 55.000 3.86 3.86 43.05 5.19
191 192 1.168714 GTTTGTAAGCTGGAGGCCTG 58.831 55.000 12.00 0.00 43.05 4.85
192 193 0.038166 TTTGTAAGCTGGAGGCCTGG 59.962 55.000 12.00 0.32 43.05 4.45
193 194 0.840288 TTGTAAGCTGGAGGCCTGGA 60.840 55.000 12.00 0.00 43.05 3.86
194 195 1.267574 TGTAAGCTGGAGGCCTGGAG 61.268 60.000 12.00 6.62 43.05 3.86
222 223 0.819582 CGGGTCGTATTGTAGGGTGT 59.180 55.000 0.00 0.00 0.00 4.16
223 224 1.205417 CGGGTCGTATTGTAGGGTGTT 59.795 52.381 0.00 0.00 0.00 3.32
234 235 3.786553 TGTAGGGTGTTGACTATGGTCT 58.213 45.455 10.82 0.00 42.54 3.85
241 242 3.008049 GTGTTGACTATGGTCTCTTGGGT 59.992 47.826 10.82 0.00 42.54 4.51
246 247 3.248024 ACTATGGTCTCTTGGGTGACAA 58.752 45.455 0.00 0.00 37.60 3.18
262 263 1.448540 CAAGGTCATCGGCTCGCTT 60.449 57.895 0.00 0.00 0.00 4.68
267 268 2.185350 CATCGGCTCGCTTGAGGT 59.815 61.111 0.00 0.00 40.26 3.85
271 272 3.123620 GGCTCGCTTGAGGTGCAG 61.124 66.667 0.00 0.00 40.26 4.41
297 298 0.035458 CCCGAGAGCTGAACCAAAGT 59.965 55.000 0.00 0.00 0.00 2.66
299 300 1.063806 CGAGAGCTGAACCAAAGTCG 58.936 55.000 0.00 0.00 0.00 4.18
303 304 2.966309 GCTGAACCAAAGTCGGCCG 61.966 63.158 22.12 22.12 0.00 6.13
316 317 2.452813 CGGCCGTTTCGAGACCATG 61.453 63.158 19.50 0.00 0.00 3.66
337 338 1.360192 GCTTTGGCTGGTGTGTGTC 59.640 57.895 0.00 0.00 35.22 3.67
338 339 1.103398 GCTTTGGCTGGTGTGTGTCT 61.103 55.000 0.00 0.00 35.22 3.41
339 340 0.947244 CTTTGGCTGGTGTGTGTCTC 59.053 55.000 0.00 0.00 0.00 3.36
340 341 0.546122 TTTGGCTGGTGTGTGTCTCT 59.454 50.000 0.00 0.00 0.00 3.10
341 342 0.179048 TTGGCTGGTGTGTGTCTCTG 60.179 55.000 0.00 0.00 0.00 3.35
342 343 1.337384 TGGCTGGTGTGTGTCTCTGT 61.337 55.000 0.00 0.00 0.00 3.41
343 344 0.882042 GGCTGGTGTGTGTCTCTGTG 60.882 60.000 0.00 0.00 0.00 3.66
344 345 0.179073 GCTGGTGTGTGTCTCTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
356 357 3.380954 TGTCTCTGTGTAACACGGTTGTA 59.619 43.478 0.00 0.00 45.67 2.41
370 371 2.415776 GGTTGTATCGGTTTTCGGTCA 58.584 47.619 0.00 0.00 39.77 4.02
376 377 4.575645 TGTATCGGTTTTCGGTCAGTTTTT 59.424 37.500 0.00 0.00 39.77 1.94
387 389 6.746745 TCGGTCAGTTTTTCTTGTTAACTT 57.253 33.333 7.22 0.00 30.08 2.66
388 390 6.548171 TCGGTCAGTTTTTCTTGTTAACTTG 58.452 36.000 7.22 0.00 30.08 3.16
389 391 6.149807 TCGGTCAGTTTTTCTTGTTAACTTGT 59.850 34.615 7.22 0.00 30.08 3.16
390 392 6.468000 CGGTCAGTTTTTCTTGTTAACTTGTC 59.532 38.462 7.22 0.00 30.08 3.18
393 395 9.353999 GTCAGTTTTTCTTGTTAACTTGTCAAT 57.646 29.630 7.22 0.00 30.08 2.57
394 396 9.921637 TCAGTTTTTCTTGTTAACTTGTCAATT 57.078 25.926 7.22 0.00 30.08 2.32
426 428 6.985653 TCTATATGAAGAGGCAAAGCTACT 57.014 37.500 0.00 0.00 0.00 2.57
427 429 8.478775 TTCTATATGAAGAGGCAAAGCTACTA 57.521 34.615 0.00 0.00 0.00 1.82
428 430 8.657387 TCTATATGAAGAGGCAAAGCTACTAT 57.343 34.615 0.00 0.00 0.00 2.12
431 433 5.420725 TGAAGAGGCAAAGCTACTATTGA 57.579 39.130 0.00 0.00 0.00 2.57
896 914 4.200283 CTCGCCTCGCCTCACCTC 62.200 72.222 0.00 0.00 0.00 3.85
991 1042 3.706668 GATCGATCTTGGCGCGGC 61.707 66.667 27.61 27.61 0.00 6.53
1287 1353 3.192001 AGAGAAAACCTGACGCGTATGTA 59.808 43.478 13.97 0.00 0.00 2.29
1314 1384 0.526662 AGGTGAGTCGGACGATGTTC 59.473 55.000 1.89 0.00 0.00 3.18
1319 1389 2.815503 TGAGTCGGACGATGTTCTTGTA 59.184 45.455 1.89 0.00 0.00 2.41
1375 1445 2.540265 AGCTGCGCTCTGCTTATTAT 57.460 45.000 9.73 0.00 43.70 1.28
1376 1446 2.843701 AGCTGCGCTCTGCTTATTATT 58.156 42.857 9.73 0.00 43.70 1.40
