Multiple sequence alignment - TraesCS5B01G334700

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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 TraesCS5B01G334700 chr5B 100.000 5767 0 0 1 5767 517870284 517864518 0.000000e+00 10650.0
1 TraesCS5B01G334700 chr5B 92.614 704 44 4 81 780 517889195 517888496 0.000000e+00 1005.0
2 TraesCS5B01G334700 chr5B 98.765 81 1 0 1 81 544518376 544518456 1.670000e-30 145.0
3 TraesCS5B01G334700 chr5A 90.966 3210 186 45 1930 5084 544568024 544564864 0.000000e+00 4226.0
4 TraesCS5B01G334700 chr5A 89.510 1468 73 37 522 1954 544569459 544568038 0.000000e+00 1783.0
5 TraesCS5B01G334700 chr5A 94.421 484 26 1 5050 5533 544563522 544563040 0.000000e+00 743.0
6 TraesCS5B01G334700 chr5A 91.765 170 7 3 317 479 544569625 544569456 4.490000e-56 230.0
7 TraesCS5B01G334700 chr5A 95.122 41 2 0 182 222 527780879 527780919 1.340000e-06 65.8
8 TraesCS5B01G334700 chr5D 91.153 1865 86 36 805 2637 428717557 428715740 0.000000e+00 2457.0
9 TraesCS5B01G334700 chr5D 93.305 1673 59 21 3230 4884 428715060 428713423 0.000000e+00 2420.0
10 TraesCS5B01G334700 chr5D 92.199 846 38 5 4947 5767 428713427 428712585 0.000000e+00 1171.0
11 TraesCS5B01G334700 chr5D 92.834 614 22 9 2634 3237 428715686 428715085 0.000000e+00 870.0
12 TraesCS5B01G334700 chr5D 84.158 303 19 18 327 627 428717980 428717705 3.430000e-67 267.0
13 TraesCS5B01G334700 chr5D 95.556 45 0 1 4882 4924 520110269 520110225 2.880000e-08 71.3
14 TraesCS5B01G334700 chr3A 82.520 246 39 4 79 322 704035585 704035828 4.530000e-51 213.0
15 TraesCS5B01G334700 chr3A 95.455 44 0 1 4884 4925 480152755 480152712 1.040000e-07 69.4
16 TraesCS5B01G334700 chr3A 95.122 41 2 0 182 222 23216130 23216090 1.340000e-06 65.8
17 TraesCS5B01G334700 chr4B 100.000 81 0 0 1 81 125423313 125423393 3.600000e-32 150.0
18 TraesCS5B01G334700 chr4B 97.531 81 2 0 1 81 125384373 125384293 7.790000e-29 139.0
19 TraesCS5B01G334700 chr4B 97.531 81 2 0 1 81 147353485 147353405 7.790000e-29 139.0
20 TraesCS5B01G334700 chr4B 96.364 55 2 0 5645 5699 585959370 585959316 2.210000e-14 91.6
21 TraesCS5B01G334700 chr7B 93.684 95 6 0 1637 1731 716024677 716024583 6.020000e-30 143.0
22 TraesCS5B01G334700 chr7B 94.643 56 3 0 5645 5700 11196783 11196838 2.860000e-13 87.9
23 TraesCS5B01G334700 chr7B 88.060 67 8 0 5701 5767 611534287 611534353 4.790000e-11 80.5
24 TraesCS5B01G334700 chr3B 97.561 82 2 0 2 83 685981592 685981511 2.170000e-29 141.0
25 TraesCS5B01G334700 chr7D 97.531 81 2 0 1 81 623785435 623785355 7.790000e-29 139.0
26 TraesCS5B01G334700 chr7D 92.632 95 7 0 1637 1731 620258100 620258006 2.800000e-28 137.0
27 TraesCS5B01G334700 chr7D 94.643 56 3 0 5644 5699 61226921 61226976 2.860000e-13 87.9
28 TraesCS5B01G334700 chr7D 92.500 40 2 1 174 213 13889154 13889192 8.070000e-04 56.5
29 TraesCS5B01G334700 chr4A 97.531 81 2 0 1 81 618192372 618192292 7.790000e-29 139.0
30 TraesCS5B01G334700 chr4A 97.531 81 2 0 1 81 618208961 618209041 7.790000e-29 139.0
31 TraesCS5B01G334700 chr4A 95.349 43 0 1 4881 4921 285485365 285485407 3.730000e-07 67.6
32 TraesCS5B01G334700 chr1D 97.531 81 2 0 1 81 348020304 348020224 7.790000e-29 139.0
33 TraesCS5B01G334700 chr1D 92.500 40 2 1 174 213 77843738 77843776 8.070000e-04 56.5
34 TraesCS5B01G334700 chr7A 92.632 95 7 0 1637 1731 714660941 714661035 2.800000e-28 137.0
35 TraesCS5B01G334700 chr7A 89.333 75 5 2 4883 4955 234912164 234912091 2.210000e-14 91.6
36 TraesCS5B01G334700 chr7A 88.060 67 8 0 5701 5767 85740723 85740657 4.790000e-11 80.5
37 TraesCS5B01G334700 chr7A 82.927 82 10 3 4875 4953 239033237 239033157 2.880000e-08 71.3
38 TraesCS5B01G334700 chr7A 88.136 59 7 0 5709 5767 671400076 671400134 2.880000e-08 71.3
39 TraesCS5B01G334700 chr7A 89.796 49 4 1 174 222 34345926 34345973 1.740000e-05 62.1
40 TraesCS5B01G334700 chr2B 78.307 189 33 7 133 318 39804384 39804201 1.310000e-21 115.0
41 TraesCS5B01G334700 chr2B 83.333 108 16 1 1624 1731 44408981 44408876 1.320000e-16 99.0
42 TraesCS5B01G334700 chr2B 96.364 55 2 0 5645 5699 383639990 383640044 2.210000e-14 91.6
43 TraesCS5B01G334700 chr2D 82.407 108 17 1 1624 1731 27912145 27912040 6.150000e-15 93.5
44 TraesCS5B01G334700 chr2D 94.643 56 3 0 5644 5699 648365455 648365400 2.860000e-13 87.9
45 TraesCS5B01G334700 chr2A 82.407 108 17 1 1624 1731 30136558 30136453 6.150000e-15 93.5
