Multiple sequence alignment - TraesCS3D01G128300

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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 TraesCS3D01G128300 chr3D 100.000 2387 0 0 1 2387 86235924 86238310 0.000000e+00 4409
1 TraesCS3D01G128300 chr3D 97.440 664 4 4 1 652 99820574 99821236 0.000000e+00 1120
2 TraesCS3D01G128300 chr3D 97.703 653 10 5 1 651 505057213 505056564 0.000000e+00 1118
3 TraesCS3D01G128300 chr3D 97.397 653 11 6 1 651 564999785 565000433 0.000000e+00 1107
4 TraesCS3D01G128300 chr3D 87.409 548 39 9 851 1391 85896275 85896799 9.440000e-169 603
5 TraesCS3D01G128300 chr3D 86.179 246 13 5 1124 1369 86357784 86358008 1.830000e-61 246
6 TraesCS3D01G128300 chr3B 91.797 1219 57 22 652 1858 136091011 136092198 0.000000e+00 1657
7 TraesCS3D01G128300 chr3B 95.050 202 9 1 2186 2387 64248849 64248649 1.380000e-82 316
8 TraesCS3D01G128300 chr3B 94.798 173 8 1 2023 2194 136092677 136092849 3.910000e-68 268
9 TraesCS3D01G128300 chr3B 86.179 246 13 5 1124 1369 136492009 136492233 1.830000e-61 246
10 TraesCS3D01G128300 chr3B 89.655 87 8 1 1940 2025 412593471 412593385 2.510000e-20 110
11 TraesCS3D01G128300 chr3B 95.312 64 3 0 1854 1917 136092619 136092682 4.200000e-18 102
12 TraesCS3D01G128300 chr3A 89.346 1239 56 32 730 1922 102554371 102555579 0.000000e+00 1487
13 TraesCS3D01G128300 chr3A 82.913 357 28 22 1028 1369 102686325 102686663 8.350000e-75 291
14 TraesCS3D01G128300 chr3A 95.858 169 7 0 2026 2194 102555569 102555737 8.410000e-70 274
15 TraesCS3D01G128300 chr1D 98.626 655 5 4 1 652 50066034 50065381 0.000000e+00 1157
16 TraesCS3D01G128300 chr1D 97.095 654 13 6 1 651 310852318 310852968 0.000000e+00 1098
17 TraesCS3D01G128300 chr1D 81.545 233 28 14 1124 1353 114083491 114083271 6.780000e-41 178
18 TraesCS3D01G128300 chr1D 88.764 89 9 1 1940 2027 341527572 341527484 9.020000e-20 108
19 TraesCS3D01G128300 chr6D 98.622 653 6 3 1 651 90435062 90435713 0.000000e+00 1153
20 TraesCS3D01G128300 chr6D 96.960 658 12 8 1 654 12480324 12479671 0.000000e+00 1098
21 TraesCS3D01G128300 chr6D 96.373 193 7 0 2195 2387 111072840 111073032 3.830000e-83 318
22 TraesCS3D01G128300 chr7D 98.162 653 9 3 1 651 574843954 574844605 0.000000e+00 1136
23 TraesCS3D01G128300 chr7D 94.241 191 10 1 2195 2384 41770595 41770405 8.350000e-75 291
24 TraesCS3D01G128300 chr2D 97.121 660 12 7 1 658 548737867 548738521 0.000000e+00 1107
25 TraesCS3D01G128300 chr2D 95.876 194 7 1 2194 2387 18900229 18900037 1.780000e-81 313
26 TraesCS3D01G128300 chr2D 95.833 192 7 1 2196 2387 19004458 19004268 2.300000e-80 309
27 TraesCS3D01G128300 chr5D 96.875 192 6 0 2196 2387 24879144 24878953 2.960000e-84 322
28 TraesCS3D01G128300 chr4A 96.373 193 7 0 2195 2387 731020501 731020693 3.830000e-83 318
29 TraesCS3D01G128300 chr7B 96.354 192 7 0 2196 2387 234905576 234905385 1.380000e-82 316
30 TraesCS3D01G128300 chr7B 95.855 193 8 0 2195 2387 392671610 392671418 1.780000e-81 313
31 TraesCS3D01G128300 chr7B 88.298 94 10 1 1940 2032 366055513 366055420 6.970000e-21 111
32 TraesCS3D01G128300 chr1B 82.479 234 29 11 1124 1354 174784124 174783900 6.730000e-46 195
33 TraesCS3D01G128300 chr1B 90.588 85 8 0 1940 2024 471177131 471177215 1.940000e-21 113
34 TraesCS3D01G128300 chr1A 81.624 234 35 8 1124 1353 124190015 124189786 1.130000e-43 187
35 TraesCS3D01G128300 chr2B 91.860 86 6 1 1940 2024 769274761 769274846 4.170000e-23 119
36 TraesCS3D01G128300 chr2B 90.805 87 8 0 1940 2026 746714636 746714550 1.500000e-22 117
37 TraesCS3D01G128300 chr5B 90.698 86 7 1 1940 2024 509185791 509185706 1.940000e-21 113
38 TraesCS3D01G128300 chr5A 89.888 89 8 1 1936 2024 606039707 606039620 1.940000e-21 113
39 TraesCS3D01G128300 chr5A 90.698 86 7 1 1941 2025 702862642 702862557 1.940000e-21 113


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 TraesCS3D01G128300 chr3D 86235924 86238310 2386 False 4409.000000 4409 100.000 1 2387 1 chr3D.!!$F2 2386
1 TraesCS3D01G128300 chr3D 99820574 99821236 662 False 1120.000000 1120 97.440 1 652 1 chr3D.!!$F4 651
2 TraesCS3D01G128300 chr3D 505056564 505057213 649 True 1118.000000 1118 97.703 1 651 1 chr3D.!!$R1 650
3 TraesCS3D01G128300 chr3D 564999785 565000433 648 False 1107.000000 1107 97.397 1 651 1 chr3D.!!$F5 650
4 TraesCS3D01G128300 chr3D 85896275 85896799 524 False 603.000000 603 87.409 851 1391 1 chr3D.!!$F1 540
5 TraesCS3D01G128300 chr3B 136091011 136092849 1838 False 675.666667 1657 93.969 652 2194 3 chr3B.!!$F2 1542
