Multiple sequence alignment - TraesCS3B01G341700

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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 TraesCS3B01G341700 chr3B 100.000 7824 0 0 1 7824 548557123 548549300 0.000000e+00 14449.0
1 TraesCS3B01G341700 chr3B 95.502 4135 125 21 4 4104 548376628 548372521 0.000000e+00 6549.0
2 TraesCS3B01G341700 chr3B 95.779 3601 102 25 4 3570 548850524 548846940 0.000000e+00 5762.0
3 TraesCS3B01G341700 chr3B 99.203 1506 11 1 5969 7473 548841707 548840202 0.000000e+00 2713.0
4 TraesCS3B01G341700 chr3B 96.605 1620 45 6 4263 5876 548084278 548082663 0.000000e+00 2678.0
5 TraesCS3B01G341700 chr3B 97.820 1422 26 3 6029 7449 548082443 548081026 0.000000e+00 2449.0
6 TraesCS3B01G341700 chr3B 95.242 1387 41 13 4358 5737 548843165 548841797 0.000000e+00 2172.0
7 TraesCS3B01G341700 chr3B 93.988 1314 50 6 4102 5391 548372418 548371110 0.000000e+00 1962.0
8 TraesCS3B01G341700 chr3B 96.915 1005 25 4 6457 7456 548370251 548369248 0.000000e+00 1679.0
9 TraesCS3B01G341700 chr3B 94.731 873 24 2 4102 4953 548846208 548845337 0.000000e+00 1338.0
10 TraesCS3B01G341700 chr3B 95.734 586 19 2 5969 6551 548370703 548370121 0.000000e+00 939.0
11 TraesCS3B01G341700 chr3B 97.575 536 13 0 3569 4104 548846846 548846311 0.000000e+00 918.0
12 TraesCS3B01G341700 chr3B 94.315 387 9 6 7442 7824 548369187 548368810 1.460000e-161 580.0
13 TraesCS3B01G341700 chr3B 94.215 363 10 5 7464 7824 548836045 548835692 1.920000e-150 544.0
14 TraesCS3B01G341700 chr3B 96.875 320 5 2 5423 5737 548371112 548370793 1.490000e-146 531.0
15 TraesCS3B01G341700 chr3B 98.010 201 4 0 3904 4104 548084963 548084763 4.490000e-92 350.0
16 TraesCS3B01G341700 chr3B 84.450 373 28 18 7455 7824 548080734 548080389 2.700000e-89 340.0
17 TraesCS3B01G341700 chr3B 93.382 136 9 0 4102 4237 548084662 548084527 1.330000e-47 202.0
18 TraesCS3B01G341700 chr3B 97.959 98 2 0 5779 5876 548841802 548841705 3.750000e-38 171.0
19 TraesCS3B01G341700 chr3B 96.939 98 3 0 5779 5876 548370798 548370701 1.750000e-36 165.0
20 TraesCS3B01G341700 chr3B 92.079 101 8 0 6418 6518 548841189 548841089 8.180000e-30 143.0
21 TraesCS3B01G341700 chr3B 100.000 63 0 0 5969 6031 548082665 548082603 4.960000e-22 117.0
22 TraesCS3B01G341700 chr3B 100.000 43 0 0 4235 4277 548084506 548084464 6.510000e-11 80.5
23 TraesCS3B01G341700 chr3B 100.000 39 0 0 2148 2186 548374349 548374311 1.090000e-08 73.1
24 TraesCS3B01G341700 chr3B 100.000 39 0 0 2148 2186 548554848 548554810 1.090000e-08 73.1
25 TraesCS3B01G341700 chr3B 100.000 39 0 0 2276 2314 548554976 548554938 1.090000e-08 73.1
26 TraesCS3B01G341700 chr3B 100.000 39 0 0 2148 2186 548848240 548848202 1.090000e-08 73.1
27 TraesCS3B01G341700 chr3B 100.000 39 0 0 2276 2314 548848368 548848330 1.090000e-08 73.1
28 TraesCS3B01G341700 chr3B 97.436 39 1 0 2276 2314 548374477 548374439 5.070000e-07 67.6
29 TraesCS3B01G341700 chr3A 92.824 3414 146 42 6 3383 529611483 529614833 0.000000e+00 4855.0
30 TraesCS3B01G341700 chr3A 95.565 1646 55 9 5969 7606 529617942 529619577 0.000000e+00 2619.0
31 TraesCS3B01G341700 chr3A 95.988 1620 49 9 4263 5876 529616335 529617944 0.000000e+00 2617.0
32 TraesCS3B01G341700 chr3A 95.740 493 9 3 3612 4104 529615396 529615876 0.000000e+00 784.0
33 TraesCS3B01G341700 chr3A 96.257 187 4 2 3429 3613 529615087 529615272 3.550000e-78 303.0
34 TraesCS3B01G341700 chr3A 89.947 189 6 4 4102 4277 529615957 529616145 1.700000e-56 231.0
35 TraesCS3B01G341700 chr3A 77.399 323 42 15 4632 4932 101888701 101888388 6.280000e-36 163.0
36 TraesCS3B01G341700 chr3A 92.079 101 8 0 6487 6587 529618388 529618488 8.180000e-30 143.0
37 TraesCS3B01G341700 chr3A 90.816 98 6 2 7726 7823 529619710 529619804 2.290000e-25 128.0
38 TraesCS3B01G341700 chr3A 89.109 101 11 0 6418 6518 529618457 529618557 8.240000e-25 126.0
39 TraesCS3B01G341700 chr3A 98.413 63 1 0 3382 3444 529614937 529614999 2.310000e-20 111.0
40 TraesCS3B01G341700 chr3A 77.251 211 27 14 1999 2190 732731965 732732173 3.860000e-18 104.0
41 TraesCS3B01G341700 chr3A 81.905 105 16 3 2930 3034 741863530 741863429 1.400000e-12 86.1
42 TraesCS3B01G341700 chr3A 77.444 133 26 4 6227 6357 529618521 529618651 8.420000e-10 76.8
