Multiple sequence alignment - TraesCS3A01G362800

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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 TraesCS3A01G362800 chr3A 100.000 6496 0 0 1 6496 611164787 611171282 0.000000e+00 11996.0
1 TraesCS3A01G362800 chr3A 93.421 76 5 0 5896 5971 611170611 611170686 5.320000e-21 113.0
2 TraesCS3A01G362800 chr3A 93.421 76 5 0 5825 5900 611170682 611170757 5.320000e-21 113.0
3 TraesCS3A01G362800 chr3D 92.031 4593 236 62 415 4913 468949854 468954410 0.000000e+00 6335.0
4 TraesCS3A01G362800 chr3D 95.144 556 19 6 5207 5755 468954469 468955023 0.000000e+00 870.0
5 TraesCS3A01G362800 chr3D 90.329 486 18 11 6016 6496 468970577 468971038 1.550000e-170 610.0
6 TraesCS3A01G362800 chr3D 89.918 486 20 11 6016 6496 468963013 468963474 3.350000e-167 599.0
7 TraesCS3A01G362800 chr3D 95.492 244 10 1 5655 5898 468970251 468970493 7.900000e-104 388.0
8 TraesCS3A01G362800 chr3D 89.873 237 20 4 1037 1273 456019207 456018975 1.060000e-77 302.0
9 TraesCS3A01G362800 chr3D 92.105 152 11 1 5747 5898 468962779 468962929 5.100000e-51 213.0
10 TraesCS3A01G362800 chr3D 90.083 121 12 0 5896 6016 468962856 468962976 2.420000e-34 158.0
11 TraesCS3A01G362800 chr3D 90.435 115 11 0 5896 6010 468970420 468970534 1.130000e-32 152.0
12 TraesCS3A01G362800 chr3D 92.857 56 4 0 2 57 468948211 468948266 1.500000e-11 82.4
13 TraesCS3A01G362800 chr3B 91.687 3284 162 42 415 3637 622759398 622762631 0.000000e+00 4449.0
14 TraesCS3A01G362800 chr3B 94.874 1034 30 6 3703 4727 622762631 622763650 0.000000e+00 1594.0
15 TraesCS3A01G362800 chr3B 92.745 827 42 8 5083 5900 622764149 622764966 0.000000e+00 1179.0
16 TraesCS3A01G362800 chr3B 93.817 372 19 2 6016 6384 622765048 622765418 2.050000e-154 556.0
17 TraesCS3A01G362800 chr3B 91.597 238 18 2 4752 4989 622763728 622763963 1.750000e-85 327.0
18 TraesCS3A01G362800 chr3B 92.667 150 10 1 207 356 622757780 622757928 1.420000e-51 215.0
19 TraesCS3A01G362800 chr3B 93.443 122 7 1 5896 6016 622764890 622765011 5.170000e-41 180.0
20 TraesCS3A01G362800 chr3B 91.579 95 1 4 6408 6496 622765531 622765624 2.460000e-24 124.0
21 TraesCS3A01G362800 chr3B 92.982 57 4 0 1 57 622757435 622757491 4.170000e-12 84.2
22 TraesCS3A01G362800 chr5D 88.670 203 20 2 1040 1242 24040977 24040778 1.810000e-60 244.0
23 TraesCS3A01G362800 chr5D 94.203 69 4 0 5018 5086 41140035 41139967 8.910000e-19 106.0
24 TraesCS3A01G362800 chr1A 90.789 76 5 2 5012 5086 6430020 6430094 4.140000e-17 100.0
25 TraesCS3A01G362800 chr4A 91.892 74 1 2 5017 5085 595568234 595568161 1.490000e-16 99.0
26 TraesCS3A01G362800 chr4A 91.667 72 1 1 5018 5084 595568162 595568233 1.930000e-15 95.3
27 TraesCS3A01G362800 chr7D 92.647 68 2 1 5018 5085 185137997 185138061 1.930000e-15 95.3
28 TraesCS3A01G362800 chr7D 89.333 75 4 2 5015 5085 383219868 383219942 2.490000e-14 91.6
29 TraesCS3A01G362800 chr1D 91.429 70 3 2 5018 5084 490579881 490579950 6.940000e-15 93.5
30 TraesCS3A01G362800 chr6D 91.304 69 3 3 5018 5086 406205748 406205683 2.490000e-14 91.6
31 TraesCS3A01G362800 chr6B 89.041 73 7 1 5014 5086 14541143 14541072 8.970000e-14 89.8


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 TraesCS3A01G362800 chr3A 611164787 611171282 6495 False 4074.000000 11996 95.614000 1 6496 3 chr3A.!!$F1 6495
1 TraesCS3A01G362800 chr3D 468948211 468955023 6812 False 2429.133333 6335 93.344000 2 5755 3 chr3D.!!$F1 5753
2 TraesCS3A01G362800 chr3D 468970251 468971038 787 False 383.333333 610 92.085333 5655 6496 3 chr3D.!!$F3 841
3 TraesCS3A01G362800 chr3D 468962779 468963474 695 False 323.333333 599 90.702000 5747 6496 3 chr3D.!!$F2 749
4 TraesCS3A01G362800 chr3B 622757435 622765624 8189 False 967.577778 4449 92.821222 1 6496 9 chr3B.!!$F1 6495

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
551 3152 0.179051 TTTTAACTGGTGGACGCGGT 60.179 50.000 12.47 0.0 0.00 5.68 F
1351 4002 0.179189 GCTCGTCTTTCCATTTGGCG 60.179 55.000 0.00 0.0 34.44 5.69 F
1488 4139 0.316360 GTACTCTCTACGAGCAGCGC 60.316 60.000 0.00 0.0 46.04 5.92 F
1981 4671 0.392706 AATCGACACTGACCTGTGCA 59.607 50.000 6.90 0.0 41.30 4.57 F
2108 4798 1.196354 CTCGTTGCCTTTGCTCTCTTG 59.804 52.381 0.00 0.0 38.71 3.02 F
3692 6413 0.552848 GGGGCATTCCTCCATTGAGA 59.447 55.000 0.00 0.0 41.42 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 4134 0.165944 AAGAAAATTCCGACGCGCTG 59.834 50.000 5.73 1.02 0.00 5.18 R
3026 5732 0.394192 CTGATAGCCGATCCTTGCCA 59.606 55.000 0.00 0.00 33.07 4.92 R
3088 5794 1.194547 CCGTGACACGATTTCCTGTTG 59.805 52.381 28.83 4.41 46.05 3.33 R
3671 6392 1.220518 TCAATGGAGGAATGCCCCCA 61.221 55.000 0.00 0.00 38.87 4.96 R
3790 6515 1.352352 ACTCCCCAGAAACATGGTCAG 59.648 52.381 0.00 0.00 38.81 3.51 R
5574 8559 0.546747 AAGGGACCTCGGTGGATGAA 60.547 55.000 2.59 0.00 39.71 2.57 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
35 36 5.772004 GCTCTATAGAGGGGAAGATGGATA 58.228 45.833 27.21 0.00 42.29 2.59
39 40 8.615360 TCTATAGAGGGGAAGATGGATATTTG 57.385 38.462 0.00 0.00 0.00 2.32
49 50 7.552687 GGGAAGATGGATATTTGCGTATAATCA 59.447 37.037 0.00 0.00 0.00 2.57