6 TraesCS3D01G128300 chr3A 102554371 102555737 1366 False 880.500000 1487 92.602 730 2194 2 chr3A.!!$F2 1464
7 TraesCS3D01G128300 chr1D 50065381 50066034 653 True 1157.000000 1157 98.626 1 652 1 chr1D.!!$R1 651
8 TraesCS3D01G128300 chr1D 310852318 310852968 650 False 1098.000000 1098 97.095 1 651 1 chr1D.!!$F1 650
9 TraesCS3D01G128300 chr6D 90435062 90435713 651 False 1153.000000 1153 98.622 1 651 1 chr6D.!!$F1 650
10 TraesCS3D01G128300 chr6D 12479671 12480324 653 True 1098.000000 1098 96.960 1 654 1 chr6D.!!$R1 653
11 TraesCS3D01G128300 chr7D 574843954 574844605 651 False 1136.000000 1136 98.162 1 651 1 chr7D.!!$F1 650
12 TraesCS3D01G128300 chr2D 548737867 548738521 654 False 1107.000000 1107 97.121 1 658 1 chr2D.!!$F1 657

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
654 671 0.095417 GCGAAGTTGCGGAACATCTC 59.905 55.0 22.29 10.82 34.17 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 2836 0.036952 GCTCACAGCCTAGCAAGACA 60.037 55.0 0.0 0.0 38.63 3.41 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
143 144 3.847037 TCACAAACTCGTCGCTAAAAC 57.153 42.857 0.00 0.00 0.00 2.43
295 296 2.105477 ACTGTGTGCTCTTTCTCCACAT 59.895 45.455 0.00 0.00 41.03 3.21
654 671 0.095417 GCGAAGTTGCGGAACATCTC 59.905 55.000 22.29 10.82 34.17 2.75
664 681 3.253188 TGCGGAACATCTCTTCCAAAAAG 59.747 43.478 0.00 0.00 39.98 2.27
666 683 3.667960 CGGAACATCTCTTCCAAAAAGCG 60.668 47.826 0.00 0.00 39.98 4.68
667 684 3.366374 GGAACATCTCTTCCAAAAAGCGG 60.366 47.826 0.00 0.00 39.78 5.52
668 685 2.162681 ACATCTCTTCCAAAAAGCGGG 58.837 47.619 0.00 0.00 0.00 6.13
720 737 2.742372 CCCCACCGTGAAAGCGAG 60.742 66.667 0.00 0.00 0.00 5.03
721 738 3.423154 CCCACCGTGAAAGCGAGC 61.423 66.667 0.00 0.00 0.00 5.03
723 740 2.733218 CACCGTGAAAGCGAGCGA 60.733 61.111 0.00 0.00 0.00 4.93
724 741 2.733593 ACCGTGAAAGCGAGCGAC 60.734 61.111 0.00 0.00 0.00 5.19
725 742 2.733218 CCGTGAAAGCGAGCGACA 60.733 61.111 0.00 0.00 0.00 4.35
727 744 1.729484 CGTGAAAGCGAGCGACAGA 60.729 57.895 0.00 0.00 0.00 3.41
728 745 1.073216 CGTGAAAGCGAGCGACAGAT 61.073 55.000 0.00 0.00 0.00 2.90
768 796 3.018901 GTGCCCCATCCCATTCCT 58.981 61.111 0.00 0.00 0.00 3.36
778 808 4.883354 CCATTCCTCGCCCAGCCC 62.883 72.222 0.00 0.00 0.00 5.19
805 835 1.741394 CGAACCTTATCCACCCGTTCC 60.741 57.143 0.00 0.00 31.24 3.62
806 836 0.622136 AACCTTATCCACCCGTTCCC 59.378 55.000 0.00 0.00 0.00 3.97
807 837 1.145377 CCTTATCCACCCGTTCCCG 59.855 63.158 0.00 0.00 0.00 5.14
808 838 1.619807 CCTTATCCACCCGTTCCCGT 61.620 60.000 0.00 0.00 0.00 5.28
809 839 0.251073 CTTATCCACCCGTTCCCGTT 59.749 55.000 0.00 0.00 0.00 4.44
810 840 0.249955 TTATCCACCCGTTCCCGTTC 59.750 55.000 0.00 0.00 0.00 3.95
811 841 1.616091 TATCCACCCGTTCCCGTTCC 61.616 60.000 0.00 0.00 0.00 3.62
849 896 1.002134 CCCACCACCATTCTCGCTT 60.002 57.895 0.00 0.00 0.00 4.68
869 918 1.354368 TCCATCCCACCACCTTTTCTC 59.646 52.381 0.00 0.00 0.00 2.87
887 940 1.208614 CAGCAGAAGCAACGAAGCC 59.791 57.895 0.00 0.00 45.49 4.35
890 943 0.386478 GCAGAAGCAACGAAGCCAAG 60.386 55.000 0.00 0.00 41.58 3.61
913 968 1.047002 AGCCAATCCATCTCCTCTCG 58.953 55.000 0.00 0.00 0.00 4.04
998 1053 1.878069 CGGCGCGAATCAGTGATCA 60.878 57.895 12.10 0.00 0.00 2.92
1490 1551 3.392769 TTCGTTTGTTTTGTCTGTCCG 57.607 42.857 0.00 0.00 0.00 4.79
1508 1569 2.819019 TCCGGTTGATCGTTACTGTACA 59.181 45.455 0.00 0.00 0.00 2.90
1546 1611 3.072211 GGCCGGTAATATTTAGGACAGC 58.928 50.000 1.90 0.00 0.00 4.40
1618 1690 8.349568 TGCTTACTTAATCTCACTAGTTCTGA 57.650 34.615 0.00 0.00 0.00 3.27
1691 1763 8.483307 AATAATTTGGTTGTGCTGATGATTTC 57.517 30.769 0.00 0.00 0.00 2.17
1751 1829 2.301870 TGGTTACGCTGAATCCAACTCT 59.698 45.455 0.00 0.00 0.00 3.24
1752 1830 2.673368 GGTTACGCTGAATCCAACTCTG 59.327 50.000 0.00 0.00 0.00 3.35
1753 1831 2.010145 TACGCTGAATCCAACTCTGC 57.990 50.000 0.00 0.00 35.19 4.26
1795 1873 3.076621 TCAAATTCAGATGCTTGCGAGT 58.923 40.909 2.14 0.00 0.00 4.18
1833 1911 2.178912 TTGATGTTTCTCCGGTCACC 57.821 50.000 0.00 0.00 0.00 4.02
1889 2393 1.931635 TTAACCCATGGGACTTTGCC 58.068 50.000 38.07 0.00 38.96 4.52
1891 2395 1.080638 AACCCATGGGACTTTGCCTA 58.919 50.000 38.07 0.00 38.96 3.93
1917 2421 1.962100 CGACCCCCTCCTGATAAGTAC 59.038 57.143 0.00 0.00 0.00 2.73
1922 2430 2.180308 CCCCTCCTGATAAGTACTCCCT 59.820 54.545 0.00 0.00 0.00 4.20
1923 2431 3.502356 CCCTCCTGATAAGTACTCCCTC 58.498 54.545 0.00 0.00 0.00 4.30
1924 2432 3.502356 CCTCCTGATAAGTACTCCCTCC 58.498 54.545 0.00 0.00 0.00 4.30
1925 2433 3.150767 CTCCTGATAAGTACTCCCTCCG 58.849 54.545 0.00 0.00 0.00 4.63