43 TraesCS3B01G341700 chr3A 95.349 43 2 0 2144 2186 529613723 529613765 1.410000e-07 69.4
44 TraesCS3B01G341700 chr3D 93.042 2199 91 25 4 2185 421377814 421375661 0.000000e+00 3157.0
45 TraesCS3B01G341700 chr3D 93.398 1863 64 23 5969 7824 421371585 421369775 0.000000e+00 2704.0
46 TraesCS3B01G341700 chr3D 97.842 1112 23 1 2272 3383 421375702 421374592 0.000000e+00 1919.0
47 TraesCS3B01G341700 chr3D 94.826 1179 35 11 4706 5876 421372743 421371583 0.000000e+00 1816.0
48 TraesCS3B01G341700 chr3D 93.480 997 34 10 3382 4355 421374433 421373445 0.000000e+00 1452.0
49 TraesCS3B01G341700 chr3D 96.000 525 21 0 4341 4865 421373265 421372741 0.000000e+00 854.0
50 TraesCS3B01G341700 chr3D 81.019 216 33 5 4722 4932 85247975 85248187 1.750000e-36 165.0
51 TraesCS3B01G341700 chr3D 77.570 321 38 15 4635 4932 84907546 84907237 6.280000e-36 163.0
52 TraesCS3B01G341700 chr3D 92.929 99 7 0 6418 6516 421371077 421370979 2.280000e-30 145.0
53 TraesCS3B01G341700 chr3D 91.346 104 9 0 6487 6590 421371146 421371043 8.180000e-30 143.0
54 TraesCS3B01G341700 chr3D 77.692 130 25 4 6233 6360 421371007 421370880 8.420000e-10 76.8
55 TraesCS3B01G341700 chr3D 92.000 50 3 1 3253 3301 42889281 42889232 1.410000e-07 69.4
56 TraesCS3B01G341700 chr5B 96.429 112 3 1 5874 5984 391643615 391643726 4.820000e-42 183.0
57 TraesCS3B01G341700 chr5B 95.614 114 4 1 5858 5971 370044305 370044193 1.730000e-41 182.0
58 TraesCS3B01G341700 chr5B 96.330 109 4 0 5867 5975 610345898 610345790 6.240000e-41 180.0
59 TraesCS3B01G341700 chr2B 96.429 112 3 1 5867 5978 397939366 397939476 4.820000e-42 183.0
60 TraesCS3B01G341700 chr2B 99.010 101 1 0 5871 5971 403101710 403101610 1.730000e-41 182.0
61 TraesCS3B01G341700 chr2B 96.364 110 2 2 5870 5979 695410955 695410848 6.240000e-41 180.0
62 TraesCS3B01G341700 chr2B 96.364 110 2 2 5870 5979 695437641 695437534 6.240000e-41 180.0
63 TraesCS3B01G341700 chr2B 96.330 109 3 1 5864 5972 182935464 182935571 2.240000e-40 178.0
64 TraesCS3B01G341700 chr2B 96.330 109 3 1 5868 5976 425527649 425527756 2.240000e-40 178.0
65 TraesCS3B01G341700 chr2B 92.562 121 5 2 5860 5980 674033931 674034047 3.750000e-38 171.0
66 TraesCS3B01G341700 chr1B 97.222 108 1 2 5875 5982 328139782 328139677 1.730000e-41 182.0
67 TraesCS3B01G341700 chr4B 96.396 111 1 3 5875 5984 32922794 32922902 6.240000e-41 180.0
68 TraesCS3B01G341700 chr7D 97.143 105 2 1 5874 5978 5023431 5023328 8.070000e-40 176.0
69 TraesCS3B01G341700 chr7B 94.690 113 6 0 5867 5979 27617354 27617242 8.070000e-40 176.0
70 TraesCS3B01G341700 chr2A 100.000 33 0 0 306 338 499175727 499175695 2.360000e-05 62.1
71 TraesCS3B01G341700 chrUn 91.111 45 1 3 294 338 38656841 38656800 3.050000e-04 58.4
72 TraesCS3B01G341700 chrUn 100.000 30 0 0 309 338 354264760 354264789 1.000000e-03 56.5
73 TraesCS3B01G341700 chr6B 97.143 35 0 1 309 343 18940240 18940273 3.050000e-04 58.4
74 TraesCS3B01G341700 chr4A 100.000 30 0 0 309 338 672187559 672187588 1.000000e-03 56.5
75 TraesCS3B01G341700 chr1D 100.000 30 0 0 309 338 28967323 28967294 1.000000e-03 56.5


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 TraesCS3B01G341700 chr3B 548549300 548557123 7823 True 4865.066667 14449 100.000000 1 7824 3 chr3B.!!$R4 7823
1 TraesCS3B01G341700 chr3B 548840202 548850524 10322 True 1484.800000 5762 96.952000 4 7473 9 chr3B.!!$R5 7469
2 TraesCS3B01G341700 chr3B 548368810 548376628 7818 True 1393.966667 6549 96.411556 4 7824 9 chr3B.!!$R3 7820
3 TraesCS3B01G341700 chr3B 548080389 548084963 4574 True 888.071429 2678 95.752429 3904 7824 7 chr3B.!!$R2 3920
4 TraesCS3B01G341700 chr3A 529611483 529619804 8321 False 1005.266667 4855 92.460917 6 7823 12 chr3A.!!$F2 7817
5 TraesCS3B01G341700 chr3D 421369775 421377814 8039 True 1362.977778 3157 92.283889 4 7824 9 chr3D.!!$R3 7820

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
479 490 1.815421 GATTCGCCACCGTGCTGAT 60.815 57.895 0.00 0.00 35.54 2.90 F
1289 1320 1.203025 CCCTACTAGCGGGTACATCCT 60.203 57.143 9.13 0.00 36.91 3.24 F
1385 1426 1.075542 CGCCTTACTTGCACGATTCA 58.924 50.000 0.00 0.00 0.00 2.57 F
2586 2644 1.056660 ACCATTCGAAGTGGTCCACT 58.943 50.000 19.42 19.42 46.79 4.00 F
