Multiple sequence alignment - TraesCS7A01G266400

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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 TraesCS7A01G266400 chr7A 100.000 4647 0 0 1 4647 268861359 268866005 0.000000e+00 8582.0
1 TraesCS7A01G266400 chr7A 87.083 240 22 5 1931 2167 74139940 74140173 3.570000e-66 263.0
2 TraesCS7A01G266400 chr7A 95.833 72 3 0 3951 4022 268865233 268865304 2.940000e-22 117.0
3 TraesCS7A01G266400 chr7A 95.833 72 3 0 3875 3946 268865309 268865380 2.940000e-22 117.0
4 TraesCS7A01G266400 chr7B 93.202 1986 101 16 2669 4647 228918728 228916770 0.000000e+00 2889.0
5 TraesCS7A01G266400 chr7B 88.128 1693 121 35 60 1705 228921567 228919908 0.000000e+00 1940.0
6 TraesCS7A01G266400 chr7B 93.295 880 50 5 1772 2647 228919675 228918801 0.000000e+00 1290.0
7 TraesCS7A01G266400 chr7B 97.059 68 2 0 3879 3946 228917456 228917389 1.060000e-21 115.0
8 TraesCS7A01G266400 chr7B 94.444 72 4 0 3951 4022 228917536 228917465 1.370000e-20 111.0
9 TraesCS7A01G266400 chr7D 92.406 1870 111 20 2796 4647 252242512 252240656 0.000000e+00 2638.0
10 TraesCS7A01G266400 chr7D 87.125 1701 112 41 60 1704 252245049 252243400 0.000000e+00 1829.0
11 TraesCS7A01G266400 chr7D 88.102 664 56 13 2166 2813 252243186 252242530 0.000000e+00 767.0
12 TraesCS7A01G266400 chr7D 81.250 304 32 16 1881 2167 63397886 63398181 6.050000e-54 222.0
13 TraesCS7A01G266400 chr7D 91.724 145 12 0 2015 2159 561701247 561701103 7.880000e-48 202.0
14 TraesCS7A01G266400 chr7D 95.833 72 3 0 3875 3946 252241345 252241274 2.940000e-22 117.0
15 TraesCS7A01G266400 chr1D 88.015 267 28 4 1903 2168 445587646 445587383 3.490000e-81 313.0
16 TraesCS7A01G266400 chr1D 83.456 272 26 13 1906 2160 389597993 389598262 7.770000e-58 235.0
17 TraesCS7A01G266400 chr3B 81.546 401 50 16 1778 2167 710386886 710387273 4.520000e-80 309.0
18 TraesCS7A01G266400 chr2D 81.388 317 41 15 1870 2173 41917876 41918187 4.650000e-60 243.0
19 TraesCS7A01G266400 chr4D 90.541 148 11 3 2013 2159 51607909 51607764 4.750000e-45 193.0
20 TraesCS7A01G266400 chr3D 95.349 43 2 0 1702 1744 347701 347659 8.340000e-08 69.4
21 TraesCS7A01G266400 chr1B 95.238 42 2 0 14 55 482945477 482945436 3.000000e-07 67.6
22 TraesCS7A01G266400 chrUn 92.857 42 3 0 1703 1744 311422372 311422413 1.400000e-05 62.1


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 TraesCS7A01G266400 chr7A 268861359 268866005 4646 False 2938.666667 8582 97.2220 1 4647 3 chr7A.!!$F2 4646
1 TraesCS7A01G266400 chr7B 228916770 228921567 4797 True 1269.000000 2889 93.2256 60 4647 5 chr7B.!!$R1 4587
2 TraesCS7A01G266400 chr7D 252240656 252245049 4393 True 1337.750000 2638 90.8665 60 4647 4 chr7D.!!$R2 4587

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
824 859 0.028902 GTTGCTGTTTTTCCTCGCGT 59.971 50.0 5.77 0.0 0.00 6.01 F
1252 1324 0.677414 GGACGAGAACGAGGAGGAGT 60.677 60.0 0.00 0.0 42.66 3.85 F
2063 2355 0.034896 GATAATGGGGCGATGACGGT 59.965 55.0 0.00 0.0 40.15 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2355 0.415429 AGAGAGAAGGAAGGGGCTCA 59.585 55.0 0.0 0.0 0.00 4.26 R
2658 2958 0.740149 GCATGATCCGCATCCAAACA 59.260 50.0 0.0 0.0 34.15 2.83 R
3700 4114 0.835543 TGAATTTTGCCTGGTGGGGG 60.836 55.0 0.0 0.0 35.12 5.40 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
25 26 6.902224 ACACATTTTTAAAAACAGGAGTGC 57.098 33.333 15.35 0.00 0.00 4.40
26 27 5.518487 ACACATTTTTAAAAACAGGAGTGCG 59.482 36.000 15.35 5.97 0.00 5.34
27 28 5.518487 CACATTTTTAAAAACAGGAGTGCGT 59.482 36.000 15.35 0.00 0.00 5.24
28 29 5.518487 ACATTTTTAAAAACAGGAGTGCGTG 59.482 36.000 15.35 8.41 36.05 5.34
29 30 2.766970 TTAAAAACAGGAGTGCGTGC 57.233 45.000 0.00 0.00 33.32 5.34
30 31 1.961793 TAAAAACAGGAGTGCGTGCT 58.038 45.000 0.00 0.00 33.32 4.40
31 32 0.663153 AAAAACAGGAGTGCGTGCTC 59.337 50.000 0.00 0.67 33.32 4.26
37 38 2.046892 GAGTGCGTGCTCCCATGT 60.047 61.111 0.00 0.00 0.00 3.21
38 39 2.359107 AGTGCGTGCTCCCATGTG 60.359 61.111 0.00 0.00 0.00 3.21
39 40 4.107051 GTGCGTGCTCCCATGTGC 62.107 66.667 0.00 0.00 0.00 4.57
42 43 2.672651 CGTGCTCCCATGTGCCAA 60.673 61.111 0.00 0.00 0.00 4.52
43 44 2.267351 CGTGCTCCCATGTGCCAAA 61.267 57.895 0.00 0.00 0.00 3.28
44 45 1.804396 CGTGCTCCCATGTGCCAAAA 61.804 55.000 0.00 0.00 0.00 2.44
45 46 0.319813 GTGCTCCCATGTGCCAAAAC 60.320 55.000 0.00 0.00 0.00 2.43
46 47 1.080569 GCTCCCATGTGCCAAAACG 60.081 57.895 0.00 0.00 0.00 3.60
