Multiple sequence alignment - TraesCS4A01G132800

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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 TraesCS4A01G132800 chr4A 100.000 5088 0 0 1 5088 179137501 179142588 0.000000e+00 9396
1 TraesCS4A01G132800 chr4A 83.775 302 34 11 269 561 647355083 647355378 6.490000e-69 272
2 TraesCS4A01G132800 chr4A 83.498 303 37 8 264 561 17670130 17669836 2.330000e-68 270
3 TraesCS4A01G132800 chr4B 90.321 2552 106 45 2278 4762 376142467 376139990 0.000000e+00 3214
4 TraesCS4A01G132800 chr4B 92.937 1430 54 13 474 1883 376144395 376142993 0.000000e+00 2037
5 TraesCS4A01G132800 chr4B 96.667 330 10 1 4759 5088 376139781 376139453 9.630000e-152 547
6 TraesCS4A01G132800 chr4B 87.354 427 29 7 1 402 376144851 376144425 2.770000e-127 466
7 TraesCS4A01G132800 chr4B 88.211 246 11 2 1995 2233 376142704 376142470 1.400000e-70 278
8 TraesCS4A01G132800 chr4B 83.333 306 40 8 264 561 167340665 167340967 6.490000e-69 272
9 TraesCS4A01G132800 chr4D 92.495 1892 81 22 34 1900 301738323 301736468 0.000000e+00 2651
10 TraesCS4A01G132800 chr4D 90.157 2032 116 32 2247 4242 301735892 301733909 0.000000e+00 2567
11 TraesCS4A01G132800 chr4D 90.122 1063 55 15 3731 4762 301734413 301733370 0.000000e+00 1336
12 TraesCS4A01G132800 chr4D 96.667 330 11 0 4759 5088 301733161 301732832 2.680000e-152 549
13 TraesCS4A01G132800 chr4D 83.819 309 37 10 264 564 497874158 497873855 1.080000e-71 281
14 TraesCS4A01G132800 chr4D 85.294 272 14 3 1973 2232 301736135 301735878 1.820000e-64 257
15 TraesCS4A01G132800 chr6B 88.645 273 23 7 1 266 234663201 234663472 4.910000e-85 326
16 TraesCS4A01G132800 chr6B 86.182 275 32 5 1 269 165856154 165855880 4.980000e-75 292
17 TraesCS4A01G132800 chr2B 88.686 274 20 8 1 269 371565096 371565363 1.770000e-84 324
18 TraesCS4A01G132800 chr5A 86.411 287 30 6 1 280 565442755 565443039 6.400000e-79 305
19 TraesCS4A01G132800 chr5B 86.716 271 29 6 1 265 357929935 357930204 1.390000e-75 294
20 TraesCS4A01G132800 chr5B 83.987 306 40 6 264 563 526191879 526191577 8.340000e-73 285
21 TraesCS4A01G132800 chr5D 86.891 267 27 6 264 526 548985739 548986001 4.980000e-75 292
22 TraesCS4A01G132800 chr6D 86.232 276 28 8 1 269 136392037 136392309 1.790000e-74 291
23 TraesCS4A01G132800 chr2D 86.182 275 31 5 2 269 557881912 557881638 1.790000e-74 291
24 TraesCS4A01G132800 chr1D 83.987 306 40 7 264 563 294746573 294746271 8.340000e-73 285
25 TraesCS4A01G132800 chr3B 83.226 310 39 6 264 563 791266795 791266489 6.490000e-69 272


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 TraesCS4A01G132800 chr4A 179137501 179142588 5087 False 9396.0 9396 100.000 1 5088 1 chr4A.!!$F1 5087
1 TraesCS4A01G132800 chr4B 376139453 376144851 5398 True 1308.4 3214 91.098 1 5088 5 chr4B.!!$R1 5087
2 TraesCS4A01G132800 chr4D 301732832 301738323 5491 True 1472.0 2651 90.947 34 5088 5 chr4D.!!$R2 5054

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
427 479 0.098025 TGTAAATTTAGCGCGCCTGC 59.902 50.000 30.33 9.59 37.91 4.85 F
1924 1998 0.029300 AGATGTTTGTGTGCGTGTGC 59.971 50.000 0.00 0.00 43.20 4.57 F
1998 2332 0.032678 CTGCGTGACTAGCTATGGGG 59.967 60.000 0.00 0.00 35.28 4.96 F
2396 2742 1.000283 CGTTGCAGGAGAGACAGACTT 60.000 52.381 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 2010 0.264955 TCTCTACATGACCCCTCCCC 59.735 60.000 0.00 0.0 0.0 4.81 R
3248 3670 0.376152 GCCATCACGTCAGCATTCAG 59.624 55.000 0.00 0.0 0.0 3.02 R
3958 4418 1.301479 GAACGGTCCGAAAGTGGCT 60.301 57.895 20.51 0.0 0.0 4.75 R
4100 4560 0.034059 CGGAGTGAACTTGCTGGAGT 59.966 55.000 0.00 0.0 0.0 3.85 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 1.739049 CGCCAGATCTGAGACCTCC 59.261 63.158 24.62 2.57 0.00 4.30
96 99 1.383248 ACGCTTCCCCTGCCTATCT 60.383 57.895 0.00 0.00 0.00 1.98
128 136 2.545810 CTTCCTCCACCTTCTCTCCTT 58.454 52.381 0.00 0.00 0.00 3.36