46 TraesCS5B01G334700 chr1A 96.429 56 2 0 5645 5700 10578529 10578474 6.150000e-15 93.5
47 TraesCS5B01G334700 chr3D 96.364 55 2 0 5645 5699 598117216 598117270 2.210000e-14 91.6
48 TraesCS5B01G334700 chr3D 89.474 57 3 2 4872 4926 74197493 74197548 1.040000e-07 69.4
49 TraesCS5B01G334700 chr3D 90.566 53 2 3 4872 4921 490836968 490837020 3.730000e-07 67.6
50 TraesCS5B01G334700 chr4D 94.545 55 3 0 5645 5699 6391248 6391194 1.030000e-12 86.1
51 TraesCS5B01G334700 chr1B 95.455 44 0 1 4883 4924 435094822 435094779 1.040000e-07 69.4
52 TraesCS5B01G334700 chr6A 95.122 41 2 0 182 222 606067142 606067102 1.340000e-06 65.8


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 TraesCS5B01G334700 chr5B 517864518 517870284 5766 True 10650.0 10650 100.0000 1 5767 1 chr5B.!!$R1 5766
1 TraesCS5B01G334700 chr5B 517888496 517889195 699 True 1005.0 1005 92.6140 81 780 1 chr5B.!!$R2 699
2 TraesCS5B01G334700 chr5A 544563040 544569625 6585 True 1745.5 4226 91.6655 317 5533 4 chr5A.!!$R1 5216
3 TraesCS5B01G334700 chr5D 428712585 428717980 5395 True 1437.0 2457 90.7298 327 5767 5 chr5D.!!$R2 5440

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
116 117 0.379669 CAGTGCCATTGCGAAGGATC 59.620 55.0 0.0 0.0 41.78 3.36 F
1426 1497 0.031314 CCCTCTCATCACCATCGTCG 59.969 60.0 0.0 0.0 0.00 5.12 F
1806 1884 0.105778 CATCTTCCTCCTCCCGCTTC 59.894 60.0 0.0 0.0 0.00 3.86 F
2463 2598 0.179116 CCTGTGCGATCTCCAGACTG 60.179 60.0 0.0 0.0 0.00 3.51 F
3125 3327 0.538057 ACTCCGGTACCTCGTTCACA 60.538 55.0 10.9 0.0 0.00 3.58 F
4515 4767 0.107945 GACCTTCTTCGCTGCCATCT 60.108 55.0 0.0 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1820 0.616111 ATTCTGGCGAGGAGAGTGGT 60.616 55.000 0.00 0.0 0.00 4.16 R
2582 2717 0.259938 GGGCTTGGGTGATCTTGGAT 59.740 55.000 0.00 0.0 0.00 3.41 R
3125 3327 0.616111 ACATTGGGTCGGAGAGAGCT 60.616 55.000 0.00 0.0 46.05 4.09 R
3902 4145 1.269448 GCGGGTCTGAAAATGAGCAAA 59.731 47.619 0.00 0.0 34.04 3.68 R
4673 4930 1.097547 TGGCCTACGTCTACCTACGC 61.098 60.000 3.32 0.0 46.71 4.42 R
5625 7294 0.175073 AAACCAGTCTATCCGCGACC 59.825 55.000 8.23 0.0 31.83 4.79 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
49 50 4.280019 GGGCCCAACCGGTCAGTT 62.280 66.667 19.95 0.00 38.37 3.16
50 51 2.203437 GGCCCAACCGGTCAGTTT 60.203 61.111 8.04 0.00 35.67 2.66
51 52 2.265904 GGCCCAACCGGTCAGTTTC 61.266 63.158 8.04 0.00 35.67 2.78
52 53 1.228154 GCCCAACCGGTCAGTTTCT 60.228 57.895 8.04 0.00 0.00 2.52
53 54 1.235281 GCCCAACCGGTCAGTTTCTC 61.235 60.000 8.04 0.00 0.00 2.87
54 55 0.396811 CCCAACCGGTCAGTTTCTCT 59.603 55.000 8.04 0.00 0.00 3.10
55 56 1.512926 CCAACCGGTCAGTTTCTCTG 58.487 55.000 8.04 0.00 44.85 3.35
56 57 1.202651 CCAACCGGTCAGTTTCTCTGT 60.203 52.381 8.04 0.00 43.97 3.41
57 58 2.135933 CAACCGGTCAGTTTCTCTGTC 58.864 52.381 8.04 0.00 43.97 3.51
58 59 1.410004 ACCGGTCAGTTTCTCTGTCA 58.590 50.000 0.00 0.00 43.97 3.58
59 60 1.760613 ACCGGTCAGTTTCTCTGTCAA 59.239 47.619 0.00 0.00 43.97 3.18
60 61 2.368875 ACCGGTCAGTTTCTCTGTCAAT 59.631 45.455 0.00 0.00 43.97 2.57
61 62 3.576982 ACCGGTCAGTTTCTCTGTCAATA 59.423 43.478 0.00 0.00 43.97 1.90
62 63 3.927142 CCGGTCAGTTTCTCTGTCAATAC 59.073 47.826 0.00 0.00 43.97 1.89
63 64 3.608506 CGGTCAGTTTCTCTGTCAATACG 59.391 47.826 0.00 0.00 43.97 3.06
64 65 4.557205 GGTCAGTTTCTCTGTCAATACGT 58.443 43.478 0.00 0.00 43.97 3.57
65 66 5.618418 CGGTCAGTTTCTCTGTCAATACGTA 60.618 44.000 0.00 0.00 43.97 3.57
66 67 6.331061 GGTCAGTTTCTCTGTCAATACGTAT 58.669 40.000 1.14 1.14 43.97 3.06
67 68 7.478322 GGTCAGTTTCTCTGTCAATACGTATA 58.522 38.462 8.83 0.00 43.97 1.47
68 69 7.972277 GGTCAGTTTCTCTGTCAATACGTATAA 59.028 37.037 8.83 0.00 43.97 0.98
69 70 9.350357 GTCAGTTTCTCTGTCAATACGTATAAA 57.650 33.333 8.83 0.24 43.97 1.40
70 71 9.917129 TCAGTTTCTCTGTCAATACGTATAAAA 57.083 29.630 8.83 0.00 43.97 1.52
71 72 9.953825 CAGTTTCTCTGTCAATACGTATAAAAC 57.046 33.333 8.83 8.04 39.17 2.43
109 110 1.929806 ATGCTGACAGTGCCATTGCG 61.930 55.000 3.99 0.00 41.78 4.85
110 111 2.327343 GCTGACAGTGCCATTGCGA 61.327 57.895 3.99 0.00 41.78 5.10
116 117 0.379669 CAGTGCCATTGCGAAGGATC 59.620 55.000 0.00 0.00 41.78 3.36
135 136 2.668550 GCTCGACCCAACCACACC 60.669 66.667 0.00 0.00 0.00 4.16
142 143 2.801342 CGACCCAACCACACCATTTTTG 60.801 50.000 0.00 0.00 0.00 2.44
161 162 7.518731 TTTTTGATCAAAACCTCGAAGTTTG 57.481 32.000 28.78 10.15 39.83 2.93