1384 1454 3.243201 GCTCTGCTTATTATTGGTGTGCC 60.243 47.826 0.00 0.00 0.00 5.01
1385 1455 3.947196 CTCTGCTTATTATTGGTGTGCCA 59.053 43.478 0.00 0.00 44.38 4.92
1461 1532 2.125391 GCAGCTGTGCGATCCTGA 60.125 61.111 16.64 0.00 40.71 3.86
1473 1544 2.362329 GATCCTGACGAGGCTGGAGC 62.362 65.000 10.32 7.48 39.57 4.70
1499 1570 0.393132 GAAAGGGAGGCCGGAGAAAG 60.393 60.000 5.05 0.00 0.00 2.62
1626 1697 1.536496 CGCCGAACGGGTATGTATTGA 60.536 52.381 15.01 0.00 38.44 2.57
1633 1704 5.048224 CGAACGGGTATGTATTGATACTCCT 60.048 44.000 3.11 0.00 34.41 3.69
1634 1705 6.149973 CGAACGGGTATGTATTGATACTCCTA 59.850 42.308 3.11 0.00 34.41 2.94
1637 1708 6.658391 ACGGGTATGTATTGATACTCCTAGTC 59.342 42.308 3.11 0.00 34.41 2.59
1638 1709 6.885376 CGGGTATGTATTGATACTCCTAGTCT 59.115 42.308 3.11 0.00 34.41 3.24
1647 1719 8.934023 ATTGATACTCCTAGTCTCCTAGAAAG 57.066 38.462 0.00 0.00 42.90 2.62
1848 1928 2.359107 AGGTCGAGGTACGCACGA 60.359 61.111 0.00 4.14 42.26 4.35
1880 1966 4.326826 CAGACCAAACCAGCTTGAATCTA 58.673 43.478 0.00 0.00 0.00 1.98
1881 1967 4.154918 CAGACCAAACCAGCTTGAATCTAC 59.845 45.833 0.00 0.00 0.00 2.59
1882 1968 4.042187 AGACCAAACCAGCTTGAATCTACT 59.958 41.667 0.00 0.00 0.00 2.57
1883 1969 4.074970 ACCAAACCAGCTTGAATCTACTG 58.925 43.478 0.00 0.00 0.00 2.74
1884 1970 4.074970 CCAAACCAGCTTGAATCTACTGT 58.925 43.478 0.00 0.00 0.00 3.55
1885 1971 5.221843 ACCAAACCAGCTTGAATCTACTGTA 60.222 40.000 0.00 0.00 0.00 2.74
1895 1981 6.419413 GCTTGAATCTACTGTATTTCTCTCGG 59.581 42.308 10.25 0.00 0.00 4.63
1918 2004 2.208074 CGTTCATCGGAGATCACGC 58.792 57.895 5.10 0.00 45.12 5.34
1933 2019 0.097674 CACGCTGCATGCTTCTTACC 59.902 55.000 20.33 0.00 40.11 2.85
1946 2032 0.981183 TCTTACCGTTGGACATGGCT 59.019 50.000 0.00 0.00 34.31 4.75
1947 2033 1.086696 CTTACCGTTGGACATGGCTG 58.913 55.000 0.00 0.00 34.31 4.85
1948 2034 0.958382 TTACCGTTGGACATGGCTGC 60.958 55.000 0.00 0.00 34.31 5.25
1949 2035 2.118233 TACCGTTGGACATGGCTGCA 62.118 55.000 0.00 0.00 34.31 4.41
2153 2255 3.631487 GATGCAACAACCGGCTGCC 62.631 63.158 9.11 9.11 35.13 4.85
2243 2345 1.006688 CACACCGGTGTCGATGTCA 60.007 57.895 36.92 0.00 39.21 3.58
2280 2388 2.423926 ATCATGCCTCGACGTATGTC 57.576 50.000 4.90 4.90 41.91 3.06
2283 2391 1.040893 ATGCCTCGACGTATGTCCCA 61.041 55.000 9.51 2.77 42.37 4.37
2290 2398 1.001268 CGACGTATGTCCCAGGAGATG 60.001 57.143 9.51 0.00 42.37 2.90
2291 2399 2.307768 GACGTATGTCCCAGGAGATGA 58.692 52.381 6.59 0.00 39.30 2.92
2301 2409 1.279271 CCAGGAGATGAACCGTCCTTT 59.721 52.381 0.00 0.00 38.75 3.11
2302 2410 2.350522 CAGGAGATGAACCGTCCTTTG 58.649 52.381 0.00 0.00 38.75 2.77
2303 2411 1.279271 AGGAGATGAACCGTCCTTTGG 59.721 52.381 0.00 0.00 37.42 3.28
2304 2412 1.003233 GGAGATGAACCGTCCTTTGGT 59.997 52.381 0.00 0.00 42.98 3.67
2305 2413 2.235402 GGAGATGAACCGTCCTTTGGTA 59.765 50.000 0.00 0.00 39.29 3.25
2306 2414 3.522553 GAGATGAACCGTCCTTTGGTAG 58.477 50.000 0.00 0.00 39.29 3.18
2307 2415 2.904434 AGATGAACCGTCCTTTGGTAGT 59.096 45.455 0.00 0.00 39.29 2.73
2314 2422 3.131396 CCGTCCTTTGGTAGTATGATGC 58.869 50.000 0.00 0.00 0.00 3.91
2316 2424 4.380531 CGTCCTTTGGTAGTATGATGCAT 58.619 43.478 0.00 0.00 0.00 3.96
2318 2426 5.368145 GTCCTTTGGTAGTATGATGCATGA 58.632 41.667 2.46 0.00 0.00 3.07
2345 2453 7.957002 TCTGGTAGATGATATTCTGAACTTCC 58.043 38.462 0.00 0.00 0.00 3.46
2346 2454 7.786943 TCTGGTAGATGATATTCTGAACTTCCT 59.213 37.037 0.00 0.00 0.00 3.36
2347 2455 7.730084 TGGTAGATGATATTCTGAACTTCCTG 58.270 38.462 0.00 0.00 0.00 3.86