131 139 1.274712 CTCCACCTTCTCTCCTTGCT 58.725 55.000 0.00 0.00 0.00 3.91
171 179 4.421479 CCTCCGACGAACAGCGCT 62.421 66.667 2.64 2.64 46.04 5.92
186 194 2.313374 GCTCGACGATCGTTTGCG 59.687 61.111 23.63 20.67 41.35 4.85
191 199 2.799540 GACGATCGTTTGCGGCTCC 61.800 63.158 23.63 1.81 38.89 4.70
283 307 7.776107 TGAATTTGGTGAACTATTTGTTGTGA 58.224 30.769 0.00 0.00 39.30 3.58
386 412 5.795441 GGTTCTATTTTGAGTGCGAAATGTC 59.205 40.000 0.00 0.00 38.32 3.06
412 464 4.610714 TGGGCGCGCACTGTGTAA 62.611 61.111 35.65 10.39 0.00 2.41
413 465 3.350612 GGGCGCGCACTGTGTAAA 61.351 61.111 34.42 0.00 0.00 2.01
414 466 2.686816 GGGCGCGCACTGTGTAAAT 61.687 57.895 34.42 0.00 0.00 1.40
415 467 1.209127 GGCGCGCACTGTGTAAATT 59.791 52.632 34.42 0.00 0.00 1.82
416 468 0.386731 GGCGCGCACTGTGTAAATTT 60.387 50.000 34.42 0.00 0.00 1.82
417 469 1.135916 GGCGCGCACTGTGTAAATTTA 60.136 47.619 34.42 0.00 0.00 1.40
418 470 2.166007 GCGCGCACTGTGTAAATTTAG 58.834 47.619 29.10 0.00 0.00 1.85
419 471 2.166007 CGCGCACTGTGTAAATTTAGC 58.834 47.619 8.75 0.00 0.00 3.09
420 472 2.166007 GCGCACTGTGTAAATTTAGCG 58.834 47.619 17.84 17.84 45.89 4.26
421 473 2.166007 CGCACTGTGTAAATTTAGCGC 58.834 47.619 9.86 0.00 37.43 5.92
422 474 2.166007 GCACTGTGTAAATTTAGCGCG 58.834 47.619 9.86 0.00 0.00 6.86
423 475 2.166007 CACTGTGTAAATTTAGCGCGC 58.834 47.619 26.66 26.66 0.00 6.86
424 476 1.129811 ACTGTGTAAATTTAGCGCGCC 59.870 47.619 30.33 10.43 0.00 6.53
425 477 1.396996 CTGTGTAAATTTAGCGCGCCT 59.603 47.619 30.33 17.79 0.00 5.52
426 478 1.129624 TGTGTAAATTTAGCGCGCCTG 59.870 47.619 30.33 0.00 0.00 4.85
427 479 0.098025 TGTAAATTTAGCGCGCCTGC 59.902 50.000 30.33 9.59 37.91 4.85
440 492 1.750930 GCCTGCTGGAGCTATAGCA 59.249 57.895 26.07 19.69 46.79 3.49
457 509 1.067516 AGCATCACGCCATATTTTGCC 59.932 47.619 0.00 0.00 44.04 4.52
467 519 0.817634 ATATTTTGCCGCGCCTGCTA 60.818 50.000 16.40 7.30 39.65 3.49
468 520 1.436195 TATTTTGCCGCGCCTGCTAG 61.436 55.000 16.40 0.00 39.65 3.42
469 521 3.770371 TATTTTGCCGCGCCTGCTAGA 62.770 52.381 16.40 6.01 39.65 2.43
481 533 2.894387 GCTAGAGCAAGCGCCCTG 60.894 66.667 2.29 2.58 41.59 4.45
482 534 2.894387 CTAGAGCAAGCGCCCTGC 60.894 66.667 21.21 21.21 46.98 4.85
528 580 5.802956 GGCACTGTAAAAATAATTTAGCGCA 59.197 36.000 11.47 0.00 0.00 6.09
564 616 2.544685 CCTGTTGGAGATGCTCTTACG 58.455 52.381 0.00 0.00 34.57 3.18
568 620 3.119459 TGTTGGAGATGCTCTTACGAGAC 60.119 47.826 0.00 0.00 39.74 3.36
581 633 0.249489 ACGAGACTCTTTTGCGTGCT 60.249 50.000 0.03 0.00 33.52 4.40
582 634 1.000607 ACGAGACTCTTTTGCGTGCTA 60.001 47.619 0.03 0.00 33.52 3.49
733 785 3.422417 TCTAAGACGATTTCAGAGGCG 57.578 47.619 0.00 0.00 0.00 5.52
876 928 5.827797 TCAAAGATTTACAGGGCCATACATC 59.172 40.000 6.18 6.10 0.00 3.06
1000 1062 7.569240 AGAAGAAACCAAGAAGAAGAAGAAGA 58.431 34.615 0.00 0.00 0.00 2.87
1001 1063 8.217111 AGAAGAAACCAAGAAGAAGAAGAAGAT 58.783 33.333 0.00 0.00 0.00 2.40
1006 1068 6.777782 ACCAAGAAGAAGAAGAAGATGATGT 58.222 36.000 0.00 0.00 0.00 3.06
1177 1239 4.667573 AGGGAAGAGAAAAAGGAATGACC 58.332 43.478 0.00 0.00 39.35 4.02
1333 1399 3.855159 GGTAAGTGATCACCGCCTT 57.145 52.632 22.21 12.22 0.00 4.35
1349 1415 2.613691 GCCTTGTTTTCTGATGGCATG 58.386 47.619 3.81 0.00 40.04 4.06
1350 1416 2.613691 CCTTGTTTTCTGATGGCATGC 58.386 47.619 9.90 9.90 0.00 4.06
1351 1417 2.232941 CCTTGTTTTCTGATGGCATGCT 59.767 45.455 18.92 0.00 0.00 3.79
1352 1418 3.250744 CTTGTTTTCTGATGGCATGCTG 58.749 45.455 18.92 1.19 0.00 4.41
1353 1419 2.516906 TGTTTTCTGATGGCATGCTGA 58.483 42.857 18.92 4.91 0.00 4.26
1417 1483 3.519107 TCAGATAACATGTCAGGCAAGGA 59.481 43.478 0.00 0.00 0.00 3.36
1424 1490 3.611674 TCAGGCAAGGACGCGACA 61.612 61.111 15.93 0.00 0.00 4.35
1612 1678 7.052873 AGATGAGGATGTGATAAGGAAAGTTG 58.947 38.462 0.00 0.00 0.00 3.16
1628 1694 4.529716 AAGTTGGGGTTAGGTGAAGAAA 57.470 40.909 0.00 0.00 0.00 2.52
1646 1712 9.834628 GTGAAGAAAACGAATTATAACCATTGA 57.165 29.630 0.00 0.00 0.00 2.57