3781 4330 1.603802 CAAATCAACCGTGCACACTCT 59.396 47.619 18.64 0.00 0.00 3.24 F
5366 9359 0.109913 AAGGAACCGAAACCCTCACC 59.890 55.000 0.00 0.00 0.00 4.02 F
6481 10677 0.037326 CAAGTGCTGAGGCGGAAGTA 60.037 55.000 0.00 0.00 42.25 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1295 1326 0.179282 CGAAGTGTTCGCGCAAGTAC 60.179 55.000 8.75 0.39 46.97 2.73 R
2586 2644 1.421268 ACCTGAACAGAGGTGCATGAA 59.579 47.619 0.00 0.00 45.20 2.57 R
3492 3820 4.461198 CCATTGTCCTATGTTCCCCTTAC 58.539 47.826 0.00 0.00 0.00 2.34 R
4451 5526 0.392461 TGGTATGCAAAGACTCGCCC 60.392 55.000 0.00 0.00 0.00 6.13 R
5873 9874 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73 R
6487 10683 0.034767 CCTTGATGCTTGGCTCTGGA 60.035 55.000 0.00 0.00 0.00 3.86 R
7571 12128 1.146452 TATCTACTCCCTCCGCTCCA 58.854 55.000 0.00 0.00 0.00 3.86 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
37 38 9.713713 TTTTTGGAAAGGTATATTTTTAGCACC 57.286 29.630 0.00 0.00 0.00 5.01
38 39 8.658840 TTTGGAAAGGTATATTTTTAGCACCT 57.341 30.769 0.00 0.00 41.38 4.00
122 124 6.072728 CGAAGTTGTGGTTGAATAATCTTCCA 60.073 38.462 0.00 0.00 0.00 3.53
132 134 9.579932 GGTTGAATAATCTTCCATCCTCTATTT 57.420 33.333 0.00 0.00 0.00 1.40
235 241 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
236 242 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
237 243 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
238 244 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
239 245 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
289 295 7.175467 TCCGGGTGTATATATGTACTGTTACTG 59.825 40.741 0.00 2.77 0.00 2.74
479 490 1.815421 GATTCGCCACCGTGCTGAT 60.815 57.895 0.00 0.00 35.54 2.90
514 526 2.722201 GCCCACCGGTCTCGATTCT 61.722 63.158 2.59 0.00 39.00 2.40
594 611 2.346803 GCGAGCTGGTCTTGATTACAA 58.653 47.619 5.23 0.00 34.65 2.41
614 631 8.789825 TTACAAAATAGCAAAAATGCCATCAT 57.210 26.923 0.00 0.00 34.90 2.45
616 633 6.655848 ACAAAATAGCAAAAATGCCATCATGT 59.344 30.769 0.00 0.00 34.90 3.21
627 644 7.591421 AAATGCCATCATGTCATCTAAATCA 57.409 32.000 0.00 0.00 32.23 2.57
1289 1320 1.203025 CCCTACTAGCGGGTACATCCT 60.203 57.143 9.13 0.00 36.91 3.24
1295 1326 2.812499 CGGGTACATCCTGGTCCG 59.188 66.667 0.00 0.00 38.86 4.79
1385 1426 1.075542 CGCCTTACTTGCACGATTCA 58.924 50.000 0.00 0.00 0.00 2.57
1505 1546 1.463553 GGCCTGAACAAACTGGGGTG 61.464 60.000 0.00 0.00 0.00 4.61
1560 1602 7.384439 TGATAGCGATTGAGATTCTAGTAGG 57.616 40.000 0.00 0.00 0.00 3.18
1625 1672 9.237187 TGCATACTTTATTGTCTATTGAACCAA 57.763 29.630 0.00 0.00 0.00 3.67
1643 1690 5.464030 ACCAATACGAGTCAACTTACACT 57.536 39.130 0.00 0.00 0.00 3.55
1644 1691 5.227908 ACCAATACGAGTCAACTTACACTG 58.772 41.667 0.00 0.00 0.00 3.66
1645 1692 4.625742 CCAATACGAGTCAACTTACACTGG 59.374 45.833 0.00 0.00 0.00 4.00
1697 1744 5.824624 ACTTTACTGGCATTATCATCACAGG 59.175 40.000 0.00 0.00 0.00 4.00
1737 1784 3.997021 CAGTTTTACCAGCAGGAGTACAG 59.003 47.826 0.35 0.00 38.69 2.74
1773 1820 5.237996 CGGTAGATAGATTCACCGTCACTAA 59.762 44.000 3.92 0.00 46.81 2.24
1851 1898 4.572909 ACGACCTCCTGTTTATTTGGTAC 58.427 43.478 0.00 0.00 0.00 3.34
1885 1932 6.542821 TCTGAAATGGTAGAAGTTTGGTGAT 58.457 36.000 0.00 0.00 0.00 3.06
1913 1960 9.539825 CTATAACAAACATAGTGAATCTGCTCT 57.460 33.333 0.00 0.00 0.00 4.09
2074 2121 6.144563 CAGAAACGTCGATGATATACATGCTT 59.855 38.462 12.58 0.00 39.56 3.91
2076 2123 7.539022 AGAAACGTCGATGATATACATGCTTAG 59.461 37.037 12.58 0.00 39.56 2.18
2077 2124 6.255596 ACGTCGATGATATACATGCTTAGT 57.744 37.500 12.58 0.00 39.56 2.24
2078 2125 7.373778 ACGTCGATGATATACATGCTTAGTA 57.626 36.000 12.58 0.00 39.56 1.82
2079 2126 7.986562 ACGTCGATGATATACATGCTTAGTAT 58.013 34.615 12.58 0.00 39.56 2.12
2193 2251 4.726035 ATCCCTCTCGGAACTAGATACA 57.274 45.455 0.00 0.00 46.47 2.29
2586 2644 1.056660 ACCATTCGAAGTGGTCCACT 58.943 50.000 19.42 19.42 46.79 4.00
2671 2729 1.620822 ATCACACAACAAAGGAGGCC 58.379 50.000 0.00 0.00 0.00 5.19
3365 3423 9.305555 CTGATAAACATATGATCCATTTTCCCT 57.694 33.333 10.38 0.00 0.00 4.20
3492 3820 8.450180 AGTGAAATTTTAACAAAAGCAACCTTG 58.550 29.630 0.00 0.00 33.22 3.61
3781 4330 1.603802 CAAATCAACCGTGCACACTCT 59.396 47.619 18.64 0.00 0.00 3.24
3843 4392 3.676646 GCAAAAACAGATGATGGTTGCTC 59.323 43.478 0.00 0.00 38.08 4.26