1926 2434 2.512896 TCCTGATAAGTACTCCCTCCGT 59.487 50.000 0.00 0.00 0.00 4.69
1927 2435 3.053095 TCCTGATAAGTACTCCCTCCGTT 60.053 47.826 0.00 0.00 0.00 4.44
1928 2436 3.705072 CCTGATAAGTACTCCCTCCGTTT 59.295 47.826 0.00 0.00 0.00 3.60
1929 2437 4.161754 CCTGATAAGTACTCCCTCCGTTTT 59.838 45.833 0.00 0.00 0.00 2.43
1930 2438 5.080969 TGATAAGTACTCCCTCCGTTTTG 57.919 43.478 0.00 0.00 0.00 2.44
1931 2439 4.529377 TGATAAGTACTCCCTCCGTTTTGT 59.471 41.667 0.00 0.00 0.00 2.83
1932 2440 5.716228 TGATAAGTACTCCCTCCGTTTTGTA 59.284 40.000 0.00 0.00 0.00 2.41
1933 2441 3.949842 AGTACTCCCTCCGTTTTGTAC 57.050 47.619 0.00 0.00 0.00 2.90
1934 2442 3.233507 AGTACTCCCTCCGTTTTGTACA 58.766 45.455 0.00 0.00 34.50 2.90
1935 2443 3.642848 AGTACTCCCTCCGTTTTGTACAA 59.357 43.478 3.59 3.59 34.50 2.41
1936 2444 3.564053 ACTCCCTCCGTTTTGTACAAA 57.436 42.857 17.01 17.01 0.00 2.83
1937 2445 3.473625 ACTCCCTCCGTTTTGTACAAAG 58.526 45.455 19.72 10.33 0.00 2.77
1938 2446 3.118149 ACTCCCTCCGTTTTGTACAAAGT 60.118 43.478 19.72 9.18 0.00 2.66
1939 2447 3.881089 CTCCCTCCGTTTTGTACAAAGTT 59.119 43.478 19.72 0.00 0.00 2.66
1940 2448 5.033589 TCCCTCCGTTTTGTACAAAGTTA 57.966 39.130 19.72 4.21 0.00 2.24
1941 2449 4.815846 TCCCTCCGTTTTGTACAAAGTTAC 59.184 41.667 19.72 14.63 0.00 2.50
1942 2450 4.818005 CCCTCCGTTTTGTACAAAGTTACT 59.182 41.667 19.72 0.00 0.00 2.24
1943 2451 5.049886 CCCTCCGTTTTGTACAAAGTTACTC 60.050 44.000 19.72 7.94 0.00 2.59
1944 2452 5.049886 CCTCCGTTTTGTACAAAGTTACTCC 60.050 44.000 19.72 4.38 0.00 3.85
1945 2453 4.815846 TCCGTTTTGTACAAAGTTACTCCC 59.184 41.667 19.72 3.21 0.00 4.30
1946 2454 4.818005 CCGTTTTGTACAAAGTTACTCCCT 59.182 41.667 19.72 0.00 0.00 4.20
1947 2455 5.049886 CCGTTTTGTACAAAGTTACTCCCTC 60.050 44.000 19.72 3.31 0.00 4.30
1948 2456 5.049886 CGTTTTGTACAAAGTTACTCCCTCC 60.050 44.000 19.72 0.00 0.00 4.30
1949 2457 3.947910 TGTACAAAGTTACTCCCTCCG 57.052 47.619 0.00 0.00 0.00 4.63
1950 2458 3.233507 TGTACAAAGTTACTCCCTCCGT 58.766 45.455 0.00 0.00 0.00 4.69
1951 2459 3.256631 TGTACAAAGTTACTCCCTCCGTC 59.743 47.826 0.00 0.00 0.00 4.79
1952 2460 1.622312 ACAAAGTTACTCCCTCCGTCC 59.378 52.381 0.00 0.00 0.00 4.79
1953 2461 1.066358 CAAAGTTACTCCCTCCGTCCC 60.066 57.143 0.00 0.00 0.00 4.46
1954 2462 0.115745 AAGTTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
1955 2463 0.115745 AGTTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
1956 2464 0.978907 GTTACTCCCTCCGTCCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
1957 2465 1.348696 GTTACTCCCTCCGTCCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
1958 2466 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1959 2467 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1960 2468 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
1961 2469 2.645797 ACTCCCTCCGTCCCAAAATAAA 59.354 45.455 0.00 0.00 0.00 1.40
1962 2470 3.268595 ACTCCCTCCGTCCCAAAATAAAT 59.731 43.478 0.00 0.00 0.00 1.40
1963 2471 3.626930 TCCCTCCGTCCCAAAATAAATG 58.373 45.455 0.00 0.00 0.00 2.32
1964 2472 3.267291 TCCCTCCGTCCCAAAATAAATGA 59.733 43.478 0.00 0.00 0.00 2.57
1965 2473 3.380320 CCCTCCGTCCCAAAATAAATGAC 59.620 47.826 0.00 0.00 0.00 3.06
1966 2474 4.270008 CCTCCGTCCCAAAATAAATGACT 58.730 43.478 0.00 0.00 0.00 3.41
1967 2475 4.335594 CCTCCGTCCCAAAATAAATGACTC 59.664 45.833 0.00 0.00 0.00 3.36
1968 2476 4.912586 TCCGTCCCAAAATAAATGACTCA 58.087 39.130 0.00 0.00 0.00 3.41
1969 2477 5.317808 TCCGTCCCAAAATAAATGACTCAA 58.682 37.500 0.00 0.00 0.00 3.02
1970 2478 5.182380 TCCGTCCCAAAATAAATGACTCAAC 59.818 40.000 0.00 0.00 0.00 3.18
1971 2479 5.183140 CCGTCCCAAAATAAATGACTCAACT 59.817 40.000 0.00 0.00 0.00 3.16
1972 2480 6.294508 CCGTCCCAAAATAAATGACTCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
1973 2481 7.145323 CGTCCCAAAATAAATGACTCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
1974 2482 8.293867 CGTCCCAAAATAAATGACTCAACTTTA 58.706 33.333 0.00 0.00 0.00 1.85
2017 2525 9.893305 AATTGAGTCACTTATTTTAAAACGGAG 57.107 29.630 1.97 4.41 0.00 4.63
2018 2526 7.429636 TGAGTCACTTATTTTAAAACGGAGG 57.570 36.000 1.97 0.00 0.00 4.30
2019 2527 6.428771 TGAGTCACTTATTTTAAAACGGAGGG 59.571 38.462 1.97 3.19 0.00 4.30
2020 2528 6.536447 AGTCACTTATTTTAAAACGGAGGGA 58.464 36.000 1.97 5.47 0.00 4.20
2021 2529 6.653740 AGTCACTTATTTTAAAACGGAGGGAG 59.346 38.462 1.97 0.00 0.00 4.30
2022 2530 6.429078 GTCACTTATTTTAAAACGGAGGGAGT 59.571 38.462 1.97 0.00 0.00 3.85
2023 2531 7.603784 GTCACTTATTTTAAAACGGAGGGAGTA 59.396 37.037 1.97 0.00 0.00 2.59