1754 1824 3.871485 AGAGCTCATGTGACTGGAATTC 58.129 45.455 17.77 0.00 0.00 2.17
1914 1988 4.780021 ACCTGGACATAGAGAGATGTTTGT 59.220 41.667 0.00 0.00 40.18 2.83
1924 1998 0.029300 AGATGTTTGTGTGCGTGTGC 59.971 50.000 0.00 0.00 43.20 4.57
1934 2008 4.803426 GCGTGTGCGGAGAGGAGG 62.803 72.222 0.00 0.00 38.78 4.30
1935 2009 4.135153 CGTGTGCGGAGAGGAGGG 62.135 72.222 0.00 0.00 0.00 4.30
1936 2010 3.775654 GTGTGCGGAGAGGAGGGG 61.776 72.222 0.00 0.00 0.00 4.79
1952 2026 3.987638 GGGGGAGGGGTCATGTAG 58.012 66.667 0.00 0.00 0.00 2.74
1953 2027 1.316969 GGGGGAGGGGTCATGTAGA 59.683 63.158 0.00 0.00 0.00 2.59
1954 2028 0.764752 GGGGGAGGGGTCATGTAGAG 60.765 65.000 0.00 0.00 0.00 2.43
1955 2029 0.264955 GGGGAGGGGTCATGTAGAGA 59.735 60.000 0.00 0.00 0.00 3.10
1956 2030 1.710816 GGGAGGGGTCATGTAGAGAG 58.289 60.000 0.00 0.00 0.00 3.20
1957 2031 1.044611 GGAGGGGTCATGTAGAGAGC 58.955 60.000 0.00 0.00 0.00 4.09
1958 2032 1.689575 GGAGGGGTCATGTAGAGAGCA 60.690 57.143 0.00 0.00 35.30 4.26
1959 2033 2.111384 GAGGGGTCATGTAGAGAGCAA 58.889 52.381 0.00 0.00 35.30 3.91
1960 2034 2.102252 GAGGGGTCATGTAGAGAGCAAG 59.898 54.545 0.00 0.00 35.30 4.01
1961 2035 1.139853 GGGGTCATGTAGAGAGCAAGG 59.860 57.143 0.00 0.00 35.30 3.61
1962 2036 1.834263 GGGTCATGTAGAGAGCAAGGT 59.166 52.381 0.00 0.00 35.30 3.50
1963 2037 2.419297 GGGTCATGTAGAGAGCAAGGTG 60.419 54.545 0.00 0.00 35.30 4.00
1964 2038 2.497675 GGTCATGTAGAGAGCAAGGTGA 59.502 50.000 0.00 0.00 33.87 4.02
1965 2039 3.430098 GGTCATGTAGAGAGCAAGGTGAG 60.430 52.174 0.00 0.00 33.87 3.51
1966 2040 2.762887 TCATGTAGAGAGCAAGGTGAGG 59.237 50.000 0.00 0.00 0.00 3.86
1967 2041 2.604912 TGTAGAGAGCAAGGTGAGGA 57.395 50.000 0.00 0.00 0.00 3.71
1968 2042 2.451490 TGTAGAGAGCAAGGTGAGGAG 58.549 52.381 0.00 0.00 0.00 3.69
1969 2043 1.754226 GTAGAGAGCAAGGTGAGGAGG 59.246 57.143 0.00 0.00 0.00 4.30
1970 2044 0.617249 AGAGAGCAAGGTGAGGAGGG 60.617 60.000 0.00 0.00 0.00 4.30
1971 2045 1.614824 AGAGCAAGGTGAGGAGGGG 60.615 63.158 0.00 0.00 0.00 4.79
1980 2314 4.439901 GAGGAGGGGAAGGGGGCT 62.440 72.222 0.00 0.00 0.00 5.19
1998 2332 0.032678 CTGCGTGACTAGCTATGGGG 59.967 60.000 0.00 0.00 35.28 4.96
2053 2399 3.352648 TGATGCGGAGTGATCGGATATA 58.647 45.455 0.00 0.00 38.71 0.86
2102 2448 1.107114 GAGCTGAATGACGAGGAGGA 58.893 55.000 0.00 0.00 0.00 3.71
2106 2452 1.821753 CTGAATGACGAGGAGGACAGT 59.178 52.381 0.00 0.00 0.00 3.55
2151 2497 2.552373 GGGGGATAAGGCGAAACATAGG 60.552 54.545 0.00 0.00 0.00 2.57
2152 2498 2.370849 GGGGATAAGGCGAAACATAGGA 59.629 50.000 0.00 0.00 0.00 2.94
2154 2500 4.065789 GGGATAAGGCGAAACATAGGAAG 58.934 47.826 0.00 0.00 0.00 3.46
2155 2501 4.065789 GGATAAGGCGAAACATAGGAAGG 58.934 47.826 0.00 0.00 0.00 3.46
2156 2502 4.444449 GGATAAGGCGAAACATAGGAAGGT 60.444 45.833 0.00 0.00 0.00 3.50
2157 2503 2.693267 AGGCGAAACATAGGAAGGTC 57.307 50.000 0.00 0.00 0.00 3.85
2158 2504 2.188817 AGGCGAAACATAGGAAGGTCT 58.811 47.619 0.00 0.00 0.00 3.85
2159 2505 2.572104 AGGCGAAACATAGGAAGGTCTT 59.428 45.455 0.00 0.00 0.00 3.01
2160 2506 3.009143 AGGCGAAACATAGGAAGGTCTTT 59.991 43.478 0.00 0.00 0.00 2.52
2161 2507 3.756963 GGCGAAACATAGGAAGGTCTTTT 59.243 43.478 0.00 0.00 0.00 2.27
2162 2508 4.217767 GGCGAAACATAGGAAGGTCTTTTT 59.782 41.667 0.00 0.00 0.00 1.94
2233 2579 3.222173 TGTGGCTTGGCTAAAGAAAGA 57.778 42.857 4.17 0.00 38.24 2.52
2234 2580 3.766545 TGTGGCTTGGCTAAAGAAAGAT 58.233 40.909 4.17 0.00 38.24 2.40
2235 2581 4.151883 TGTGGCTTGGCTAAAGAAAGATT 58.848 39.130 4.17 0.00 38.24 2.40
2236 2582 4.588528 TGTGGCTTGGCTAAAGAAAGATTT 59.411 37.500 4.17 0.00 38.24 2.17
2237 2583 5.070313 TGTGGCTTGGCTAAAGAAAGATTTT 59.930 36.000 4.17 0.00 38.24 1.82
2238 2584 5.991606 GTGGCTTGGCTAAAGAAAGATTTTT 59.008 36.000 4.17 0.00 38.24 1.94
2239 2585 5.990996 TGGCTTGGCTAAAGAAAGATTTTTG 59.009 36.000 4.17 0.00 38.24 2.44
2240 2586 6.183360 TGGCTTGGCTAAAGAAAGATTTTTGA 60.183 34.615 4.17 0.00 38.24 2.69
2241 2587 6.705825 GGCTTGGCTAAAGAAAGATTTTTGAA 59.294 34.615 4.17 0.00 38.24 2.69