47 48 1.080569 CTCCCATGTGCCAAAACGC 60.081 57.895 0.00 0.00 0.00 4.84
48 49 2.048316 CCCATGTGCCAAAACGCC 60.048 61.111 0.00 0.00 0.00 5.68
49 50 2.733301 CCATGTGCCAAAACGCCA 59.267 55.556 0.00 0.00 0.00 5.69
50 51 1.292860 CCATGTGCCAAAACGCCAT 59.707 52.632 0.00 0.00 0.00 4.40
51 52 0.320596 CCATGTGCCAAAACGCCATT 60.321 50.000 0.00 0.00 0.00 3.16
52 53 1.070038 CATGTGCCAAAACGCCATTC 58.930 50.000 0.00 0.00 0.00 2.67
53 54 0.968405 ATGTGCCAAAACGCCATTCT 59.032 45.000 0.00 0.00 0.00 2.40
54 55 0.313672 TGTGCCAAAACGCCATTCTC 59.686 50.000 0.00 0.00 0.00 2.87
55 56 0.729140 GTGCCAAAACGCCATTCTCG 60.729 55.000 0.00 0.00 0.00 4.04
56 57 1.169661 TGCCAAAACGCCATTCTCGT 61.170 50.000 0.00 0.00 42.54 4.18
57 58 0.729140 GCCAAAACGCCATTCTCGTG 60.729 55.000 0.00 0.00 40.36 4.35
58 59 0.109781 CCAAAACGCCATTCTCGTGG 60.110 55.000 0.00 0.00 40.36 4.94
59 60 0.591170 CAAAACGCCATTCTCGTGGT 59.409 50.000 0.00 0.00 41.47 4.16
60 61 0.872388 AAAACGCCATTCTCGTGGTC 59.128 50.000 0.00 0.00 41.47 4.02
61 62 0.953960 AAACGCCATTCTCGTGGTCC 60.954 55.000 0.00 0.00 41.47 4.46
62 63 2.107041 AACGCCATTCTCGTGGTCCA 62.107 55.000 0.00 0.00 41.47 4.02
63 64 1.811266 CGCCATTCTCGTGGTCCAG 60.811 63.158 0.00 0.00 41.47 3.86
64 65 2.109126 GCCATTCTCGTGGTCCAGC 61.109 63.158 0.00 0.00 41.47 4.85
112 113 7.518731 TCGTGTTTCAAATTTCAAGGAAAAG 57.481 32.000 3.71 0.93 35.11 2.27
132 143 8.971321 GGAAAAGCACATGCATATAAACAATAG 58.029 33.333 6.64 0.00 45.16 1.73
155 166 5.242393 AGAATACAAGCATGCCCATTGATAC 59.758 40.000 21.12 11.04 0.00 2.24
156 167 2.737544 ACAAGCATGCCCATTGATACA 58.262 42.857 21.12 0.00 0.00 2.29
157 168 3.098377 ACAAGCATGCCCATTGATACAA 58.902 40.909 21.12 0.00 0.00 2.41
158 169 3.514706 ACAAGCATGCCCATTGATACAAA 59.485 39.130 21.12 0.00 0.00 2.83
159 170 4.020396 ACAAGCATGCCCATTGATACAAAA 60.020 37.500 21.12 0.00 0.00 2.44
160 171 4.822685 AGCATGCCCATTGATACAAAAA 57.177 36.364 15.66 0.00 0.00 1.94
191 202 8.837788 ATCATTTGCAAGATACGATAGAATCA 57.162 30.769 0.00 0.00 41.38 2.57
207 218 9.694520 CGATAGAATCACAACATAAGTTCTTTG 57.305 33.333 0.00 0.00 34.52 2.77
232 246 8.726988 TGCAGTAAGTTAACTAATGGCTTAAAG 58.273 33.333 8.92 0.00 0.00 1.85
267 281 2.181975 CCCCAAGGAGAAGTACCGTAA 58.818 52.381 0.00 0.00 33.47 3.18
273 287 6.040878 CCAAGGAGAAGTACCGTAACATAAG 58.959 44.000 0.00 0.00 0.00 1.73
281 296 4.809426 AGTACCGTAACATAAGCTTGATGC 59.191 41.667 9.86 0.00 43.29 3.91
296 311 8.556213 AAGCTTGATGCAAATCAATTAATGTT 57.444 26.923 0.00 0.00 45.94 2.71
300 315 7.062906 TGATGCAAATCAATTAATGTTGTGC 57.937 32.000 0.00 0.00 0.00 4.57
308 323 8.721019 AATCAATTAATGTTGTGCCCATTAAG 57.279 30.769 10.30 0.96 43.91 1.85
381 396 7.712204 ATTATTTTTGGGTCGAATTGGTACT 57.288 32.000 0.00 0.00 0.00 2.73
382 397 7.527568 TTATTTTTGGGTCGAATTGGTACTT 57.472 32.000 0.00 0.00 0.00 2.24
444 459 6.366340 TGTACAACCTTAATCCTTTCCACAA 58.634 36.000 0.00 0.00 0.00 3.33
451 466 5.393461 CCTTAATCCTTTCCACAAGTGCATC 60.393 44.000 0.00 0.00 0.00 3.91
452 467 2.655090 TCCTTTCCACAAGTGCATCA 57.345 45.000 0.00 0.00 0.00 3.07
477 492 8.957028 CATGATACAAATGCTAAACGTTTATGG 58.043 33.333 20.39 11.42 35.68 2.74
486 501 1.541379 AACGTTTATGGGTTGCCCTC 58.459 50.000 5.73 0.00 45.70 4.30
497 512 1.150536 TTGCCCTCCAACACACCTC 59.849 57.895 0.00 0.00 0.00 3.85
500 515 1.484444 GCCCTCCAACACACCTCTCT 61.484 60.000 0.00 0.00 0.00 3.10
502 517 1.421646 CCCTCCAACACACCTCTCTTT 59.578 52.381 0.00 0.00 0.00 2.52
504 519 3.555966 CCTCCAACACACCTCTCTTTTT 58.444 45.455 0.00 0.00 0.00 1.94
505 520 3.316308 CCTCCAACACACCTCTCTTTTTG 59.684 47.826 0.00 0.00 0.00 2.44
521 551 5.651530 TCTTTTTGCCAAAACGTGTATGAA 58.348 33.333 1.25 0.00 0.00 2.57
552 583 6.559521 GCTTACATTGCAAGTAAAACGTGTTG 60.560 38.462 4.94 0.00 31.66 3.33
596 627 2.254546 TTGCACGGTTTCACTCTCAT 57.745 45.000 0.00 0.00 0.00 2.90
605 636 3.503748 GGTTTCACTCTCATCCACCAAAG 59.496 47.826 0.00 0.00 0.00 2.77
631 662 2.933495 TCTCCACGAGATAAACGGTG 57.067 50.000 0.00 0.00 33.35 4.94
633 664 0.604073 TCCACGAGATAAACGGTGCA 59.396 50.000 0.00 0.00 34.93 4.57
634 665 1.001068 TCCACGAGATAAACGGTGCAA 59.999 47.619 0.00 0.00 34.93 4.08
637 668 1.396996 ACGAGATAAACGGTGCAATGC 59.603 47.619 0.00 0.00 34.93 3.56
638 669 1.268032 CGAGATAAACGGTGCAATGCC 60.268 52.381 1.53 0.00 0.00 4.40
639 670 1.065551 GAGATAAACGGTGCAATGCCC 59.934 52.381 1.53 2.50 0.00 5.36