2024 2532 7.603784 TCACTTATTTTAAAACGGAGGGAGTAC 59.396 37.037 1.97 0.00 0.00 2.73
2025 2533 7.605309 CACTTATTTTAAAACGGAGGGAGTACT 59.395 37.037 1.97 0.00 0.00 2.73
2026 2534 8.815912 ACTTATTTTAAAACGGAGGGAGTACTA 58.184 33.333 1.97 0.00 0.00 1.82
2027 2535 9.657419 CTTATTTTAAAACGGAGGGAGTACTAA 57.343 33.333 1.97 0.00 0.00 2.24
2028 2536 9.657419 TTATTTTAAAACGGAGGGAGTACTAAG 57.343 33.333 1.97 0.00 0.00 2.18
2029 2537 6.670695 TTTAAAACGGAGGGAGTACTAAGT 57.329 37.500 0.00 0.00 0.00 2.24
2030 2538 7.775053 TTTAAAACGGAGGGAGTACTAAGTA 57.225 36.000 0.00 0.00 0.00 2.24
2031 2539 7.775053 TTAAAACGGAGGGAGTACTAAGTAA 57.225 36.000 0.00 0.00 0.00 2.24
2032 2540 6.864151 AAAACGGAGGGAGTACTAAGTAAT 57.136 37.500 0.00 0.00 0.00 1.89
2033 2541 6.462552 AAACGGAGGGAGTACTAAGTAATC 57.537 41.667 0.00 0.00 33.15 1.75
2077 2585 4.634004 GGATTAACACATCCAACGTCATCA 59.366 41.667 0.00 0.00 42.35 3.07
2102 2610 5.277974 CCATTTGATTCAACTCTGTGTCGTT 60.278 40.000 0.00 0.00 0.00 3.85
2163 2671 0.462759 GACCTCTGCCTTTGATCCGG 60.463 60.000 0.00 0.00 0.00 5.14
2194 2702 9.653516 ATCCGATCCATGTTAGATTAGATATCT 57.346 33.333 10.73 10.73 0.00 1.98
2195 2703 9.480861 TCCGATCCATGTTAGATTAGATATCTT 57.519 33.333 11.25 0.00 0.00 2.40
2244 2752 7.504924 TTCCATTATAAATTTAGACTGGCCG 57.495 36.000 19.26 0.00 28.33 6.13
2245 2753 6.833041 TCCATTATAAATTTAGACTGGCCGA 58.167 36.000 19.26 5.16 28.33 5.54
2246 2754 7.284074 TCCATTATAAATTTAGACTGGCCGAA 58.716 34.615 19.26 4.87 28.33 4.30
2247 2755 7.942341 TCCATTATAAATTTAGACTGGCCGAAT 59.058 33.333 19.26 0.00 28.33 3.34
2248 2756 8.237267 CCATTATAAATTTAGACTGGCCGAATC 58.763 37.037 14.12 0.00 0.00 2.52
2249 2757 5.924475 ATAAATTTAGACTGGCCGAATCG 57.076 39.130 3.94 0.00 0.00 3.34
2250 2758 1.583054 ATTTAGACTGGCCGAATCGC 58.417 50.000 0.00 0.00 0.00 4.58
2258 2766 2.202878 GCCGAATCGCCAGCTACA 60.203 61.111 0.00 0.00 0.00 2.74
2259 2767 2.240500 GCCGAATCGCCAGCTACAG 61.241 63.158 0.00 0.00 0.00 2.74
2260 2768 1.437573 CCGAATCGCCAGCTACAGA 59.562 57.895 0.00 0.00 0.00 3.41
2261 2769 0.596083 CCGAATCGCCAGCTACAGAG 60.596 60.000 0.00 0.00 0.00 3.35
2262 2770 0.101399 CGAATCGCCAGCTACAGAGT 59.899 55.000 0.00 0.00 0.00 3.24
2263 2771 1.469940 CGAATCGCCAGCTACAGAGTT 60.470 52.381 0.00 0.00 0.00 3.01
2264 2772 2.622436 GAATCGCCAGCTACAGAGTTT 58.378 47.619 0.00 0.00 0.00 2.66
2265 2773 3.733988 CGAATCGCCAGCTACAGAGTTTA 60.734 47.826 0.00 0.00 0.00 2.01
2266 2774 2.649331 TCGCCAGCTACAGAGTTTAC 57.351 50.000 0.00 0.00 0.00 2.01
2267 2775 1.890489 TCGCCAGCTACAGAGTTTACA 59.110 47.619 0.00 0.00 0.00 2.41
2268 2776 2.297880 TCGCCAGCTACAGAGTTTACAA 59.702 45.455 0.00 0.00 0.00 2.41
2269 2777 2.412089 CGCCAGCTACAGAGTTTACAAC 59.588 50.000 0.00 0.00 0.00 3.32
2270 2778 3.399330 GCCAGCTACAGAGTTTACAACA 58.601 45.455 0.00 0.00 0.00 3.33
2271 2779 3.813166 GCCAGCTACAGAGTTTACAACAA 59.187 43.478 0.00 0.00 0.00 2.83
2272 2780 4.274950 GCCAGCTACAGAGTTTACAACAAA 59.725 41.667 0.00 0.00 0.00 2.83
2273 2781 5.748592 CCAGCTACAGAGTTTACAACAAAC 58.251 41.667 0.00 0.00 0.00 2.93
2274 2782 5.527582 CCAGCTACAGAGTTTACAACAAACT 59.472 40.000 2.18 2.18 42.62 2.66
2285 2793 8.166422 AGTTTACAACAAACTCAGGGAAATAG 57.834 34.615 0.00 0.00 35.76 1.73
2286 2794 6.569179 TTACAACAAACTCAGGGAAATAGC 57.431 37.500 0.00 0.00 0.00 2.97
2287 2795 3.826729 ACAACAAACTCAGGGAAATAGCC 59.173 43.478 0.00 0.00 0.00 3.93
2288 2796 4.082125 CAACAAACTCAGGGAAATAGCCT 58.918 43.478 0.00 0.00 0.00 4.58
2289 2797 5.222048 ACAACAAACTCAGGGAAATAGCCTA 60.222 40.000 0.00 0.00 0.00 3.93
2290 2798 5.104259 ACAAACTCAGGGAAATAGCCTAG 57.896 43.478 0.00 0.00 0.00 3.02
2291 2799 3.847671 AACTCAGGGAAATAGCCTAGC 57.152 47.619 0.00 0.00 0.00 3.42
2292 2800 2.050918 ACTCAGGGAAATAGCCTAGCC 58.949 52.381 0.00 0.00 0.00 3.93
2293 2801 2.050144 CTCAGGGAAATAGCCTAGCCA 58.950 52.381 0.00 0.00 0.00 4.75
2294 2802 2.439507 CTCAGGGAAATAGCCTAGCCAA 59.560 50.000 0.00 0.00 0.00 4.52
2295 2803 2.439507 TCAGGGAAATAGCCTAGCCAAG 59.560 50.000 0.00 0.00 0.00 3.61
2296 2804 2.173569 CAGGGAAATAGCCTAGCCAAGT 59.826 50.000 0.00 0.00 0.00 3.16
2297 2805 2.853077 AGGGAAATAGCCTAGCCAAGTT 59.147 45.455 0.00 0.00 0.00 2.66
2298 2806 3.269643 AGGGAAATAGCCTAGCCAAGTTT 59.730 43.478 0.00 0.00 0.00 2.66
2299 2807 3.632604 GGGAAATAGCCTAGCCAAGTTTC 59.367 47.826 0.00 0.00 0.00 2.78
2300 2808 4.270008 GGAAATAGCCTAGCCAAGTTTCA 58.730 43.478 0.00 0.00 0.00 2.69
2301 2809 4.889995 GGAAATAGCCTAGCCAAGTTTCAT 59.110 41.667 0.00 0.00 0.00 2.57
2302 2810 6.062095 GGAAATAGCCTAGCCAAGTTTCATA 58.938 40.000 0.00 0.00 0.00 2.15