2242 2588 7.226523 GGCTTGGCTAAAGAAAGATTTTTGAAA 59.773 33.333 4.17 0.00 38.24 2.69
2243 2589 8.064222 GCTTGGCTAAAGAAAGATTTTTGAAAC 58.936 33.333 4.17 0.00 38.24 2.78
2244 2590 9.317936 CTTGGCTAAAGAAAGATTTTTGAAACT 57.682 29.630 0.00 0.00 38.24 2.66
2246 2592 9.965824 TGGCTAAAGAAAGATTTTTGAAACTAG 57.034 29.630 0.00 0.00 0.00 2.57
2247 2593 8.916654 GGCTAAAGAAAGATTTTTGAAACTAGC 58.083 33.333 0.00 0.00 0.00 3.42
2248 2594 9.684448 GCTAAAGAAAGATTTTTGAAACTAGCT 57.316 29.630 0.00 0.00 0.00 3.32
2251 2597 8.877808 AAGAAAGATTTTTGAAACTAGCTTGG 57.122 30.769 0.00 0.00 0.00 3.61
2252 2598 6.925718 AGAAAGATTTTTGAAACTAGCTTGGC 59.074 34.615 0.00 0.00 0.00 4.52
2253 2599 6.410942 AAGATTTTTGAAACTAGCTTGGCT 57.589 33.333 0.00 0.00 43.41 4.75
2254 2600 7.524717 AAGATTTTTGAAACTAGCTTGGCTA 57.475 32.000 0.00 0.00 40.44 3.93
2255 2601 7.524717 AGATTTTTGAAACTAGCTTGGCTAA 57.475 32.000 0.00 0.00 40.82 3.09
2256 2602 7.951591 AGATTTTTGAAACTAGCTTGGCTAAA 58.048 30.769 0.00 0.00 40.82 1.85
2257 2603 8.084684 AGATTTTTGAAACTAGCTTGGCTAAAG 58.915 33.333 0.00 0.00 40.82 1.85
2258 2604 6.952773 TTTTGAAACTAGCTTGGCTAAAGA 57.047 33.333 0.00 0.00 40.82 2.52
2259 2605 6.952773 TTTGAAACTAGCTTGGCTAAAGAA 57.047 33.333 0.00 0.00 40.82 2.52
2260 2606 6.952773 TTGAAACTAGCTTGGCTAAAGAAA 57.047 33.333 0.00 0.00 40.82 2.52
2261 2607 6.560253 TGAAACTAGCTTGGCTAAAGAAAG 57.440 37.500 0.00 3.18 40.82 2.62
2262 2608 6.062095 TGAAACTAGCTTGGCTAAAGAAAGT 58.938 36.000 0.00 3.68 40.82 2.66
2312 2658 4.947147 TGTTGGTCGGGCTGTGGC 62.947 66.667 0.00 0.00 37.82 5.01
2396 2742 1.000283 CGTTGCAGGAGAGACAGACTT 60.000 52.381 0.00 0.00 0.00 3.01
2438 2784 2.308570 TGACATCCAGGTAAACCATGCT 59.691 45.455 1.26 0.00 38.89 3.79
2482 2828 5.823570 TGAAATTTCCCCTCGCGATTTATAA 59.176 36.000 10.36 2.17 0.00 0.98
2498 2847 7.431084 GCGATTTATAAATGGAAACGTTGACAT 59.569 33.333 20.55 6.87 40.16 3.06
2543 2910 1.902918 GTGCAGGTGGGTGATTGCA 60.903 57.895 0.00 0.00 43.62 4.08
2572 2939 1.745320 TAGAGAGGCCCGGCGATTTC 61.745 60.000 9.30 0.01 0.00 2.17
2605 2972 1.808945 CAGAAGAACACAGATGGCACC 59.191 52.381 0.00 0.00 0.00 5.01
2614 2981 1.066858 ACAGATGGCACCTACAAGACG 60.067 52.381 0.00 0.00 0.00 4.18
2663 3030 7.519809 CGTCTCATTCATTGTTCCTGTTGTTTA 60.520 37.037 0.00 0.00 0.00 2.01
2665 3032 8.859090 TCTCATTCATTGTTCCTGTTGTTTATT 58.141 29.630 0.00 0.00 0.00 1.40
2666 3033 9.480053 CTCATTCATTGTTCCTGTTGTTTATTT 57.520 29.630 0.00 0.00 0.00 1.40
2667 3034 9.829507 TCATTCATTGTTCCTGTTGTTTATTTT 57.170 25.926 0.00 0.00 0.00 1.82
2670 3037 9.883142 TTCATTGTTCCTGTTGTTTATTTTTCT 57.117 25.926 0.00 0.00 0.00 2.52
2671 3038 9.883142 TCATTGTTCCTGTTGTTTATTTTTCTT 57.117 25.926 0.00 0.00 0.00 2.52
2674 3041 9.936759 TTGTTCCTGTTGTTTATTTTTCTTTCT 57.063 25.926 0.00 0.00 0.00 2.52
2675 3042 9.936759 TGTTCCTGTTGTTTATTTTTCTTTCTT 57.063 25.926 0.00 0.00 0.00 2.52
2831 3221 6.708285 ACACCATACCTTACAAAGAGGTTAG 58.292 40.000 0.59 0.00 45.06 2.34
2855 3248 4.868171 TCGGTCGTTCATTCCTCAATTAAG 59.132 41.667 0.00 0.00 0.00 1.85
3001 3402 3.462678 GAGTCGGACCTCCTGGCC 61.463 72.222 4.14 0.00 36.63 5.36
3155 3571 1.626356 CCAGATCGGCAAGGGAGGAA 61.626 60.000 0.00 0.00 0.00 3.36
3207 3628 5.491982 AGCAAGAAAAGGTAATGAGTCGAT 58.508 37.500 0.00 0.00 0.00 3.59
3248 3670 3.248266 GCACATCCAAAGAGAACATTGC 58.752 45.455 0.00 0.00 0.00 3.56
3348 3770 2.353803 GGAGGCTCACTTACAACGATGT 60.354 50.000 17.69 3.12 43.74 3.06
3506 3963 2.228138 AGTTTTGGTGCAGCAACATG 57.772 45.000 29.69 0.00 28.36 3.21
3595 4052 3.133365 AAGGCTGGCCACCGAGTTT 62.133 57.895 14.39 0.00 38.92 2.66
3838 4295 1.612395 CCGCCTTCTTGGAGAGAGCT 61.612 60.000 0.00 0.00 37.90 4.09
3934 4394 2.356313 ACAGAAGCGCCACAGACG 60.356 61.111 2.29 0.00 0.00 4.18
3940 4400 2.755542 AAGCGCCACAGACGAGTGAG 62.756 60.000 2.29 4.55 42.05 3.51
3941 4401 2.807045 CGCCACAGACGAGTGAGC 60.807 66.667 8.54 8.86 42.05 4.26