2358 2466 4.107622 CTGAACTTCCTGTTTTTGCTGTG 58.892 43.478 0.00 0.00 39.30 3.66
2360 2468 3.508744 ACTTCCTGTTTTTGCTGTGTG 57.491 42.857 0.00 0.00 0.00 3.82
2365 2473 3.006323 TCCTGTTTTTGCTGTGTGTTTGT 59.994 39.130 0.00 0.00 0.00 2.83
2427 2535 3.642848 AGCATTTGTTCAGTGGGTTTGAT 59.357 39.130 0.00 0.00 0.00 2.57
2440 2548 2.397549 GGTTTGATGCACAGTTTCAGC 58.602 47.619 0.00 0.00 0.00 4.26
2465 2573 3.045601 TCAAAGTGAGTAGCTGCTTCC 57.954 47.619 7.79 0.00 0.00 3.46
2466 2574 1.728971 CAAAGTGAGTAGCTGCTTCCG 59.271 52.381 7.79 0.00 0.00 4.30
2495 2603 6.443876 CAAAGCTTGCTTTGTTCTGAATAC 57.556 37.500 29.35 0.00 38.94 1.89
2496 2604 6.211515 CAAAGCTTGCTTTGTTCTGAATACT 58.788 36.000 29.35 1.66 38.94 2.12
2502 2620 6.486253 TGCTTTGTTCTGAATACTCATGTC 57.514 37.500 0.00 0.00 0.00 3.06
2555 2684 9.830975 AAGAAAAATAAAATGTTACAGTTGGCT 57.169 25.926 0.00 0.00 0.00 4.75
2588 2717 5.009110 TCACATAGCTGCTATACTGACAGAC 59.991 44.000 20.91 0.00 33.10 3.51
2590 2719 2.644676 AGCTGCTATACTGACAGACGA 58.355 47.619 10.08 0.00 33.10 4.20
2605 2734 7.704472 ACTGACAGACGATTAAAGAATCTCATC 59.296 37.037 10.08 0.00 39.56 2.92
2679 2834 6.334989 ACAATTTGGAAGATGCATGTGTATG 58.665 36.000 2.46 0.00 37.36 2.39
2684 2839 3.947196 GGAAGATGCATGTGTATGGTCAA 59.053 43.478 2.46 0.00 34.79 3.18
2685 2840 4.036027 GGAAGATGCATGTGTATGGTCAAG 59.964 45.833 2.46 0.00 34.79 3.02
2686 2841 2.947652 AGATGCATGTGTATGGTCAAGC 59.052 45.455 2.46 0.00 34.79 4.01
2703 2858 0.677098 AGCTGAGCACAGGAAGCATG 60.677 55.000 13.26 0.00 43.62 4.06
2725 2880 3.983344 GTGCCATGAACACATTGAAACTC 59.017 43.478 12.37 0.00 37.96 3.01
2728 2883 4.556501 GCCATGAACACATTGAAACTCGAA 60.557 41.667 0.00 0.00 0.00 3.71
2734 2889 6.204688 TGAACACATTGAAACTCGAATAAGCT 59.795 34.615 0.00 0.00 0.00 3.74
2736 2891 4.790140 CACATTGAAACTCGAATAAGCTGC 59.210 41.667 0.00 0.00 0.00 5.25
2737 2892 4.455533 ACATTGAAACTCGAATAAGCTGCA 59.544 37.500 1.02 0.00 0.00 4.41
2741 2896 4.455533 TGAAACTCGAATAAGCTGCAATGT 59.544 37.500 1.02 0.00 0.00 2.71
2744 2899 3.127548 ACTCGAATAAGCTGCAATGTTGG 59.872 43.478 1.02 0.00 0.00 3.77
2745 2900 3.081061 TCGAATAAGCTGCAATGTTGGT 58.919 40.909 1.02 0.00 0.00 3.67
2747 2902 3.731867 CGAATAAGCTGCAATGTTGGTCC 60.732 47.826 1.02 0.00 0.00 4.46
2749 2904 0.963962 AAGCTGCAATGTTGGTCCTG 59.036 50.000 1.02 0.00 0.00 3.86
2751 2906 1.073763 AGCTGCAATGTTGGTCCTGTA 59.926 47.619 1.02 0.00 0.00 2.74
2752 2907 1.885887 GCTGCAATGTTGGTCCTGTAA 59.114 47.619 0.00 0.00 0.00 2.41
2753 2908 2.493278 GCTGCAATGTTGGTCCTGTAAT 59.507 45.455 0.00 0.00 0.00 1.89
2754 2909 3.674138 GCTGCAATGTTGGTCCTGTAATG 60.674 47.826 0.00 0.00 0.00 1.90
2755 2910 3.758023 CTGCAATGTTGGTCCTGTAATGA 59.242 43.478 0.00 0.00 0.00 2.57
2757 2912 4.771577 TGCAATGTTGGTCCTGTAATGAAT 59.228 37.500 0.00 0.00 0.00 2.57
2758 2913 5.948758 TGCAATGTTGGTCCTGTAATGAATA 59.051 36.000 0.00 0.00 0.00 1.75
2759 2914 6.606796 TGCAATGTTGGTCCTGTAATGAATAT 59.393 34.615 0.00 0.00 0.00 1.28
2760 2915 7.777440 TGCAATGTTGGTCCTGTAATGAATATA 59.223 33.333 0.00 0.00 0.00 0.86
2761 2916 8.796475 GCAATGTTGGTCCTGTAATGAATATAT 58.204 33.333 0.00 0.00 0.00 0.86
2800 2955 1.080995 GCGATGCAGTGTCAGGACTC 61.081 60.000 0.00 0.00 0.00 3.36
2801 2956 0.799917 CGATGCAGTGTCAGGACTCG 60.800 60.000 0.00 0.00 0.00 4.18
2854 3009 5.125097 CAGAAGAACATTTCCCCTGAATCAG 59.875 44.000 2.68 2.68 33.87 2.90
2894 3049 4.357918 AGGTGACTGTTTGCTAGACAAT 57.642 40.909 0.00 0.00 41.13 2.71