640 671 0.102300 GATAAACGGTGCAATGCCCC 59.898 55.000 1.53 0.00 0.00 5.80
641 672 1.662438 ATAAACGGTGCAATGCCCCG 61.662 55.000 26.39 26.39 46.93 5.73
648 679 2.130426 TGCAATGCCCCGTGTGTTT 61.130 52.632 1.53 0.00 0.00 2.83
662 693 6.152154 CCCCGTGTGTTTTAAATAGAAATCCT 59.848 38.462 0.00 0.00 0.00 3.24
663 694 7.337436 CCCCGTGTGTTTTAAATAGAAATCCTA 59.663 37.037 0.00 0.00 0.00 2.94
690 722 2.418083 CCCTGCGATTTTCCAGGCC 61.418 63.158 0.00 0.00 45.75 5.19
691 723 1.379044 CCTGCGATTTTCCAGGCCT 60.379 57.895 0.00 0.00 41.86 5.19
702 736 0.687354 TCCAGGCCTCTTCACTGTTC 59.313 55.000 0.00 0.00 0.00 3.18
814 849 2.086610 ATCCAAGGTGGTTGCTGTTT 57.913 45.000 0.00 0.00 39.03 2.83
824 859 0.028902 GTTGCTGTTTTTCCTCGCGT 59.971 50.000 5.77 0.00 0.00 6.01
835 870 4.492791 TTTCCTCGCGTGATCGATATAA 57.507 40.909 10.21 0.00 37.87 0.98
846 881 6.300902 GCGTGATCGATATAACAGAAAAATGC 59.699 38.462 0.00 0.00 39.71 3.56
855 890 4.510038 AACAGAAAAATGCTGCGATCTT 57.490 36.364 0.00 0.00 36.86 2.40
898 933 1.269936 CCTTTTTGCAGTGCCTTCCAG 60.270 52.381 13.72 2.13 0.00 3.86
908 943 1.376037 GCCTTCCAGACCTCAACGG 60.376 63.158 0.00 0.00 39.35 4.44
978 1035 9.151471 CAAGAAGAACGTTGGATAATCTAAAGA 57.849 33.333 5.00 0.00 0.00 2.52
1197 1266 2.745492 GACGACCTCGACCTCGGT 60.745 66.667 10.80 3.07 43.02 4.69
1252 1324 0.677414 GGACGAGAACGAGGAGGAGT 60.677 60.000 0.00 0.00 42.66 3.85
1407 1479 2.951458 TCGAGCTCTTTCGACGCA 59.049 55.556 12.85 0.00 44.00 5.24
1601 1673 9.283768 ACTGTTCATCACAATTTGATAAGTACA 57.716 29.630 2.79 0.74 43.68 2.90
1633 1710 4.873746 TCCCAGGCTATTTCTTATCGAG 57.126 45.455 0.00 0.00 0.00 4.04
1635 1712 4.654262 TCCCAGGCTATTTCTTATCGAGTT 59.346 41.667 0.00 0.00 0.00 3.01
1698 1775 5.172053 GTCTGAAATGCTGTCAAAAGAAACG 59.828 40.000 0.00 0.00 0.00 3.60
1714 1841 4.492611 AGAAACGAAATACTCCTTCCGTC 58.507 43.478 0.00 0.00 0.00 4.79
1715 1842 2.955477 ACGAAATACTCCTTCCGTCC 57.045 50.000 0.00 0.00 0.00 4.79
1717 1844 1.479323 CGAAATACTCCTTCCGTCCCA 59.521 52.381 0.00 0.00 0.00 4.37
1718 1845 2.481449 CGAAATACTCCTTCCGTCCCAG 60.481 54.545 0.00 0.00 0.00 4.45
1728 1855 5.213519 TCCTTCCGTCCCAGAATATAAGAA 58.786 41.667 0.00 0.00 0.00 2.52
1736 1863 7.915397 CCGTCCCAGAATATAAGAACATTTTTG 59.085 37.037 0.00 0.00 0.00 2.44
1751 1878 8.157476 AGAACATTTTTGTCACTAGGAGTACAT 58.843 33.333 0.00 0.00 0.00 2.29
1752 1879 9.431887 GAACATTTTTGTCACTAGGAGTACATA 57.568 33.333 0.00 0.00 0.00 2.29
1753 1880 9.436957 AACATTTTTGTCACTAGGAGTACATAG 57.563 33.333 0.00 0.00 36.60 2.23
1754 1881 8.812972 ACATTTTTGTCACTAGGAGTACATAGA 58.187 33.333 0.00 0.00 34.90 1.98
1755 1882 9.653287 CATTTTTGTCACTAGGAGTACATAGAA 57.347 33.333 0.00 0.00 34.90 2.10
1756 1883 9.654663 ATTTTTGTCACTAGGAGTACATAGAAC 57.345 33.333 0.00 0.71 34.90 3.01
1757 1884 7.770366 TTTGTCACTAGGAGTACATAGAACA 57.230 36.000 0.00 3.01 34.90 3.18
1758 1885 7.956328 TTGTCACTAGGAGTACATAGAACAT 57.044 36.000 0.00 0.00 33.64 2.71
1760 1887 9.470399 TTGTCACTAGGAGTACATAGAACATTA 57.530 33.333 0.00 0.00 33.64 1.90
1761 1888 9.121658 TGTCACTAGGAGTACATAGAACATTAG 57.878 37.037 0.00 0.00 34.90 1.73
1762 1889 9.339850 GTCACTAGGAGTACATAGAACATTAGA 57.660 37.037 0.00 0.00 34.90 2.10
1785 2076 7.059156 AGAAGATTTATCCTGGATCAGTTTGG 58.941 38.462 13.54 0.00 0.00 3.28
1789 2080 1.361204 TCCTGGATCAGTTTGGAGCA 58.639 50.000 0.00 0.00 0.00 4.26
1812 2103 1.181786 GATGGAAAATGAACGGCCCA 58.818 50.000 0.00 0.00 0.00 5.36
1813 2104 0.894835 ATGGAAAATGAACGGCCCAC 59.105 50.000 0.00 0.00 0.00 4.61
1832 2123 4.080356 CCCACATTATGTCTTCTTCCTCCA 60.080 45.833 0.00 0.00 0.00 3.86
1835 2126 5.008415 CACATTATGTCTTCTTCCTCCATGC 59.992 44.000 0.00 0.00 0.00 4.06
1852 2143 3.255725 CATGCGTTTTCCAGATTGCATT 58.744 40.909 0.00 0.00 40.77 3.56
1854 2145 3.726607 TGCGTTTTCCAGATTGCATTTT 58.273 36.364 0.00 0.00 0.00 1.82
1855 2146 3.740321 TGCGTTTTCCAGATTGCATTTTC 59.260 39.130 0.00 0.00 0.00 2.29
1856 2147 3.989817 GCGTTTTCCAGATTGCATTTTCT 59.010 39.130 0.00 0.00 0.00 2.52
1857 2148 4.448732 GCGTTTTCCAGATTGCATTTTCTT 59.551 37.500 0.00 0.00 0.00 2.52
1858 2149 5.633182 GCGTTTTCCAGATTGCATTTTCTTA 59.367 36.000 0.00 0.00 0.00 2.10
1869 2160 3.142174 GCATTTTCTTATCCTCCTCCCG 58.858 50.000 0.00 0.00 0.00 5.14
1983 2275 4.964241 ATCCCTCTAGCCCCGCCC 62.964 72.222 0.00 0.00 0.00 6.13
2049 2341 6.013293 GCACCCTGAACCCTAAGATAGATAAT 60.013 42.308 0.00 0.00 0.00 1.28
2053 2345 6.069963 CCTGAACCCTAAGATAGATAATGGGG 60.070 46.154 0.00 0.00 37.56 4.96