3952 4412 3.781770 GAGTGAGCCAGGCGATCCG 62.782 68.421 5.55 0.00 37.47 4.18
4064 4524 4.434725 CGTTCATGGTGAAGTCGAATTCTG 60.435 45.833 24.25 14.98 37.00 3.02
4066 4526 1.808411 TGGTGAAGTCGAATTCTGCC 58.192 50.000 24.25 23.57 0.00 4.85
4100 4560 2.611971 CGAGAATGAAGGACGAACCCAA 60.612 50.000 0.00 0.00 40.05 4.12
4140 4608 2.616842 GTCCATTTTGTGTCGTGTCCTT 59.383 45.455 0.00 0.00 0.00 3.36
4161 4629 4.790765 TGACTCCCATTATATCGCTCAG 57.209 45.455 0.00 0.00 0.00 3.35
4280 4776 6.990798 TCATCAAATGTATGCAAGTTCCAAA 58.009 32.000 0.00 0.00 0.00 3.28
4281 4777 7.440198 TCATCAAATGTATGCAAGTTCCAAAA 58.560 30.769 0.00 0.00 0.00 2.44
4311 4807 7.394641 TCACAGACTTCAGATATACACAAGACT 59.605 37.037 0.00 0.00 0.00 3.24
4365 4863 4.223556 TGCCAAGAAATAACATACCGGA 57.776 40.909 9.46 0.00 0.00 5.14
4402 4900 4.268405 CCACAACAGTTGTTTTCTGATTGC 59.732 41.667 16.70 0.00 43.23 3.56
4407 4905 4.278419 ACAGTTGTTTTCTGATTGCTACCC 59.722 41.667 0.00 0.00 36.81 3.69
4498 4996 5.090757 TCTTAACACGTATGTAGCTCGTTG 58.909 41.667 0.00 0.00 38.45 4.10
4567 5065 4.082571 ACAATTACTGCATCAGCCAACTTC 60.083 41.667 0.00 0.00 41.13 3.01
4574 5072 2.787994 CATCAGCCAACTTCAAGAGGT 58.212 47.619 0.00 0.00 0.00 3.85
4620 5118 2.168521 GCAGCAGGACCTACAGTATGAA 59.831 50.000 0.00 0.00 39.69 2.57
4631 5129 1.340308 ACAGTATGAATGGCAGCTGCA 60.340 47.619 37.63 24.48 40.55 4.41
4753 5251 2.025155 ACCAAATGTGTGCCGTTTGTA 58.975 42.857 6.34 0.00 44.95 2.41
4788 5499 2.781681 AACTAGCGGGTGTGCTTTAT 57.218 45.000 0.00 0.00 44.46 1.40
4877 5588 0.109919 GAACCGTCGGTTGATTTGCC 60.110 55.000 33.41 13.71 46.95 4.52
5039 5750 7.586714 TCTGTTCAAGCATATCATATTAGCG 57.413 36.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.039785 TGGAGGTCTCAGATCTGGCG 61.040 60.000 22.42 13.71 0.00 5.69
76 79 2.701163 GATAGGCAGGGGAAGCGTCG 62.701 65.000 0.00 0.00 0.00 5.12
78 81 1.383248 AGATAGGCAGGGGAAGCGT 60.383 57.895 0.00 0.00 0.00 5.07
171 179 3.176578 GCCGCAAACGATCGTCGA 61.177 61.111 22.98 0.00 43.74 4.20
191 199 3.645975 AAACACCTTGTCGGCGCG 61.646 61.111 0.00 0.00 35.61 6.86
197 205 2.596862 GCGTTTTGTCAAACACCTTGTC 59.403 45.455 0.00 0.00 42.30 3.18
221 229 7.759489 AAAGTTGAAGCAATACATACCTTGA 57.241 32.000 0.00 0.00 0.00 3.02
402 454 2.166007 CGCGCTAAATTTACACAGTGC 58.834 47.619 5.56 12.26 40.31 4.40
403 455 2.166007 GCGCGCTAAATTTACACAGTG 58.834 47.619 26.67 0.00 0.00 3.66
404 456 1.129811 GGCGCGCTAAATTTACACAGT 59.870 47.619 32.29 0.00 0.00 3.55
405 457 1.396996 AGGCGCGCTAAATTTACACAG 59.603 47.619 32.29 0.00 0.00 3.66
406 458 1.129624 CAGGCGCGCTAAATTTACACA 59.870 47.619 32.29 0.00 0.00 3.72
407 459 1.810197 CAGGCGCGCTAAATTTACAC 58.190 50.000 32.29 9.98 0.00 2.90
408 460 0.098025 GCAGGCGCGCTAAATTTACA 59.902 50.000 32.29 0.00 0.00 2.41
409 461 0.377203 AGCAGGCGCGCTAAATTTAC 59.623 50.000 32.29 11.63 45.49 2.01
410 462 0.376852 CAGCAGGCGCGCTAAATTTA 59.623 50.000 32.29 0.00 45.49 1.40
411 463 1.137404 CAGCAGGCGCGCTAAATTT 59.863 52.632 32.29 9.28 45.49 1.82
412 464 2.764314 CCAGCAGGCGCGCTAAATT 61.764 57.895 32.29 10.43 45.49 1.82
413 465 3.204827 CCAGCAGGCGCGCTAAAT 61.205 61.111 32.29 12.41 45.49 1.40
414 466 4.386951 TCCAGCAGGCGCGCTAAA 62.387 61.111 32.29 6.90 45.49 1.85
415 467 4.819761 CTCCAGCAGGCGCGCTAA 62.820 66.667 32.29 7.65 45.49 3.09
420 472 1.373999 CTATAGCTCCAGCAGGCGC 60.374 63.158 1.15 1.15 46.09 6.53
421 473 1.373999 GCTATAGCTCCAGCAGGCG 60.374 63.158 17.75 0.00 45.16 5.52
422 474 1.750930 TGCTATAGCTCCAGCAGGC 59.249 57.895 24.61 2.27 42.68 4.85
426 478 1.707632 CGTGATGCTATAGCTCCAGC 58.292 55.000 24.61 8.92 42.66 4.85
427 479 1.671261 GGCGTGATGCTATAGCTCCAG 60.671 57.143 24.61 15.28 45.43 3.86
495 547 5.897377 ATTTTTACAGTGCCGAAATAGCT 57.103 34.783 0.00 0.00 0.00 3.32
534 586 3.047280 CCAACAGGCGCGCAACTA 61.047 61.111 34.42 0.00 0.00 2.24
535 587 4.927782 TCCAACAGGCGCGCAACT 62.928 61.111 34.42 19.33 0.00 3.16
564 616 4.031878 GTGTATAGCACGCAAAAGAGTCTC 59.968 45.833 0.00 0.00 38.45 3.36