2907 3062 7.523293 TTGCTAGACAATCTCAAAATGGAAA 57.477 32.000 0.00 0.00 31.73 3.13
2989 3144 9.671279 TGAAGATTCTTTATTCATAGCAACTGA 57.329 29.630 0.00 0.00 0.00 3.41
3016 3171 3.011818 TGCAGTATTCTGTCAGCAATGG 58.988 45.455 1.02 0.00 43.05 3.16
3069 3224 9.687210 TTATATTCTTGTATTGCTAGTGTACCG 57.313 33.333 0.00 0.00 0.00 4.02
3087 3242 1.872952 CCGAATCATAAGCAATCCGCA 59.127 47.619 0.00 0.00 46.13 5.69
3202 3357 7.502226 TCTCACTACAAACAAATCCAGAACAAT 59.498 33.333 0.00 0.00 0.00 2.71
3261 3416 2.300152 TGAAAGTGCAACACCAAACCAA 59.700 40.909 0.00 0.00 41.43 3.67
3262 3417 3.244215 TGAAAGTGCAACACCAAACCAAA 60.244 39.130 0.00 0.00 41.43 3.28
3266 3421 0.581053 GCAACACCAAACCAAATGCG 59.419 50.000 0.00 0.00 0.00 4.73
3283 3438 2.001361 GCGCCGCTGTCTCCTACTTA 62.001 60.000 0.00 0.00 0.00 2.24
3285 3440 1.067212 CGCCGCTGTCTCCTACTTATT 59.933 52.381 0.00 0.00 0.00 1.40
3313 3471 4.084328 CCTCTTTAAAGCACAGACTGTTCG 60.084 45.833 5.04 0.00 0.00 3.95
3440 3614 0.103937 GATCCCTCTCGAGCAAGGTG 59.896 60.000 16.66 9.76 0.00 4.00
3479 3654 7.921786 TTCATGGGTACTACTCAAATTTCAG 57.078 36.000 0.00 0.00 28.99 3.02
3486 3661 8.697292 GGGTACTACTCAAATTTCAGTATCTCT 58.303 37.037 2.13 0.00 0.00 3.10
3550 3725 7.462731 GCATAAGATAACTATGCTCTCATTGC 58.537 38.462 7.41 0.00 42.23 3.56
3751 3930 6.291377 ACAGCAGAAATTACTCTCTGTGAAA 58.709 36.000 6.71 0.00 41.02 2.69
3774 3953 7.981102 AAATAAGGTGGACTTGTAGAGAAAC 57.019 36.000 0.00 0.00 40.37 2.78
3781 3960 3.186613 GGACTTGTAGAGAAACGGCAAAG 59.813 47.826 0.00 0.00 0.00 2.77
3811 3990 6.465948 TGCTTGAATATCTTGTGGCAAAAAT 58.534 32.000 0.00 0.00 0.00 1.82
3818 3997 3.976169 TCTTGTGGCAAAAATTTCCTCG 58.024 40.909 0.00 0.00 0.00 4.63
3819 3998 2.810439 TGTGGCAAAAATTTCCTCGG 57.190 45.000 0.00 0.00 0.00 4.63
3824 4003 3.243704 TGGCAAAAATTTCCTCGGAACTG 60.244 43.478 0.00 0.00 33.41 3.16
3825 4004 2.731451 GCAAAAATTTCCTCGGAACTGC 59.269 45.455 0.00 0.10 33.41 4.40
3826 4005 3.552890 GCAAAAATTTCCTCGGAACTGCT 60.553 43.478 0.00 0.00 33.41 4.24
3829 4008 4.553330 AAATTTCCTCGGAACTGCTAGA 57.447 40.909 0.00 0.00 33.41 2.43
3879 4064 3.347216 ACAAATCTGGGCATACACAGAC 58.653 45.455 0.00 0.00 45.54 3.51
3890 4075 2.278026 TACACAGACGCACATGCTAG 57.722 50.000 1.82 0.00 39.32 3.42
3899 4084 1.532505 CGCACATGCTAGATTTGGCAC 60.533 52.381 0.00 0.00 43.99 5.01
3910 4095 4.826274 AGATTTGGCACTAGCACTTCTA 57.174 40.909 0.00 0.00 44.61 2.10
3911 4096 5.365021 AGATTTGGCACTAGCACTTCTAT 57.635 39.130 0.00 0.00 44.61 1.98
3912 4097 5.363939 AGATTTGGCACTAGCACTTCTATC 58.636 41.667 0.00 0.00 44.61 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.018856 ACGTACCCGATGAGTTGACATA 58.981 45.455 0.00 0.00 37.88 2.29
10 11 1.822990 ACGTACCCGATGAGTTGACAT 59.177 47.619 0.00 0.00 37.88 3.06
11 12 1.068125 CACGTACCCGATGAGTTGACA 60.068 52.381 0.00 0.00 37.88 3.58
15 16 1.217244 GCCACGTACCCGATGAGTT 59.783 57.895 0.00 0.00 37.88 3.01
40 41 0.246360 GTTCCGGCTTCCAAATTGGG 59.754 55.000 12.67 0.00 38.32 4.12
41 42 0.246360 GGTTCCGGCTTCCAAATTGG 59.754 55.000 5.48 5.48 39.43 3.16
42 43 0.109319 CGGTTCCGGCTTCCAAATTG 60.109 55.000 0.00 0.00 0.00 2.32
43 44 1.873270 GCGGTTCCGGCTTCCAAATT 61.873 55.000 13.16 0.00 0.00 1.82
63 64 4.421479 ACGCTCTCCGAAGCCGTG 62.421 66.667 0.00 0.00 39.17 4.94
65 66 3.816524 AGACGCTCTCCGAAGCCG 61.817 66.667 0.00 0.00 39.17 5.52
66 67 2.202676 CAGACGCTCTCCGAAGCC 60.203 66.667 0.00 0.00 39.17 4.35
70 71 1.285950 CAACACAGACGCTCTCCGA 59.714 57.895 0.00 0.00 41.02 4.55