2303 2811 6.717084 GGAAATAGCCTAGCCAAGTTTCATAT 59.283 38.462 0.00 0.00 0.00 1.78
2304 2812 7.231519 GGAAATAGCCTAGCCAAGTTTCATATT 59.768 37.037 0.00 0.00 0.00 1.28
2305 2813 7.751768 AATAGCCTAGCCAAGTTTCATATTC 57.248 36.000 0.00 0.00 0.00 1.75
2306 2814 5.116084 AGCCTAGCCAAGTTTCATATTCA 57.884 39.130 0.00 0.00 0.00 2.57
2307 2815 4.884164 AGCCTAGCCAAGTTTCATATTCAC 59.116 41.667 0.00 0.00 0.00 3.18
2308 2816 4.036852 GCCTAGCCAAGTTTCATATTCACC 59.963 45.833 0.00 0.00 0.00 4.02
2309 2817 5.192927 CCTAGCCAAGTTTCATATTCACCA 58.807 41.667 0.00 0.00 0.00 4.17
2310 2818 5.829924 CCTAGCCAAGTTTCATATTCACCAT 59.170 40.000 0.00 0.00 0.00 3.55
2311 2819 5.841957 AGCCAAGTTTCATATTCACCATC 57.158 39.130 0.00 0.00 0.00 3.51
2312 2820 5.513233 AGCCAAGTTTCATATTCACCATCT 58.487 37.500 0.00 0.00 0.00 2.90
2313 2821 5.591877 AGCCAAGTTTCATATTCACCATCTC 59.408 40.000 0.00 0.00 0.00 2.75
2314 2822 5.221126 GCCAAGTTTCATATTCACCATCTCC 60.221 44.000 0.00 0.00 0.00 3.71
2315 2823 6.125029 CCAAGTTTCATATTCACCATCTCCT 58.875 40.000 0.00 0.00 0.00 3.69
2316 2824 7.282585 CCAAGTTTCATATTCACCATCTCCTA 58.717 38.462 0.00 0.00 0.00 2.94
2317 2825 7.775093 CCAAGTTTCATATTCACCATCTCCTAA 59.225 37.037 0.00 0.00 0.00 2.69
2318 2826 9.347240 CAAGTTTCATATTCACCATCTCCTAAT 57.653 33.333 0.00 0.00 0.00 1.73
2319 2827 9.566432 AAGTTTCATATTCACCATCTCCTAATC 57.434 33.333 0.00 0.00 0.00 1.75
2320 2828 8.943085 AGTTTCATATTCACCATCTCCTAATCT 58.057 33.333 0.00 0.00 0.00 2.40
2321 2829 9.566432 GTTTCATATTCACCATCTCCTAATCTT 57.434 33.333 0.00 0.00 0.00 2.40
2324 2832 9.379770 TCATATTCACCATCTCCTAATCTTACA 57.620 33.333 0.00 0.00 0.00 2.41
2325 2833 9.429359 CATATTCACCATCTCCTAATCTTACAC 57.571 37.037 0.00 0.00 0.00 2.90
2326 2834 5.871396 TCACCATCTCCTAATCTTACACC 57.129 43.478 0.00 0.00 0.00 4.16
2327 2835 5.277250 TCACCATCTCCTAATCTTACACCA 58.723 41.667 0.00 0.00 0.00 4.17
2328 2836 5.905331 TCACCATCTCCTAATCTTACACCAT 59.095 40.000 0.00 0.00 0.00 3.55
2329 2837 5.994054 CACCATCTCCTAATCTTACACCATG 59.006 44.000 0.00 0.00 0.00 3.66
2330 2838 5.667626 ACCATCTCCTAATCTTACACCATGT 59.332 40.000 0.00 0.00 0.00 3.21
2331 2839 6.183361 ACCATCTCCTAATCTTACACCATGTC 60.183 42.308 0.00 0.00 0.00 3.06
2332 2840 6.042552 CCATCTCCTAATCTTACACCATGTCT 59.957 42.308 0.00 0.00 0.00 3.41
2333 2841 7.419518 CCATCTCCTAATCTTACACCATGTCTT 60.420 40.741 0.00 0.00 0.00 3.01
2334 2842 6.878317 TCTCCTAATCTTACACCATGTCTTG 58.122 40.000 0.00 0.00 0.00 3.02
2335 2843 5.428253 TCCTAATCTTACACCATGTCTTGC 58.572 41.667 0.00 0.00 0.00 4.01
2336 2844 5.189736 TCCTAATCTTACACCATGTCTTGCT 59.810 40.000 0.00 0.00 0.00 3.91
2337 2845 6.382859 TCCTAATCTTACACCATGTCTTGCTA 59.617 38.462 0.00 0.00 0.00 3.49
2338 2846 6.703607 CCTAATCTTACACCATGTCTTGCTAG 59.296 42.308 0.00 0.00 0.00 3.42
2339 2847 4.471904 TCTTACACCATGTCTTGCTAGG 57.528 45.455 0.00 0.00 0.00 3.02
2340 2848 2.691409 TACACCATGTCTTGCTAGGC 57.309 50.000 0.00 0.00 0.00 3.93
2341 2849 0.987294 ACACCATGTCTTGCTAGGCT 59.013 50.000 0.64 0.00 0.00 4.58
2342 2850 1.339438 ACACCATGTCTTGCTAGGCTG 60.339 52.381 0.64 0.00 0.00 4.85
2343 2851 0.987294 ACCATGTCTTGCTAGGCTGT 59.013 50.000 0.64 0.00 0.00 4.40
2344 2852 1.339438 ACCATGTCTTGCTAGGCTGTG 60.339 52.381 0.64 0.51 0.00 3.66
2345 2853 1.065926 CCATGTCTTGCTAGGCTGTGA 60.066 52.381 0.64 0.00 0.00 3.58
2346 2854 2.277969 CATGTCTTGCTAGGCTGTGAG 58.722 52.381 0.64 0.00 0.00 3.51
2347 2855 0.036952 TGTCTTGCTAGGCTGTGAGC 60.037 55.000 0.64 0.00 41.46 4.26
2348 2856 0.248843 GTCTTGCTAGGCTGTGAGCT 59.751 55.000 9.04 0.00 41.99 4.09
2349 2857 0.248565 TCTTGCTAGGCTGTGAGCTG 59.751 55.000 9.04 2.98 41.99 4.24
2350 2858 1.367599 CTTGCTAGGCTGTGAGCTGC 61.368 60.000 9.04 0.00 41.99 5.25
2351 2859 1.834856 TTGCTAGGCTGTGAGCTGCT 61.835 55.000 0.00 0.00 41.99 4.24
2352 2860 0.972471 TGCTAGGCTGTGAGCTGCTA 60.972 55.000 0.15 0.00 41.99 3.49
2353 2861 0.529555 GCTAGGCTGTGAGCTGCTAC 60.530 60.000 0.15 2.25 41.99 3.58
2354 2862 0.820226 CTAGGCTGTGAGCTGCTACA 59.180 55.000 0.15 6.94 41.99 2.74
2355 2863 1.411977 CTAGGCTGTGAGCTGCTACAT 59.588 52.381 0.15 0.00 41.99 2.29
2356 2864 0.617413 AGGCTGTGAGCTGCTACATT 59.383 50.000 0.15 0.00 41.99 2.71
2357 2865 1.833630 AGGCTGTGAGCTGCTACATTA 59.166 47.619 0.15 0.00 41.99 1.90
2358 2866 1.936547 GGCTGTGAGCTGCTACATTAC 59.063 52.381 0.15 0.00 41.99 1.89
2359 2867 2.621338 GCTGTGAGCTGCTACATTACA 58.379 47.619 0.15 2.82 38.45 2.41
2360 2868 3.002791 GCTGTGAGCTGCTACATTACAA 58.997 45.455 0.15 0.00 38.45 2.41