164 165 4.878971 TGATCAAAACCTCGAAGTTTGTGA 59.121 37.500 12.70 16.20 39.83 3.58
180 181 3.266510 TGTGACACTCAAGCAAGAAGT 57.733 42.857 7.20 0.00 0.00 3.01
198 199 4.814771 AGAAGTTCCCAGTTAACTTTGTCG 59.185 41.667 5.07 0.00 44.94 4.35
236 237 3.073356 TCGAGTTTAAGAACCAACCCCAT 59.927 43.478 0.00 0.00 36.39 4.00
240 241 3.732048 TTAAGAACCAACCCCATCCTC 57.268 47.619 0.00 0.00 0.00 3.71
251 252 4.946160 ACCCCATCCTCTTTTTGACATA 57.054 40.909 0.00 0.00 0.00 2.29
252 253 5.269554 ACCCCATCCTCTTTTTGACATAA 57.730 39.130 0.00 0.00 0.00 1.90
282 286 1.486726 AGTAACTCATGTAGGGCCAGC 59.513 52.381 6.18 0.00 0.00 4.85
283 287 0.464036 TAACTCATGTAGGGCCAGCG 59.536 55.000 6.18 0.00 0.00 5.18
478 490 1.002142 GAAAACCTACACCACGTTGGC 60.002 52.381 4.23 0.00 43.61 4.52
480 492 2.740826 CCTACACCACGTTGGCCG 60.741 66.667 0.00 0.00 42.67 6.13
512 524 0.894184 TGGAGACTGGACTCGACCAC 60.894 60.000 0.00 0.00 37.74 4.16
514 526 0.806241 GAGACTGGACTCGACCACTC 59.194 60.000 0.00 0.00 35.91 3.51
548 560 0.947660 CCGTGATCATCATCGCCCAG 60.948 60.000 0.00 0.00 36.32 4.45
747 780 1.723288 GGAAAACCAAACCCCATCCA 58.277 50.000 0.00 0.00 0.00 3.41
802 843 4.994471 CCACGGCAGCAGCACAGA 62.994 66.667 2.65 0.00 44.61 3.41
1090 1143 2.603776 GGGGTGGAGACGTGGAGT 60.604 66.667 0.00 0.00 0.00 3.85
1157 1215 2.125350 CTGCTTCTGGCCCTCGTC 60.125 66.667 0.00 0.00 40.92 4.20
1418 1489 4.554036 GCCCGCCCCTCTCATCAC 62.554 72.222 0.00 0.00 0.00 3.06
1423 1494 1.070445 GCCCCTCTCATCACCATCG 59.930 63.158 0.00 0.00 0.00 3.84
1426 1497 0.031314 CCCTCTCATCACCATCGTCG 59.969 60.000 0.00 0.00 0.00 5.12
1438 1509 2.193447 CCATCGTCGTCGTCAATTCAT 58.807 47.619 1.33 0.00 38.33 2.57
1484 1555 6.926313 AGGAGAGATTGGTAGCGATAATAAC 58.074 40.000 0.00 0.00 0.00 1.89
1537 1612 1.150536 GGAGGTTGCTGTCACCCAA 59.849 57.895 0.00 0.00 0.00 4.12
1742 1820 2.666190 GACTGCCTCAAGTGCGCA 60.666 61.111 5.66 5.66 0.00 6.09
1745 1823 4.560743 TGCCTCAAGTGCGCACCA 62.561 61.111 35.51 22.36 0.00 4.17
1798 1876 2.350863 ACCACCTTCATCTTCCTCCT 57.649 50.000 0.00 0.00 0.00 3.69
1801 1879 1.488393 CACCTTCATCTTCCTCCTCCC 59.512 57.143 0.00 0.00 0.00 4.30
1804 1882 0.325671 TTCATCTTCCTCCTCCCGCT 60.326 55.000 0.00 0.00 0.00 5.52
1805 1883 0.325671 TCATCTTCCTCCTCCCGCTT 60.326 55.000 0.00 0.00 0.00 4.68
1806 1884 0.105778 CATCTTCCTCCTCCCGCTTC 59.894 60.000 0.00 0.00 0.00 3.86
1807 1885 1.395826 ATCTTCCTCCTCCCGCTTCG 61.396 60.000 0.00 0.00 0.00 3.79
1808 1886 2.036731 TTCCTCCTCCCGCTTCGA 59.963 61.111 0.00 0.00 0.00 3.71
1858 1938 0.522915 GATTCGACCTCGTGTCCGTC 60.523 60.000 0.00 0.00 41.18 4.79
1864 1944 2.408022 CTCGTGTCCGTCGATCCC 59.592 66.667 0.00 0.00 36.73 3.85
1886 1967 3.264450 CAGAGATATTTCCGGGGGCTAAT 59.736 47.826 0.00 0.00 0.00 1.73
1894 1975 3.843893 TCCGGGGGCTAATTAGTTAAC 57.156 47.619 13.91 0.00 0.00 2.01
1920 2001 9.282569 CTACCAGAAGATTACGGTAGTATTAGT 57.717 37.037 6.34 0.00 43.96 2.24
1922 2003 8.411683 ACCAGAAGATTACGGTAGTATTAGTTG 58.588 37.037 0.00 0.00 32.12 3.16
1924 2005 9.798994 CAGAAGATTACGGTAGTATTAGTTGTT 57.201 33.333 0.00 0.00 32.12 2.83
1925 2006 9.798994 AGAAGATTACGGTAGTATTAGTTGTTG 57.201 33.333 0.00 0.00 32.12 3.33
1926 2007 7.998753 AGATTACGGTAGTATTAGTTGTTGC 57.001 36.000 0.00 0.00 32.12 4.17
1927 2008 7.549839 AGATTACGGTAGTATTAGTTGTTGCA 58.450 34.615 0.00 0.00 32.12 4.08
1928 2009 6.949578 TTACGGTAGTATTAGTTGTTGCAC 57.050 37.500 0.00 0.00 32.12 4.57
1945 2026 1.332997 GCACTTGCATGGTAGAGATGC 59.667 52.381 4.44 0.00 45.45 3.91
1983 2101 3.152261 ACTACTAGTCGACATGCTTGC 57.848 47.619 19.50 0.00 0.00 4.01
2011 2129 3.126858 GGAGTTGTTGCGAGCATAATTCA 59.873 43.478 14.72 3.46 0.00 2.57
2023 2141 5.355350 CGAGCATAATTCAGGGAAGAAAAGT 59.645 40.000 0.00 0.00 0.00 2.66
2050 2169 1.300311 CACGGAAGCACCACACGTA 60.300 57.895 0.00 0.00 38.90 3.57
2059 2178 2.431942 CCACACGTACCGTCCTGC 60.432 66.667 0.00 0.00 38.32 4.85
2063 2182 0.961019 ACACGTACCGTCCTGCTTTA 59.039 50.000 0.00 0.00 38.32 1.85
2150 2275 8.482128 ACACTACTACTACTACTACTAACCCAG 58.518 40.741 0.00 0.00 0.00 4.45
2208 2333 5.972107 AATCTTGTTGGAGGTTGAGATTG 57.028 39.130 0.00 0.00 33.83 2.67
2212 2337 3.689347 TGTTGGAGGTTGAGATTGATGG 58.311 45.455 0.00 0.00 0.00 3.51
2250 2375 8.352936 GTGAAAATTATTTACGCTTTACACACG 58.647 33.333 0.00 0.00 0.00 4.49
2265 2390 2.030893 ACACACGTTTGCTGAATCATGG 60.031 45.455 0.61 0.00 0.00 3.66
2282 2410 5.209818 TCATGGTATCCTAATTGACGACC 57.790 43.478 0.00 0.00 0.00 4.79