733 785 4.274950 TGAAACGGAAACAATCTGGAGTTC 59.725 41.667 0.00 0.00 38.87 3.01
876 928 4.589908 ACCATGCTAGTTACTTTTCCAGG 58.410 43.478 0.00 0.00 0.00 4.45
1000 1062 5.124645 GGATCTCTTCTTTGCAGACATCAT 58.875 41.667 0.00 0.00 0.00 2.45
1001 1063 4.019950 TGGATCTCTTCTTTGCAGACATCA 60.020 41.667 0.00 0.00 0.00 3.07
1006 1068 4.224594 AGACATGGATCTCTTCTTTGCAGA 59.775 41.667 0.00 0.00 0.00 4.26
1177 1239 6.991938 TGATGGAAATTTTTACCTGGACTTG 58.008 36.000 0.00 0.00 0.00 3.16
1319 1385 1.880027 GAAAACAAGGCGGTGATCACT 59.120 47.619 24.50 2.45 0.00 3.41
1333 1399 2.516906 TCAGCATGCCATCAGAAAACA 58.483 42.857 15.66 0.00 34.76 2.83
1349 1415 1.970114 ACACACAGGCAGCATCAGC 60.970 57.895 0.00 0.00 42.56 4.26
1350 1416 1.873863 CACACACAGGCAGCATCAG 59.126 57.895 0.00 0.00 0.00 2.90
1351 1417 2.263021 GCACACACAGGCAGCATCA 61.263 57.895 0.00 0.00 0.00 3.07
1352 1418 1.592400 ATGCACACACAGGCAGCATC 61.592 55.000 0.00 0.00 41.70 3.91
1353 1419 1.605451 ATGCACACACAGGCAGCAT 60.605 52.632 0.00 0.00 44.24 3.79
1417 1483 2.669808 GATCTGCTCCGATGTCGCGT 62.670 60.000 5.77 0.00 38.18 6.01
1424 1490 1.614996 AGTCGATGATCTGCTCCGAT 58.385 50.000 0.00 0.00 0.00 4.18
1524 1590 2.407090 CACTCTCTCATCAACGCAACA 58.593 47.619 0.00 0.00 0.00 3.33
1580 1646 4.888326 ATCACATCCTCATCTTCTAGCC 57.112 45.455 0.00 0.00 0.00 3.93
1612 1678 3.130280 TCGTTTTCTTCACCTAACCCC 57.870 47.619 0.00 0.00 0.00 4.95
1825 1895 3.383825 TCTCTTTACGGCCATCTCCTTAC 59.616 47.826 2.24 0.00 0.00 2.34
1888 1962 3.303938 CATCTCTCTATGTCCAGGTGGT 58.696 50.000 0.00 0.00 36.34 4.16
1914 1988 4.662961 CCTCTCCGCACACGCACA 62.663 66.667 0.00 0.00 38.40 4.57
1935 2009 0.764752 CTCTACATGACCCCTCCCCC 60.765 65.000 0.00 0.00 0.00 5.40
1936 2010 0.264955 TCTCTACATGACCCCTCCCC 59.735 60.000 0.00 0.00 0.00 4.81
1937 2011 1.710816 CTCTCTACATGACCCCTCCC 58.289 60.000 0.00 0.00 0.00 4.30
1938 2012 1.044611 GCTCTCTACATGACCCCTCC 58.955 60.000 0.00 0.00 0.00 4.30
1939 2013 1.781786 TGCTCTCTACATGACCCCTC 58.218 55.000 0.00 0.00 0.00 4.30
1940 2014 2.114616 CTTGCTCTCTACATGACCCCT 58.885 52.381 0.00 0.00 0.00 4.79
1941 2015 1.139853 CCTTGCTCTCTACATGACCCC 59.860 57.143 0.00 0.00 0.00 4.95
1942 2016 1.834263 ACCTTGCTCTCTACATGACCC 59.166 52.381 0.00 0.00 0.00 4.46
1943 2017 2.497675 TCACCTTGCTCTCTACATGACC 59.502 50.000 0.00 0.00 0.00 4.02
1944 2018 3.430098 CCTCACCTTGCTCTCTACATGAC 60.430 52.174 0.00 0.00 0.00 3.06
1945 2019 2.762887 CCTCACCTTGCTCTCTACATGA 59.237 50.000 0.00 0.00 0.00 3.07
1946 2020 2.762887 TCCTCACCTTGCTCTCTACATG 59.237 50.000 0.00 0.00 0.00 3.21
1947 2021 3.030291 CTCCTCACCTTGCTCTCTACAT 58.970 50.000 0.00 0.00 0.00 2.29
1948 2022 2.451490 CTCCTCACCTTGCTCTCTACA 58.549 52.381 0.00 0.00 0.00 2.74
1949 2023 1.754226 CCTCCTCACCTTGCTCTCTAC 59.246 57.143 0.00 0.00 0.00 2.59
1950 2024 1.342474 CCCTCCTCACCTTGCTCTCTA 60.342 57.143 0.00 0.00 0.00 2.43
1951 2025 0.617249 CCCTCCTCACCTTGCTCTCT 60.617 60.000 0.00 0.00 0.00 3.10
1952 2026 1.621672 CCCCTCCTCACCTTGCTCTC 61.622 65.000 0.00 0.00 0.00 3.20
1953 2027 1.614824 CCCCTCCTCACCTTGCTCT 60.615 63.158 0.00 0.00 0.00 4.09
1954 2028 1.201429 TTCCCCTCCTCACCTTGCTC 61.201 60.000 0.00 0.00 0.00 4.26
1955 2029 1.151810 TTCCCCTCCTCACCTTGCT 60.152 57.895 0.00 0.00 0.00 3.91
1956 2030 1.301293 CTTCCCCTCCTCACCTTGC 59.699 63.158 0.00 0.00 0.00 4.01
1957 2031 1.566298 CCCTTCCCCTCCTCACCTTG 61.566 65.000 0.00 0.00 0.00 3.61
1958 2032 1.229984 CCCTTCCCCTCCTCACCTT 60.230 63.158 0.00 0.00 0.00 3.50
1959 2033 2.456840 CCCTTCCCCTCCTCACCT 59.543 66.667 0.00 0.00 0.00 4.00
1960 2034 2.692741 CCCCTTCCCCTCCTCACC 60.693 72.222 0.00 0.00 0.00 4.02
1961 2035 2.692741 CCCCCTTCCCCTCCTCAC 60.693 72.222 0.00 0.00 0.00 3.51
1962 2036 4.760220 GCCCCCTTCCCCTCCTCA 62.760 72.222 0.00 0.00 0.00 3.86
1963 2037 4.439901 AGCCCCCTTCCCCTCCTC 62.440 72.222 0.00 0.00 0.00 3.71
1964 2038 4.767892 CAGCCCCCTTCCCCTCCT 62.768 72.222 0.00 0.00 0.00 3.69