3941 4490 2.752903 AGTTTTTGGTGGTGTGTCAGAC 59.247 45.455 0.00 0.00 0.00 3.51
3950 4499 4.299978 GTGGTGTGTCAGACTAGAGAAAC 58.700 47.826 1.31 0.00 0.00 2.78
4162 4816 6.610456 TGTTGATACGCATTATTATGGCATG 58.390 36.000 10.98 0.00 32.15 4.06
4212 4866 5.286438 TGACATGCAGACCATATACGTAAC 58.714 41.667 0.00 0.00 31.47 2.50
4453 5528 5.603170 ATGACTTCCATTTTATTGCTGGG 57.397 39.130 0.00 0.00 29.34 4.45
4568 5643 6.149973 CCGGCTATCAAAATCATACATGACAT 59.850 38.462 0.00 0.00 40.03 3.06
4672 5747 6.740401 GCATTTCATTGTGGATAGGATGCATT 60.740 38.462 0.00 0.00 37.78 3.56
4756 5988 6.731292 AACCATTTTTACCAGAGAAAGCTT 57.269 33.333 0.00 0.00 0.00 3.74
4772 6004 8.515414 AGAGAAAGCTTGTTACCATTTGTTATC 58.485 33.333 0.00 0.00 0.00 1.75
4871 6103 1.815421 CCTCCCTCAATCAACGGCG 60.815 63.158 4.80 4.80 0.00 6.46
5039 9024 5.899631 TCCCCTAAATGACAGTATTACCC 57.100 43.478 0.00 0.00 0.00 3.69
5053 9038 1.352622 TTACCCCCAGCCTATGCCTG 61.353 60.000 0.00 0.00 38.69 4.85
5128 9114 8.740123 ACGAGACTAATCTGATTTCTCTAAGA 57.260 34.615 21.13 0.00 34.34 2.10
5181 9169 9.443323 TTTTTGCTATACTTCTACTTGTATGCA 57.557 29.630 0.00 0.00 34.62 3.96
5204 9192 6.510638 GCAATGCTTTAAAATTATGCTCTGCC 60.511 38.462 0.00 0.00 0.00 4.85
5215 9203 1.466856 TGCTCTGCCTATTGCTTTGG 58.533 50.000 0.00 0.00 42.00 3.28
5257 9245 6.432403 TTTTTATTCAATTGCTCCCACCTT 57.568 33.333 0.00 0.00 0.00 3.50
5366 9359 0.109913 AAGGAACCGAAACCCTCACC 59.890 55.000 0.00 0.00 0.00 4.02
5482 9475 6.203072 AGTTTTCTGCCTACCTTCCTATCTA 58.797 40.000 0.00 0.00 0.00 1.98
5655 9653 0.237498 GTGACAAGTAAACTGCGGGC 59.763 55.000 0.00 0.00 0.00 6.13
5738 9738 5.597813 AGTTCTCTGTTCTACAATTTGCG 57.402 39.130 0.00 0.00 0.00 4.85
5847 9848 6.392354 ACATTGTAGCAATCCAAATGAACTG 58.608 36.000 0.00 0.00 0.00 3.16
5873 9874 9.612620 GTACCTTTTCTGTTGATTGTTATCTTG 57.387 33.333 0.00 0.00 0.00 3.02
5874 9875 8.237811 ACCTTTTCTGTTGATTGTTATCTTGT 57.762 30.769 0.00 0.00 0.00 3.16
5875 9876 9.349713 ACCTTTTCTGTTGATTGTTATCTTGTA 57.650 29.630 0.00 0.00 0.00 2.41
5876 9877 9.612620 CCTTTTCTGTTGATTGTTATCTTGTAC 57.387 33.333 0.00 0.00 0.00 2.90
5879 9880 8.547967 TTCTGTTGATTGTTATCTTGTACTCC 57.452 34.615 0.00 0.00 0.00 3.85
5880 9881 7.103641 TCTGTTGATTGTTATCTTGTACTCCC 58.896 38.462 0.00 0.00 0.00 4.30
5881 9882 7.016153 TGTTGATTGTTATCTTGTACTCCCT 57.984 36.000 0.00 0.00 0.00 4.20
5882 9883 7.103641 TGTTGATTGTTATCTTGTACTCCCTC 58.896 38.462 0.00 0.00 0.00 4.30
5883 9884 6.235231 TGATTGTTATCTTGTACTCCCTCC 57.765 41.667 0.00 0.00 0.00 4.30
5884 9885 4.730949 TTGTTATCTTGTACTCCCTCCG 57.269 45.455 0.00 0.00 0.00 4.63
5885 9886 3.705051 TGTTATCTTGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
5886 9887 3.698040 TGTTATCTTGTACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
5887 9888 1.777941 ATCTTGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
5888 9889 0.324091 TCTTGTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
5889 9890 0.613853 CTTGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
5890 9891 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
5891 9892 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
5892 9893 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
5893 9894 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
5894 9895 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5895 9896 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5896 9897 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5897 9898 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5898 9899 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5899 9900 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
5900 9901 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
5901 9902 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
5902 9903 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
5903 9904 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
5904 9905 4.069304 CCGTCCCAAAATAAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
5905 9906 4.154195 CCGTCCCAAAATAAGTGTCTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
5906 9907 4.378459 CGTCCCAAAATAAGTGTCTTGAGC 60.378 45.833 0.00 0.00 0.00 4.26
5907 9908 4.762251 GTCCCAAAATAAGTGTCTTGAGCT 59.238 41.667 0.00 0.00 0.00 4.09