73 74 1.402984 CCCTACAACACAGACGCTCTC 60.403 57.143 0.00 0.00 0.00 3.20
86 87 2.253610 ACCAGAATCGACACCCTACAA 58.746 47.619 0.00 0.00 0.00 2.41
87 88 1.933021 ACCAGAATCGACACCCTACA 58.067 50.000 0.00 0.00 0.00 2.74
99 100 3.091545 CTGCAACCCATGTTACCAGAAT 58.908 45.455 0.00 0.00 36.14 2.40
111 112 1.523154 GCCAACGATTCTGCAACCCA 61.523 55.000 0.00 0.00 0.00 4.51
114 115 0.179215 CGAGCCAACGATTCTGCAAC 60.179 55.000 0.00 0.00 35.09 4.17
119 120 0.108615 CCAGACGAGCCAACGATTCT 60.109 55.000 0.00 0.00 37.03 2.40
121 122 0.892755 TACCAGACGAGCCAACGATT 59.107 50.000 0.00 0.00 37.03 3.34
122 123 1.112113 ATACCAGACGAGCCAACGAT 58.888 50.000 0.00 0.00 37.03 3.73
153 154 1.355210 CTCAACAACACACACCGGC 59.645 57.895 0.00 0.00 0.00 6.13
155 156 1.091537 AACCTCAACAACACACACCG 58.908 50.000 0.00 0.00 0.00 4.94
173 174 0.038166 CCAGGCCTCCAGCTTACAAA 59.962 55.000 0.00 0.00 43.05 2.83
207 208 5.163488 CCATAGTCAACACCCTACAATACGA 60.163 44.000 0.00 0.00 0.00 3.43
222 223 3.260884 GTCACCCAAGAGACCATAGTCAA 59.739 47.826 0.00 0.00 46.15 3.18
223 224 2.832129 GTCACCCAAGAGACCATAGTCA 59.168 50.000 0.00 0.00 46.15 3.41
241 242 1.215382 CGAGCCGATGACCTTGTCA 59.785 57.895 0.00 0.00 46.90 3.58
246 247 2.185350 CAAGCGAGCCGATGACCT 59.815 61.111 0.00 0.00 0.00 3.85
251 252 2.185350 CACCTCAAGCGAGCCGAT 59.815 61.111 0.00 0.00 38.00 4.18
252 253 4.742201 GCACCTCAAGCGAGCCGA 62.742 66.667 0.00 0.00 38.00 5.54
262 263 4.783621 GGGCGATGCTGCACCTCA 62.784 66.667 3.57 0.00 36.28 3.86
297 298 2.642254 ATGGTCTCGAAACGGCCGA 61.642 57.895 35.90 7.96 34.61 5.54
299 300 2.106683 CCATGGTCTCGAAACGGCC 61.107 63.158 2.57 0.00 0.00 6.13
303 304 2.100605 AAGCTCCATGGTCTCGAAAC 57.899 50.000 12.58 0.00 0.00 2.78
337 338 3.606777 CGATACAACCGTGTTACACAGAG 59.393 47.826 16.09 6.01 39.30 3.35
338 339 3.567530 CGATACAACCGTGTTACACAGA 58.432 45.455 16.09 0.00 39.30 3.41
339 340 2.664568 CCGATACAACCGTGTTACACAG 59.335 50.000 16.09 6.74 39.30 3.66
340 341 2.035704 ACCGATACAACCGTGTTACACA 59.964 45.455 16.09 0.00 39.30 3.72
341 342 2.676076 ACCGATACAACCGTGTTACAC 58.324 47.619 5.27 5.27 39.30 2.90
342 343 3.383620 AACCGATACAACCGTGTTACA 57.616 42.857 0.00 0.00 39.30 2.41
343 344 4.663889 CGAAAACCGATACAACCGTGTTAC 60.664 45.833 0.00 0.00 41.76 2.50
344 345 3.428198 CGAAAACCGATACAACCGTGTTA 59.572 43.478 0.00 0.00 41.76 2.41
348 349 1.270252 ACCGAAAACCGATACAACCGT 60.270 47.619 0.00 0.00 41.76 4.83
356 357 3.881089 AGAAAAACTGACCGAAAACCGAT 59.119 39.130 0.00 0.00 41.76 4.18
406 408 7.739825 TCAATAGTAGCTTTGCCTCTTCATAT 58.260 34.615 0.00 0.00 0.00 1.78
413 415 4.578105 AGCAATCAATAGTAGCTTTGCCTC 59.422 41.667 10.94 0.00 40.11 4.70
419 421 5.521906 TCTCGAGCAATCAATAGTAGCTT 57.478 39.130 7.81 0.00 35.36 3.74
448 450 7.335627 TGATCAGAAATGGGTATACGAAACTT 58.664 34.615 0.00 0.00 0.00 2.66
449 451 6.884832 TGATCAGAAATGGGTATACGAAACT 58.115 36.000 0.00 0.00 0.00 2.66
450 452 7.548196 TTGATCAGAAATGGGTATACGAAAC 57.452 36.000 0.00 0.00 0.00 2.78
805 822 1.979155 GCCCTCTTTTGTGCTCCCC 60.979 63.158 0.00 0.00 0.00 4.81
886 904 2.357517 AAGCAACGAGGTGAGGCG 60.358 61.111 0.00 0.00 0.00 5.52
888 906 0.034059 AGACAAGCAACGAGGTGAGG 59.966 55.000 0.00 0.00 0.00 3.86
889 907 1.795286 GAAGACAAGCAACGAGGTGAG 59.205 52.381 0.00 0.00 0.00 3.51
890 908 1.865865 GAAGACAAGCAACGAGGTGA 58.134 50.000 0.00 0.00 0.00 4.02
892 910 0.387929 TCGAAGACAAGCAACGAGGT 59.612 50.000 0.00 0.00 0.00 3.85