61 112 3.244078 GCGTATAATCACATCCACCCTCA 60.244 47.826 0.00 0.00 0.00 3.86
139 190 4.451150 CCGCTACTTGCTGGCCGA 62.451 66.667 0.00 0.00 40.11 5.54
198 257 3.459063 ACCCGCTTCTCCGCTACC 61.459 66.667 0.00 0.00 0.00 3.18
251 1435 4.804139 CCGAATGTAGAGTCGCAACTAAAT 59.196 41.667 3.96 0.00 38.35 1.40
253 1437 5.515270 CGAATGTAGAGTCGCAACTAAATCA 59.485 40.000 0.00 0.00 35.28 2.57
273 1457 2.791383 TGTTGAAGACAATTTGGGCG 57.209 45.000 0.78 0.00 38.32 6.13
294 1478 6.128553 GGGCGTATACATGACATTAAGTGATG 60.129 42.308 0.00 0.00 45.88 3.07
307 1491 3.287867 AAGTGATGGCATCCGAATTCT 57.712 42.857 23.92 9.97 0.00 2.40
347 1532 4.421058 CTGCAATGGACAAAGATGATGTG 58.579 43.478 0.00 0.00 0.00 3.21
383 1592 8.611654 AAAAAGCATCCCATTATATTTGCATC 57.388 30.769 0.00 0.00 32.66 3.91
431 3027 5.063880 CCATAGTTTGGGAGCATAACCTAC 58.936 45.833 0.00 0.00 42.33 3.18
437 3033 1.227147 GAGCATAACCTACGCCGCA 60.227 57.895 0.00 0.00 0.00 5.69
551 3152 0.179051 TTTTAACTGGTGGACGCGGT 60.179 50.000 12.47 0.00 0.00 5.68
553 3154 2.718747 TTAACTGGTGGACGCGGTGG 62.719 60.000 12.47 0.00 0.00 4.61
600 3203 2.120053 TACCGGTAGCCCCACACA 59.880 61.111 11.16 0.00 0.00 3.72
663 3279 3.282745 CTGCTGACACGTACGCCCT 62.283 63.158 16.72 0.00 0.00 5.19
664 3280 2.809601 GCTGACACGTACGCCCTG 60.810 66.667 16.72 9.09 0.00 4.45
749 3366 4.899239 CCGGATCCAGCGGCTCAC 62.899 72.222 13.41 0.00 0.00 3.51
751 3368 4.554036 GGATCCAGCGGCTCACCC 62.554 72.222 6.95 0.00 0.00 4.61
967 3600 3.437795 GGTTCGAGACGGAGGCGA 61.438 66.667 0.00 0.00 0.00 5.54
1116 3758 4.475135 GCGGGGAAGGAGCAGGTC 62.475 72.222 0.00 0.00 0.00 3.85
1287 3933 3.717294 GCCGCCCTCCCTTCTCAA 61.717 66.667 0.00 0.00 0.00 3.02
1315 3966 3.057734 CTCCGTTTGTGTTCTGGTACTC 58.942 50.000 0.00 0.00 0.00 2.59
1316 3967 2.140717 CCGTTTGTGTTCTGGTACTCC 58.859 52.381 0.00 0.00 0.00 3.85
1338 3989 2.248431 GCGTTGGTTGTGCTCGTC 59.752 61.111 0.00 0.00 0.00 4.20
1339 3990 2.244651 GCGTTGGTTGTGCTCGTCT 61.245 57.895 0.00 0.00 0.00 4.18
1351 4002 0.179189 GCTCGTCTTTCCATTTGGCG 60.179 55.000 0.00 0.00 34.44 5.69
1414 4065 4.604976 GCAGGATTGCTTATTTGCTAGTG 58.395 43.478 0.00 0.00 46.95 2.74
1452 4103 0.329261 TTGGCCTGATGAGTGAAGGG 59.671 55.000 3.32 0.00 0.00 3.95
1457 4108 1.406614 CCTGATGAGTGAAGGGCTGTC 60.407 57.143 0.00 0.00 0.00 3.51
1459 4110 1.552337 TGATGAGTGAAGGGCTGTCTC 59.448 52.381 0.00 0.00 0.00 3.36
1476 4127 3.309138 TGTCTCGCGATACAAGTACTCTC 59.691 47.826 23.05 0.00 0.00 3.20
1483 4134 4.608890 GCGATACAAGTACTCTCTACGAGC 60.609 50.000 0.00 0.00 43.85 5.03
1486 4137 2.420722 ACAAGTACTCTCTACGAGCAGC 59.579 50.000 0.00 0.00 43.85 5.25
1488 4139 0.316360 GTACTCTCTACGAGCAGCGC 60.316 60.000 0.00 0.00 46.04 5.92
1489 4140 1.763200 TACTCTCTACGAGCAGCGCG 61.763 60.000 17.71 17.71 46.04 6.86
1507 4162 3.488489 CGCGTCGGAATTTTCTTGAATT 58.512 40.909 0.00 0.00 32.16 2.17
1508 4163 4.643953 CGCGTCGGAATTTTCTTGAATTA 58.356 39.130 0.00 0.00 29.75 1.40
1509 4164 4.723862 CGCGTCGGAATTTTCTTGAATTAG 59.276 41.667 0.00 0.00 29.75 1.73
1510 4165 4.495828 GCGTCGGAATTTTCTTGAATTAGC 59.504 41.667 0.00 0.00 29.75 3.09
1511 4166 5.627172 CGTCGGAATTTTCTTGAATTAGCA 58.373 37.500 0.00 0.00 29.75 3.49
1523 4178 9.844790 TTTCTTGAATTAGCATATCACACTTTG 57.155 29.630 0.00 0.00 0.00 2.77
1544 4199 5.329035 TGGAATCTGCTTTTGAAATAGCC 57.671 39.130 8.75 0.00 36.56 3.93
1621 4277 5.790593 TGGGATTTGTGTTCTACTGAGTAC 58.209 41.667 0.00 0.00 0.00 2.73
1650 4316 7.387397 AGTGCTAAACAATGAAAAGAGAGAGAG 59.613 37.037 0.00 0.00 0.00 3.20
1651 4317 6.652481 TGCTAAACAATGAAAAGAGAGAGAGG 59.348 38.462 0.00 0.00 0.00 3.69
1727 4393 7.719778 TTTCTTATGATGTTCTCATGGATCG 57.280 36.000 0.00 0.00 44.48 3.69
1732 4398 4.798574 TGATGTTCTCATGGATCGTATCG 58.201 43.478 0.00 0.00 34.06 2.92
1746 4412 4.282950 TCGTATCGTTACTGGTGTGATC 57.717 45.455 2.39 0.00 0.00 2.92
1804 4470 5.701750 TCGAATGTCCGTTCAAATCCTTTAA 59.298 36.000 0.64 0.00 0.00 1.52
1830 4519 5.659440 AAATATGCCTTTTGTCGTTGGAT 57.341 34.783 0.00 0.00 0.00 3.41
1880 4569 9.903682 GTACTGTACAAATTCAGACTGTTAGTA 57.096 33.333 12.89 1.19 35.84 1.82
1889 4578 6.531503 TTCAGACTGTTAGTAATAGCTGCT 57.468 37.500 7.57 7.57 0.00 4.24
1924 4613 8.584157 AGTGATATGCCAAACTGAAACATTTTA 58.416 29.630 0.00 0.00 0.00 1.52
1938 4627 7.859598 TGAAACATTTTATGTCATTTGTTGGC 58.140 30.769 0.00 0.00 44.07 4.52
1940 4629 6.112927 ACATTTTATGTCATTTGTTGGCCT 57.887 33.333 3.32 0.00 39.92 5.19
1966 4656 6.313658 TGGTCAATGTGATCAAGTTCTAATCG 59.686 38.462 0.00 0.00 34.00 3.34
1980 4670 2.094700 TCTAATCGACACTGACCTGTGC 60.095 50.000 6.90 0.87 41.30 4.57
1981 4671 0.392706 AATCGACACTGACCTGTGCA 59.607 50.000 6.90 0.00 41.30 4.57
2079 4769 2.633967 TGGGAAGCACGAGGTAAAGTTA 59.366 45.455 0.00 0.00 0.00 2.24
2080 4770 3.071312 TGGGAAGCACGAGGTAAAGTTAA 59.929 43.478 0.00 0.00 0.00 2.01
2081 4771 3.434641 GGGAAGCACGAGGTAAAGTTAAC 59.565 47.826 0.00 0.00 0.00 2.01
2107 4797 1.202698 ACTCGTTGCCTTTGCTCTCTT 60.203 47.619 0.00 0.00 38.71 2.85
2108 4798 1.196354 CTCGTTGCCTTTGCTCTCTTG 59.804 52.381 0.00 0.00 38.71 3.02