2054 2346 5.250774 TGAACCCTAAGATAGATAATGGGGC 59.749 44.000 0.00 0.00 37.56 5.80
2063 2355 0.034896 GATAATGGGGCGATGACGGT 59.965 55.000 0.00 0.00 40.15 4.83
2082 2374 0.415429 TGAGCCCCTTCCTTCTCTCT 59.585 55.000 0.00 0.00 0.00 3.10
2084 2376 0.620121 AGCCCCTTCCTTCTCTCTGG 60.620 60.000 0.00 0.00 0.00 3.86
2085 2377 1.911471 CCCCTTCCTTCTCTCTGGC 59.089 63.158 0.00 0.00 0.00 4.85
2105 2397 2.703405 AGGCCCTTCCTTCTCCTTC 58.297 57.895 0.00 0.00 44.75 3.46
2108 2400 0.544223 GCCCTTCCTTCTCCTTCCTC 59.456 60.000 0.00 0.00 0.00 3.71
2135 2427 1.922570 AATCGACTGACCCGAATTCG 58.077 50.000 20.92 20.92 39.62 3.34
2173 2465 3.704061 ACATGTAGCCAAACTGGTGTTTT 59.296 39.130 0.00 0.00 43.13 2.43
2251 2543 2.600420 CACGATGTGATCCGAAGAACAG 59.400 50.000 0.00 0.00 35.23 3.16
2504 2800 1.282157 ACATGTAAGAACTGCCCCTCC 59.718 52.381 0.00 0.00 0.00 4.30
2581 2880 4.819105 TGACCTATCTGTTTTGATCGGT 57.181 40.909 0.00 0.00 42.72 4.69
2586 2885 5.895534 ACCTATCTGTTTTGATCGGTACCTA 59.104 40.000 10.90 0.00 39.67 3.08
2600 2899 8.372459 TGATCGGTACCTATAATGCTTGTTTAT 58.628 33.333 10.90 0.00 0.00 1.40
2684 3035 0.391661 ATGCGGATCATGCGTATCCC 60.392 55.000 0.00 1.54 39.92 3.85
2705 3056 6.202331 TCCCTCTCCTGTAGATTTCATGTAA 58.798 40.000 0.00 0.00 32.41 2.41
2712 3064 8.506168 TCCTGTAGATTTCATGTAATTTCACC 57.494 34.615 0.00 0.00 0.00 4.02
2742 3098 5.471556 TGAAAATTGTCCAAGCATGTCAT 57.528 34.783 0.00 0.00 0.00 3.06
2779 3137 2.107204 GGTAGACAATGCCATCATCCCT 59.893 50.000 0.00 0.00 32.98 4.20
2876 3272 5.057149 TGGCTAACAACAGAGAGAAGAAAC 58.943 41.667 0.00 0.00 0.00 2.78
2962 3361 0.032615 ACCTTGTTCCCTTTGCCACA 60.033 50.000 0.00 0.00 0.00 4.17
3117 3516 0.868406 CACCTTCTTCGTTCTGCCAC 59.132 55.000 0.00 0.00 0.00 5.01
3146 3545 2.485426 AGACAATCTTGCATGTTCACCG 59.515 45.455 0.00 0.00 0.00 4.94
3149 3548 1.167851 ATCTTGCATGTTCACCGTGG 58.832 50.000 0.00 0.00 0.00 4.94
3172 3583 4.508584 GGGGAGAAGGTGATTAAAAGGTGT 60.509 45.833 0.00 0.00 0.00 4.16
3186 3597 3.782889 AAGGTGTTGTGAACTTCTTGC 57.217 42.857 0.00 0.00 0.00 4.01
3273 3684 5.972973 GGTTTTTCGTCGAAAACTTACCATT 59.027 36.000 30.28 0.00 44.77 3.16
3708 4122 0.033405 TGAAACGAAAACCCCCACCA 60.033 50.000 0.00 0.00 0.00 4.17
3834 4251 1.070134 TCAAGGCTGCTCAAGTTACGT 59.930 47.619 0.00 0.00 0.00 3.57
3947 4364 4.573607 TCATGCAGATTCTTCGGATTTGAG 59.426 41.667 0.00 0.00 0.00 3.02
4027 4444 3.062639 CAGATTCTTCGGGTTTGTCGATG 59.937 47.826 0.00 0.00 36.49 3.84
4045 4462 3.121092 CGATGCGCTGTCAATCTGATTAG 60.121 47.826 9.73 0.00 0.00 1.73
4075 4492 4.479619 GTTTACAAAGGAAGATGCTGCTG 58.520 43.478 0.00 0.00 0.00 4.41
4132 4549 9.868277 ATGTACAGATTGTTTTCTTTGTTTTGA 57.132 25.926 0.33 0.00 0.00 2.69
4201 4618 4.216257 GCAAGTTTTAATGTCCTCTCTGCA 59.784 41.667 0.00 0.00 0.00 4.41
4318 4735 3.118519 AGGTTCACCAACAGAGTACGTTT 60.119 43.478 0.00 0.00 38.89 3.60
4320 4737 4.992951 GGTTCACCAACAGAGTACGTTTAT 59.007 41.667 0.00 0.00 33.70 1.40
4321 4738 6.015180 AGGTTCACCAACAGAGTACGTTTATA 60.015 38.462 0.00 0.00 38.89 0.98
4322 4739 6.089954 GGTTCACCAACAGAGTACGTTTATAC 59.910 42.308 0.00 0.00 33.70 1.47
4329 4746 8.239314 CCAACAGAGTACGTTTATACTAGTTGA 58.761 37.037 22.66 0.00 44.37 3.18
4333 4750 9.275231 CAGAGTACGTTTATACTAGTTGAGTTG 57.725 37.037 0.00 0.00 39.81 3.16
4339 4756 7.111139 CGTTTATACTAGTTGAGTTGATTGCG 58.889 38.462 0.00 0.00 39.81 4.85
4367 4784 3.506067 CACATGTTTTGGGACTAGGGTTC 59.494 47.826 0.00 0.00 0.00 3.62
4382 4799 0.519961 GGTTCCACGTAACCACATGC 59.480 55.000 14.14 0.00 46.85 4.06
4391 4808 1.613437 GTAACCACATGCCTTGCAAGT 59.387 47.619 24.35 3.84 43.62 3.16
4435 4852 4.528596 TCAAAAAGGAAAAACACAGACCCA 59.471 37.500 0.00 0.00 0.00 4.51
4438 4855 3.593442 AGGAAAAACACAGACCCATGA 57.407 42.857 0.00 0.00 0.00 3.07
4440 4857 4.482990 AGGAAAAACACAGACCCATGAAT 58.517 39.130 0.00 0.00 0.00 2.57
4441 4858 4.901250 AGGAAAAACACAGACCCATGAATT 59.099 37.500 0.00 0.00 0.00 2.17
4524 4941 0.678950 TGGTGAGCGAATCTGACACA 59.321 50.000 0.00 0.00 29.89 3.72
4526 4943 1.662629 GGTGAGCGAATCTGACACATG 59.337 52.381 0.00 0.00 29.89 3.21
4534 4951 4.093998 GCGAATCTGACACATGACTGAAAT 59.906 41.667 0.00 0.00 0.00 2.17
4535 4952 5.557388 CGAATCTGACACATGACTGAAATG 58.443 41.667 0.00 0.00 0.00 2.32
4546 4963 5.243507 ACATGACTGAAATGCACACCAAATA 59.756 36.000 0.00 0.00 0.00 1.40
4552 4969 4.525874 TGAAATGCACACCAAATATCCACA 59.474 37.500 0.00 0.00 0.00 4.17