893 911 1.457303 CTTCGAAGACAAGCAACGAGG 59.543 52.381 20.74 0.00 34.32 4.63
894 912 2.394708 TCTTCGAAGACAAGCAACGAG 58.605 47.619 23.74 0.00 34.32 4.18
895 913 2.502213 TCTTCGAAGACAAGCAACGA 57.498 45.000 23.74 0.00 34.32 3.85
896 914 2.092838 GGATCTTCGAAGACAAGCAACG 59.907 50.000 29.24 0.00 37.98 4.10
897 915 2.092838 CGGATCTTCGAAGACAAGCAAC 59.907 50.000 29.24 13.10 37.98 4.17
993 1044 3.539253 GCAGTGCGCCATTAATCAG 57.461 52.632 4.18 0.00 32.94 2.90
1048 1099 0.911769 AAATGGCTCTCCACGGATGA 59.088 50.000 0.00 0.00 46.92 2.92
1050 1101 0.181350 GGAAATGGCTCTCCACGGAT 59.819 55.000 0.00 0.00 46.92 4.18
1257 1323 4.238514 CGTCAGGTTTTCTCTTAGTGGAG 58.761 47.826 0.00 0.00 34.88 3.86
1263 1329 2.806608 ACGCGTCAGGTTTTCTCTTA 57.193 45.000 5.58 0.00 0.00 2.10
1287 1353 1.006102 CCGACTCACCTTTGCGTCT 60.006 57.895 0.00 0.00 35.63 4.18
1314 1384 1.346197 CTCGCAGCGCATGTACAAG 59.654 57.895 10.87 0.00 0.00 3.16
1376 1446 0.546122 AGTCAAAGACTGGCACACCA 59.454 50.000 0.00 0.00 46.51 4.17
1638 1709 9.793259 ACACAAGATTAATTGTTCTTTCTAGGA 57.207 29.630 2.85 0.00 41.41 2.94
1670 1742 3.367600 GCATCAGGATCAAATTGTGCACA 60.368 43.478 17.42 17.42 0.00 4.57
1671 1743 3.184541 GCATCAGGATCAAATTGTGCAC 58.815 45.455 10.75 10.75 0.00 4.57
1848 1928 0.951558 GTTTGGTCTGGTTGATGCGT 59.048 50.000 0.00 0.00 0.00 5.24
1849 1929 0.240945 GGTTTGGTCTGGTTGATGCG 59.759 55.000 0.00 0.00 0.00 4.73
1850 1930 1.270550 CTGGTTTGGTCTGGTTGATGC 59.729 52.381 0.00 0.00 0.00 3.91
1853 1933 0.550914 AGCTGGTTTGGTCTGGTTGA 59.449 50.000 0.00 0.00 0.00 3.18
1855 1935 1.064017 TCAAGCTGGTTTGGTCTGGTT 60.064 47.619 0.00 0.00 0.00 3.67
1880 1966 3.870633 GGACACCGAGAGAAATACAGT 57.129 47.619 0.00 0.00 0.00 3.55
1918 2004 1.131126 CCAACGGTAAGAAGCATGCAG 59.869 52.381 21.98 2.94 0.00 4.41
1933 2019 2.562912 GTGCAGCCATGTCCAACG 59.437 61.111 0.00 0.00 0.00 4.10
1946 2032 4.908687 AGGAACTGCGTGCGTGCA 62.909 61.111 2.51 2.51 43.95 4.57
2058 2148 4.794439 CGGCAGCGTCGTCATGGA 62.794 66.667 0.00 0.00 0.00 3.41
2060 2150 2.583319 ATCGGCAGCGTCGTCATG 60.583 61.111 2.79 0.00 30.45 3.07
2061 2151 2.583319 CATCGGCAGCGTCGTCAT 60.583 61.111 2.79 0.00 30.45 3.06
2153 2255 4.096003 ATGTCCTGCCCGAACCCG 62.096 66.667 0.00 0.00 0.00 5.28
2164 2266 1.512926 GTTGTTGACGAGCATGTCCT 58.487 50.000 5.97 0.00 38.11 3.85
2228 2330 2.261671 GCTGACATCGACACCGGT 59.738 61.111 0.00 0.00 36.24 5.28
2261 2369 1.000163 GGACATACGTCGAGGCATGAT 60.000 52.381 21.83 8.67 43.61 2.45
2280 2388 0.978146 AGGACGGTTCATCTCCTGGG 60.978 60.000 0.00 0.00 32.85 4.45
2283 2391 1.279271 CCAAAGGACGGTTCATCTCCT 59.721 52.381 0.00 0.00 35.83 3.69
2290 2398 4.460948 TCATACTACCAAAGGACGGTTC 57.539 45.455 0.00 0.00 37.99 3.62
2291 2399 4.766375 CATCATACTACCAAAGGACGGTT 58.234 43.478 0.00 0.00 37.99 4.44
2301 2409 5.072193 ACCAGAATCATGCATCATACTACCA 59.928 40.000 0.00 0.00 0.00 3.25
2302 2410 5.555017 ACCAGAATCATGCATCATACTACC 58.445 41.667 0.00 0.00 0.00 3.18
2303 2411 7.606349 TCTACCAGAATCATGCATCATACTAC 58.394 38.462 0.00 0.00 0.00 2.73
2304 2412 7.781324 TCTACCAGAATCATGCATCATACTA 57.219 36.000 0.00 0.00 0.00 1.82
2305 2413 6.676990 TCTACCAGAATCATGCATCATACT 57.323 37.500 0.00 0.00 0.00 2.12
2306 2414 7.101700 TCATCTACCAGAATCATGCATCATAC 58.898 38.462 0.00 0.00 0.00 2.39
2307 2415 7.248743 TCATCTACCAGAATCATGCATCATA 57.751 36.000 0.00 0.00 0.00 2.15
2314 2422 9.939802 TTCAGAATATCATCTACCAGAATCATG 57.060 33.333 0.00 0.00 0.00 3.07