5908 9909 5.241728 GTCCCAAAATAAGTGTCTTGAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
5909 9910 6.430000 GTCCCAAAATAAGTGTCTTGAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
5910 9911 6.655003 TCCCAAAATAAGTGTCTTGAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
5911 9912 6.431234 CCCAAAATAAGTGTCTTGAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
5912 9913 7.606456 CCCAAAATAAGTGTCTTGAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
5913 9914 9.167311 CCAAAATAAGTGTCTTGAGCTTAGTAT 57.833 33.333 0.00 0.00 0.00 2.12
5921 9922 9.726438 AGTGTCTTGAGCTTAGTATAAATTTGT 57.274 29.630 0.00 0.00 0.00 2.83
5946 9947 7.148355 ACTAGAGCTAGTACAAAGTTGAGAC 57.852 40.000 8.35 0.00 43.98 3.36
5947 9948 6.715718 ACTAGAGCTAGTACAAAGTTGAGACA 59.284 38.462 8.35 0.00 43.98 3.41
5948 9949 5.774630 AGAGCTAGTACAAAGTTGAGACAC 58.225 41.667 0.00 0.00 0.00 3.67
5949 9950 5.536916 AGAGCTAGTACAAAGTTGAGACACT 59.463 40.000 0.00 0.00 0.00 3.55
5950 9951 6.041069 AGAGCTAGTACAAAGTTGAGACACTT 59.959 38.462 0.00 0.00 38.74 3.16
5951 9952 7.230913 AGAGCTAGTACAAAGTTGAGACACTTA 59.769 37.037 0.00 0.00 35.87 2.24
5952 9953 7.897864 AGCTAGTACAAAGTTGAGACACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
5953 9954 8.368668 AGCTAGTACAAAGTTGAGACACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
5954 9955 8.989980 GCTAGTACAAAGTTGAGACACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
5957 9958 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
5958 9959 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
5959 9960 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
5960 9961 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
5961 9962 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
5962 9963 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
5963 9964 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
5964 9965 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
5965 9966 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5966 9967 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
5967 9968 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
6475 10671 1.302033 AGAACCAAGTGCTGAGGCG 60.302 57.895 0.00 0.00 42.25 5.52
6476 10672 2.281761 AACCAAGTGCTGAGGCGG 60.282 61.111 0.00 0.00 42.25 6.13
6477 10673 2.731691 GAACCAAGTGCTGAGGCGGA 62.732 60.000 0.00 0.00 42.25 5.54
6478 10674 2.032528 CCAAGTGCTGAGGCGGAA 59.967 61.111 0.00 0.00 42.25 4.30
6479 10675 2.037136 CCAAGTGCTGAGGCGGAAG 61.037 63.158 0.00 0.00 42.25 3.46
6480 10676 1.302033 CAAGTGCTGAGGCGGAAGT 60.302 57.895 0.00 0.00 42.25 3.01
6481 10677 0.037326 CAAGTGCTGAGGCGGAAGTA 60.037 55.000 0.00 0.00 42.25 2.24
6482 10678 0.247736 AAGTGCTGAGGCGGAAGTAG 59.752 55.000 0.00 0.00 42.25 2.57
6483 10679 0.612174 AGTGCTGAGGCGGAAGTAGA 60.612 55.000 0.00 0.00 42.25 2.59
6484 10680 0.458716 GTGCTGAGGCGGAAGTAGAC 60.459 60.000 0.00 0.00 42.25 2.59
6485 10681 1.226717 GCTGAGGCGGAAGTAGACG 60.227 63.158 0.00 0.00 0.00 4.18
6486 10682 1.935327 GCTGAGGCGGAAGTAGACGT 61.935 60.000 0.00 0.00 0.00 4.34
6487 10683 0.526662 CTGAGGCGGAAGTAGACGTT 59.473 55.000 0.00 0.00 0.00 3.99
6488 10684 0.524862 TGAGGCGGAAGTAGACGTTC 59.475 55.000 0.00 0.00 0.00 3.95
6489 10685 0.179142 GAGGCGGAAGTAGACGTTCC 60.179 60.000 0.00 0.00 40.25 3.62
6490 10686 0.896940 AGGCGGAAGTAGACGTTCCA 60.897 55.000 4.22 0.00 43.35 3.53
6491 10687 0.458025 GGCGGAAGTAGACGTTCCAG 60.458 60.000 4.22 0.00 43.35 3.86
6492 10688 0.524862 GCGGAAGTAGACGTTCCAGA 59.475 55.000 4.22 0.00 43.35 3.86
6493 10689 1.467713 GCGGAAGTAGACGTTCCAGAG 60.468 57.143 4.22 0.00 43.35 3.35
6494 10690 1.467713 CGGAAGTAGACGTTCCAGAGC 60.468 57.143 4.22 0.00 43.35 4.09
6495 10691 1.135053 GGAAGTAGACGTTCCAGAGCC 60.135 57.143 0.00 0.00 42.79 4.70
6496 10692 1.544691 GAAGTAGACGTTCCAGAGCCA 59.455 52.381 0.00 0.00 0.00 4.75
6497 10693 1.629043 AGTAGACGTTCCAGAGCCAA 58.371 50.000 0.00 0.00 0.00 4.52
6498 10694 1.546476 AGTAGACGTTCCAGAGCCAAG 59.454 52.381 0.00 0.00 0.00 3.61
6499 10695 0.246635 TAGACGTTCCAGAGCCAAGC 59.753 55.000 0.00 0.00 0.00 4.01
6500 10696 1.301716 GACGTTCCAGAGCCAAGCA 60.302 57.895 0.00 0.00 0.00 3.91
6501 10697 0.674895 GACGTTCCAGAGCCAAGCAT 60.675 55.000 0.00 0.00 0.00 3.79