2432 5137 3.217626 AGCTTCAGTTGGAACTTTGGAG 58.782 45.455 0.00 0.00 37.08 3.86
2524 5229 9.403110 CAGTTCTTCATTAAAAACATCTTCAGG 57.597 33.333 0.00 0.00 0.00 3.86
2529 5234 5.418840 TCATTAAAAACATCTTCAGGAGGGC 59.581 40.000 0.00 0.00 0.00 5.19
2877 5583 6.457159 TTTAACCTATCTGGGGAACTTTGA 57.543 37.500 0.00 0.00 41.11 2.69
2886 5592 4.018415 TCTGGGGAACTTTGAGGATTAAGG 60.018 45.833 0.00 0.00 0.00 2.69
3026 5732 5.357878 ACCTTGCATTGAATCAACATCGTAT 59.642 36.000 0.00 0.00 0.00 3.06
3088 5794 4.504097 CGCTGAAGGGCAAATTAATAAAGC 59.496 41.667 0.00 0.00 0.00 3.51
3104 5810 3.626028 AAAGCAACAGGAAATCGTGTC 57.374 42.857 8.98 0.00 43.25 3.67
3176 5882 7.560368 AGTTCTTTCTTTCAGTCTCTTTCTGA 58.440 34.615 0.00 0.00 39.71 3.27
3196 5902 6.263344 TCTGATACTTCTTTTGTCGTATCCG 58.737 40.000 0.00 0.00 38.14 4.18
3211 5917 3.867493 CGTATCCGTGTAGAGACAGTACA 59.133 47.826 0.00 0.00 35.82 2.90
3416 6123 2.215196 CAATTGCTGCCAGCTTGTTTT 58.785 42.857 18.96 1.62 42.97 2.43
3506 6222 8.023021 AGTCAAGCATGTAAGATACCATTAGA 57.977 34.615 0.00 0.00 0.00 2.10
3620 6341 8.217111 ACCAAAATGTTGAATGGGAGTATTTTT 58.783 29.630 0.00 0.00 36.83 1.94
3676 6397 3.303351 AGATGAGTTGCTTATTGGGGG 57.697 47.619 0.00 0.00 0.00 5.40
3691 6412 3.122369 GGGGCATTCCTCCATTGAG 57.878 57.895 0.00 0.00 38.42 3.02
3692 6413 0.552848 GGGGCATTCCTCCATTGAGA 59.447 55.000 0.00 0.00 41.42 3.27
3790 6515 1.602771 GTCTAGGGAGTTGGTGGCC 59.397 63.158 0.00 0.00 0.00 5.36
3879 6604 1.478105 GCCTTGTCCCCTTAAATGCAG 59.522 52.381 0.00 0.00 0.00 4.41
4089 6816 7.875971 AGTCTTTTCTATTTCAACACATGGTC 58.124 34.615 0.00 0.00 0.00 4.02
4239 6966 3.014623 ACATGATCAGCCACTCACAATG 58.985 45.455 0.00 0.00 0.00 2.82
4376 7106 4.282195 TGTGTCAGAAACTGTTTGGGTTTT 59.718 37.500 11.03 0.00 37.07 2.43
4389 7127 9.114952 ACTGTTTGGGTTTTATTTTTGTATTGG 57.885 29.630 0.00 0.00 0.00 3.16
4521 7264 6.198966 GTGCTTTTATTTTTCAGTGTGGACAG 59.801 38.462 0.00 0.00 0.00 3.51
4712 7455 1.988107 TGAGGTGGGAGCTTTGATTCT 59.012 47.619 0.00 0.00 0.00 2.40
4800 7595 6.658816 TCACTACACCAAATGCATAAGAATGT 59.341 34.615 0.00 4.26 35.38 2.71
4922 7717 6.927381 GCAATAATAACAGGTATAGTGGTCGT 59.073 38.462 0.00 0.00 0.00 4.34
4929 7724 5.910614 ACAGGTATAGTGGTCGTATTTTCC 58.089 41.667 0.00 0.00 0.00 3.13
4933 7728 6.040616 AGGTATAGTGGTCGTATTTTCCTCTG 59.959 42.308 0.00 0.00 0.00 3.35
4960 7755 1.002624 TCACCGTTCCAATCTGCCC 60.003 57.895 0.00 0.00 0.00 5.36
4970 7765 0.107703 CAATCTGCCCGAGTGCCTTA 60.108 55.000 0.00 0.00 30.27 2.69
4971 7766 0.107654 AATCTGCCCGAGTGCCTTAC 60.108 55.000 0.00 0.00 0.00 2.34
4974 7769 2.436115 GCCCGAGTGCCTTACCAC 60.436 66.667 0.00 0.00 35.98 4.16
4999 7954 5.048713 CCTTGGCTTGTACTTTAGAACCTTG 60.049 44.000 0.00 0.00 0.00 3.61
5001 7956 4.819630 TGGCTTGTACTTTAGAACCTTGTG 59.180 41.667 0.00 0.00 0.00 3.33
5012 7967 8.322091 ACTTTAGAACCTTGTGCTGTCTATTAT 58.678 33.333 0.00 0.00 0.00 1.28
5015 7970 9.817809 TTAGAACCTTGTGCTGTCTATTATTAG 57.182 33.333 0.00 0.00 0.00 1.73
5016 7971 7.852263 AGAACCTTGTGCTGTCTATTATTAGT 58.148 34.615 0.00 0.00 0.00 2.24
5017 7972 8.322091 AGAACCTTGTGCTGTCTATTATTAGTT 58.678 33.333 0.00 0.00 0.00 2.24
5018 7973 9.595823 GAACCTTGTGCTGTCTATTATTAGTTA 57.404 33.333 0.00 0.00 0.00 2.24
5019 7974 8.943909 ACCTTGTGCTGTCTATTATTAGTTAC 57.056 34.615 0.00 0.00 0.00 2.50
5020 7975 8.759782 ACCTTGTGCTGTCTATTATTAGTTACT 58.240 33.333 0.00 0.00 0.00 2.24
5021 7976 9.250624 CCTTGTGCTGTCTATTATTAGTTACTC 57.749 37.037 0.00 0.00 0.00 2.59
5022 7977 9.250624 CTTGTGCTGTCTATTATTAGTTACTCC 57.749 37.037 0.00 0.00 0.00 3.85
5023 7978 7.723324 TGTGCTGTCTATTATTAGTTACTCCC 58.277 38.462 0.00 0.00 0.00 4.30
5024 7979 7.563924 TGTGCTGTCTATTATTAGTTACTCCCT 59.436 37.037 0.00 0.00 0.00 4.20
5025 7980 7.868415 GTGCTGTCTATTATTAGTTACTCCCTG 59.132 40.741 0.00 0.00 0.00 4.45
5026 7981 7.563924 TGCTGTCTATTATTAGTTACTCCCTGT 59.436 37.037 0.00 0.00 0.00 4.00
5027 7982 7.868415 GCTGTCTATTATTAGTTACTCCCTGTG 59.132 40.741 0.00 0.00 0.00 3.66
5028 7983 8.834004 TGTCTATTATTAGTTACTCCCTGTGT 57.166 34.615 0.00 0.00 0.00 3.72
5029 7984 9.925545 TGTCTATTATTAGTTACTCCCTGTGTA 57.074 33.333 0.00 0.00 0.00 2.90
5045 8000 9.197694 CTCCCTGTGTAAAGAAATATAAGATCG 57.802 37.037 0.00 0.00 0.00 3.69
5046 8001 8.701895 TCCCTGTGTAAAGAAATATAAGATCGT 58.298 33.333 0.00 0.00 0.00 3.73
5047 8002 9.326413 CCCTGTGTAAAGAAATATAAGATCGTT 57.674 33.333 0.00 0.00 0.00 3.85
5079 8034 9.765795 AACGATCTTATATTTCTTTACAGAGGG 57.234 33.333 0.00 0.00 0.00 4.30
5080 8035 9.144298 ACGATCTTATATTTCTTTACAGAGGGA 57.856 33.333 0.00 0.00 0.00 4.20
5081 8036 9.632807 CGATCTTATATTTCTTTACAGAGGGAG 57.367 37.037 0.00 0.00 0.00 4.30
5097 8052 4.409247 AGAGGGAGTACAACTTTGTTCTGT 59.591 41.667 6.03 0.00 42.35 3.41
5099 8054 5.608449 AGGGAGTACAACTTTGTTCTGTAC 58.392 41.667 6.03 3.90 43.71 2.90
5126 8084 4.081972 GCTATTAGCTAGCCTGCATCAGTA 60.082 45.833 12.13 0.00 46.08 2.74
5137 8095 2.797156 CTGCATCAGTATCTTACCGCAC 59.203 50.000 0.00 0.00 0.00 5.34
5139 8097 2.540101 GCATCAGTATCTTACCGCACAC 59.460 50.000 0.00 0.00 0.00 3.82
5140 8098 3.780902 CATCAGTATCTTACCGCACACA 58.219 45.455 0.00 0.00 0.00 3.72