2316 2424 9.152327 AGTTCAGAATATCATCTACCAGAATCA 57.848 33.333 0.00 0.00 0.00 2.57
2318 2426 9.995003 GAAGTTCAGAATATCATCTACCAGAAT 57.005 33.333 0.00 0.00 0.00 2.40
2345 2453 4.700332 CAACAAACACACAGCAAAAACAG 58.300 39.130 0.00 0.00 0.00 3.16
2346 2454 3.059325 GCAACAAACACACAGCAAAAACA 60.059 39.130 0.00 0.00 0.00 2.83
2347 2455 3.059325 TGCAACAAACACACAGCAAAAAC 60.059 39.130 0.00 0.00 0.00 2.43
2358 2466 2.100584 TCCATTCACCTGCAACAAACAC 59.899 45.455 0.00 0.00 0.00 3.32
2360 2468 2.863704 GCTCCATTCACCTGCAACAAAC 60.864 50.000 0.00 0.00 0.00 2.93
2365 2473 2.951269 CAGCTCCATTCACCTGCAA 58.049 52.632 0.00 0.00 0.00 4.08
2427 2535 1.024271 GAACTGGCTGAAACTGTGCA 58.976 50.000 0.00 0.00 0.00 4.57
2440 2548 2.481952 GCAGCTACTCACTTTGAACTGG 59.518 50.000 0.00 0.00 0.00 4.00
2482 2590 8.675705 TCTTTGACATGAGTATTCAGAACAAA 57.324 30.769 0.00 12.21 36.61 2.83
2483 2591 8.559536 GTTCTTTGACATGAGTATTCAGAACAA 58.440 33.333 0.00 5.19 36.61 2.83
2484 2592 7.714813 TGTTCTTTGACATGAGTATTCAGAACA 59.285 33.333 0.00 10.36 36.77 3.18
2488 2596 9.591792 TCTATGTTCTTTGACATGAGTATTCAG 57.408 33.333 0.00 0.00 40.33 3.02
2494 2602 8.753133 TCTGTATCTATGTTCTTTGACATGAGT 58.247 33.333 0.00 0.00 40.33 3.41
2495 2603 9.247126 CTCTGTATCTATGTTCTTTGACATGAG 57.753 37.037 0.00 0.00 40.33 2.90
2496 2604 8.753133 ACTCTGTATCTATGTTCTTTGACATGA 58.247 33.333 0.00 0.00 40.33 3.07
2540 2659 4.202419 TGACCACTAGCCAACTGTAACATT 60.202 41.667 0.00 0.00 0.00 2.71
2555 2684 3.033909 AGCAGCTATGTGATGACCACTA 58.966 45.455 0.00 0.00 45.86 2.74
2568 2697 4.390264 TCGTCTGTCAGTATAGCAGCTAT 58.610 43.478 19.07 19.07 0.00 2.97
2571 2700 3.634568 ATCGTCTGTCAGTATAGCAGC 57.365 47.619 0.00 0.00 0.00 5.25
2588 2717 8.417780 AGTTCTGTGATGAGATTCTTTAATCG 57.582 34.615 0.00 0.00 45.24 3.34
2590 2719 9.381033 CAGAGTTCTGTGATGAGATTCTTTAAT 57.619 33.333 0.91 0.00 39.09 1.40
2639 2768 9.770097 TTCCAAATTGTACAAATGAAGCAAATA 57.230 25.926 20.41 0.00 0.00 1.40
2640 2769 8.674263 TTCCAAATTGTACAAATGAAGCAAAT 57.326 26.923 20.41 0.00 0.00 2.32
2645 2781 7.599621 TGCATCTTCCAAATTGTACAAATGAAG 59.400 33.333 20.41 21.04 0.00 3.02
2679 2834 0.250467 TTCCTGTGCTCAGCTTGACC 60.250 55.000 10.32 0.00 40.09 4.02
2684 2839 0.677098 CATGCTTCCTGTGCTCAGCT 60.677 55.000 10.32 0.00 40.09 4.24
2685 2840 0.959372 ACATGCTTCCTGTGCTCAGC 60.959 55.000 10.32 0.00 40.09 4.26
2686 2841 0.803117 CACATGCTTCCTGTGCTCAG 59.197 55.000 8.84 8.84 37.76 3.35
2703 2858 3.981211 AGTTTCAATGTGTTCATGGCAC 58.019 40.909 12.38 12.38 37.37 5.01
2706 2861 4.747540 TCGAGTTTCAATGTGTTCATGG 57.252 40.909 0.00 0.00 34.19 3.66
2707 2862 7.007725 GCTTATTCGAGTTTCAATGTGTTCATG 59.992 37.037 0.00 0.00 34.19 3.07
2725 2880 3.429085 GACCAACATTGCAGCTTATTCG 58.571 45.455 0.00 0.00 0.00 3.34
2728 2883 2.756760 CAGGACCAACATTGCAGCTTAT 59.243 45.455 0.00 0.00 0.00 1.73
2734 2889 3.760738 TCATTACAGGACCAACATTGCA 58.239 40.909 0.00 0.00 0.00 4.08
2761 2916 8.659491 GCATCGCATACTAGAAATATGAATTCA 58.341 33.333 11.26 11.26 32.66 2.57
2763 2918 8.552083 TGCATCGCATACTAGAAATATGAATT 57.448 30.769 0.00 0.00 32.66 2.17
2764 2919 7.821359 ACTGCATCGCATACTAGAAATATGAAT 59.179 33.333 0.00 0.00 38.13 2.57
2766 2921 6.587608 CACTGCATCGCATACTAGAAATATGA 59.412 38.462 0.00 0.00 38.13 2.15
2767 2922 6.367149 ACACTGCATCGCATACTAGAAATATG 59.633 38.462 0.00 0.00 38.13 1.78
2768 2923 6.459066 ACACTGCATCGCATACTAGAAATAT 58.541 36.000 0.00 0.00 38.13 1.28
2771 2926 4.112634 GACACTGCATCGCATACTAGAAA 58.887 43.478 0.00 0.00 38.13 2.52