2331 2459 9.155975 GTCTCTTCTTCATGTTCTTGCTTAATA 57.844 33.333 0.00 0.00 0.00 0.98
2332 2460 9.725019 TCTCTTCTTCATGTTCTTGCTTAATAA 57.275 29.630 0.00 0.00 0.00 1.40
2349 2478 9.776158 TGCTTAATAATGTGTTAAATGTAACCG 57.224 29.630 3.27 0.00 39.16 4.44
2356 2485 4.034858 TGTGTTAAATGTAACCGCGTTTCA 59.965 37.500 4.92 4.34 39.16 2.69
2357 2486 4.968788 GTGTTAAATGTAACCGCGTTTCAA 59.031 37.500 4.92 0.00 39.16 2.69
2463 2598 0.179116 CCTGTGCGATCTCCAGACTG 60.179 60.000 0.00 0.00 0.00 3.51
2507 2642 1.522092 CTGCCCCTACAGCATCGAA 59.478 57.895 0.00 0.00 40.04 3.71
2655 2847 3.691118 AGTACATGACAATGCGCAATTCT 59.309 39.130 17.11 0.00 37.29 2.40
2669 2861 2.159234 GCAATTCTGAGTCACTGCTCAC 59.841 50.000 0.00 0.00 40.23 3.51
2683 2875 2.615447 CTGCTCACTTTTCTGTGCTGAA 59.385 45.455 0.00 0.00 37.81 3.02
2684 2876 3.216800 TGCTCACTTTTCTGTGCTGAAT 58.783 40.909 0.00 0.00 37.81 2.57
2685 2877 3.633525 TGCTCACTTTTCTGTGCTGAATT 59.366 39.130 0.00 0.00 37.81 2.17
2686 2878 4.098349 TGCTCACTTTTCTGTGCTGAATTT 59.902 37.500 0.00 0.00 37.81 1.82
2687 2879 4.443394 GCTCACTTTTCTGTGCTGAATTTG 59.557 41.667 0.00 0.00 37.81 2.32
2688 2880 5.734220 GCTCACTTTTCTGTGCTGAATTTGA 60.734 40.000 0.00 0.00 37.81 2.69
2689 2881 6.206395 TCACTTTTCTGTGCTGAATTTGAA 57.794 33.333 0.00 0.00 37.81 2.69
2690 2882 6.808829 TCACTTTTCTGTGCTGAATTTGAAT 58.191 32.000 0.00 0.00 37.81 2.57
2691 2883 7.267128 TCACTTTTCTGTGCTGAATTTGAATT 58.733 30.769 0.00 0.00 37.81 2.17
2749 2941 1.458777 ACAGGTCCAGACGGGTTCA 60.459 57.895 0.00 0.00 38.11 3.18
3047 3249 6.154534 TCTGCAGTCCATACTACAACATTAGT 59.845 38.462 14.67 0.00 36.28 2.24
3125 3327 0.538057 ACTCCGGTACCTCGTTCACA 60.538 55.000 10.90 0.00 0.00 3.58
3177 3379 3.522553 ACCAGCGCTGTAAGTAGATTTC 58.477 45.455 33.75 0.00 35.30 2.17
3180 3382 2.500098 AGCGCTGTAAGTAGATTTCCCA 59.500 45.455 10.39 0.00 35.30 4.37
3201 3403 5.007034 CCACATTATACAAGTGGTTCCACA 58.993 41.667 21.71 3.78 45.95 4.17
3219 3421 9.482627 GGTTCCACAATGTTTTATATTTTCACA 57.517 29.630 0.00 0.00 0.00 3.58
3277 3511 7.780008 TCAGTTCGATAAACAAGTCAAAGAA 57.220 32.000 0.00 0.00 40.56 2.52
3307 3541 1.745489 GGCCGATTCTTCGTTGCCT 60.745 57.895 7.96 0.00 44.47 4.75
3397 3631 4.209080 GCACATTTTTACAAACCACTGCTC 59.791 41.667 0.00 0.00 0.00 4.26
3398 3632 4.744631 CACATTTTTACAAACCACTGCTCC 59.255 41.667 0.00 0.00 0.00 4.70
3458 3694 1.698506 AGGGAGCTCTTAGTCATCCG 58.301 55.000 14.64 0.00 0.00 4.18
3500 3736 3.123273 AGGTGGCAGTATATTCCCTGTT 58.877 45.455 0.00 0.00 0.00 3.16
3509 3745 6.313905 GCAGTATATTCCCTGTTAATGATCCG 59.686 42.308 0.00 0.00 0.00 4.18
3553 3789 3.924686 TCTTCGGTAAGAAAACTCGATGC 59.075 43.478 0.00 0.00 38.81 3.91
3554 3790 3.306917 TCGGTAAGAAAACTCGATGCA 57.693 42.857 0.00 0.00 0.00 3.96
3555 3791 3.857052 TCGGTAAGAAAACTCGATGCAT 58.143 40.909 0.00 0.00 0.00 3.96
3556 3792 5.001237 TCGGTAAGAAAACTCGATGCATA 57.999 39.130 0.00 0.00 0.00 3.14
3762 4004 8.737168 TTTATTAGATTCAGTCTGAACCATGG 57.263 34.615 17.49 11.19 39.45 3.66
3765 4007 5.350504 AGATTCAGTCTGAACCATGGTAG 57.649 43.478 20.12 13.39 39.45 3.18
3769 4012 3.258372 TCAGTCTGAACCATGGTAGTGAC 59.742 47.826 20.12 23.10 0.00 3.67
3771 4014 3.259374 AGTCTGAACCATGGTAGTGACAG 59.741 47.826 29.33 24.77 0.00 3.51
3818 4061 9.890915 AATTAGATTCTCTCTAACCCATCTAGT 57.109 33.333 0.00 0.00 46.61 2.57
3819 4062 9.890915 ATTAGATTCTCTCTAACCCATCTAGTT 57.109 33.333 0.00 0.00 46.61 2.24
3902 4145 8.540388 TGAATAACTACTACTTTTCAGATGCCT 58.460 33.333 0.00 0.00 0.00 4.75
3920 4163 2.353109 GCCTTTGCTCATTTTCAGACCC 60.353 50.000 0.00 0.00 33.53 4.46
4000 4245 8.099537 AGATATTTCAGCACTAACTATCCATGG 58.900 37.037 4.97 4.97 0.00 3.66
4073 4318 2.375174 TGCCTTGATGTGTCCTAAACCT 59.625 45.455 0.00 0.00 0.00 3.50
4158 4403 0.616395 TCATGTCCGGGCTCAAGGTA 60.616 55.000 7.97 0.00 0.00 3.08
4216 4461 7.148623 GGAAATCTTTCAACTGTAAGTACCTCG 60.149 40.741 5.14 0.00 41.90 4.63
4234 4479 1.437986 GACTCGACATCCCCCGAAG 59.562 63.158 0.00 0.00 34.17 3.79
4255 4500 5.262588 AGCGGTTCTTCAGTTTCAATTTT 57.737 34.783 0.00 0.00 0.00 1.82
4260 4505 6.975772 CGGTTCTTCAGTTTCAATTTTGGTTA 59.024 34.615 0.00 0.00 0.00 2.85
4269 4515 7.651704 CAGTTTCAATTTTGGTTACCGAGAAAT 59.348 33.333 6.94 5.95 0.00 2.17
4289 4535 0.684153 ATGCCCTTACACACCATGCC 60.684 55.000 0.00 0.00 0.00 4.40
4297 4546 0.674581 ACACACCATGCCTGTCATCG 60.675 55.000 0.00 0.00 31.79 3.84