5141 8099 3.945981 TCAGTATCTTACCGCACACAA 57.054 42.857 0.00 0.00 0.00 3.33
5150 8108 0.179140 ACCGCACACAAAGCAAACAG 60.179 50.000 0.00 0.00 0.00 3.16
5204 8162 5.013704 TGTTGAGGTATGGAGGTAACATTGT 59.986 40.000 0.00 0.00 41.41 2.71
5387 8371 4.473520 CAGTTGGGCCTCGGCGAT 62.474 66.667 11.27 0.00 43.06 4.58
5417 8401 1.004320 AAACGTGCCCTGCATCGTA 60.004 52.632 13.86 0.00 41.99 3.43
5533 8518 2.204059 AGGAGCTGAACTGCCCCT 60.204 61.111 0.00 1.42 37.47 4.79
5574 8559 3.865571 TGTTAGGAGTTTGGTAGACCCT 58.134 45.455 0.00 0.00 34.29 4.34
5584 8573 0.464452 GGTAGACCCTTCATCCACCG 59.536 60.000 0.00 0.00 0.00 4.94
5610 8599 5.760253 GGTCCCTTGTACATACATGAATGAG 59.240 44.000 0.00 0.00 35.89 2.90
5653 8642 3.589951 ATCCATCCATTCTTCCCTGTG 57.410 47.619 0.00 0.00 0.00 3.66
5692 8687 4.260784 GCATTGGACGGACAGATTTGTATC 60.261 45.833 0.00 0.00 37.76 2.24
5757 8752 8.286800 GCACTGTTTGATTGTGTATACTTACAA 58.713 33.333 10.26 10.26 39.96 2.41
5782 8777 3.187700 ACTATTAGGTTCAAAGAGCGCG 58.812 45.455 0.00 0.00 0.00 6.86
5808 8803 0.322456 TGTGCTTGTATGGTGCTCCC 60.322 55.000 1.59 0.00 0.00 4.30
5843 8838 8.972127 AGCTATCTTAACAGAGATGTAACTTCA 58.028 33.333 0.00 0.00 37.01 3.02
5844 8839 9.587772 GCTATCTTAACAGAGATGTAACTTCAA 57.412 33.333 0.00 0.00 37.01 2.69
5847 8842 8.818141 TCTTAACAGAGATGTAACTTCAACTG 57.182 34.615 0.00 0.00 0.00 3.16
5848 8843 5.931441 AACAGAGATGTAACTTCAACTGC 57.069 39.130 0.00 0.00 0.00 4.40
5849 8844 3.990469 ACAGAGATGTAACTTCAACTGCG 59.010 43.478 0.00 0.00 0.00 5.18
5850 8845 4.237724 CAGAGATGTAACTTCAACTGCGA 58.762 43.478 0.00 0.00 0.00 5.10
5851 8846 4.686091 CAGAGATGTAACTTCAACTGCGAA 59.314 41.667 0.00 0.00 0.00 4.70
5852 8847 4.926238 AGAGATGTAACTTCAACTGCGAAG 59.074 41.667 6.02 6.02 46.47 3.79
5859 8854 2.708514 CTTCAACTGCGAAGTGTGTTG 58.291 47.619 0.00 0.00 38.07 3.33
5860 8855 1.732941 TCAACTGCGAAGTGTGTTGT 58.267 45.000 0.00 0.00 40.20 3.32
5861 8856 1.663643 TCAACTGCGAAGTGTGTTGTC 59.336 47.619 0.00 0.00 40.20 3.18
5862 8857 0.650512 AACTGCGAAGTGTGTTGTCG 59.349 50.000 0.00 0.00 37.82 4.35
5863 8858 0.459585 ACTGCGAAGTGTGTTGTCGT 60.460 50.000 0.00 0.00 37.12 4.34
5864 8859 0.229753 CTGCGAAGTGTGTTGTCGTC 59.770 55.000 0.00 0.00 37.12 4.20
5865 8860 0.179121 TGCGAAGTGTGTTGTCGTCT 60.179 50.000 0.00 0.00 37.12 4.18
5866 8861 0.229753 GCGAAGTGTGTTGTCGTCTG 59.770 55.000 0.00 0.00 37.12 3.51
5867 8862 1.556564 CGAAGTGTGTTGTCGTCTGT 58.443 50.000 0.00 0.00 0.00 3.41
5868 8863 1.517276 CGAAGTGTGTTGTCGTCTGTC 59.483 52.381 0.00 0.00 0.00 3.51
5869 8864 2.536365 GAAGTGTGTTGTCGTCTGTCA 58.464 47.619 0.00 0.00 0.00 3.58
5870 8865 1.922570 AGTGTGTTGTCGTCTGTCAC 58.077 50.000 0.00 0.00 0.00 3.67
5871 8866 0.928229 GTGTGTTGTCGTCTGTCACC 59.072 55.000 0.00 0.00 0.00 4.02
5872 8867 0.821517 TGTGTTGTCGTCTGTCACCT 59.178 50.000 0.00 0.00 0.00 4.00
5873 8868 1.206132 TGTGTTGTCGTCTGTCACCTT 59.794 47.619 0.00 0.00 0.00 3.50
5874 8869 2.277084 GTGTTGTCGTCTGTCACCTTT 58.723 47.619 0.00 0.00 0.00 3.11
5875 8870 2.030457 GTGTTGTCGTCTGTCACCTTTG 59.970 50.000 0.00 0.00 0.00 2.77
5876 8871 2.277084 GTTGTCGTCTGTCACCTTTGT 58.723 47.619 0.00 0.00 0.00 2.83
5877 8872 2.676342 GTTGTCGTCTGTCACCTTTGTT 59.324 45.455 0.00 0.00 0.00 2.83
5878 8873 2.980568 TGTCGTCTGTCACCTTTGTTT 58.019 42.857 0.00 0.00 0.00 2.83
5879 8874 3.340034 TGTCGTCTGTCACCTTTGTTTT 58.660 40.909 0.00 0.00 0.00 2.43
5880 8875 3.126171 TGTCGTCTGTCACCTTTGTTTTG 59.874 43.478 0.00 0.00 0.00 2.44
5881 8876 2.096819 TCGTCTGTCACCTTTGTTTTGC 59.903 45.455 0.00 0.00 0.00 3.68
5882 8877 2.097466 CGTCTGTCACCTTTGTTTTGCT 59.903 45.455 0.00 0.00 0.00 3.91
5883 8878 3.695816 GTCTGTCACCTTTGTTTTGCTC 58.304 45.455 0.00 0.00 0.00 4.26
5884 8879 2.687935 TCTGTCACCTTTGTTTTGCTCC 59.312 45.455 0.00 0.00 0.00 4.70
5885 8880 2.689983 CTGTCACCTTTGTTTTGCTCCT 59.310 45.455 0.00 0.00 0.00 3.69
5886 8881 2.426738 TGTCACCTTTGTTTTGCTCCTG 59.573 45.455 0.00 0.00 0.00 3.86
5887 8882 2.687935 GTCACCTTTGTTTTGCTCCTGA 59.312 45.455 0.00 0.00 0.00 3.86
5888 8883 3.130340 GTCACCTTTGTTTTGCTCCTGAA 59.870 43.478 0.00 0.00 0.00 3.02
5889 8884 3.766591 TCACCTTTGTTTTGCTCCTGAAA 59.233 39.130 0.00 0.00 0.00 2.69
5890 8885 4.221703 TCACCTTTGTTTTGCTCCTGAAAA 59.778 37.500 0.00 0.00 0.00 2.29
5891 8886 4.934602 CACCTTTGTTTTGCTCCTGAAAAA 59.065 37.500 0.00 0.00 0.00 1.94
5892 8887 4.935205 ACCTTTGTTTTGCTCCTGAAAAAC 59.065 37.500 5.64 5.64 46.71 2.43
5893 8888 5.178061 CCTTTGTTTTGCTCCTGAAAAACT 58.822 37.500 11.98 0.00 46.68 2.66
5894 8889 5.643348 CCTTTGTTTTGCTCCTGAAAAACTT 59.357 36.000 11.98 0.00 46.68 2.66
5895 8890 6.149308 CCTTTGTTTTGCTCCTGAAAAACTTT 59.851 34.615 11.98 0.00 46.68 2.66
5896 8891 7.308529 CCTTTGTTTTGCTCCTGAAAAACTTTT 60.309 33.333 11.98 0.00 46.68 2.27
5897 8892 8.608844 TTTGTTTTGCTCCTGAAAAACTTTTA 57.391 26.923 11.98 0.00 46.68 1.52
5898 8893 8.608844 TTGTTTTGCTCCTGAAAAACTTTTAA 57.391 26.923 11.98 0.00 46.68 1.52
5899 8894 8.024146 TGTTTTGCTCCTGAAAAACTTTTAAC 57.976 30.769 11.98 0.00 46.68 2.01
5900 8895 7.657761 TGTTTTGCTCCTGAAAAACTTTTAACA 59.342 29.630 11.98 0.00 46.68 2.41