2361 2869 3.063180 GCTGTGAGCTGCTACATTACAAG 59.937 47.826 0.15 0.00 38.45 3.16
2362 2870 4.498241 CTGTGAGCTGCTACATTACAAGA 58.502 43.478 0.15 0.00 0.00 3.02
2363 2871 5.089970 TGTGAGCTGCTACATTACAAGAT 57.910 39.130 0.15 0.00 0.00 2.40
2364 2872 5.111989 TGTGAGCTGCTACATTACAAGATC 58.888 41.667 0.15 0.00 0.00 2.75
2365 2873 5.105187 TGTGAGCTGCTACATTACAAGATCT 60.105 40.000 0.15 0.00 0.00 2.75
2366 2874 5.814705 GTGAGCTGCTACATTACAAGATCTT 59.185 40.000 0.15 0.88 0.00 2.40
2367 2875 5.814188 TGAGCTGCTACATTACAAGATCTTG 59.186 40.000 29.74 29.74 45.58 3.02
2368 2876 5.121811 AGCTGCTACATTACAAGATCTTGG 58.878 41.667 33.11 20.37 44.45 3.61
2369 2877 5.104776 AGCTGCTACATTACAAGATCTTGGA 60.105 40.000 33.11 26.14 44.45 3.53
2370 2878 5.007136 GCTGCTACATTACAAGATCTTGGAC 59.993 44.000 33.11 16.41 44.45 4.02
2371 2879 6.048732 TGCTACATTACAAGATCTTGGACA 57.951 37.500 33.11 18.57 44.45 4.02
2372 2880 6.472016 TGCTACATTACAAGATCTTGGACAA 58.528 36.000 33.11 24.27 44.45 3.18
2373 2881 6.939730 TGCTACATTACAAGATCTTGGACAAA 59.060 34.615 33.11 22.48 44.45 2.83
2374 2882 7.094805 TGCTACATTACAAGATCTTGGACAAAC 60.095 37.037 33.11 18.18 44.45 2.93
2375 2883 7.094805 GCTACATTACAAGATCTTGGACAAACA 60.095 37.037 33.11 14.83 44.45 2.83
2376 2884 6.970484 ACATTACAAGATCTTGGACAAACAC 58.030 36.000 33.11 0.00 44.45 3.32
2377 2885 6.772716 ACATTACAAGATCTTGGACAAACACT 59.227 34.615 33.11 15.41 44.45 3.55
2378 2886 7.936847 ACATTACAAGATCTTGGACAAACACTA 59.063 33.333 33.11 12.77 44.45 2.74
2379 2887 8.783093 CATTACAAGATCTTGGACAAACACTAA 58.217 33.333 33.11 20.77 44.45 2.24
2380 2888 6.619801 ACAAGATCTTGGACAAACACTAAC 57.380 37.500 33.11 0.00 44.45 2.34
2381 2889 6.119536 ACAAGATCTTGGACAAACACTAACA 58.880 36.000 33.11 0.00 44.45 2.41
2382 2890 6.772716 ACAAGATCTTGGACAAACACTAACAT 59.227 34.615 33.11 8.94 44.45 2.71
2383 2891 7.285401 ACAAGATCTTGGACAAACACTAACATT 59.715 33.333 33.11 8.59 44.45 2.71
2384 2892 7.823745 AGATCTTGGACAAACACTAACATTT 57.176 32.000 0.00 0.00 0.00 2.32
2385 2893 8.918202 AGATCTTGGACAAACACTAACATTTA 57.082 30.769 0.00 0.00 0.00 1.40
2386 2894 8.784043 AGATCTTGGACAAACACTAACATTTAC 58.216 33.333 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
654 671 1.371635 CGTGCCCGCTTTTTGGAAG 60.372 57.895 0.00 0.00 0.00 3.46
702 719 4.323477 TCGCTTTCACGGTGGGGG 62.323 66.667 8.50 7.65 0.00 5.40
712 729 1.913685 CGATCTGTCGCTCGCTTTC 59.086 57.895 0.00 0.00 41.49 2.62
754 772 2.113986 GCGAGGAATGGGATGGGG 59.886 66.667 0.00 0.00 0.00 4.96
757 775 1.228063 CTGGGCGAGGAATGGGATG 60.228 63.158 0.00 0.00 0.00 3.51
758 776 3.125376 GCTGGGCGAGGAATGGGAT 62.125 63.158 0.00 0.00 0.00 3.85
759 777 3.797353 GCTGGGCGAGGAATGGGA 61.797 66.667 0.00 0.00 0.00 4.37
779 809 3.637030 GGATAAGGTTCGCGCCGC 61.637 66.667 0.00 0.00 0.00 6.53
780 810 2.202824 TGGATAAGGTTCGCGCCG 60.203 61.111 0.00 0.00 0.00 6.46
781 811 2.178235 GGTGGATAAGGTTCGCGCC 61.178 63.158 0.00 0.00 0.00 6.53
782 812 2.178235 GGGTGGATAAGGTTCGCGC 61.178 63.158 0.00 0.00 0.00 6.86
808 838 2.868790 ATAAAGCGGGGGAGGGGGAA 62.869 60.000 0.00 0.00 0.00 3.97
809 839 1.975758 TATAAAGCGGGGGAGGGGGA 61.976 60.000 0.00 0.00 0.00 4.81
810 840 1.063654 TTATAAAGCGGGGGAGGGGG 61.064 60.000 0.00 0.00 0.00 5.40
811 841 0.109913 GTTATAAAGCGGGGGAGGGG 59.890 60.000 0.00 0.00 0.00 4.79
849 896 1.354368 GAGAAAAGGTGGTGGGATGGA 59.646 52.381 0.00 0.00 0.00 3.41
869 918 1.208614 GGCTTCGTTGCTTCTGCTG 59.791 57.895 2.92 0.00 40.48 4.41
887 940 1.407979 GAGATGGATTGGCTTGGCTTG 59.592 52.381 0.00 0.00 0.00 4.01
890 943 0.106318 AGGAGATGGATTGGCTTGGC 60.106 55.000 0.00 0.00 0.00 4.52
913 968 0.382515 ATTCGCAGCCGAGAGTAGAC 59.617 55.000 0.00 0.00 45.35 2.59
962 1017 2.105128 CGCCGCGAGAGGAAGAAT 59.895 61.111 8.23 0.00 0.00 2.40
998 1053 0.107410 TCCCGATGCTAACGCCATTT 60.107 50.000 0.00 0.00 34.43 2.32
1161 1216 2.005960 GCTGGGCGTCGATGTAGTCT 62.006 60.000 6.48 0.00 0.00 3.24
1480 1541 0.677288 ACGATCAACCGGACAGACAA 59.323 50.000 9.46 0.00 0.00 3.18
1490 1551 3.916761 TGGTGTACAGTAACGATCAACC 58.083 45.455 0.00 0.00 0.00 3.77
1508 1569 2.093447 CGGCCTCTTCTTGTCTAATGGT 60.093 50.000 0.00 0.00 0.00 3.55
1546 1611 3.787001 GGAGGGTCTGAAGGGGCG 61.787 72.222 0.00 0.00 0.00 6.13
1618 1690 3.935828 GCTACTGCTAGCTAGTTTTGCTT 59.064 43.478 21.62 2.87 42.11 3.91
1691 1763 2.549754 ACTGATGAGCAAACCGAAACTG 59.450 45.455 0.00 0.00 0.00 3.16
1751 1829 1.374125 CGACTGTGATTCCACCGCA 60.374 57.895 0.00 0.00 42.53 5.69
1752 1830 0.460284 ATCGACTGTGATTCCACCGC 60.460 55.000 0.00 0.00 42.53 5.68
1753 1831 1.660607 CAATCGACTGTGATTCCACCG 59.339 52.381 0.00 0.00 42.53 4.94