4331 4580 1.226046 CTACAGCGTCGACCACTCG 60.226 63.158 10.58 0.00 41.65 4.18
4340 4589 2.091112 CGACCACTCGAGCAAGCTG 61.091 63.158 13.61 2.31 43.06 4.24
4361 4610 3.319198 GTGAGCCCGAACCCCTCA 61.319 66.667 0.00 0.00 33.53 3.86
4508 4760 1.188219 TCAGCAGGACCTTCTTCGCT 61.188 55.000 0.00 0.00 0.00 4.93
4515 4767 0.107945 GACCTTCTTCGCTGCCATCT 60.108 55.000 0.00 0.00 0.00 2.90
4583 4838 7.722949 ATTGGTTTGAAGTTGACATGGATAT 57.277 32.000 0.00 0.00 0.00 1.63
4584 4839 8.821686 ATTGGTTTGAAGTTGACATGGATATA 57.178 30.769 0.00 0.00 0.00 0.86
4673 4930 3.470709 ACACACAGGATGAGTTGAGTTG 58.529 45.455 0.00 0.00 38.01 3.16
4723 4985 8.918202 ACTTTGATTACTTCAGGTGTTGATAA 57.082 30.769 0.00 0.00 35.27 1.75
4769 5031 1.663739 CGAGGGGTTTGTGACGAGA 59.336 57.895 0.00 0.00 0.00 4.04
4869 5131 5.983720 TGTCTACTGTTTCTTTCAGCTACAC 59.016 40.000 0.00 0.00 36.50 2.90
4895 5164 4.537751 TGTATCAGGTACTCCCTCTGAAG 58.462 47.826 3.36 0.00 43.86 3.02
4904 5173 8.364142 CAGGTACTCCCTCTGAAGAAATATAAG 58.636 40.741 0.00 0.00 43.86 1.73
4907 5176 7.061566 ACTCCCTCTGAAGAAATATAAGAGC 57.938 40.000 0.00 0.00 34.35 4.09
4909 5178 4.688413 CCCTCTGAAGAAATATAAGAGCGC 59.312 45.833 0.00 0.00 34.35 5.92
4922 5191 9.982651 AAATATAAGAGCGCTTAGATCACTAAA 57.017 29.630 13.26 0.00 37.50 1.85
4923 5192 9.632807 AATATAAGAGCGCTTAGATCACTAAAG 57.367 33.333 13.26 0.00 37.50 1.85
4935 5204 9.601971 CTTAGATCACTAAAGACGCTCTTATAC 57.398 37.037 0.00 0.00 35.27 1.47
4946 5215 7.584122 AGACGCTCTTATACTTCTTTATGGA 57.416 36.000 0.00 0.00 0.00 3.41
4947 5216 7.653647 AGACGCTCTTATACTTCTTTATGGAG 58.346 38.462 0.00 0.00 0.00 3.86
4949 5218 6.550108 ACGCTCTTATACTTCTTTATGGAGGA 59.450 38.462 0.00 0.00 0.00 3.71
4991 5261 6.866010 TGGAGTCGAATCAATCAATTATGG 57.134 37.500 15.56 0.00 0.00 2.74
5054 5324 6.967199 GGGAGCGTGTTTATTCATAGAAAAAG 59.033 38.462 0.00 0.00 0.00 2.27
5213 6858 3.799281 TCCACTTGCACTTTTTGAAGG 57.201 42.857 0.00 0.00 0.00 3.46
5348 6993 3.563390 TCTCTCACGCAGATCAGACATAG 59.437 47.826 0.00 0.00 0.00 2.23
5508 7153 3.250744 CAAACGTAGATGGCTTCTTCGA 58.749 45.455 27.52 2.39 45.11 3.71
5521 7166 3.127030 GCTTCTTCGAACAGGTAAATGGG 59.873 47.826 0.00 0.00 0.00 4.00
5555 7224 6.071728 ACAATTGGAGCCATCACTTTTAGAAG 60.072 38.462 10.83 0.00 38.87 2.85
5581 7250 3.920446 TGCAAGCACTCACGTTTAGATA 58.080 40.909 1.76 0.00 0.00 1.98
5591 7260 8.440833 GCACTCACGTTTAGATAAATTAACTGT 58.559 33.333 1.76 0.00 0.00 3.55
5625 7294 0.376152 GAGCTGATGTGGATGCAACG 59.624 55.000 0.00 0.00 0.00 4.10
5660 7329 5.238583 ACTGGTTTGTAGAAGTGCATACTC 58.761 41.667 0.00 0.00 35.69 2.59
5666 7335 5.736486 TGTAGAAGTGCATACTCTAGTCG 57.264 43.478 0.00 0.00 35.69 4.18
5670 7339 3.634568 AGTGCATACTCTAGTCGATGC 57.365 47.619 14.54 14.54 44.00 3.91
5686 7355 3.309682 TCGATGCAATCAAAAGACCGATC 59.690 43.478 0.00 0.00 45.97 3.69
5692 7361 4.497006 GCAATCAAAAGACCGATCTGATGG 60.497 45.833 0.00 0.00 34.48 3.51
5704 7373 3.119884 CGATCTGATGGAAGAGATCTCCG 60.120 52.174 19.30 7.11 41.67 4.63
5706 7375 3.636679 TCTGATGGAAGAGATCTCCGTT 58.363 45.455 19.30 8.02 0.00 4.44
5710 7379 2.032620 TGGAAGAGATCTCCGTTAGGC 58.967 52.381 19.30 1.42 37.47 3.93
5716 7385 3.892588 AGAGATCTCCGTTAGGCCTAAAG 59.107 47.826 26.78 26.49 37.47 1.85
5719 7388 1.829222 TCTCCGTTAGGCCTAAAGGTG 59.171 52.381 39.66 37.31 42.66 4.00
5724 7393 1.631898 GTTAGGCCTAAAGGTGGACCA 59.368 52.381 26.78 0.00 38.89 4.02
5728 7397 2.090999 AGGCCTAAAGGTGGACCAAAAA 60.091 45.455 1.29 0.00 38.89 1.94
5746 7415 6.267242 ACCAAAAATGGGCTGCAATTTAATTT 59.733 30.769 11.43 2.75 0.00 1.82
5749 7418 3.951775 TGGGCTGCAATTTAATTTCGT 57.048 38.095 0.50 0.00 0.00 3.85
5755 7424 4.484236 CTGCAATTTAATTTCGTCAGCCA 58.516 39.130 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.802852 AAACTGACCGGTTGGGCCC 62.803 63.158 17.59 17.59 46.01 5.80
33 34 2.203437 AAACTGACCGGTTGGGCC 60.203 61.111 9.42 0.00 46.01 5.80
35 36 0.396811 AGAGAAACTGACCGGTTGGG 59.603 55.000 9.42 4.56 40.75 4.12
46 47 8.857216 CGTTTTATACGTATTGACAGAGAAACT 58.143 33.333 14.33 0.00 45.14 2.66
67 68 8.272866 GCATCAAACTTAATAAAAGTGCGTTTT 58.727 29.630 2.53 2.53 41.45 2.43
68 69 7.651704 AGCATCAAACTTAATAAAAGTGCGTTT 59.348 29.630 0.00 0.00 0.00 3.60
69 70 7.114811 CAGCATCAAACTTAATAAAAGTGCGTT 59.885 33.333 0.00 0.00 0.00 4.84
70 71 6.582295 CAGCATCAAACTTAATAAAAGTGCGT 59.418 34.615 0.00 0.00 0.00 5.24