6502 10698 0.674895 ACGTTCCAGAGCCAAGCATC 60.675 55.000 0.00 0.00 0.00 3.91
6503 10699 0.674581 CGTTCCAGAGCCAAGCATCA 60.675 55.000 0.00 0.00 0.00 3.07
6504 10700 1.538047 GTTCCAGAGCCAAGCATCAA 58.462 50.000 0.00 0.00 0.00 2.57
6505 10701 1.471684 GTTCCAGAGCCAAGCATCAAG 59.528 52.381 0.00 0.00 0.00 3.02
6506 10702 0.034767 TCCAGAGCCAAGCATCAAGG 60.035 55.000 0.00 0.00 0.00 3.61
6520 10749 3.563223 CATCAAGGCTGAAGGAATGGAT 58.437 45.455 0.00 0.00 34.49 3.41
7246 11481 2.687700 TGATCTTGAGCTTGCTCTCC 57.312 50.000 21.17 8.20 32.22 3.71
7418 11655 5.584649 CGTCATTGCTGAATACCCTAGAAAA 59.415 40.000 0.00 0.00 31.85 2.29
7571 12128 8.138928 TGAGAAACGATCTTATATCATGGGAT 57.861 34.615 0.00 0.00 38.96 3.85
7572 12129 8.037166 TGAGAAACGATCTTATATCATGGGATG 58.963 37.037 0.00 0.00 38.96 3.51
7573 12130 7.334090 AGAAACGATCTTATATCATGGGATGG 58.666 38.462 0.00 0.00 33.39 3.51
7574 12131 6.874278 AACGATCTTATATCATGGGATGGA 57.126 37.500 0.00 0.00 34.89 3.41
7575 12132 6.477053 ACGATCTTATATCATGGGATGGAG 57.523 41.667 0.00 0.00 34.89 3.86
7780 12409 9.442047 AATACATAAATAGGCTGTTGATAGCTC 57.558 33.333 0.00 0.00 43.22 4.09
7781 12410 7.072263 ACATAAATAGGCTGTTGATAGCTCT 57.928 36.000 0.00 0.00 43.22 4.09
7804 12433 2.823747 GGAACGCCCTAAAAAGGTTCAT 59.176 45.455 4.83 0.00 38.90 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.437741 CCTTTCCAAAAATCCTTGCATGC 59.562 43.478 11.82 11.82 0.00 4.06
1 2 4.644498 ACCTTTCCAAAAATCCTTGCATG 58.356 39.130 0.00 0.00 0.00 4.06
2 3 4.980339 ACCTTTCCAAAAATCCTTGCAT 57.020 36.364 0.00 0.00 0.00 3.96
37 38 1.674611 CGGTTAGCTTCACGCGTGAG 61.675 60.000 37.06 30.16 45.59 3.51
38 39 1.731613 CGGTTAGCTTCACGCGTGA 60.732 57.895 36.40 36.40 45.59 4.35
122 124 8.883731 CATCAACAACTAACGAAAATAGAGGAT 58.116 33.333 0.00 0.00 0.00 3.24
132 134 9.214957 AGAAATACATCATCAACAACTAACGAA 57.785 29.630 0.00 0.00 0.00 3.85
425 435 1.194781 AGGAGACACATGGGCGAAGT 61.195 55.000 0.00 0.00 0.00 3.01
514 526 1.681327 GACTAGGTGGGCGGTGAGA 60.681 63.158 0.00 0.00 0.00 3.27
560 572 1.738099 CTCGCCTTCGTGGAACTGG 60.738 63.158 1.63 0.00 38.35 4.00
564 576 2.048222 CAGCTCGCCTTCGTGGAA 60.048 61.111 1.63 0.00 38.35 3.53
594 611 6.408035 TGACATGATGGCATTTTTGCTATTT 58.592 32.000 0.00 0.00 36.13 1.40
614 631 3.384789 CCTCCGTCCTGATTTAGATGACA 59.615 47.826 0.00 0.00 0.00 3.58
616 633 2.965831 CCCTCCGTCCTGATTTAGATGA 59.034 50.000 0.00 0.00 0.00 2.92
627 644 0.338814 ATCAACTACCCCTCCGTCCT 59.661 55.000 0.00 0.00 0.00 3.85
689 718 9.598517 ACACAATTCACAAGTAACAAATGAATT 57.401 25.926 5.00 5.00 46.02 2.17
1289 1320 3.210223 TTCGCGCAAGTACGGACCA 62.210 57.895 8.75 0.00 41.68 4.02
1295 1326 0.179282 CGAAGTGTTCGCGCAAGTAC 60.179 55.000 8.75 0.39 46.97 2.73
1385 1426 0.606401 CTGAACCAACAGCCGTCCAT 60.606 55.000 0.00 0.00 0.00 3.41
1505 1546 7.410485 GCTTAAGCCTTTATACAGTTGATGAC 58.590 38.462 17.00 0.00 34.31 3.06
1560 1602 8.150945 TCTCAATAGCCAGTAAACTATCCATTC 58.849 37.037 0.00 0.00 0.00 2.67
1625 1672 4.321750 CCACCAGTGTAAGTTGACTCGTAT 60.322 45.833 0.00 0.00 0.00 3.06
1645 1692 5.554822 TTTTTGCGAGGTGATAATACCAC 57.445 39.130 0.00 0.00 43.37 4.16
1737 1784 7.976175 TGAATCTATCTACCGATATGAATGCAC 59.024 37.037 0.00 0.00 31.98 4.57
1766 1813 7.652300 TCAAGTGATATTGTGTGTTAGTGAC 57.348 36.000 0.00 0.00 0.00 3.67
1773 1820 6.899393 ACCAAATCAAGTGATATTGTGTGT 57.101 33.333 0.00 0.00 33.73 3.72
1800 1847 3.737559 TGAATGCAGTAACTCCCCATT 57.262 42.857 0.00 0.00 0.00 3.16
1851 1898 8.428063 ACTTCTACCATTTCAGAATCAGATAGG 58.572 37.037 0.00 0.00 30.70 2.57
1885 1932 7.770433 AGCAGATTCACTATGTTTGTTATAGCA 59.230 33.333 0.00 0.00 32.58 3.49
1913 1960 1.320507 TACTGTGTACACGCTCCACA 58.679 50.000 20.61 0.79 37.52 4.17
2586 2644 1.421268 ACCTGAACAGAGGTGCATGAA 59.579 47.619 0.00 0.00 45.20 2.57
3492 3820 4.461198 CCATTGTCCTATGTTCCCCTTAC 58.539 47.826 0.00 0.00 0.00 2.34
3781 4330 2.290071 CCCTCCTGAAAACTTTCGCCTA 60.290 50.000 0.00 0.00 40.01 3.93
3843 4392 4.402474 ACTGTCTTTGGAAGGTTGAAAAGG 59.598 41.667 0.00 0.00 31.87 3.11
3941 4490 5.126779 GGGGGCATCTTAAAGTTTCTCTAG 58.873 45.833 0.00 0.00 0.00 2.43
3950 4499 5.619132 AATCATTTGGGGGCATCTTAAAG 57.381 39.130 0.00 0.00 0.00 1.85
4124 4778 5.356426 CGTATCAACATGTCCATCCTACAA 58.644 41.667 0.00 0.00 0.00 2.41