1754 1832 2.673368 GACAATCGACTGTGATTCCACC 59.327 50.000 3.28 0.00 42.53 4.61
1795 1873 7.156000 ACATCAATCAGTGATCATTTTTGCAA 58.844 30.769 5.98 0.00 44.01 4.08
1807 1885 3.007940 ACCGGAGAAACATCAATCAGTGA 59.992 43.478 9.46 0.00 41.67 3.41
1833 1911 2.173433 TGCAGTGATGCAATCCACG 58.827 52.632 0.00 7.65 44.73 4.94
1889 2393 1.757340 GGAGGGGGTCGACAGGTAG 60.757 68.421 18.91 0.00 0.00 3.18
1891 2395 3.602030 AGGAGGGGGTCGACAGGT 61.602 66.667 18.91 0.00 0.00 4.00
1917 2421 3.473625 ACTTTGTACAAAACGGAGGGAG 58.526 45.455 20.89 9.16 0.00 4.30
1922 2430 4.815846 GGGAGTAACTTTGTACAAAACGGA 59.184 41.667 20.89 5.34 0.00 4.69
1923 2431 4.818005 AGGGAGTAACTTTGTACAAAACGG 59.182 41.667 20.89 12.50 0.00 4.44
1924 2432 5.049886 GGAGGGAGTAACTTTGTACAAAACG 60.050 44.000 20.89 13.17 0.00 3.60
1925 2433 5.049886 CGGAGGGAGTAACTTTGTACAAAAC 60.050 44.000 20.89 16.05 0.00 2.43
1926 2434 5.058490 CGGAGGGAGTAACTTTGTACAAAA 58.942 41.667 20.89 4.87 0.00 2.44
1927 2435 4.101430 ACGGAGGGAGTAACTTTGTACAAA 59.899 41.667 19.53 19.53 0.00 2.83
1928 2436 3.642848 ACGGAGGGAGTAACTTTGTACAA 59.357 43.478 3.59 3.59 0.00 2.41
1929 2437 3.233507 ACGGAGGGAGTAACTTTGTACA 58.766 45.455 0.00 0.00 0.00 2.90
1930 2438 3.367806 GGACGGAGGGAGTAACTTTGTAC 60.368 52.174 0.00 0.00 0.00 2.90
1931 2439 2.827921 GGACGGAGGGAGTAACTTTGTA 59.172 50.000 0.00 0.00 0.00 2.41
1932 2440 1.622312 GGACGGAGGGAGTAACTTTGT 59.378 52.381 0.00 0.00 0.00 2.83
1933 2441 1.066358 GGGACGGAGGGAGTAACTTTG 60.066 57.143 0.00 0.00 0.00 2.77
1934 2442 1.273759 GGGACGGAGGGAGTAACTTT 58.726 55.000 0.00 0.00 0.00 2.66
1935 2443 0.115745 TGGGACGGAGGGAGTAACTT 59.884 55.000 0.00 0.00 0.00 2.66
1936 2444 0.115745 TTGGGACGGAGGGAGTAACT 59.884 55.000 0.00 0.00 0.00 2.24
1937 2445 0.978907 TTTGGGACGGAGGGAGTAAC 59.021 55.000 0.00 0.00 0.00 2.50
1938 2446 1.732117 TTTTGGGACGGAGGGAGTAA 58.268 50.000 0.00 0.00 0.00 2.24
1939 2447 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1940 2448 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
1941 2449 3.359695 TTTATTTTGGGACGGAGGGAG 57.640 47.619 0.00 0.00 0.00 4.30
1942 2450 3.267291 TCATTTATTTTGGGACGGAGGGA 59.733 43.478 0.00 0.00 0.00 4.20
1943 2451 3.380320 GTCATTTATTTTGGGACGGAGGG 59.620 47.826 0.00 0.00 0.00 4.30
1944 2452 4.270008 AGTCATTTATTTTGGGACGGAGG 58.730 43.478 0.00 0.00 33.84 4.30
1945 2453 4.941263 TGAGTCATTTATTTTGGGACGGAG 59.059 41.667 0.00 0.00 33.84 4.63
1946 2454 4.912586 TGAGTCATTTATTTTGGGACGGA 58.087 39.130 0.00 0.00 33.84 4.69
1947 2455 5.183140 AGTTGAGTCATTTATTTTGGGACGG 59.817 40.000 0.00 0.00 33.84 4.79
1948 2456 6.254281 AGTTGAGTCATTTATTTTGGGACG 57.746 37.500 0.00 0.00 33.84 4.79
1991 2499 9.893305 CTCCGTTTTAAAATAAGTGACTCAATT 57.107 29.630 3.52 0.00 0.00 2.32
1992 2500 8.512138 CCTCCGTTTTAAAATAAGTGACTCAAT 58.488 33.333 3.52 0.00 0.00 2.57
1993 2501 7.040961 CCCTCCGTTTTAAAATAAGTGACTCAA 60.041 37.037 3.52 0.00 0.00 3.02
1994 2502 6.428771 CCCTCCGTTTTAAAATAAGTGACTCA 59.571 38.462 3.52 0.00 0.00 3.41
1995 2503 6.652062 TCCCTCCGTTTTAAAATAAGTGACTC 59.348 38.462 3.52 0.00 0.00 3.36
1996 2504 6.536447 TCCCTCCGTTTTAAAATAAGTGACT 58.464 36.000 3.52 0.00 0.00 3.41
1997 2505 6.429078 ACTCCCTCCGTTTTAAAATAAGTGAC 59.571 38.462 3.52 0.00 0.00 3.67
1998 2506 6.536447 ACTCCCTCCGTTTTAAAATAAGTGA 58.464 36.000 3.52 0.00 0.00 3.41
1999 2507 6.812879 ACTCCCTCCGTTTTAAAATAAGTG 57.187 37.500 3.52 0.00 0.00 3.16
2000 2508 7.683578 AGTACTCCCTCCGTTTTAAAATAAGT 58.316 34.615 3.52 3.73 0.00 2.24
2001 2509 9.657419 TTAGTACTCCCTCCGTTTTAAAATAAG 57.343 33.333 0.00 2.61 0.00 1.73
2002 2510 9.657419 CTTAGTACTCCCTCCGTTTTAAAATAA 57.343 33.333 0.00 0.00 0.00 1.40
2003 2511 8.815912 ACTTAGTACTCCCTCCGTTTTAAAATA 58.184 33.333 0.00 0.00 0.00 1.40
2004 2512 7.683578 ACTTAGTACTCCCTCCGTTTTAAAAT 58.316 34.615 0.00 0.00 0.00 1.82
2005 2513 7.066307 ACTTAGTACTCCCTCCGTTTTAAAA 57.934 36.000 0.00 0.00 0.00 1.52
2006 2514 6.670695 ACTTAGTACTCCCTCCGTTTTAAA 57.329 37.500 0.00 0.00 0.00 1.52
2007 2515 7.775053 TTACTTAGTACTCCCTCCGTTTTAA 57.225 36.000 0.00 0.00 0.00 1.52
2008 2516 7.068716 GGATTACTTAGTACTCCCTCCGTTTTA 59.931 40.741 15.37 0.00 33.51 1.52
2009 2517 6.127225 GGATTACTTAGTACTCCCTCCGTTTT 60.127 42.308 15.37 0.00 33.51 2.43
2010 2518 5.362143 GGATTACTTAGTACTCCCTCCGTTT 59.638 44.000 15.37 0.00 33.51 3.60
2011 2519 4.892345 GGATTACTTAGTACTCCCTCCGTT 59.108 45.833 15.37 0.00 33.51 4.44
2012 2520 4.167697 AGGATTACTTAGTACTCCCTCCGT 59.832 45.833 20.56 4.04 38.21 4.69