71 72 6.801377 TCAGCATCAAACTTAATAAAAGTGCG 59.199 34.615 0.00 0.00 0.00 5.34
72 73 7.594758 TGTCAGCATCAAACTTAATAAAAGTGC 59.405 33.333 0.00 0.00 0.00 4.40
73 74 9.121517 CTGTCAGCATCAAACTTAATAAAAGTG 57.878 33.333 0.00 0.00 0.00 3.16
74 75 8.850156 ACTGTCAGCATCAAACTTAATAAAAGT 58.150 29.630 0.00 0.00 0.00 2.66
75 76 9.121517 CACTGTCAGCATCAAACTTAATAAAAG 57.878 33.333 0.00 0.00 0.00 2.27
76 77 7.594758 GCACTGTCAGCATCAAACTTAATAAAA 59.405 33.333 0.00 0.00 0.00 1.52
77 78 7.083858 GCACTGTCAGCATCAAACTTAATAAA 58.916 34.615 0.00 0.00 0.00 1.40
78 79 6.349280 GGCACTGTCAGCATCAAACTTAATAA 60.349 38.462 0.00 0.00 0.00 1.40
79 80 5.123820 GGCACTGTCAGCATCAAACTTAATA 59.876 40.000 0.00 0.00 0.00 0.98
84 85 1.242076 GGCACTGTCAGCATCAAACT 58.758 50.000 0.00 0.00 0.00 2.66
89 90 0.179145 GCAATGGCACTGTCAGCATC 60.179 55.000 0.00 0.00 40.72 3.91
116 117 1.961277 GTGTGGTTGGGTCGAGCAG 60.961 63.158 17.59 0.00 0.00 4.24
135 136 7.698836 AACTTCGAGGTTTTGATCAAAAATG 57.301 32.000 30.07 20.36 41.37 2.32
142 143 5.205565 GTCACAAACTTCGAGGTTTTGATC 58.794 41.667 25.32 19.20 37.32 2.92
161 162 3.002759 GGAACTTCTTGCTTGAGTGTCAC 59.997 47.826 0.00 0.00 0.00 3.67
164 165 2.092429 TGGGAACTTCTTGCTTGAGTGT 60.092 45.455 0.00 0.00 0.00 3.55
180 181 4.512571 GCTTACGACAAAGTTAACTGGGAA 59.487 41.667 9.34 0.00 0.00 3.97
219 220 3.660669 AGAGGATGGGGTTGGTTCTTAAA 59.339 43.478 0.00 0.00 0.00 1.52
230 231 3.833559 ATGTCAAAAAGAGGATGGGGT 57.166 42.857 0.00 0.00 0.00 4.95
236 237 9.567776 TCAATTACACTTATGTCAAAAAGAGGA 57.432 29.630 5.54 0.00 40.48 3.71
251 252 8.041323 CCCTACATGAGTTACTCAATTACACTT 58.959 37.037 19.42 0.00 44.04 3.16
252 253 7.556844 CCCTACATGAGTTACTCAATTACACT 58.443 38.462 19.42 0.00 44.04 3.55
267 271 2.590007 GCGCTGGCCCTACATGAG 60.590 66.667 0.00 0.00 0.00 2.90
282 286 2.030540 CAGAAGCATTATGAATGGGGCG 60.031 50.000 0.00 0.00 40.36 6.13
283 287 2.288640 GCAGAAGCATTATGAATGGGGC 60.289 50.000 0.00 0.00 40.36 5.80
290 294 4.334552 TGTGAAAGGCAGAAGCATTATGA 58.665 39.130 0.00 0.00 45.14 2.15
489 501 2.183046 GAGTCCAGTCTCCAGCGC 59.817 66.667 0.00 0.00 0.00 5.92
491 503 1.509004 GTCGAGTCCAGTCTCCAGC 59.491 63.158 0.00 0.00 0.00 4.85
492 504 0.609406 TGGTCGAGTCCAGTCTCCAG 60.609 60.000 0.00 0.00 33.19 3.86
548 560 5.177696 CGCCTAGTTTATTATTCAGGTCAGC 59.822 44.000 0.00 0.00 0.00 4.26
697 730 2.511600 GATTCTCCCGTGCGGTGG 60.512 66.667 9.90 2.23 0.00 4.61
747 780 2.200092 GGAGGGAGAGCCGGAGAT 59.800 66.667 5.05 0.00 33.83 2.75
802 843 4.309950 GTTGGACTGGACCGGCGT 62.310 66.667 6.01 0.00 0.00 5.68
1074 1127 2.971452 GACTCCACGTCTCCACCC 59.029 66.667 0.00 0.00 39.61 4.61
1090 1143 1.220206 GCAGAGCAGGCAAGCTAGA 59.780 57.895 4.39 0.00 46.75 2.43
1418 1489 1.624487 TGAATTGACGACGACGATGG 58.376 50.000 15.32 0.00 42.66 3.51
1423 1494 2.516923 AGACGATGAATTGACGACGAC 58.483 47.619 0.00 0.00 0.00 4.34
1426 1497 4.562789 TCATTGAGACGATGAATTGACGAC 59.437 41.667 0.00 0.00 30.96 4.34
1438 1509 2.432146 CTCTTGGGGATCATTGAGACGA 59.568 50.000 0.00 0.00 32.06 4.20
1484 1555 3.742353 GATCGATCGATCGGTGCG 58.258 61.111 38.80 20.35 44.81 5.34
1505 1580 1.394532 ACCTCCTCCTAGTTCCTCCA 58.605 55.000 0.00 0.00 0.00 3.86
1537 1612 3.314331 CAGTCTGGCCGTCTGGGT 61.314 66.667 12.04 0.00 38.44 4.51
1742 1820 0.616111 ATTCTGGCGAGGAGAGTGGT 60.616 55.000 0.00 0.00 0.00 4.16
1745 1823 1.025812 CGTATTCTGGCGAGGAGAGT 58.974 55.000 0.00 0.00 0.00 3.24
1798 1876 2.101575 CGTCGAATCGAAGCGGGA 59.898 61.111 7.01 0.00 37.72 5.14
1804 1882 1.713246 GCAATGGCGTCGAATCGAA 59.287 52.632 7.01 0.00 37.72 3.71
1805 1883 3.394588 GCAATGGCGTCGAATCGA 58.605 55.556 0.00 0.00 0.00 3.59
1858 1938 3.238108 CCGGAAATATCTCTGGGATCG 57.762 52.381 0.00 0.00 38.10 3.69
1864 1944 1.059913 AGCCCCCGGAAATATCTCTG 58.940 55.000 0.73 0.00 0.00 3.35
1886 1967 8.353423 ACCGTAATCTTCTGGTAGTTAACTAA 57.647 34.615 16.82 2.41 31.60 2.24
1925 2006 1.332997 GCATCTCTACCATGCAAGTGC 59.667 52.381 0.00 0.00 45.19 4.40
1945 2026 7.871463 ACTAGTAGTAGCAGTACCAACTTTTTG 59.129 37.037 0.00 0.00 31.97 2.44
1983 2101 0.994995 CTCGCAACAACTCCATCTCG 59.005 55.000 0.00 0.00 0.00 4.04
2023 2141 1.606668 GGTGCTTCCGTGATTGTTTCA 59.393 47.619 0.00 0.00 0.00 2.69
2077 2196 1.521010 CTGAGGCTGTCATGCTCCG 60.521 63.158 0.00 0.00 33.51 4.63
2141 2260 0.541998 GCCAAAAGCCCTGGGTTAGT 60.542 55.000 15.56 0.00 35.18 2.24
2208 2333 2.462456 TCACTGTCACAAGAGCCATC 57.538 50.000 0.00 0.00 0.00 3.51