4212 4866 9.806203 TCAATAAAAAGGTGATAATGCATTCTG 57.194 29.630 16.86 0.00 0.00 3.02
4386 5461 8.863049 CAATGACACAAATTTGTAAATAGCTCC 58.137 33.333 22.87 5.26 39.91 4.70
4451 5526 0.392461 TGGTATGCAAAGACTCGCCC 60.392 55.000 0.00 0.00 0.00 6.13
4453 5528 1.599542 GGATGGTATGCAAAGACTCGC 59.400 52.381 0.00 0.00 0.00 5.03
4568 5643 4.022413 AGAGAGACAGCTGTGTAGTACA 57.978 45.455 27.27 0.00 36.88 2.90
4695 5770 4.573021 TCACAATGGGATCTTGATCACA 57.427 40.909 16.61 16.61 38.48 3.58
4772 6004 6.558771 TGTATAATTGGCATGAATCCTTCG 57.441 37.500 0.00 0.00 0.00 3.79
4871 6103 8.831550 CAGAGGTAAGATAAGGTTTAAATCTGC 58.168 37.037 0.68 0.00 30.50 4.26
4963 8948 6.540995 AGTACTACTGTCAACTAGGTTCAGA 58.459 40.000 14.39 0.00 0.00 3.27
5128 9114 2.706350 TGGGGAGCTATTGAGGCTATT 58.294 47.619 0.00 0.00 40.40 1.73
5181 9169 6.881570 AGGCAGAGCATAATTTTAAAGCATT 58.118 32.000 0.02 0.00 0.00 3.56
5237 9225 6.432403 AAAAAGGTGGGAGCAATTGAATAA 57.568 33.333 10.34 0.00 0.00 1.40
5366 9359 1.000283 ACAGTCTTGACCTCTTGCTCG 60.000 52.381 0.00 0.00 0.00 5.03
5738 9738 4.926140 AAGCAGCATAAATTAAGCTCCC 57.074 40.909 0.00 0.00 36.26 4.30
5847 9848 9.612620 CAAGATAACAATCAACAGAAAAGGTAC 57.387 33.333 0.00 0.00 0.00 3.34
5873 9874 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
5874 9875 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
5875 9876 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
5876 9877 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
5877 9878 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
5878 9879 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
5879 9880 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5880 9881 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
5881 9882 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
5882 9883 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
5883 9884 4.378459 GCTCAAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
5884 9885 4.762251 AGCTCAAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
5885 9886 4.985538 AGCTCAAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
5886 9887 5.712152 AAGCTCAAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
5887 9888 7.440523 ACTAAGCTCAAGACACTTATTTTGG 57.559 36.000 3.19 0.00 0.00 3.28
5895 9896 9.726438 ACAAATTTATACTAAGCTCAAGACACT 57.274 29.630 3.19 0.00 0.00 3.55
5921 9922 7.881751 TGTCTCAACTTTGTACTAGCTCTAGTA 59.118 37.037 11.59 11.59 43.98 1.82
5923 9924 7.024768 GTGTCTCAACTTTGTACTAGCTCTAG 58.975 42.308 0.00 2.55 39.04 2.43
5924 9925 6.715718 AGTGTCTCAACTTTGTACTAGCTCTA 59.284 38.462 0.00 0.00 0.00 2.43
5925 9926 5.536916 AGTGTCTCAACTTTGTACTAGCTCT 59.463 40.000 0.00 0.00 0.00 4.09
5926 9927 5.774630 AGTGTCTCAACTTTGTACTAGCTC 58.225 41.667 0.00 0.00 0.00 4.09
5927 9928 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
5928 9929 8.535690 AATAAGTGTCTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
5931 9932 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
5932 9933 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
5933 9934 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
5934 9935 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
5935 9936 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
5936 9937 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
5937 9938 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
5938 9939 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
5939 9940 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
5940 9941 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
5941 9942 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
5942 9943 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
5943 9944 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
5944 9945 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
5945 9946 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
5946 9947 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5947 9948 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5948 9949 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5949 9950 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5950 9951 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5951 9952 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