4568 4985 3.505386 TCCACATAAAACACTGGGCAAT 58.495 40.909 0.00 0.00 0.00 3.56
4632 5049 7.319646 GCTACATTATTCCATTCACAACCAAA 58.680 34.615 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.412455 CGCACTCCTGTTTTTAAAAATGTGTTT 60.412 33.333 16.02 0.00 0.00 2.83
1 2 6.035542 CGCACTCCTGTTTTTAAAAATGTGTT 59.964 34.615 16.02 0.00 0.00 3.32
2 3 5.518487 CGCACTCCTGTTTTTAAAAATGTGT 59.482 36.000 16.02 11.42 0.00 3.72
3 4 5.518487 ACGCACTCCTGTTTTTAAAAATGTG 59.482 36.000 16.02 16.10 0.00 3.21
4 5 5.518487 CACGCACTCCTGTTTTTAAAAATGT 59.482 36.000 16.02 8.07 0.00 2.71
5 6 5.556194 GCACGCACTCCTGTTTTTAAAAATG 60.556 40.000 16.02 10.24 0.00 2.32
6 7 4.506288 GCACGCACTCCTGTTTTTAAAAAT 59.494 37.500 16.02 0.00 0.00 1.82
7 8 3.860536 GCACGCACTCCTGTTTTTAAAAA 59.139 39.130 9.31 9.31 0.00 1.94
8 9 3.129638 AGCACGCACTCCTGTTTTTAAAA 59.870 39.130 0.00 0.00 0.00 1.52
9 10 2.685897 AGCACGCACTCCTGTTTTTAAA 59.314 40.909 0.00 0.00 0.00 1.52
10 11 2.289547 GAGCACGCACTCCTGTTTTTAA 59.710 45.455 0.00 0.00 0.00 1.52
11 12 1.871039 GAGCACGCACTCCTGTTTTTA 59.129 47.619 0.00 0.00 0.00 1.52
12 13 0.663153 GAGCACGCACTCCTGTTTTT 59.337 50.000 0.00 0.00 0.00 1.94
13 14 2.321213 GAGCACGCACTCCTGTTTT 58.679 52.632 0.00 0.00 0.00 2.43
14 15 4.049393 GAGCACGCACTCCTGTTT 57.951 55.556 0.00 0.00 0.00 2.83
20 21 2.046892 ACATGGGAGCACGCACTC 60.047 61.111 2.41 0.00 41.49 3.51
21 22 2.359107 CACATGGGAGCACGCACT 60.359 61.111 2.41 0.00 41.49 4.40
22 23 4.107051 GCACATGGGAGCACGCAC 62.107 66.667 0.00 0.00 41.49 5.34
25 26 1.804396 TTTTGGCACATGGGAGCACG 61.804 55.000 0.00 0.00 39.30 5.34
26 27 0.319813 GTTTTGGCACATGGGAGCAC 60.320 55.000 0.00 0.00 39.30 4.40
27 28 1.804396 CGTTTTGGCACATGGGAGCA 61.804 55.000 0.00 0.00 39.30 4.26
28 29 1.080569 CGTTTTGGCACATGGGAGC 60.081 57.895 0.00 0.00 39.30 4.70
29 30 1.080569 GCGTTTTGGCACATGGGAG 60.081 57.895 0.00 0.00 39.30 4.30
30 31 2.569354 GGCGTTTTGGCACATGGGA 61.569 57.895 0.00 0.00 44.08 4.37
31 32 2.048316 GGCGTTTTGGCACATGGG 60.048 61.111 0.00 0.00 44.08 4.00
38 39 0.729140 CACGAGAATGGCGTTTTGGC 60.729 55.000 0.00 0.00 40.44 4.52
39 40 0.109781 CCACGAGAATGGCGTTTTGG 60.110 55.000 0.00 0.00 40.44 3.28
40 41 0.591170 ACCACGAGAATGGCGTTTTG 59.409 50.000 0.00 0.00 44.33 2.44
41 42 0.872388 GACCACGAGAATGGCGTTTT 59.128 50.000 0.00 0.00 44.33 2.43
42 43 0.953960 GGACCACGAGAATGGCGTTT 60.954 55.000 0.00 0.00 44.33 3.60
43 44 1.375523 GGACCACGAGAATGGCGTT 60.376 57.895 0.00 0.00 44.33 4.84
44 45 2.264794 GGACCACGAGAATGGCGT 59.735 61.111 0.00 0.00 44.33 5.68
45 46 1.811266 CTGGACCACGAGAATGGCG 60.811 63.158 0.00 0.00 44.33 5.69
46 47 2.109126 GCTGGACCACGAGAATGGC 61.109 63.158 0.00 0.00 44.33 4.40
47 48 0.460987 GAGCTGGACCACGAGAATGG 60.461 60.000 0.00 0.00 46.10 3.16
48 49 0.534412 AGAGCTGGACCACGAGAATG 59.466 55.000 0.00 0.00 0.00 2.67
49 50 0.820871 GAGAGCTGGACCACGAGAAT 59.179 55.000 0.00 0.00 0.00 2.40
50 51 0.539669 TGAGAGCTGGACCACGAGAA 60.540 55.000 0.00 0.00 0.00 2.87
51 52 0.539669 TTGAGAGCTGGACCACGAGA 60.540 55.000 0.00 0.00 0.00 4.04
52 53 0.318441 TTTGAGAGCTGGACCACGAG 59.682 55.000 0.00 0.00 0.00 4.18
53 54 0.976641 ATTTGAGAGCTGGACCACGA 59.023 50.000 0.00 0.00 0.00 4.35
54 55 1.813513 AATTTGAGAGCTGGACCACG 58.186 50.000 0.00 0.00 0.00 4.94
55 56 3.057946 GTCAAATTTGAGAGCTGGACCAC 60.058 47.826 21.05 2.08 37.98 4.16
56 57 3.149196 GTCAAATTTGAGAGCTGGACCA 58.851 45.455 21.05 0.00 37.98 4.02
57 58 2.489722 GGTCAAATTTGAGAGCTGGACC 59.510 50.000 21.05 12.56 37.98 4.46
58 59 3.149196 TGGTCAAATTTGAGAGCTGGAC 58.851 45.455 21.05 7.40 37.98 4.02
59 60 3.507162 TGGTCAAATTTGAGAGCTGGA 57.493 42.857 21.05 0.00 37.98 3.86
60 61 4.589216 TTTGGTCAAATTTGAGAGCTGG 57.411 40.909 21.05 0.00 37.98 4.85
61 62 8.767478 ATAATTTTGGTCAAATTTGAGAGCTG 57.233 30.769 21.05 0.00 41.57 4.24
90 91 6.960992 GTGCTTTTCCTTGAAATTTGAAACAC 59.039 34.615 0.00 1.85 31.34 3.32
107 108 9.734620 TCTATTGTTTATATGCATGTGCTTTTC 57.265 29.630 10.16 0.00 42.66 2.29
132 143 4.595762 ATCAATGGGCATGCTTGTATTC 57.404 40.909 18.92 0.00 0.00 1.75
136 147 2.737544 TGTATCAATGGGCATGCTTGT 58.262 42.857 18.92 7.81 0.00 3.16
160 171 9.888878 CTATCGTATCTTGCAAATGATCATTTT 57.111 29.630 27.30 16.12 38.84 1.82
161 172 9.276590 TCTATCGTATCTTGCAAATGATCATTT 57.723 29.630 24.83 24.83 41.33 2.32
162 173 8.837788 TCTATCGTATCTTGCAAATGATCATT 57.162 30.769 15.36 15.36 0.00 2.57
163 174 8.837788 TTCTATCGTATCTTGCAAATGATCAT 57.162 30.769 1.18 1.18 0.00 2.45