5901 8896 7.826260 TTTGCTCCTGAAAAACTTTTAACAG 57.174 32.000 11.38 11.38 0.00 3.16
5902 8897 6.767524 TGCTCCTGAAAAACTTTTAACAGA 57.232 33.333 16.42 7.47 0.00 3.41
5903 8898 6.795399 TGCTCCTGAAAAACTTTTAACAGAG 58.205 36.000 16.42 13.51 0.00 3.35
5904 8899 6.601613 TGCTCCTGAAAAACTTTTAACAGAGA 59.398 34.615 16.42 12.55 0.00 3.10
5905 8900 7.285401 TGCTCCTGAAAAACTTTTAACAGAGAT 59.715 33.333 16.42 0.00 0.00 2.75
5906 8901 7.592903 GCTCCTGAAAAACTTTTAACAGAGATG 59.407 37.037 16.42 6.24 0.00 2.90
5907 8902 8.519799 TCCTGAAAAACTTTTAACAGAGATGT 57.480 30.769 16.42 0.00 0.00 3.06
5908 8903 9.621629 TCCTGAAAAACTTTTAACAGAGATGTA 57.378 29.630 16.42 0.00 0.00 2.29
5909 8904 9.884465 CCTGAAAAACTTTTAACAGAGATGTAG 57.116 33.333 16.42 0.00 0.00 2.74
5910 8905 9.387123 CTGAAAAACTTTTAACAGAGATGTAGC 57.613 33.333 12.33 0.00 0.00 3.58
5911 8906 9.120538 TGAAAAACTTTTAACAGAGATGTAGCT 57.879 29.630 0.00 0.00 0.00 3.32
5984 8979 7.918643 AGAACTTTTAACCGTGTCGAAAAATA 58.081 30.769 0.00 0.00 0.00 1.40
5985 8980 8.066000 AGAACTTTTAACCGTGTCGAAAAATAG 58.934 33.333 0.00 0.00 0.00 1.73
6011 9006 6.062258 ACCAAGTAACAAGGCATACATACT 57.938 37.500 0.00 0.00 0.00 2.12
6049 9081 4.695396 TCAACAAGAACATGCAATTGCTT 58.305 34.783 29.37 21.33 42.66 3.91
6082 9114 5.065218 CGATCCAGTTAGCTAGCAAATGTTT 59.935 40.000 18.83 7.92 0.00 2.83
6282 9320 2.743664 CAATTCCAACTGATCAGACGCA 59.256 45.455 29.27 9.02 0.00 5.24
6288 9326 1.719600 ACTGATCAGACGCAAGAAGC 58.280 50.000 29.27 0.00 43.62 3.86
6386 9424 9.982651 ACTAATTACGCACACTTTCATATAGAT 57.017 29.630 0.00 0.00 0.00 1.98
6485 9620 1.448893 GACGGCCCATCAACGCTAA 60.449 57.895 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.518970 GGGTGGATGTGATTATACGCAAAT 59.481 41.667 0.00 0.00 34.01 2.32
39 40 3.244078 TGAGGGTGGATGTGATTATACGC 60.244 47.826 0.00 0.00 0.00 4.42
49 50 3.717294 GGCGGTGAGGGTGGATGT 61.717 66.667 0.00 0.00 0.00 3.06
139 190 2.202797 CTGCATCTACGCCGCTGT 60.203 61.111 0.00 0.00 0.00 4.40
181 240 3.459063 GGTAGCGGAGAAGCGGGT 61.459 66.667 0.00 0.00 43.00 5.28
223 1407 0.179171 CGACTCTACATTCGGTGCGT 60.179 55.000 0.00 0.00 0.00 5.24
251 1435 3.305267 CGCCCAAATTGTCTTCAACATGA 60.305 43.478 0.00 0.00 37.82 3.07
253 1437 2.627699 ACGCCCAAATTGTCTTCAACAT 59.372 40.909 0.00 0.00 37.82 2.71
273 1457 7.728847 TGCCATCACTTAATGTCATGTATAC 57.271 36.000 0.00 0.00 0.00 1.47
394 1603 0.533755 CTATGGAAAGCAGGAGCCGG 60.534 60.000 0.00 0.00 43.56 6.13
431 3027 2.892373 TCTTAAAACAAGATGCGGCG 57.108 45.000 0.51 0.51 0.00 6.46
437 3033 8.624776 CACACCTCTTCTTTCTTAAAACAAGAT 58.375 33.333 0.00 0.00 31.60 2.40
551 3152 1.497309 ATTTTGACCTCCGCCTCCCA 61.497 55.000 0.00 0.00 0.00 4.37
553 3154 1.090052 CGATTTTGACCTCCGCCTCC 61.090 60.000 0.00 0.00 0.00 4.30
557 3158 0.094730 CGAACGATTTTGACCTCCGC 59.905 55.000 0.00 0.00 0.00 5.54
646 3262 3.299977 AGGGCGTACGTGTCAGCA 61.300 61.111 17.90 0.00 0.00 4.41
648 3264 1.733041 CACAGGGCGTACGTGTCAG 60.733 63.158 17.90 6.25 45.71 3.51
734 3351 4.554036 GGGTGAGCCGCTGGATCC 62.554 72.222 4.20 4.20 37.30 3.36
891 3508 0.744771 GAGGGAGATGGCGTTGGTTC 60.745 60.000 0.00 0.00 0.00 3.62
967 3600 4.323843 CGTACTCGCCGCCGCTAT 62.324 66.667 0.00 0.00 0.00 2.97
1020 3662 2.018086 CTCCCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1023 3665 2.204705 ACCTCCCCTCCTCCTCCT 60.205 66.667 0.00 0.00 0.00 3.69
1024 3666 2.041405 CACCTCCCCTCCTCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
1025 3667 2.041405 CCACCTCCCCTCCTCCTC 60.041 72.222 0.00 0.00 0.00 3.71
1026 3668 3.700350 CCCACCTCCCCTCCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
1116 3758 1.815421 GTAGCCCCACATCAGCACG 60.815 63.158 0.00 0.00 0.00 5.34
1215 3857 2.187946 CCGCAGACATCCCTCCAC 59.812 66.667 0.00 0.00 0.00 4.02
1275 3921 3.194329 GGAGCAAAAATTGAGAAGGGAGG 59.806 47.826 0.00 0.00 0.00 4.30
1287 3933 4.111916 CAGAACACAAACGGAGCAAAAAT 58.888 39.130 0.00 0.00 0.00 1.82
1315 3966 3.959975 CACAACCAACGCACCGGG 61.960 66.667 6.32 0.00 0.00 5.73
1316 3967 4.622456 GCACAACCAACGCACCGG 62.622 66.667 0.00 0.00 0.00 5.28
1338 3989 2.506881 GCGCCGCCAAATGGAAAG 60.507 61.111 0.00 0.00 37.39 2.62
1339 3990 3.279974 CTGCGCCGCCAAATGGAAA 62.280 57.895 6.63 0.00 37.39 3.13
1414 4065 4.201980 GCCAAAAATCCACTACCGAATACC 60.202 45.833 0.00 0.00 0.00 2.73
1452 4103 2.110226 GTACTTGTATCGCGAGACAGC 58.890 52.381 32.02 20.72 46.97 4.40
1457 4108 4.375205 CGTAGAGAGTACTTGTATCGCGAG 60.375 50.000 16.66 2.26 34.71 5.03
1459 4110 3.488678 TCGTAGAGAGTACTTGTATCGCG 59.511 47.826 0.00 0.00 0.00 5.87
1483 4134 0.165944 AAGAAAATTCCGACGCGCTG 59.834 50.000 5.73 1.02 0.00 5.18
1486 4137 2.587612 TTCAAGAAAATTCCGACGCG 57.412 45.000 3.53 3.53 0.00 6.01
1488 4139 5.627172 TGCTAATTCAAGAAAATTCCGACG 58.373 37.500 0.00 0.00 31.50 5.12
1489 4140 9.387123 GATATGCTAATTCAAGAAAATTCCGAC 57.613 33.333 0.00 0.00 31.50 4.79
1507 4162 5.528690 GCAGATTCCAAAGTGTGATATGCTA 59.471 40.000 0.00 0.00 0.00 3.49
1508 4163 4.337555 GCAGATTCCAAAGTGTGATATGCT 59.662 41.667 0.00 0.00 0.00 3.79
1509 4164 4.337555 AGCAGATTCCAAAGTGTGATATGC 59.662 41.667 0.00 0.00 0.00 3.14
1510 4165 6.446781 AAGCAGATTCCAAAGTGTGATATG 57.553 37.500 0.00 0.00 0.00 1.78