5952 9953 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
5953 9954 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
5954 9955 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
5955 9956 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
5956 9957 1.893801 CATACATACTCCCTCCGTCCC 59.106 57.143 0.00 0.00 0.00 4.46
5957 9958 2.595238 ACATACATACTCCCTCCGTCC 58.405 52.381 0.00 0.00 0.00 4.79
5958 9959 5.979288 AATACATACATACTCCCTCCGTC 57.021 43.478 0.00 0.00 0.00 4.79
5959 9960 5.836898 TCAAATACATACATACTCCCTCCGT 59.163 40.000 0.00 0.00 0.00 4.69
5960 9961 6.340962 TCAAATACATACATACTCCCTCCG 57.659 41.667 0.00 0.00 0.00 4.63
5961 9962 7.680730 ACATCAAATACATACATACTCCCTCC 58.319 38.462 0.00 0.00 0.00 4.30
5962 9963 8.367911 TGACATCAAATACATACATACTCCCTC 58.632 37.037 0.00 0.00 0.00 4.30
5963 9964 8.262601 TGACATCAAATACATACATACTCCCT 57.737 34.615 0.00 0.00 0.00 4.20
5964 9965 8.902540 TTGACATCAAATACATACATACTCCC 57.097 34.615 0.00 0.00 32.11 4.30
6199 10362 6.509418 TTAACATTTTCCATACTGCCAGAC 57.491 37.500 0.00 0.00 0.00 3.51
6475 10671 1.135053 GGCTCTGGAACGTCTACTTCC 60.135 57.143 0.00 0.00 38.18 3.46
6476 10672 1.544691 TGGCTCTGGAACGTCTACTTC 59.455 52.381 0.00 0.00 0.00 3.01
6477 10673 1.629043 TGGCTCTGGAACGTCTACTT 58.371 50.000 0.00 0.00 0.00 2.24
6478 10674 1.546476 CTTGGCTCTGGAACGTCTACT 59.454 52.381 0.00 0.00 0.00 2.57
6479 10675 1.997669 CTTGGCTCTGGAACGTCTAC 58.002 55.000 0.00 0.00 0.00 2.59
6480 10676 0.246635 GCTTGGCTCTGGAACGTCTA 59.753 55.000 0.00 0.00 0.00 2.59
6481 10677 1.004440 GCTTGGCTCTGGAACGTCT 60.004 57.895 0.00 0.00 0.00 4.18
6482 10678 0.674895 ATGCTTGGCTCTGGAACGTC 60.675 55.000 0.00 0.00 0.00 4.34
6483 10679 0.674895 GATGCTTGGCTCTGGAACGT 60.675 55.000 0.00 0.00 0.00 3.99
6484 10680 0.674581 TGATGCTTGGCTCTGGAACG 60.675 55.000 0.00 0.00 0.00 3.95
6485 10681 1.471684 CTTGATGCTTGGCTCTGGAAC 59.528 52.381 0.00 0.00 0.00 3.62
6486 10682 1.615116 CCTTGATGCTTGGCTCTGGAA 60.615 52.381 0.00 0.00 0.00 3.53
6487 10683 0.034767 CCTTGATGCTTGGCTCTGGA 60.035 55.000 0.00 0.00 0.00 3.86
6488 10684 1.664321 GCCTTGATGCTTGGCTCTGG 61.664 60.000 0.00 0.00 43.05 3.86
6489 10685 1.807886 GCCTTGATGCTTGGCTCTG 59.192 57.895 0.00 0.00 43.05 3.35
6490 10686 4.333417 GCCTTGATGCTTGGCTCT 57.667 55.556 0.00 0.00 43.05 4.09
6493 10689 0.172803 CTTCAGCCTTGATGCTTGGC 59.827 55.000 0.00 0.00 46.42 4.52
6494 10690 0.815734 CCTTCAGCCTTGATGCTTGG 59.184 55.000 0.00 0.00 40.32 3.61
6495 10691 1.830279 TCCTTCAGCCTTGATGCTTG 58.170 50.000 0.00 0.00 40.32 4.01
6496 10692 2.592102 TTCCTTCAGCCTTGATGCTT 57.408 45.000 0.00 0.00 40.32 3.91
6497 10693 2.376109 CATTCCTTCAGCCTTGATGCT 58.624 47.619 0.00 0.00 44.00 3.79
6498 10694 1.407979 CCATTCCTTCAGCCTTGATGC 59.592 52.381 0.00 0.00 32.27 3.91
6499 10695 3.008835 TCCATTCCTTCAGCCTTGATG 57.991 47.619 0.00 0.00 32.27 3.07
6500 10696 3.053095 ACATCCATTCCTTCAGCCTTGAT 60.053 43.478 0.00 0.00 32.27 2.57
6501 10697 2.309755 ACATCCATTCCTTCAGCCTTGA 59.690 45.455 0.00 0.00 0.00 3.02
6502 10698 2.731572 ACATCCATTCCTTCAGCCTTG 58.268 47.619 0.00 0.00 0.00 3.61
6503 10699 3.094572 CAACATCCATTCCTTCAGCCTT 58.905 45.455 0.00 0.00 0.00 4.35
6504 10700 2.731572 CAACATCCATTCCTTCAGCCT 58.268 47.619 0.00 0.00 0.00 4.58
6505 10701 1.135721 GCAACATCCATTCCTTCAGCC 59.864 52.381 0.00 0.00 0.00 4.85
6506 10702 1.820519 TGCAACATCCATTCCTTCAGC 59.179 47.619 0.00 0.00 0.00 4.26
6507 10703 3.349927 TCTGCAACATCCATTCCTTCAG 58.650 45.455 0.00 0.00 0.00 3.02
6520 10749 1.823470 AGCGCTTGGTTCTGCAACA 60.823 52.632 2.64 0.00 33.70 3.33
7246 11481 6.302313 CGTCTAAACAAAATAGAAAGCAACCG 59.698 38.462 0.00 0.00 31.52 4.44
7571 12128 1.146452 TATCTACTCCCTCCGCTCCA 58.854 55.000 0.00 0.00 0.00 3.86
7572 12129 2.289592 TTATCTACTCCCTCCGCTCC 57.710 55.000 0.00 0.00 0.00 4.70
7573 12130 3.615351 GCAATTATCTACTCCCTCCGCTC 60.615 52.174 0.00 0.00 0.00 5.03
7574 12131 2.300437 GCAATTATCTACTCCCTCCGCT 59.700 50.000 0.00 0.00 0.00 5.52
7575 12132 2.613223 GGCAATTATCTACTCCCTCCGC 60.613 54.545 0.00 0.00 0.00 5.54
7781 12410 3.072768 TGAACCTTTTTAGGGCGTTCCTA 59.927 43.478 3.11 3.11 45.98 2.94


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

AutoCloner maintained by Alex Coulton.