164 175 8.837788 ATTCTATCGTATCTTGCAAATGATCA 57.162 30.769 7.44 0.00 0.00 2.92
165 176 8.929746 TGATTCTATCGTATCTTGCAAATGATC 58.070 33.333 7.44 0.00 0.00 2.92
166 177 8.715998 GTGATTCTATCGTATCTTGCAAATGAT 58.284 33.333 0.00 5.11 0.00 2.45
167 178 7.710475 TGTGATTCTATCGTATCTTGCAAATGA 59.290 33.333 0.00 0.00 0.00 2.57
182 193 9.495754 GCAAAGAACTTATGTTGTGATTCTATC 57.504 33.333 0.00 0.00 36.39 2.08
183 194 9.013229 TGCAAAGAACTTATGTTGTGATTCTAT 57.987 29.630 0.00 0.00 36.39 1.98
184 195 8.389779 TGCAAAGAACTTATGTTGTGATTCTA 57.610 30.769 0.00 0.00 36.39 2.10
191 202 7.568199 ACTTACTGCAAAGAACTTATGTTGT 57.432 32.000 5.15 0.00 36.39 3.32
207 218 8.727910 ACTTTAAGCCATTAGTTAACTTACTGC 58.272 33.333 14.49 10.76 0.00 4.40
252 266 4.954826 AGCTTATGTTACGGTACTTCTCCT 59.045 41.667 0.00 0.00 0.00 3.69
253 267 5.259832 AGCTTATGTTACGGTACTTCTCC 57.740 43.478 0.00 0.00 0.00 3.71
262 276 4.614555 TTGCATCAAGCTTATGTTACGG 57.385 40.909 0.00 0.00 45.94 4.02
281 296 6.988622 ATGGGCACAACATTAATTGATTTG 57.011 33.333 0.00 0.00 33.57 2.32
296 311 4.321899 GCATTCAGTTTCTTAATGGGCACA 60.322 41.667 0.00 0.00 32.44 4.57
300 315 5.416952 AGAGTGCATTCAGTTTCTTAATGGG 59.583 40.000 12.16 0.00 32.44 4.00
308 323 6.690194 AATATGGAGAGTGCATTCAGTTTC 57.310 37.500 12.16 0.00 29.08 2.78
354 369 9.458374 GTACCAATTCGACCCAAAAATAATATG 57.542 33.333 0.00 0.00 0.00 1.78
355 370 9.416284 AGTACCAATTCGACCCAAAAATAATAT 57.584 29.630 0.00 0.00 0.00 1.28
359 374 7.527568 AAAGTACCAATTCGACCCAAAAATA 57.472 32.000 0.00 0.00 0.00 1.40
360 375 6.413783 AAAGTACCAATTCGACCCAAAAAT 57.586 33.333 0.00 0.00 0.00 1.82
382 397 8.604640 AATACATGATGACAACAATGCAAAAA 57.395 26.923 0.00 0.00 0.00 1.94
421 436 6.489022 ACTTGTGGAAAGGATTAAGGTTGTAC 59.511 38.462 0.00 0.00 0.00 2.90
423 438 5.301805 CACTTGTGGAAAGGATTAAGGTTGT 59.698 40.000 0.00 0.00 0.00 3.32
444 459 6.947644 TTAGCATTTGTATCATGATGCACT 57.052 33.333 23.98 19.14 45.47 4.40
451 466 8.957028 CCATAAACGTTTAGCATTTGTATCATG 58.043 33.333 23.78 13.76 0.00 3.07
452 467 8.134895 CCCATAAACGTTTAGCATTTGTATCAT 58.865 33.333 23.78 2.93 0.00 2.45
486 501 2.223805 GGCAAAAAGAGAGGTGTGTTGG 60.224 50.000 0.00 0.00 0.00 3.77
492 507 3.115554 CGTTTTGGCAAAAAGAGAGGTG 58.884 45.455 27.34 8.35 35.96 4.00
493 508 2.758423 ACGTTTTGGCAAAAAGAGAGGT 59.242 40.909 34.33 19.32 35.96 3.85
494 509 3.115554 CACGTTTTGGCAAAAAGAGAGG 58.884 45.455 34.33 18.76 35.96 3.69
497 512 5.277825 TCATACACGTTTTGGCAAAAAGAG 58.722 37.500 34.33 29.63 35.96 2.85
500 515 5.651530 TCTTCATACACGTTTTGGCAAAAA 58.348 33.333 25.60 11.37 32.82 1.94
502 517 4.902443 TCTTCATACACGTTTTGGCAAA 57.098 36.364 8.93 8.93 0.00 3.68
504 519 5.391523 GCTTATCTTCATACACGTTTTGGCA 60.392 40.000 0.00 0.00 0.00 4.92
505 520 5.028375 GCTTATCTTCATACACGTTTTGGC 58.972 41.667 0.00 0.00 0.00 4.52
521 551 7.962918 CGTTTTACTTGCAATGTAAGCTTATCT 59.037 33.333 9.88 0.00 37.68 1.98
583 614 2.859165 TGGTGGATGAGAGTGAAACC 57.141 50.000 0.00 0.00 37.80 3.27
596 627 0.039618 GAGATTGGGCCTTTGGTGGA 59.960 55.000 4.53 0.00 0.00 4.02
605 636 1.048601 TATCTCGTGGAGATTGGGCC 58.951 55.000 12.86 0.00 45.86 5.80
629 660 2.362329 AAACACACGGGGCATTGCAC 62.362 55.000 11.39 6.67 0.00 4.57
631 662 0.315568 TAAAACACACGGGGCATTGC 59.684 50.000 0.00 0.00 0.00 3.56
633 664 4.767928 TCTATTTAAAACACACGGGGCATT 59.232 37.500 0.00 0.00 0.00 3.56
634 665 4.337145 TCTATTTAAAACACACGGGGCAT 58.663 39.130 0.00 0.00 0.00 4.40
637 668 6.152154 AGGATTTCTATTTAAAACACACGGGG 59.848 38.462 0.00 0.00 0.00 5.73
638 669 7.153217 AGGATTTCTATTTAAAACACACGGG 57.847 36.000 0.00 0.00 0.00 5.28
639 670 9.550811 GTTAGGATTTCTATTTAAAACACACGG 57.449 33.333 0.00 0.00 0.00 4.94
640 671 9.257865 CGTTAGGATTTCTATTTAAAACACACG 57.742 33.333 0.00 0.00 0.00 4.49
648 679 7.983484 GGGACACTCGTTAGGATTTCTATTTAA 59.017 37.037 0.00 0.00 0.00 1.52
662 693 0.892755 AATCGCAGGGACACTCGTTA 59.107 50.000 0.00 0.00 0.00 3.18
663 694 0.034896 AAATCGCAGGGACACTCGTT 59.965 50.000 0.00 0.00 0.00 3.85
690 722 1.687628 GGACGACGAACAGTGAAGAG 58.312 55.000 0.00 0.00 0.00 2.85
691 723 3.859650 GGACGACGAACAGTGAAGA 57.140 52.632 0.00 0.00 0.00 2.87
702 736 1.477030 CGCCTATTTTCCGGACGACG 61.477 60.000 1.83 0.00 43.80 5.12
735 769 0.674581 TCTGTTCATCGGCTTGCAGG 60.675 55.000 0.00 0.00 0.00 4.85
814 849 4.224433 GTTATATCGATCACGCGAGGAAA 58.776 43.478 15.93 0.71 44.26 3.13