2774 2929 3.048501 CTGACACTGCATCGCATACTAG 58.951 50.000 0.00 0.00 38.13 2.57
2780 2935 1.374631 GTCCTGACACTGCATCGCA 60.375 57.895 0.00 0.00 36.92 5.10
2782 2937 0.799917 CGAGTCCTGACACTGCATCG 60.800 60.000 0.00 0.00 0.00 3.84
2783 2938 0.528017 TCGAGTCCTGACACTGCATC 59.472 55.000 0.00 0.00 0.00 3.91
2800 2955 4.685169 AATAGCACAAAATGGACACTCG 57.315 40.909 0.00 0.00 0.00 4.18
2801 2956 8.699749 GTTAAAAATAGCACAAAATGGACACTC 58.300 33.333 0.00 0.00 0.00 3.51
2854 3009 0.609131 TGCAAGGGAAAGTAGCAGCC 60.609 55.000 0.00 0.00 0.00 4.85
2894 3049 4.157656 CCCGCTTACATTTCCATTTTGAGA 59.842 41.667 0.00 0.00 0.00 3.27
2907 3062 6.431234 GGAATGAGAATTAATCCCGCTTACAT 59.569 38.462 0.00 0.00 0.00 2.29
2989 3144 5.491070 TGCTGACAGAATACTGCATTAGTT 58.509 37.500 6.65 0.00 46.95 2.24
3069 3224 6.211515 AGAATTTGCGGATTGCTTATGATTC 58.788 36.000 0.00 0.00 46.63 2.52
3087 3242 5.169295 GTGTAGCTCGGTAGTGAAGAATTT 58.831 41.667 0.00 0.00 0.00 1.82
3146 3301 4.537135 TCTGAACAAGGTAGCGAGAATT 57.463 40.909 0.00 0.00 0.00 2.17
3147 3302 4.537135 TTCTGAACAAGGTAGCGAGAAT 57.463 40.909 0.00 0.00 0.00 2.40
3202 3357 5.066968 TCTGATAAGACGTGTGCATGTTA 57.933 39.130 0.00 0.00 0.00 2.41
3244 3399 2.903798 CATTTGGTTTGGTGTTGCACT 58.096 42.857 0.00 0.00 34.40 4.40
3249 3404 0.531753 GGCGCATTTGGTTTGGTGTT 60.532 50.000 10.83 0.00 0.00 3.32
3261 3416 2.721167 TAGGAGACAGCGGCGCATT 61.721 57.895 35.02 20.40 0.00 3.56
3262 3417 3.147595 TAGGAGACAGCGGCGCAT 61.148 61.111 35.02 22.06 0.00 4.73
3266 3421 2.159085 ACAATAAGTAGGAGACAGCGGC 60.159 50.000 0.00 0.00 0.00 6.53
3283 3438 4.082125 CTGTGCTTTAAAGAGGGGACAAT 58.918 43.478 19.48 0.00 30.43 2.71
3285 3440 2.708861 TCTGTGCTTTAAAGAGGGGACA 59.291 45.455 19.48 9.07 0.00 4.02
3313 3471 0.886563 ATGTCTTTGCAGAAGCTGGC 59.113 50.000 0.00 0.00 42.74 4.85
3440 3614 8.739972 AGTACCCATGAAAATCTGAAACAATAC 58.260 33.333 0.00 0.00 0.00 1.89
3486 3661 8.778358 GTGGCAAAACATATTTGATGGTTTAAA 58.222 29.630 5.17 0.00 36.86 1.52
3550 3725 3.424529 GTGTAACTTTCTTGACCGAGTCG 59.575 47.826 5.29 5.29 34.95 4.18
3751 3930 6.164176 CGTTTCTCTACAAGTCCACCTTATT 58.836 40.000 0.00 0.00 0.00 1.40
3781 3960 5.517770 GCCACAAGATATTCAAGCAAATGAC 59.482 40.000 0.00 0.00 0.00 3.06
3800 3979 2.311463 TCCGAGGAAATTTTTGCCACA 58.689 42.857 0.00 0.00 0.00 4.17
3801 3980 3.057019 GTTCCGAGGAAATTTTTGCCAC 58.943 45.455 6.09 0.00 35.75 5.01
3811 3990 4.553330 ATTTCTAGCAGTTCCGAGGAAA 57.447 40.909 6.09 0.00 35.75 3.13
3818 3997 6.458888 GCAAGTGGATAATTTCTAGCAGTTCC 60.459 42.308 0.00 0.00 0.00 3.62
3819 3998 6.094048 TGCAAGTGGATAATTTCTAGCAGTTC 59.906 38.462 0.00 0.00 0.00 3.01
3824 4003 5.532406 TGGATGCAAGTGGATAATTTCTAGC 59.468 40.000 0.00 0.00 0.00 3.42
3825 4004 6.016777 GGTGGATGCAAGTGGATAATTTCTAG 60.017 42.308 0.00 0.00 0.00 2.43
3826 4005 5.827797 GGTGGATGCAAGTGGATAATTTCTA 59.172 40.000 0.00 0.00 0.00 2.10
3829 4008 4.352009 TGGTGGATGCAAGTGGATAATTT 58.648 39.130 0.00 0.00 0.00 1.82
3859 4044 2.352651 CGTCTGTGTATGCCCAGATTTG 59.647 50.000 0.00 0.00 39.70 2.32
3860 4045 2.632377 CGTCTGTGTATGCCCAGATTT 58.368 47.619 0.00 0.00 39.70 2.17
3862 4047 0.179073 GCGTCTGTGTATGCCCAGAT 60.179 55.000 0.00 0.00 39.70 2.90
3864 4049 1.079197 TGCGTCTGTGTATGCCCAG 60.079 57.895 0.00 0.00 0.00 4.45
3890 4075 5.665381 GATAGAAGTGCTAGTGCCAAATC 57.335 43.478 0.00 0.00 38.71 2.17


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

AutoCloner maintained by Alex Coulton.