1971 2045 2.579684 CTAGTCACGCAGCCCCCTTC 62.580 65.000 0.00 0.00 0.00 3.46
1980 2314 0.686441 ACCCCATAGCTAGTCACGCA 60.686 55.000 0.00 0.00 0.00 5.24
1984 2318 0.341961 ACCCACCCCATAGCTAGTCA 59.658 55.000 0.00 0.00 0.00 3.41
1985 2319 0.759346 CACCCACCCCATAGCTAGTC 59.241 60.000 0.00 0.00 0.00 2.59
1998 2332 1.603739 GCTCTTTGACCCCACCCAC 60.604 63.158 0.00 0.00 0.00 4.61
2053 2399 2.756283 CGTCGCCCTCTTCTCCCT 60.756 66.667 0.00 0.00 0.00 4.20
2080 2426 2.023673 CTCCTCGTCATTCAGCTCTCT 58.976 52.381 0.00 0.00 0.00 3.10
2159 2505 5.362143 TCACATGAGTTCCATCCAACAAAAA 59.638 36.000 0.00 0.00 31.94 1.94
2160 2506 4.892345 TCACATGAGTTCCATCCAACAAAA 59.108 37.500 0.00 0.00 31.94 2.44
2161 2507 4.468713 TCACATGAGTTCCATCCAACAAA 58.531 39.130 0.00 0.00 31.94 2.83
2162 2508 4.097551 TCACATGAGTTCCATCCAACAA 57.902 40.909 0.00 0.00 31.94 2.83
2163 2509 3.786368 TCACATGAGTTCCATCCAACA 57.214 42.857 0.00 0.00 31.94 3.33
2164 2510 4.326826 TCTTCACATGAGTTCCATCCAAC 58.673 43.478 0.00 0.00 31.94 3.77
2233 2579 7.951591 TCTTTAGCCAAGCTAGTTTCAAAAAT 58.048 30.769 0.00 0.00 42.34 1.82
2234 2580 7.341445 TCTTTAGCCAAGCTAGTTTCAAAAA 57.659 32.000 0.00 0.00 42.34 1.94
2235 2581 6.952773 TCTTTAGCCAAGCTAGTTTCAAAA 57.047 33.333 0.00 0.00 42.34 2.44
2236 2582 6.952773 TTCTTTAGCCAAGCTAGTTTCAAA 57.047 33.333 0.00 0.00 42.34 2.69
2237 2583 6.546034 ACTTTCTTTAGCCAAGCTAGTTTCAA 59.454 34.615 0.00 0.00 42.34 2.69
2238 2584 6.017109 CACTTTCTTTAGCCAAGCTAGTTTCA 60.017 38.462 0.00 0.00 42.34 2.69
2239 2585 6.204882 TCACTTTCTTTAGCCAAGCTAGTTTC 59.795 38.462 0.00 0.00 42.34 2.78
2240 2586 6.017026 GTCACTTTCTTTAGCCAAGCTAGTTT 60.017 38.462 0.00 0.00 42.34 2.66
2241 2587 5.470437 GTCACTTTCTTTAGCCAAGCTAGTT 59.530 40.000 0.00 0.00 42.34 2.24
2242 2588 4.998033 GTCACTTTCTTTAGCCAAGCTAGT 59.002 41.667 0.00 0.00 42.34 2.57
2243 2589 4.393371 GGTCACTTTCTTTAGCCAAGCTAG 59.607 45.833 0.00 0.00 42.34 3.42
2244 2590 4.202419 TGGTCACTTTCTTTAGCCAAGCTA 60.202 41.667 0.00 0.00 40.44 3.32
2245 2591 3.149981 GGTCACTTTCTTTAGCCAAGCT 58.850 45.455 0.00 0.00 43.41 3.74
2246 2592 2.884639 TGGTCACTTTCTTTAGCCAAGC 59.115 45.455 0.00 0.00 31.70 4.01
2247 2593 3.503748 CCTGGTCACTTTCTTTAGCCAAG 59.496 47.826 0.00 0.00 0.00 3.61
2248 2594 3.486383 CCTGGTCACTTTCTTTAGCCAA 58.514 45.455 0.00 0.00 0.00 4.52
2249 2595 2.814097 GCCTGGTCACTTTCTTTAGCCA 60.814 50.000 0.00 0.00 0.00 4.75
2250 2596 1.813178 GCCTGGTCACTTTCTTTAGCC 59.187 52.381 0.00 0.00 0.00 3.93
2251 2597 2.504367 TGCCTGGTCACTTTCTTTAGC 58.496 47.619 0.00 0.00 0.00 3.09
2252 2598 4.023707 CAGTTGCCTGGTCACTTTCTTTAG 60.024 45.833 0.00 0.00 34.90 1.85
2253 2599 3.882888 CAGTTGCCTGGTCACTTTCTTTA 59.117 43.478 0.00 0.00 34.90 1.85
2254 2600 2.689983 CAGTTGCCTGGTCACTTTCTTT 59.310 45.455 0.00 0.00 34.90 2.52
2255 2601 2.301346 CAGTTGCCTGGTCACTTTCTT 58.699 47.619 0.00 0.00 34.90 2.52
2256 2602 1.212935 ACAGTTGCCTGGTCACTTTCT 59.787 47.619 0.00 0.00 43.36 2.52
2257 2603 1.680338 ACAGTTGCCTGGTCACTTTC 58.320 50.000 0.00 0.00 43.36 2.62
2258 2604 2.172717 AGTACAGTTGCCTGGTCACTTT 59.827 45.455 0.00 0.00 43.36 2.66
2259 2605 1.768870 AGTACAGTTGCCTGGTCACTT 59.231 47.619 0.00 0.00 43.36 3.16
2260 2606 1.344763 GAGTACAGTTGCCTGGTCACT 59.655 52.381 0.00 0.00 43.36 3.41
2261 2607 1.070134 TGAGTACAGTTGCCTGGTCAC 59.930 52.381 0.00 0.00 43.36 3.67
2262 2608 1.419381 TGAGTACAGTTGCCTGGTCA 58.581 50.000 0.00 0.00 43.36 4.02
2275 2621 6.348050 CCAACAAGAAAGAGATGCTTGAGTAC 60.348 42.308 0.00 0.00 41.03 2.73
2312 2658 0.389296 TGTGCTCCCGATACACAACG 60.389 55.000 0.00 0.00 41.11 4.10
2368 2714 0.534203 TCTCCTGCAACGGGACAAAC 60.534 55.000 0.00 0.00 33.41 2.93
2396 2742 1.573932 CGGCATCGCAAACAACTCA 59.426 52.632 0.00 0.00 0.00 3.41
2438 2784 1.565156 GACGTGCCTTGTTCATGCGA 61.565 55.000 0.00 0.00 0.00 5.10
2451 2797 1.468914 GAGGGGAAATTTCAGACGTGC 59.531 52.381 19.49 0.55 0.00 5.34