2212 2337 9.118236 GTAAATAATTTTCACTGTCACAAGAGC 57.882 33.333 0.00 0.00 0.00 4.09
2250 2375 6.942532 TTAGGATACCATGATTCAGCAAAC 57.057 37.500 0.00 0.00 37.17 2.93
2265 2390 5.048507 GTCAAGGGTCGTCAATTAGGATAC 58.951 45.833 0.00 0.00 0.00 2.24
2282 2410 8.246180 AGACATGCATAATTTTTACTGTCAAGG 58.754 33.333 0.00 0.00 35.40 3.61
2331 2459 4.752661 ACGCGGTTACATTTAACACATT 57.247 36.364 12.47 0.00 39.64 2.71
2332 2460 4.752661 AACGCGGTTACATTTAACACAT 57.247 36.364 12.47 0.00 39.64 3.21
2333 2461 4.034858 TGAAACGCGGTTACATTTAACACA 59.965 37.500 10.60 0.00 39.64 3.72
2334 2462 4.525686 TGAAACGCGGTTACATTTAACAC 58.474 39.130 10.60 0.00 39.64 3.32
2349 2478 3.183373 TCAAAATTTCGCCATTGAAACGC 59.817 39.130 0.00 0.00 40.40 4.84
2356 2485 3.940209 TCTGCTCAAAATTTCGCCATT 57.060 38.095 0.00 0.00 0.00 3.16
2357 2486 3.940209 TTCTGCTCAAAATTTCGCCAT 57.060 38.095 0.00 0.00 0.00 4.40
2405 2540 2.876645 CGGCTCGTGCTCGACTTC 60.877 66.667 6.80 0.00 41.35 3.01
2507 2642 0.963962 ACGTGTTGTCCGACAGGTAT 59.036 50.000 10.46 0.00 44.19 2.73
2582 2717 0.259938 GGGCTTGGGTGATCTTGGAT 59.740 55.000 0.00 0.00 0.00 3.41
2655 2847 3.118629 ACAGAAAAGTGAGCAGTGACTCA 60.119 43.478 11.66 11.66 44.32 3.41
2669 2861 8.133754 TCAAATTCAAATTCAGCACAGAAAAG 57.866 30.769 0.00 0.00 0.00 2.27
2690 2882 9.286946 GCACACAAATTCAAATTCAAATTCAAA 57.713 25.926 0.08 0.00 0.00 2.69
2691 2883 8.456471 TGCACACAAATTCAAATTCAAATTCAA 58.544 25.926 0.00 0.00 0.00 2.69
2785 2977 2.046023 TTGCTGTCCATGCCGAGG 60.046 61.111 0.00 0.00 0.00 4.63
2806 2998 4.385405 GCCAGCAGACTCGGCACT 62.385 66.667 3.90 0.00 45.52 4.40
3011 3204 4.890158 TGGACTGCAGAAATAGAAGTCA 57.110 40.909 23.35 0.47 42.41 3.41
3015 3208 7.418337 TGTAGTATGGACTGCAGAAATAGAA 57.582 36.000 23.35 3.50 42.61 2.10
3047 3249 2.024369 TCCCGCCATAGCTCCTATGATA 60.024 50.000 12.53 0.00 44.55 2.15
3125 3327 0.616111 ACATTGGGTCGGAGAGAGCT 60.616 55.000 0.00 0.00 46.05 4.09
3180 3382 6.719370 ACATTGTGGAACCACTTGTATAATGT 59.281 34.615 21.38 21.38 46.30 2.71
3197 3399 9.689976 TCACTGTGAAAATATAAAACATTGTGG 57.310 29.630 8.27 0.00 0.00 4.17
3307 3541 8.588290 ACCTTATGGTGTAGCAATATTCAAAA 57.412 30.769 0.00 0.00 46.51 2.44
3397 3631 5.123502 GCAGCATATCCATCAGATACAAAGG 59.876 44.000 0.00 0.00 40.31 3.11
3398 3632 5.938710 AGCAGCATATCCATCAGATACAAAG 59.061 40.000 0.00 0.00 40.31 2.77
3500 3736 7.039270 CCGTTATGGTGATTATCGGATCATTA 58.961 38.462 0.00 0.00 38.25 1.90
3509 3745 7.730364 AGAAATGTCCGTTATGGTGATTATC 57.270 36.000 0.00 0.00 39.52 1.75
3547 3783 5.355071 GGCTGGATGAAATTATATGCATCGA 59.645 40.000 0.19 0.00 38.36 3.59
3548 3784 5.124297 TGGCTGGATGAAATTATATGCATCG 59.876 40.000 0.19 0.00 38.36 3.84
3549 3785 6.519679 TGGCTGGATGAAATTATATGCATC 57.480 37.500 0.19 0.00 37.11 3.91
3550 3786 6.439375 ACATGGCTGGATGAAATTATATGCAT 59.561 34.615 3.79 3.79 0.00 3.96
3551 3787 5.776208 ACATGGCTGGATGAAATTATATGCA 59.224 36.000 0.00 0.00 0.00 3.96
3552 3788 6.276832 ACATGGCTGGATGAAATTATATGC 57.723 37.500 0.00 0.00 0.00 3.14
3553 3789 7.972277 GCTTACATGGCTGGATGAAATTATATG 59.028 37.037 0.00 0.00 0.00 1.78
3554 3790 7.892241 AGCTTACATGGCTGGATGAAATTATAT 59.108 33.333 0.00 0.00 38.73 0.86
3555 3791 7.233632 AGCTTACATGGCTGGATGAAATTATA 58.766 34.615 0.00 0.00 38.73 0.98
3556 3792 6.073314 AGCTTACATGGCTGGATGAAATTAT 58.927 36.000 0.00 0.00 38.73 1.28
3585 3826 5.573337 AGAGCAGCAAGATTAAATTCACC 57.427 39.130 0.00 0.00 0.00 4.02
3761 4003 2.755650 CACACCTCAACTGTCACTACC 58.244 52.381 0.00 0.00 0.00 3.18
3762 4004 2.135933 GCACACCTCAACTGTCACTAC 58.864 52.381 0.00 0.00 0.00 2.73
3765 4007 1.378531 TTGCACACCTCAACTGTCAC 58.621 50.000 0.00 0.00 0.00 3.67
3769 4012 2.223572 GGTTCTTTGCACACCTCAACTG 60.224 50.000 0.00 0.00 0.00 3.16
3771 4014 1.748493 TGGTTCTTTGCACACCTCAAC 59.252 47.619 0.00 0.00 0.00 3.18
3841 4084 6.205784 GTTCTTTGCAACTAACACATGCTAA 58.794 36.000 15.04 0.00 40.66 3.09
3884 4127 5.560724 AGCAAAGGCATCTGAAAAGTAGTA 58.439 37.500 0.00 0.00 44.61 1.82
3902 4145 1.269448 GCGGGTCTGAAAATGAGCAAA 59.731 47.619 0.00 0.00 34.04 3.68
3938 4181 8.486210 AGCATATAAGAGGACATAAAACTGACA 58.514 33.333 0.00 0.00 0.00 3.58
4073 4318 1.679680 GTGGATTATCGACGGTGAGGA 59.320 52.381 0.00 0.00 0.00 3.71
4158 4403 1.957562 CCTCTCACGGTCGAACACT 59.042 57.895 0.00 0.00 0.00 3.55
4216 4461 1.437986 CTTCGGGGGATGTCGAGTC 59.562 63.158 0.00 0.00 36.72 3.36
4234 4479 4.209080 CCAAAATTGAAACTGAAGAACCGC 59.791 41.667 0.00 0.00 0.00 5.68