1511 4166 7.177216 TCAAAAGCAGATTCCAAAGTGTGATAT 59.823 33.333 0.00 0.00 0.00 1.63
1523 4178 4.096382 TCGGCTATTTCAAAAGCAGATTCC 59.904 41.667 6.63 0.00 37.89 3.01
1544 4199 2.286713 TGAAAATGCAACTTCACGGTCG 60.287 45.455 9.19 0.00 0.00 4.79
1577 4233 0.937304 CCACACAACTTCACTCACCG 59.063 55.000 0.00 0.00 0.00 4.94
1621 4277 7.172190 TCTCTCTTTTCATTGTTTAGCACTCAG 59.828 37.037 0.00 0.00 0.00 3.35
1650 4316 2.089201 CGACAAATGTAACCCTTCCCC 58.911 52.381 0.00 0.00 0.00 4.81
1651 4317 3.007635 CTCGACAAATGTAACCCTTCCC 58.992 50.000 0.00 0.00 0.00 3.97
1727 4393 4.282950 TCGATCACACCAGTAACGATAC 57.717 45.455 0.00 0.00 0.00 2.24
1732 4398 3.056749 ACTCCTTCGATCACACCAGTAAC 60.057 47.826 0.00 0.00 0.00 2.50
1746 4412 3.131223 TCCTTCATCTTGCTACTCCTTCG 59.869 47.826 0.00 0.00 0.00 3.79
1804 4470 6.151985 TCCAACGACAAAAGGCATATTTACAT 59.848 34.615 0.00 0.00 0.00 2.29
1830 4519 6.209192 ACATCAGCAAATTCTGTTGGTATTGA 59.791 34.615 9.02 0.00 37.12 2.57
1880 4569 8.781196 CATATCACTGAATAAACAGCAGCTATT 58.219 33.333 0.00 0.00 41.06 1.73
1881 4570 7.094890 GCATATCACTGAATAAACAGCAGCTAT 60.095 37.037 0.00 0.00 41.06 2.97
1889 4578 7.392953 TCAGTTTGGCATATCACTGAATAAACA 59.607 33.333 13.74 0.00 42.09 2.83
1924 4613 2.299867 GACCAAGGCCAACAAATGACAT 59.700 45.455 5.01 0.00 0.00 3.06
1938 4627 4.763793 AGAACTTGATCACATTGACCAAGG 59.236 41.667 13.66 0.00 0.00 3.61
1940 4629 7.148423 CGATTAGAACTTGATCACATTGACCAA 60.148 37.037 0.00 0.00 0.00 3.67
1966 4656 2.221169 TGAAATGCACAGGTCAGTGTC 58.779 47.619 0.00 0.00 41.52 3.67
1980 4670 7.149569 TCCAGACTCTAAAGCAAATGAAATG 57.850 36.000 0.00 0.00 0.00 2.32
1981 4671 7.765695 TTCCAGACTCTAAAGCAAATGAAAT 57.234 32.000 0.00 0.00 0.00 2.17
2107 4797 5.583457 TCTTCGAGTATTCTCATCGTGTACA 59.417 40.000 0.00 0.00 40.44 2.90
2108 4798 6.045698 TCTTCGAGTATTCTCATCGTGTAC 57.954 41.667 0.00 0.00 40.44 2.90
2334 5039 1.516110 ACCCCTTCATCTGATCCAGG 58.484 55.000 5.08 5.08 31.51 4.45
2408 5113 3.381272 CCAAAGTTCCAACTGAAGCTTGA 59.619 43.478 2.10 0.00 39.66 3.02
2432 5137 1.663135 GCGCTCTGTCTTTCATCCTTC 59.337 52.381 0.00 0.00 0.00 3.46
2840 5546 9.482627 CAGATAGGTTAAAAATAGCACTAGAGG 57.517 37.037 0.00 0.00 0.00 3.69
2877 5583 6.682537 TCAAGAAATATTGGGCCTTAATCCT 58.317 36.000 4.53 0.00 0.00 3.24
2886 5592 7.378181 TCTGAAGTTTTCAAGAAATATTGGGC 58.622 34.615 0.00 0.00 39.58 5.36
3026 5732 0.394192 CTGATAGCCGATCCTTGCCA 59.606 55.000 0.00 0.00 33.07 4.92
3088 5794 1.194547 CCGTGACACGATTTCCTGTTG 59.805 52.381 28.83 4.41 46.05 3.33
3104 5810 4.403137 CCACACGCAATGGCCGTG 62.403 66.667 13.33 13.33 44.43 4.94
3196 5902 9.599322 CAAAAATGATTTGTACTGTCTCTACAC 57.401 33.333 0.00 0.00 0.00 2.90
3211 5917 5.393461 GCCATCTCGAGACCAAAAATGATTT 60.393 40.000 19.30 0.00 0.00 2.17
3313 6020 5.428253 TGACCAGTTGGAAATATCTACTGC 58.572 41.667 4.92 0.00 37.12 4.40
3342 6049 3.967203 TTTACACTGTTACGCCAAACC 57.033 42.857 0.00 0.00 0.00 3.27
3416 6123 7.997991 TAAGCACCATCACTTTGCTACAGCA 62.998 44.000 0.00 0.00 45.93 4.41
3556 6275 7.389053 GGATGGATATTTCCTACAAGTAAGCTG 59.611 40.741 3.72 0.00 43.07 4.24
3582 6303 6.520272 TCAACATTTTGGTTGGAAATACCTG 58.480 36.000 6.24 0.00 46.29 4.00
3620 6341 7.591421 ATCTCATGATTATGCATTTGTCCAA 57.409 32.000 3.54 0.00 34.21 3.53
3671 6392 1.220518 TCAATGGAGGAATGCCCCCA 61.221 55.000 0.00 0.00 38.87 4.96
3676 6397 2.019984 GTGGTCTCAATGGAGGAATGC 58.980 52.381 0.00 0.00 41.69 3.56
3691 6412 7.945033 ATGAACAATTGTTAATGTTGTGGTC 57.055 32.000 23.33 7.58 39.73 4.02
3692 6413 8.729805 AAATGAACAATTGTTAATGTTGTGGT 57.270 26.923 23.33 2.62 39.73 4.16
3727 6448 6.265196 TCCATGATATGTACAATGGAAAAGGC 59.735 38.462 20.03 0.00 35.50 4.35
3790 6515 1.352352 ACTCCCCAGAAACATGGTCAG 59.648 52.381 0.00 0.00 38.81 3.51
3939 6664 2.814336 GGGCTGTGTTTTCTGAAGTAGG 59.186 50.000 0.00 0.00 0.00 3.18
3940 6665 2.814336 GGGGCTGTGTTTTCTGAAGTAG 59.186 50.000 0.00 0.00 0.00 2.57
4239 6966 9.129209 GAGATGGTATTTTTCAACTAAACAAGC 57.871 33.333 0.00 0.00 0.00 4.01
4433 7176 8.142551 GGTCAAAACATATAGACTAATCGACCT 58.857 37.037 0.00 0.00 35.05 3.85
4521 7264 4.780815 TCAACACATCATCTGTATTCCCC 58.219 43.478 0.00 0.00 35.91 4.81
4741 7484 9.415544 GCTTGATCAGAAACAAAATAACATTCT 57.584 29.630 0.00 0.00 0.00 2.40
4742 7485 9.415544 AGCTTGATCAGAAACAAAATAACATTC 57.584 29.630 0.00 0.00 0.00 2.67
4745 7488 7.715657 ACAGCTTGATCAGAAACAAAATAACA 58.284 30.769 0.00 0.00 0.00 2.41
4746 7489 8.078596 AGACAGCTTGATCAGAAACAAAATAAC 58.921 33.333 0.00 0.00 0.00 1.89
4748 7491 7.229306 ACAGACAGCTTGATCAGAAACAAAATA 59.771 33.333 0.00 0.00 0.00 1.40
4751 7494 4.883585 ACAGACAGCTTGATCAGAAACAAA 59.116 37.500 0.00 0.00 0.00 2.83
4752 7495 4.454678 ACAGACAGCTTGATCAGAAACAA 58.545 39.130 0.00 0.00 0.00 2.83
4754 7497 4.512944 TGAACAGACAGCTTGATCAGAAAC 59.487 41.667 0.00 0.00 0.00 2.78
4755 7498 4.512944 GTGAACAGACAGCTTGATCAGAAA 59.487 41.667 0.00 0.00 0.00 2.52
4811 7606 6.851222 CCAGTTTTGGTATAGTCTGCATAG 57.149 41.667 0.00 0.00 39.79 2.23
4836 7631 1.803453 TTTCCAAGCTGGGGGCATCT 61.803 55.000 7.48 0.00 44.79 2.90
4929 7724 0.900647 ACGGTGAGTTCCTCCCAGAG 60.901 60.000 0.00 0.00 0.00 3.35