2482 2828 7.657336 ACAAGAAATATGTCAACGTTTCCATT 58.343 30.769 13.06 0.99 32.43 3.16
2498 2847 8.298854 CACCATGTCAAGATGAAACAAGAAATA 58.701 33.333 0.00 0.00 0.00 1.40
2543 2910 2.050934 GCCTCTCTACCCGTTCCGT 61.051 63.158 0.00 0.00 0.00 4.69
2572 2939 0.731514 TCTTCTGCCTTAACGTCGCG 60.732 55.000 0.00 0.00 0.00 5.87
2605 2972 3.483922 CGAATTGCTCTAGCGTCTTGTAG 59.516 47.826 0.00 0.00 45.83 2.74
2614 2981 2.468831 CTGACCTCGAATTGCTCTAGC 58.531 52.381 0.00 0.00 42.50 3.42
2831 3221 2.074547 TTGAGGAATGAACGACCGAC 57.925 50.000 0.00 0.00 0.00 4.79
2894 3295 5.481200 TGCACCAAAAACAAACATTCATG 57.519 34.783 0.00 0.00 0.00 3.07
2895 3296 4.575645 CCTGCACCAAAAACAAACATTCAT 59.424 37.500 0.00 0.00 0.00 2.57
2896 3297 3.937706 CCTGCACCAAAAACAAACATTCA 59.062 39.130 0.00 0.00 0.00 2.57
2897 3298 3.242706 GCCTGCACCAAAAACAAACATTC 60.243 43.478 0.00 0.00 0.00 2.67
3001 3402 1.571460 GAGTTGCTTGTGACGCCAG 59.429 57.895 0.00 0.00 0.00 4.85
3155 3571 2.176273 GCGATGGCGTGCTTCTGAT 61.176 57.895 0.00 0.00 40.36 2.90
3207 3628 2.799562 GCATTGGATCGATGTCGTCTCA 60.800 50.000 0.54 0.00 40.80 3.27
3248 3670 0.376152 GCCATCACGTCAGCATTCAG 59.624 55.000 0.00 0.00 0.00 3.02
3445 3867 8.531982 GCATCCATGATTGTTACTCCTACTATA 58.468 37.037 0.00 0.00 0.00 1.31
3446 3868 7.390027 GCATCCATGATTGTTACTCCTACTAT 58.610 38.462 0.00 0.00 0.00 2.12
3448 3870 5.615289 GCATCCATGATTGTTACTCCTACT 58.385 41.667 0.00 0.00 0.00 2.57
3449 3871 4.449068 CGCATCCATGATTGTTACTCCTAC 59.551 45.833 0.00 0.00 0.00 3.18
3520 3977 1.412453 TTTCCTGGTACGTGTGCCCT 61.412 55.000 0.00 0.00 34.17 5.19
3595 4052 4.201920 CGAGTGTCACATTCGAGGATCTTA 60.202 45.833 17.22 0.00 44.29 2.10
3720 4177 2.358125 CCGGTGACATTGTGCGGA 60.358 61.111 0.00 0.00 0.00 5.54
3838 4295 3.251245 CCGTGTAACCAAACATGTGCTTA 59.749 43.478 0.00 0.00 35.08 3.09
3928 4388 2.936912 GCCTGGCTCACTCGTCTGT 61.937 63.158 12.43 0.00 0.00 3.41
3934 4394 2.107953 GGATCGCCTGGCTCACTC 59.892 66.667 17.92 7.52 0.00 3.51
3956 4416 3.423154 CGGTCCGAAAGTGGCTGC 61.423 66.667 4.91 0.00 0.00 5.25
3957 4417 1.566018 GAACGGTCCGAAAGTGGCTG 61.566 60.000 20.51 0.00 0.00 4.85
3958 4418 1.301479 GAACGGTCCGAAAGTGGCT 60.301 57.895 20.51 0.00 0.00 4.75
4064 4524 2.754658 TCGTCTCTTCTCCCCGGC 60.755 66.667 0.00 0.00 0.00 6.13
4066 4526 1.066303 CATTCTCGTCTCTTCTCCCCG 59.934 57.143 0.00 0.00 0.00 5.73
4100 4560 0.034059 CGGAGTGAACTTGCTGGAGT 59.966 55.000 0.00 0.00 0.00 3.85
4140 4608 3.056536 GCTGAGCGATATAATGGGAGTCA 60.057 47.826 0.00 0.00 0.00 3.41
4161 4629 0.531974 TATCATTTCCCCGCTGACGC 60.532 55.000 0.00 0.00 38.22 5.19
4280 4776 7.093333 TGTGTATATCTGAAGTCTGTGATGGTT 60.093 37.037 0.00 0.00 0.00 3.67
4281 4777 6.381133 TGTGTATATCTGAAGTCTGTGATGGT 59.619 38.462 0.00 0.00 0.00 3.55
4340 4838 6.015350 TCCGGTATGTTATTTCTTGGCAAAAA 60.015 34.615 0.00 5.78 0.00 1.94
4363 4861 6.019779 TGTTGTGGCATGTTAATTACTTCC 57.980 37.500 0.00 0.00 0.00 3.46
4365 4863 6.648879 ACTGTTGTGGCATGTTAATTACTT 57.351 33.333 0.00 0.00 0.00 2.24
4402 4900 4.993584 CAGTCTGCTAATATGCTTGGGTAG 59.006 45.833 0.00 0.00 0.00 3.18
4407 4905 4.701765 AGTCCAGTCTGCTAATATGCTTG 58.298 43.478 0.00 0.00 0.00 4.01
4498 4996 1.300971 TGCGATGCTTTGAGAGTGGC 61.301 55.000 0.00 0.00 0.00 5.01
4567 5065 5.205565 GTTTTAAGTTTGCGAGACCTCTTG 58.794 41.667 0.00 0.00 0.00 3.02
4574 5072 5.163703 TGCTTCTTGTTTTAAGTTTGCGAGA 60.164 36.000 0.00 0.00 0.00 4.04
4620 5118 2.101917 GGTTGATAAATGCAGCTGCCAT 59.898 45.455 34.64 23.90 41.18 4.40
4631 5129 7.226059 AGGATACCTGGAAAGGTTGATAAAT 57.774 36.000 0.00 0.00 42.99 1.40
4753 5251 6.448006 CCGCTAGTTACTATGCTTCTGTAAT 58.552 40.000 10.40 0.00 0.00 1.89
4922 5633 1.476085 CTGACAGTCGAGCCAGAGAAT 59.524 52.381 0.00 0.00 0.00 2.40
5039 5750 7.870445 ACCCAACAATAATTTGTGTTATGTGTC 59.130 33.333 6.22 0.00 45.30 3.67
5065 5776 1.093972 CCATTAACTCCATGTGCGCA 58.906 50.000 5.66 5.66 0.00 6.09


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

AutoCloner maintained by Alex Coulton.