4246 4491 9.632807 CATATTTCTCGGTAACCAAAATTGAAA 57.367 29.630 0.00 0.00 0.00 2.69
4250 4495 6.406512 GGGCATATTTCTCGGTAACCAAAATT 60.407 38.462 0.00 0.00 0.00 1.82
4251 4496 5.068591 GGGCATATTTCTCGGTAACCAAAAT 59.931 40.000 0.00 0.00 0.00 1.82
4255 4500 2.775384 AGGGCATATTTCTCGGTAACCA 59.225 45.455 0.00 0.00 0.00 3.67
4260 4505 3.199071 TGTGTAAGGGCATATTTCTCGGT 59.801 43.478 0.00 0.00 0.00 4.69
4269 4515 1.409521 GGCATGGTGTGTAAGGGCATA 60.410 52.381 0.00 0.00 0.00 3.14
4289 4535 3.524541 TGGTTCATGATGACGATGACAG 58.475 45.455 0.00 0.00 29.39 3.51
4297 4546 3.201290 CTGTAGCCTGGTTCATGATGAC 58.799 50.000 0.00 0.00 0.00 3.06
4331 4580 3.123620 CTCACCGGCAGCTTGCTC 61.124 66.667 0.00 0.00 44.28 4.26
4430 4679 1.275291 ACGTCGATCTGGGTGATGTTT 59.725 47.619 0.00 0.00 35.14 2.83
4508 4760 1.620739 GGAGCAGTGGAGAGATGGCA 61.621 60.000 0.00 0.00 0.00 4.92
4583 4838 2.491693 TGTGAGAGCGTGTGATCATGTA 59.508 45.455 0.00 0.00 31.29 2.29
4584 4839 1.273327 TGTGAGAGCGTGTGATCATGT 59.727 47.619 0.00 0.00 31.29 3.21
4673 4930 1.097547 TGGCCTACGTCTACCTACGC 61.098 60.000 3.32 0.00 46.71 4.42
4723 4985 1.990563 GCGTTATTGCGAGTGTACACT 59.009 47.619 28.27 28.27 45.84 3.55
4769 5031 2.455674 ACATATACATGCGCGTCCAT 57.544 45.000 8.43 0.00 35.39 3.41
4895 5164 9.627395 TTAGTGATCTAAGCGCTCTTATATTTC 57.373 33.333 12.06 0.76 34.54 2.17
4904 5173 3.726730 CGTCTTTAGTGATCTAAGCGCTC 59.273 47.826 12.06 0.00 37.44 5.03
4907 5176 3.696898 AGCGTCTTTAGTGATCTAAGCG 58.303 45.455 0.00 3.10 37.44 4.68
4909 5178 9.601971 GTATAAGAGCGTCTTTAGTGATCTAAG 57.398 37.037 5.74 0.00 37.89 2.18
4922 5191 7.255660 CCTCCATAAAGAAGTATAAGAGCGTCT 60.256 40.741 0.00 0.00 0.00 4.18
4923 5192 6.864165 CCTCCATAAAGAAGTATAAGAGCGTC 59.136 42.308 0.00 0.00 0.00 5.19
4935 5204 7.394816 TCAAACCTACTTCCTCCATAAAGAAG 58.605 38.462 0.00 0.00 42.19 2.85
4943 5212 5.367352 TGTAAGTTCAAACCTACTTCCTCCA 59.633 40.000 0.00 0.00 36.16 3.86
4944 5213 5.861727 TGTAAGTTCAAACCTACTTCCTCC 58.138 41.667 0.00 0.00 36.16 4.30
4946 5215 6.043938 TCCATGTAAGTTCAAACCTACTTCCT 59.956 38.462 0.00 0.00 36.16 3.36
4947 5216 6.235664 TCCATGTAAGTTCAAACCTACTTCC 58.764 40.000 0.00 0.00 36.16 3.46
4949 5218 6.838382 ACTCCATGTAAGTTCAAACCTACTT 58.162 36.000 3.94 0.00 38.16 2.24
4991 5261 1.450312 CCACGGTGCAGGGAGATTC 60.450 63.158 1.68 0.00 0.00 2.52
5027 5297 3.709653 TCTATGAATAAACACGCTCCCCT 59.290 43.478 0.00 0.00 0.00 4.79
5054 5324 5.163513 CCAAATGATAAGTGCCACAAGTTC 58.836 41.667 0.00 0.00 0.00 3.01
5213 6858 4.514816 ACCAAACCTAAATTTGCATGCAAC 59.485 37.500 31.99 0.00 38.10 4.17
5302 6947 8.242739 AGAGTGTTATTTCTAAGTCGGTAGAAC 58.757 37.037 4.33 0.00 39.31 3.01
5348 6993 5.705902 ACACTAAAAATACATCGGGTTTGC 58.294 37.500 0.00 0.00 0.00 3.68
5486 7131 2.993899 CGAAGAAGCCATCTACGTTTGT 59.006 45.455 0.00 0.00 37.42 2.83
5508 7153 2.574369 TCGTCCATCCCATTTACCTGTT 59.426 45.455 0.00 0.00 0.00 3.16
5521 7166 1.401905 GGCTCCAATTGTTCGTCCATC 59.598 52.381 4.43 0.00 0.00 3.51
5581 7250 7.554835 TCCTCTGTGTACAACAACAGTTAATTT 59.445 33.333 0.00 0.00 38.67 1.82
5591 7260 2.698274 TCAGCTCCTCTGTGTACAACAA 59.302 45.455 0.00 0.00 43.32 2.83
5625 7294 0.175073 AAACCAGTCTATCCGCGACC 59.825 55.000 8.23 0.00 31.83 4.79
5660 7329 4.259970 CGGTCTTTTGATTGCATCGACTAG 60.260 45.833 0.00 0.00 0.00 2.57
5666 7335 4.333649 TCAGATCGGTCTTTTGATTGCATC 59.666 41.667 0.00 0.00 30.42 3.91
5670 7339 4.877823 TCCATCAGATCGGTCTTTTGATTG 59.122 41.667 0.00 0.00 30.42 2.67
5673 7342 4.222810 TCTTCCATCAGATCGGTCTTTTGA 59.777 41.667 0.00 0.00 30.42 2.69
5686 7355 4.022416 CCTAACGGAGATCTCTTCCATCAG 60.022 50.000 21.81 10.00 0.00 2.90
5692 7361 2.312390 AGGCCTAACGGAGATCTCTTC 58.688 52.381 21.81 5.83 0.00 2.87
5704 7373 1.631898 TGGTCCACCTTTAGGCCTAAC 59.368 52.381 25.13 12.11 39.32 2.34
5706 7375 2.047769 TTGGTCCACCTTTAGGCCTA 57.952 50.000 8.91 8.91 39.32 3.93
5710 7379 3.260632 CCCATTTTTGGTCCACCTTTAGG 59.739 47.826 0.00 0.00 42.17 2.69
5716 7385 0.321346 CAGCCCATTTTTGGTCCACC 59.679 55.000 0.00 0.00 0.00 4.61
5719 7388 0.396060 TTGCAGCCCATTTTTGGTCC 59.604 50.000 0.00 0.00 0.00 4.46
5724 7393 6.206438 ACGAAATTAAATTGCAGCCCATTTTT 59.794 30.769 5.24 0.00 31.54 1.94
5728 7397 4.081752 TGACGAAATTAAATTGCAGCCCAT 60.082 37.500 0.00 0.00 0.00 4.00
5746 7415 1.968493 AGTTTAAGACCTGGCTGACGA 59.032 47.619 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.