824 859 7.355017 GCAGCATTTTTCTGTTATATCGATCA 58.645 34.615 0.00 0.00 34.21 2.92
835 870 4.510038 AAAGATCGCAGCATTTTTCTGT 57.490 36.364 0.00 0.00 34.21 3.41
846 881 2.073816 ACAAACCCGTAAAGATCGCAG 58.926 47.619 0.00 0.00 0.00 5.18
855 890 5.702209 GGACAAGATCTAAACAAACCCGTAA 59.298 40.000 0.00 0.00 0.00 3.18
908 943 1.725164 GTCAGGAATCGTGACGGAAAC 59.275 52.381 18.41 0.00 38.99 2.78
1252 1324 2.094700 CGTCGAGGAACATGGAGAAGAA 60.095 50.000 0.00 0.00 0.00 2.52
1429 1501 2.758327 CGACATCCCCTCCACCGA 60.758 66.667 0.00 0.00 0.00 4.69
1633 1710 9.722056 CTTCATCCATATAACAGCTGTAAAAAC 57.278 33.333 22.01 0.00 0.00 2.43
1635 1712 9.679661 TTCTTCATCCATATAACAGCTGTAAAA 57.320 29.630 22.01 9.43 0.00 1.52
1698 1775 2.764572 TCTGGGACGGAAGGAGTATTTC 59.235 50.000 0.00 0.00 43.00 2.17
1714 1841 9.573133 GTGACAAAAATGTTCTTATATTCTGGG 57.427 33.333 0.00 0.00 0.00 4.45
1728 1855 8.812972 TCTATGTACTCCTAGTGACAAAAATGT 58.187 33.333 0.00 0.00 0.00 2.71
1736 1863 9.339850 TCTAATGTTCTATGTACTCCTAGTGAC 57.660 37.037 0.00 0.00 0.00 3.67
1753 1880 9.784531 TGATCCAGGATAAATCTTCTAATGTTC 57.215 33.333 0.32 0.00 0.00 3.18
1754 1881 9.790344 CTGATCCAGGATAAATCTTCTAATGTT 57.210 33.333 0.32 0.00 0.00 2.71
1755 1882 8.943085 ACTGATCCAGGATAAATCTTCTAATGT 58.057 33.333 0.32 0.00 35.51 2.71
1756 1883 9.790344 AACTGATCCAGGATAAATCTTCTAATG 57.210 33.333 0.32 0.00 35.51 1.90
1758 1885 9.618890 CAAACTGATCCAGGATAAATCTTCTAA 57.381 33.333 0.32 0.00 35.51 2.10
1760 1887 7.059156 CCAAACTGATCCAGGATAAATCTTCT 58.941 38.462 0.32 0.00 35.51 2.85
1761 1888 7.056635 TCCAAACTGATCCAGGATAAATCTTC 58.943 38.462 0.32 0.00 35.51 2.87
1762 1889 6.973642 TCCAAACTGATCCAGGATAAATCTT 58.026 36.000 0.32 0.00 35.51 2.40
1764 1891 5.240403 GCTCCAAACTGATCCAGGATAAATC 59.760 44.000 0.32 0.00 35.51 2.17
1765 1892 5.136105 GCTCCAAACTGATCCAGGATAAAT 58.864 41.667 0.32 0.00 35.51 1.40
1767 1894 3.523157 TGCTCCAAACTGATCCAGGATAA 59.477 43.478 0.32 0.00 35.51 1.75
1769 1896 1.918262 TGCTCCAAACTGATCCAGGAT 59.082 47.619 0.00 0.00 35.51 3.24
1771 1898 2.431954 ATGCTCCAAACTGATCCAGG 57.568 50.000 0.00 0.00 35.51 4.45
1785 2076 5.514279 CCGTTCATTTTCCATCTAATGCTC 58.486 41.667 0.00 0.00 32.96 4.26
1789 2080 3.636764 GGGCCGTTCATTTTCCATCTAAT 59.363 43.478 0.00 0.00 0.00 1.73
1812 2103 5.128919 GCATGGAGGAAGAAGACATAATGT 58.871 41.667 0.00 0.00 0.00 2.71
1813 2104 4.212847 CGCATGGAGGAAGAAGACATAATG 59.787 45.833 0.00 0.00 0.00 1.90
1832 2123 3.598019 AATGCAATCTGGAAAACGCAT 57.402 38.095 0.00 0.00 41.60 4.73
1835 2126 7.009540 GGATAAGAAAATGCAATCTGGAAAACG 59.990 37.037 0.00 0.00 0.00 3.60
1852 2143 1.129058 GGCGGGAGGAGGATAAGAAA 58.871 55.000 0.00 0.00 0.00 2.52
1854 2145 1.530891 CGGCGGGAGGAGGATAAGA 60.531 63.158 0.00 0.00 0.00 2.10
1855 2146 1.530891 TCGGCGGGAGGAGGATAAG 60.531 63.158 7.21 0.00 0.00 1.73
1856 2147 1.831286 GTCGGCGGGAGGAGGATAA 60.831 63.158 7.21 0.00 0.00 1.75
1857 2148 2.203451 GTCGGCGGGAGGAGGATA 60.203 66.667 7.21 0.00 0.00 2.59
1858 2149 4.144727 AGTCGGCGGGAGGAGGAT 62.145 66.667 7.21 0.00 0.00 3.24
1925 2216 2.271173 GCGGTGGGGGAGGTTAAG 59.729 66.667 0.00 0.00 0.00 1.85
2003 2295 4.974721 CGGTGGTGGGGCTTTGCT 62.975 66.667 0.00 0.00 0.00 3.91
2025 2317 6.996180 TTATCTATCTTAGGGTTCAGGGTG 57.004 41.667 0.00 0.00 0.00 4.61
2036 2328 6.276847 GTCATCGCCCCATTATCTATCTTAG 58.723 44.000 0.00 0.00 0.00 2.18
2049 2341 3.770040 CTCACCGTCATCGCCCCA 61.770 66.667 0.00 0.00 35.54 4.96
2054 2346 2.907897 GAAGGGGCTCACCGTCATCG 62.908 65.000 0.00 0.00 41.60 3.84
2063 2355 0.415429 AGAGAGAAGGAAGGGGCTCA 59.585 55.000 0.00 0.00 0.00 4.26
2105 2397 3.375299 GGTCAGTCGATTTTGAATGGAGG 59.625 47.826 0.00 0.00 34.85 4.30
2108 2400 2.095853 CGGGTCAGTCGATTTTGAATGG 59.904 50.000 0.00 0.00 34.85 3.16
2160 2452 7.659652 TTTTGACCTTAAAAACACCAGTTTG 57.340 32.000 0.00 0.00 46.79 2.93
2173 2465 6.294361 TCATCCGAGAGATTTTGACCTTAA 57.706 37.500 0.00 0.00 30.59 1.85
2251 2543 6.042777 GCCATTTTCTAGGTAAAGATTTGCC 58.957 40.000 4.43 4.43 42.43 4.52
2504 2800 6.816140 GGAGAAGAGGAATAACAGAAGTTGAG 59.184 42.308 0.00 0.00 38.69 3.02
2541 2840 7.872113 AGGTCAAGATATTCTTCCACATTTC 57.128 36.000 0.00 0.00 33.78 2.17
2555 2854 7.147724 ACCGATCAAAACAGATAGGTCAAGATA 60.148 37.037 3.36 0.00 46.79 1.98
2581 2880 7.443477 TGCCGTATAAACAAGCATTATAGGTA 58.557 34.615 0.00 0.00 32.88 3.08
2586 2885 6.935741 TCTTGCCGTATAAACAAGCATTAT 57.064 33.333 0.00 0.00 40.45 1.28