4953 7748 1.522569 GTAAGGCACTCGGGCAGAT 59.477 57.895 0.00 0.00 46.44 2.90
4960 7755 0.673644 CAAGGGTGGTAAGGCACTCG 60.674 60.000 0.00 0.00 38.49 4.18
4974 7769 3.756963 GGTTCTAAAGTACAAGCCAAGGG 59.243 47.826 0.00 0.00 0.00 3.95
4999 7954 7.868415 CAGGGAGTAACTAATAATAGACAGCAC 59.132 40.741 0.00 0.00 33.15 4.40
5001 7956 7.868415 CACAGGGAGTAACTAATAATAGACAGC 59.132 40.741 0.00 0.00 33.15 4.40
5019 7974 9.197694 CGATCTTATATTTCTTTACACAGGGAG 57.802 37.037 0.00 0.00 0.00 4.30
5020 7975 8.701895 ACGATCTTATATTTCTTTACACAGGGA 58.298 33.333 0.00 0.00 0.00 4.20
5021 7976 8.888579 ACGATCTTATATTTCTTTACACAGGG 57.111 34.615 0.00 0.00 0.00 4.45
5053 8008 9.765795 CCCTCTGTAAAGAAATATAAGATCGTT 57.234 33.333 0.00 0.00 0.00 3.85
5054 8009 9.144298 TCCCTCTGTAAAGAAATATAAGATCGT 57.856 33.333 0.00 0.00 0.00 3.73
5055 8010 9.632807 CTCCCTCTGTAAAGAAATATAAGATCG 57.367 37.037 0.00 0.00 0.00 3.69
5062 8017 9.047947 AGTTGTACTCCCTCTGTAAAGAAATAT 57.952 33.333 0.00 0.00 0.00 1.28
5063 8018 8.431910 AGTTGTACTCCCTCTGTAAAGAAATA 57.568 34.615 0.00 0.00 0.00 1.40
5064 8019 7.317722 AGTTGTACTCCCTCTGTAAAGAAAT 57.682 36.000 0.00 0.00 0.00 2.17
5065 8020 6.742559 AGTTGTACTCCCTCTGTAAAGAAA 57.257 37.500 0.00 0.00 0.00 2.52
5066 8021 6.742559 AAGTTGTACTCCCTCTGTAAAGAA 57.257 37.500 0.00 0.00 0.00 2.52
5067 8022 6.099269 ACAAAGTTGTACTCCCTCTGTAAAGA 59.901 38.462 0.00 0.00 40.16 2.52
5068 8023 6.289064 ACAAAGTTGTACTCCCTCTGTAAAG 58.711 40.000 0.00 0.00 40.16 1.85
5069 8024 6.243216 ACAAAGTTGTACTCCCTCTGTAAA 57.757 37.500 0.00 0.00 40.16 2.01
5070 8025 5.881923 ACAAAGTTGTACTCCCTCTGTAA 57.118 39.130 0.00 0.00 40.16 2.41
5071 8026 5.601313 AGAACAAAGTTGTACTCCCTCTGTA 59.399 40.000 0.00 0.00 41.31 2.74
5072 8027 4.409247 AGAACAAAGTTGTACTCCCTCTGT 59.591 41.667 0.00 0.00 41.31 3.41
5073 8028 4.752101 CAGAACAAAGTTGTACTCCCTCTG 59.248 45.833 0.00 2.54 41.31 3.35
5074 8029 4.409247 ACAGAACAAAGTTGTACTCCCTCT 59.591 41.667 0.00 0.00 41.31 3.69
5075 8030 4.704965 ACAGAACAAAGTTGTACTCCCTC 58.295 43.478 0.00 0.00 41.31 4.30
5076 8031 4.772886 ACAGAACAAAGTTGTACTCCCT 57.227 40.909 0.00 0.00 41.31 4.20
5077 8032 4.753610 GGTACAGAACAAAGTTGTACTCCC 59.246 45.833 12.15 0.00 44.03 4.30
5078 8033 5.362263 TGGTACAGAACAAAGTTGTACTCC 58.638 41.667 12.15 0.48 44.03 3.85
5120 8078 4.465632 TTGTGTGCGGTAAGATACTGAT 57.534 40.909 0.60 0.00 37.22 2.90
5126 8084 1.890876 TGCTTTGTGTGCGGTAAGAT 58.109 45.000 0.00 0.00 0.00 2.40
5150 8108 0.601841 AGCAGCAACAATGGCAAAGC 60.602 50.000 0.00 0.00 0.00 3.51
5204 8162 3.765511 CCCTCATCTGCAGGAAATTTCAA 59.234 43.478 19.49 1.82 31.91 2.69
5319 8303 4.964897 TCAGAGATCATATCACACCAAGGT 59.035 41.667 0.00 0.00 0.00 3.50
5332 8316 4.654724 TCCAAAGCTCAGATCAGAGATCAT 59.345 41.667 18.52 2.90 37.87 2.45
5373 8357 4.483243 GGAATCGCCGAGGCCCAA 62.483 66.667 8.72 0.00 37.98 4.12
5387 8371 1.234821 GCACGTTTCTGTCCATGGAA 58.765 50.000 18.20 6.23 0.00 3.53
5533 8518 4.787551 ACAAAATTGTCACCTGACCTACA 58.212 39.130 2.98 0.00 44.15 2.74
5574 8559 0.546747 AAGGGACCTCGGTGGATGAA 60.547 55.000 2.59 0.00 39.71 2.57
5584 8573 5.353394 TTCATGTATGTACAAGGGACCTC 57.647 43.478 0.00 0.00 39.99 3.85
5610 8599 2.162208 CACAATGTCACTGTATGCACCC 59.838 50.000 0.00 0.00 0.00 4.61
5653 8642 2.815647 GCTGCACTCTGTACCGGC 60.816 66.667 0.00 0.00 0.00 6.13
5692 8687 1.469126 GACCGTATACACACAGCGCG 61.469 60.000 0.00 0.00 0.00 6.86
5757 8752 6.217294 GCGCTCTTTGAACCTAATAGTAGAT 58.783 40.000 0.00 0.00 0.00 1.98
5765 8760 2.380084 ATCGCGCTCTTTGAACCTAA 57.620 45.000 5.56 0.00 0.00 2.69
5782 8777 5.894807 AGCACCATACAAGCACAAATTATC 58.105 37.500 0.00 0.00 0.00 1.75
5808 8803 4.811024 TCTGTTAAGATAGCTGGAAATGCG 59.189 41.667 0.00 0.00 35.28 4.73
5843 8838 0.650512 CGACAACACACTTCGCAGTT 59.349 50.000 0.00 0.00 0.00 3.16
5844 8839 0.459585 ACGACAACACACTTCGCAGT 60.460 50.000 0.00 0.00 36.18 4.40
5845 8840 0.229753 GACGACAACACACTTCGCAG 59.770 55.000 0.00 0.00 36.18 5.18
5846 8841 0.179121 AGACGACAACACACTTCGCA 60.179 50.000 0.00 0.00 36.18 5.10
5847 8842 0.229753 CAGACGACAACACACTTCGC 59.770 55.000 0.00 0.00 36.18 4.70
5848 8843 1.517276 GACAGACGACAACACACTTCG 59.483 52.381 0.00 0.00 38.73 3.79
5849 8844 2.281762 GTGACAGACGACAACACACTTC 59.718 50.000 0.00 0.00 0.00 3.01
5850 8845 2.268298 GTGACAGACGACAACACACTT 58.732 47.619 0.00 0.00 0.00 3.16
5851 8846 1.470979 GGTGACAGACGACAACACACT 60.471 52.381 0.00 0.00 33.82 3.55
5852 8847 0.928229 GGTGACAGACGACAACACAC 59.072 55.000 0.00 0.00 33.82 3.82
5853 8848 0.821517 AGGTGACAGACGACAACACA 59.178 50.000 0.00 0.00 33.82 3.72
5854 8849 1.935933 AAGGTGACAGACGACAACAC 58.064 50.000 0.00 0.00 0.00 3.32
5855 8850 2.276201 CAAAGGTGACAGACGACAACA 58.724 47.619 0.00 0.00 0.00 3.33
5856 8851 2.277084 ACAAAGGTGACAGACGACAAC 58.723 47.619 0.00 0.00 0.00 3.32
5857 8852 2.684001 ACAAAGGTGACAGACGACAA 57.316 45.000 0.00 0.00 0.00 3.18
5858 8853 2.684001 AACAAAGGTGACAGACGACA 57.316 45.000 0.00 0.00 0.00 4.35
5859 8854 3.680789 CAAAACAAAGGTGACAGACGAC 58.319 45.455 0.00 0.00 0.00 4.34
5860 8855 2.096819 GCAAAACAAAGGTGACAGACGA 59.903 45.455 0.00 0.00 0.00 4.20
5861 8856 2.097466 AGCAAAACAAAGGTGACAGACG 59.903 45.455 0.00 0.00 0.00 4.18
5862 8857 3.489229 GGAGCAAAACAAAGGTGACAGAC 60.489 47.826 0.00 0.00 0.00 3.51
5863 8858 2.687935 GGAGCAAAACAAAGGTGACAGA 59.312 45.455 0.00 0.00 0.00 3.41
5864 8859 2.689983 AGGAGCAAAACAAAGGTGACAG 59.310 45.455 0.00 0.00 0.00 3.51
5865 8860 2.426738 CAGGAGCAAAACAAAGGTGACA 59.573 45.455 0.00 0.00 0.00 3.58
5866 8861 2.687935 TCAGGAGCAAAACAAAGGTGAC 59.312 45.455 0.00 0.00 0.00 3.67
5867 8862 3.011566 TCAGGAGCAAAACAAAGGTGA 57.988 42.857 0.00 0.00 0.00 4.02
5868 8863 3.799281 TTCAGGAGCAAAACAAAGGTG 57.201 42.857 0.00 0.00 0.00 4.00
5869 8864 4.817318 TTTTCAGGAGCAAAACAAAGGT 57.183 36.364 0.00 0.00 0.00 3.50
5870 8865 5.178061 AGTTTTTCAGGAGCAAAACAAAGG 58.822 37.500 9.61 0.00 42.80 3.11
5871 8866 6.726258 AAGTTTTTCAGGAGCAAAACAAAG 57.274 33.333 9.61 0.00 42.80 2.77
5872 8867 7.503521 AAAAGTTTTTCAGGAGCAAAACAAA 57.496 28.000 9.61 0.00 42.80 2.83
5873 8868 8.499967 GTTAAAAGTTTTTCAGGAGCAAAACAA 58.500 29.630 6.10 0.00 42.80 2.83
5874 8869 7.657761 TGTTAAAAGTTTTTCAGGAGCAAAACA 59.342 29.630 6.10 4.31 42.80 2.83
5875 8870 8.024146 TGTTAAAAGTTTTTCAGGAGCAAAAC 57.976 30.769 6.10 1.79 41.35 2.43
5876 8871 8.091449 TCTGTTAAAAGTTTTTCAGGAGCAAAA 58.909 29.630 21.76 7.99 0.00 2.44
5877 8872 7.607250 TCTGTTAAAAGTTTTTCAGGAGCAAA 58.393 30.769 21.76 8.45 0.00 3.68
5878 8873 7.122055 TCTCTGTTAAAAGTTTTTCAGGAGCAA 59.878 33.333 21.76 9.97 0.00 3.91
5879 8874 6.601613 TCTCTGTTAAAAGTTTTTCAGGAGCA 59.398 34.615 21.76 8.17 0.00 4.26
5880 8875 7.027778 TCTCTGTTAAAAGTTTTTCAGGAGC 57.972 36.000 21.76 4.87 0.00 4.70
5881 8876 8.624776 ACATCTCTGTTAAAAGTTTTTCAGGAG 58.375 33.333 21.76 18.46 28.70 3.69
5882 8877 8.519799 ACATCTCTGTTAAAAGTTTTTCAGGA 57.480 30.769 21.76 18.89 28.70 3.86
5883 8878 9.884465 CTACATCTCTGTTAAAAGTTTTTCAGG 57.116 33.333 21.76 16.16 36.79 3.86
5884 8879 9.387123 GCTACATCTCTGTTAAAAGTTTTTCAG 57.613 33.333 18.74 18.74 36.79 3.02
5885 8880 9.120538 AGCTACATCTCTGTTAAAAGTTTTTCA 57.879 29.630 6.10 6.04 36.79 2.69
5891 8886 9.780186 AGTTTTAGCTACATCTCTGTTAAAAGT 57.220 29.630 0.00 0.00 36.79 2.66
5893 8888 8.504005 GCAGTTTTAGCTACATCTCTGTTAAAA 58.496 33.333 0.00 0.00 36.79 1.52
5894 8889 7.659799 TGCAGTTTTAGCTACATCTCTGTTAAA 59.340 33.333 0.00 0.00 36.79 1.52
5895 8890 7.158697 TGCAGTTTTAGCTACATCTCTGTTAA 58.841 34.615 0.00 0.00 36.79 2.01
5896 8891 6.697395 TGCAGTTTTAGCTACATCTCTGTTA 58.303 36.000 0.00 0.00 36.79 2.41
5897 8892 5.551233 TGCAGTTTTAGCTACATCTCTGTT 58.449 37.500 0.00 0.00 36.79 3.16
5898 8893 5.152623 TGCAGTTTTAGCTACATCTCTGT 57.847 39.130 0.00 0.00 39.49 3.41
5899 8894 6.148480 ACTTTGCAGTTTTAGCTACATCTCTG 59.852 38.462 0.00 0.00 0.00 3.35
5900 8895 6.148480 CACTTTGCAGTTTTAGCTACATCTCT 59.852 38.462 0.00 0.00 0.00 3.10
5901 8896 6.073003 ACACTTTGCAGTTTTAGCTACATCTC 60.073 38.462 0.00 0.00 0.00 2.75
5902 8897 5.765182 ACACTTTGCAGTTTTAGCTACATCT 59.235 36.000 0.00 0.00 0.00 2.90
5903 8898 5.853282 CACACTTTGCAGTTTTAGCTACATC 59.147 40.000 0.00 0.00 0.00 3.06
5904 8899 5.299279 ACACACTTTGCAGTTTTAGCTACAT 59.701 36.000 0.00 0.00 0.00 2.29
5905 8900 4.638421 ACACACTTTGCAGTTTTAGCTACA 59.362 37.500 0.00 0.00 0.00 2.74
5906 8901 5.169836 ACACACTTTGCAGTTTTAGCTAC 57.830 39.130 0.00 0.00 0.00 3.58
5907 8902 5.124776 ACAACACACTTTGCAGTTTTAGCTA 59.875 36.000 0.00 0.00 0.00 3.32
5908 8903 4.082245 ACAACACACTTTGCAGTTTTAGCT 60.082 37.500 0.00 0.00 0.00 3.32
5909 8904 4.173256 ACAACACACTTTGCAGTTTTAGC 58.827 39.130 0.00 0.00 0.00 3.09
5910 8905 4.495472 CGACAACACACTTTGCAGTTTTAG 59.505 41.667 0.00 0.00 0.00 1.85
5911 8906 4.083217 ACGACAACACACTTTGCAGTTTTA 60.083 37.500 0.00 0.00 0.00 1.52
5912 8907 3.241701 CGACAACACACTTTGCAGTTTT 58.758 40.909 0.00 0.00 0.00 2.43
5913 8908 2.227865 ACGACAACACACTTTGCAGTTT 59.772 40.909 0.00 0.00 0.00 2.66
5984 8979 5.381757 TGTATGCCTTGTTACTTGGTTTCT 58.618 37.500 0.00 0.00 0.00 2.52
5985 8980 5.699097 TGTATGCCTTGTTACTTGGTTTC 57.301 39.130 0.00 0.00 0.00 2.78
6011 9006 9.638239 GTTCTTGTTGATATGCTATTTCCAAAA 57.362 29.630 0.00 0.00 0.00 2.44
6027 9059 4.325028 AGCAATTGCATGTTCTTGTTGA 57.675 36.364 30.89 0.00 45.16 3.18
6049 9081 2.225491 GCTAACTGGATCGTTTGCAACA 59.775 45.455 0.00 0.00 42.47 3.33
6082 9114 8.615878 TGTCTCAAAATCGAAGGAAAAGATAA 57.384 30.769 0.00 0.00 0.00 1.75
6101 9133 1.407299 CCAATCCGGATGCTTGTCTCA 60.407 52.381 19.95 0.00 36.56 3.27
6151 9183 3.493873 GCACAGTGGATAGATCATCTGCA 60.494 47.826 1.84 0.00 32.69 4.41
6282 9320 2.751259 ACGATGTTGCATCATGCTTCTT 59.249 40.909 14.89 2.21 45.31 2.52
6288 9326 4.799419 TGTATCACGATGTTGCATCATG 57.201 40.909 14.89 9.59 0.00 3.07
6404 9442 9.823647 GGGGTGACTGATATAACAATCTATATG 57.176 37.037 0.00 0.00 0.00 1.78
6405 9443 9.560860 TGGGGTGACTGATATAACAATCTATAT 57.439 33.333 0.00 0.00 0.00 0.86
6406 9444 8.966155 TGGGGTGACTGATATAACAATCTATA 57.034 34.615 0.00 0.00 0.00 1.31
6419 9546 1.043816 CGCTCTATGGGGTGACTGAT 58.956 55.000 0.00 0.00 0.00 2.90
6420 9547 0.033503 TCGCTCTATGGGGTGACTGA 60.034 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.