2600 2899 5.972107 AGTTAGTTCTAGTTCTTGCCGTA 57.028 39.130 0.00 0.00 0.00 4.02
2649 2949 1.068434 CGCATCCAAACACAAAAGGGT 59.932 47.619 0.00 0.00 0.00 4.34
2650 2950 1.605202 CCGCATCCAAACACAAAAGGG 60.605 52.381 0.00 0.00 0.00 3.95
2652 2952 2.791383 TCCGCATCCAAACACAAAAG 57.209 45.000 0.00 0.00 0.00 2.27
2653 2953 2.625314 TGATCCGCATCCAAACACAAAA 59.375 40.909 0.00 0.00 0.00 2.44
2654 2954 2.234143 TGATCCGCATCCAAACACAAA 58.766 42.857 0.00 0.00 0.00 2.83
2655 2955 1.902938 TGATCCGCATCCAAACACAA 58.097 45.000 0.00 0.00 0.00 3.33
2657 2957 1.534595 GCATGATCCGCATCCAAACAC 60.535 52.381 0.00 0.00 34.15 3.32
2658 2958 0.740149 GCATGATCCGCATCCAAACA 59.260 50.000 0.00 0.00 34.15 2.83
2684 3035 9.605275 TGAAATTACATGAAATCTACAGGAGAG 57.395 33.333 0.00 0.00 37.70 3.20
2705 3056 9.603921 GGACAATTTTCATTATGATGGTGAAAT 57.396 29.630 0.00 0.00 40.37 2.17
2712 3064 8.547894 CATGCTTGGACAATTTTCATTATGATG 58.452 33.333 0.00 0.00 34.46 3.07
2779 3137 6.821665 GGATAAAGCTACCTGACACAAACATA 59.178 38.462 0.00 0.00 0.00 2.29
2876 3272 5.359009 ACCCTCAGTCATATCAAGCAAATTG 59.641 40.000 0.00 0.00 40.52 2.32
2962 3361 5.934625 GTGTCTCTCTGTGTCATTTACCAAT 59.065 40.000 0.00 0.00 0.00 3.16
3117 3516 5.872635 ACATGCAAGATTGTCTTACATTCG 58.127 37.500 0.00 0.00 38.15 3.34
3146 3545 3.732048 TTTAATCACCTTCTCCCCCAC 57.268 47.619 0.00 0.00 0.00 4.61
3149 3548 4.017126 CACCTTTTAATCACCTTCTCCCC 58.983 47.826 0.00 0.00 0.00 4.81
3172 3583 2.923121 AGCTGAGCAAGAAGTTCACAA 58.077 42.857 7.39 0.00 33.60 3.33
3186 3597 4.093291 AGCGCCCCTCAAGCTGAG 62.093 66.667 2.29 6.28 43.91 3.35
3209 3620 9.508567 GACAAATTATCTTTCCTTCTTGTATGC 57.491 33.333 0.00 0.00 0.00 3.14
3403 3814 1.710996 TTGGCTGGTTCCCTCCGAAA 61.711 55.000 0.00 0.00 30.39 3.46
3700 4114 0.835543 TGAATTTTGCCTGGTGGGGG 60.836 55.000 0.00 0.00 35.12 5.40
3708 4122 4.951715 TGACAGATAGCATGAATTTTGCCT 59.048 37.500 0.00 0.35 41.06 4.75
3834 4251 3.637229 AGAAGGAAGACTCGACAACTGAA 59.363 43.478 0.00 0.00 0.00 3.02
3864 4281 6.258354 TGTAGACCCCATAAGAACAGAACTA 58.742 40.000 0.00 0.00 0.00 2.24
3869 4286 3.775316 ACCTGTAGACCCCATAAGAACAG 59.225 47.826 0.00 0.00 34.15 3.16
3947 4364 2.028020 CACCTGTAGACCCCAGAAGTTC 60.028 54.545 0.00 0.00 31.38 3.01
4027 4444 2.826428 TCCTAATCAGATTGACAGCGC 58.174 47.619 5.85 0.00 0.00 5.92
4045 4462 4.142038 TCTTCCTTTGTAAACCAGCTTCC 58.858 43.478 0.00 0.00 0.00 3.46
4075 4492 3.973135 CAGCGCATGAGATTAAGAAATGC 59.027 43.478 11.47 0.00 40.14 3.56
4132 4549 0.625849 ACGATGAAAAGGCCCCAGAT 59.374 50.000 0.00 0.00 0.00 2.90
4201 4618 6.785191 ACGCATCATTTTGTATTCGAAGAAT 58.215 32.000 3.35 0.79 45.90 2.40
4292 4709 4.334481 CGTACTCTGTTGGTGAACCTTTTT 59.666 41.667 0.37 0.00 36.82 1.94
4298 4715 6.865205 AGTATAAACGTACTCTGTTGGTGAAC 59.135 38.462 0.00 0.00 28.99 3.18
4299 4716 6.985117 AGTATAAACGTACTCTGTTGGTGAA 58.015 36.000 0.00 0.00 28.99 3.18
4307 4724 9.275231 CAACTCAACTAGTATAAACGTACTCTG 57.725 37.037 0.00 0.00 37.50 3.35
4318 4735 5.656480 TGCGCAATCAACTCAACTAGTATA 58.344 37.500 8.16 0.00 37.50 1.47
4320 4737 3.920446 TGCGCAATCAACTCAACTAGTA 58.080 40.909 8.16 0.00 37.50 1.82
4321 4738 2.766313 TGCGCAATCAACTCAACTAGT 58.234 42.857 8.16 0.00 41.49 2.57
4322 4739 3.811722 TTGCGCAATCAACTCAACTAG 57.188 42.857 21.02 0.00 0.00 2.57
4329 4746 0.743688 TGTGGTTTGCGCAATCAACT 59.256 45.000 29.52 0.00 0.00 3.16
4333 4750 1.782044 AACATGTGGTTTGCGCAATC 58.218 45.000 25.64 22.70 35.82 2.67
4367 4784 0.521291 CAAGGCATGTGGTTACGTGG 59.479 55.000 0.00 0.00 42.76 4.94
4382 4799 4.280677 TGTGATTCCCTTTTACTTGCAAGG 59.719 41.667 29.18 12.07 39.58 3.61
4464 4881 6.542370 GCACCCAATAGAGCAGTTTCTTAATA 59.458 38.462 0.00 0.00 0.00 0.98
4508 4925 2.232208 AGTCATGTGTCAGATTCGCTCA 59.768 45.455 0.00 0.00 0.00 4.26
4513 4930 5.106436 TGCATTTCAGTCATGTGTCAGATTC 60.106 40.000 0.00 0.00 0.00 2.52
4524 4941 4.877378 ATTTGGTGTGCATTTCAGTCAT 57.123 36.364 0.00 0.00 0.00 3.06
4526 4943 5.105797 TGGATATTTGGTGTGCATTTCAGTC 60.106 40.000 0.00 0.00 0.00 3.51
4534 4951 6.015095 TGTTTTATGTGGATATTTGGTGTGCA 60.015 34.615 0.00 0.00 0.00 4.57
4535 4952 6.310224 GTGTTTTATGTGGATATTTGGTGTGC 59.690 38.462 0.00 0.00 0.00 4.57
4546 4963 3.168035 TGCCCAGTGTTTTATGTGGAT 57.832 42.857 0.00 0.00 31.04 3.41
4552 4969 6.245408 TCTACTCAATTGCCCAGTGTTTTAT 58.755 36.000 0.00 0.00 0.00 1.40
4568 4985 8.484214 AGATATGTGCTAATCCTTCTACTCAA 57.516 34.615 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.