2013 2521 4.727677 AGGATTACTTAGTACTCCCTCCG 58.272 47.826 20.56 0.00 38.21 4.63
2014 2522 6.851318 ACTAGGATTACTTAGTACTCCCTCC 58.149 44.000 20.56 9.49 38.21 4.30
2015 2523 8.659527 ACTACTAGGATTACTTAGTACTCCCTC 58.340 40.741 20.56 1.96 38.21 4.30
2016 2524 8.580024 ACTACTAGGATTACTTAGTACTCCCT 57.420 38.462 20.56 15.00 38.21 4.20
2017 2525 9.639563 AAACTACTAGGATTACTTAGTACTCCC 57.360 37.037 20.56 9.58 38.21 4.30
2077 2585 4.214119 CGACACAGAGTTGAATCAAATGGT 59.786 41.667 0.00 0.00 33.04 3.55
2163 2671 4.855715 TCTAACATGGATCGGATCAGAC 57.144 45.455 18.99 3.36 0.00 3.51
2218 2726 9.226606 CGGCCAGTCTAAATTTATAATGGAATA 57.773 33.333 25.53 0.00 29.66 1.75
2219 2727 7.942341 TCGGCCAGTCTAAATTTATAATGGAAT 59.058 33.333 25.53 6.44 29.66 3.01
2220 2728 7.284074 TCGGCCAGTCTAAATTTATAATGGAA 58.716 34.615 25.53 12.36 29.66 3.53
2221 2729 6.833041 TCGGCCAGTCTAAATTTATAATGGA 58.167 36.000 25.53 9.12 29.66 3.41
2222 2730 7.504924 TTCGGCCAGTCTAAATTTATAATGG 57.495 36.000 19.98 19.98 30.90 3.16
2223 2731 7.957484 CGATTCGGCCAGTCTAAATTTATAATG 59.043 37.037 2.24 1.41 0.00 1.90
2224 2732 7.360946 GCGATTCGGCCAGTCTAAATTTATAAT 60.361 37.037 2.24 0.00 0.00 1.28
2225 2733 6.073440 GCGATTCGGCCAGTCTAAATTTATAA 60.073 38.462 2.24 0.00 0.00 0.98
2226 2734 5.407387 GCGATTCGGCCAGTCTAAATTTATA 59.593 40.000 2.24 0.00 0.00 0.98
2227 2735 4.213482 GCGATTCGGCCAGTCTAAATTTAT 59.787 41.667 2.24 0.00 0.00 1.40
2228 2736 3.558418 GCGATTCGGCCAGTCTAAATTTA 59.442 43.478 2.24 0.00 0.00 1.40
2229 2737 2.354821 GCGATTCGGCCAGTCTAAATTT 59.645 45.455 2.24 0.00 0.00 1.82
2230 2738 1.940613 GCGATTCGGCCAGTCTAAATT 59.059 47.619 2.24 0.00 0.00 1.82
2231 2739 1.583054 GCGATTCGGCCAGTCTAAAT 58.417 50.000 2.24 0.00 0.00 1.40
2232 2740 3.059603 GCGATTCGGCCAGTCTAAA 57.940 52.632 2.24 0.00 0.00 1.85
2233 2741 4.827481 GCGATTCGGCCAGTCTAA 57.173 55.556 2.24 0.00 0.00 2.10
2242 2750 0.596083 CTCTGTAGCTGGCGATTCGG 60.596 60.000 8.34 0.00 0.00 4.30
2243 2751 0.101399 ACTCTGTAGCTGGCGATTCG 59.899 55.000 0.62 0.62 0.00 3.34
2244 2752 2.301577 AACTCTGTAGCTGGCGATTC 57.698 50.000 0.00 0.00 0.00 2.52
2245 2753 2.770164 AAACTCTGTAGCTGGCGATT 57.230 45.000 0.00 0.00 0.00 3.34
2246 2754 2.496070 TGTAAACTCTGTAGCTGGCGAT 59.504 45.455 0.00 0.00 0.00 4.58
2247 2755 1.890489 TGTAAACTCTGTAGCTGGCGA 59.110 47.619 0.00 0.00 0.00 5.54
2248 2756 2.363788 TGTAAACTCTGTAGCTGGCG 57.636 50.000 0.00 0.00 0.00 5.69
2262 2770 6.015772 GGCTATTTCCCTGAGTTTGTTGTAAA 60.016 38.462 0.00 0.00 0.00 2.01
2263 2771 5.475564 GGCTATTTCCCTGAGTTTGTTGTAA 59.524 40.000 0.00 0.00 0.00 2.41
2264 2772 5.007682 GGCTATTTCCCTGAGTTTGTTGTA 58.992 41.667 0.00 0.00 0.00 2.41
2265 2773 3.826729 GGCTATTTCCCTGAGTTTGTTGT 59.173 43.478 0.00 0.00 0.00 3.32
2266 2774 4.082125 AGGCTATTTCCCTGAGTTTGTTG 58.918 43.478 0.00 0.00 0.00 3.33
2267 2775 4.388577 AGGCTATTTCCCTGAGTTTGTT 57.611 40.909 0.00 0.00 0.00 2.83
2268 2776 4.626529 GCTAGGCTATTTCCCTGAGTTTGT 60.627 45.833 0.00 0.00 33.88 2.83
2269 2777 3.879892 GCTAGGCTATTTCCCTGAGTTTG 59.120 47.826 0.00 0.00 33.88 2.93
2270 2778 3.117851 GGCTAGGCTATTTCCCTGAGTTT 60.118 47.826 9.46 0.00 33.88 2.66
2271 2779 2.439880 GGCTAGGCTATTTCCCTGAGTT 59.560 50.000 9.46 0.00 33.88 3.01
2272 2780 2.050918 GGCTAGGCTATTTCCCTGAGT 58.949 52.381 9.46 0.00 33.88 3.41
2273 2781 2.050144 TGGCTAGGCTATTTCCCTGAG 58.950 52.381 18.18 0.00 33.88 3.35
2274 2782 2.190398 TGGCTAGGCTATTTCCCTGA 57.810 50.000 18.18 0.00 33.88 3.86
2275 2783 2.173569 ACTTGGCTAGGCTATTTCCCTG 59.826 50.000 18.18 0.00 33.88 4.45
2276 2784 2.493091 ACTTGGCTAGGCTATTTCCCT 58.507 47.619 18.18 0.00 36.47 4.20
2277 2785 3.298686 AACTTGGCTAGGCTATTTCCC 57.701 47.619 18.18 0.00 0.00 3.97
2278 2786 4.270008 TGAAACTTGGCTAGGCTATTTCC 58.730 43.478 24.20 8.40 0.00 3.13
2279 2787 7.751768 ATATGAAACTTGGCTAGGCTATTTC 57.248 36.000 18.18 20.77 0.00 2.17
2280 2788 7.779798 TGAATATGAAACTTGGCTAGGCTATTT 59.220 33.333 18.18 14.02 0.00 1.40
2281 2789 7.229506 GTGAATATGAAACTTGGCTAGGCTATT 59.770 37.037 18.18 9.92 0.00 1.73
2282 2790 6.712547 GTGAATATGAAACTTGGCTAGGCTAT 59.287 38.462 18.18 1.38 0.00 2.97
2283 2791 6.055588 GTGAATATGAAACTTGGCTAGGCTA 58.944 40.000 18.18 9.18 0.00 3.93
2284 2792 4.884164 GTGAATATGAAACTTGGCTAGGCT 59.116 41.667 18.18 0.00 0.00 4.58
2285 2793 4.036852 GGTGAATATGAAACTTGGCTAGGC 59.963 45.833 9.85 9.85 0.00 3.93
2286 2794 5.192927 TGGTGAATATGAAACTTGGCTAGG 58.807 41.667 0.20 0.00 0.00 3.02
2287 2795 6.769822 AGATGGTGAATATGAAACTTGGCTAG 59.230 38.462 0.00 0.00 0.00 3.42
2288 2796 6.662755 AGATGGTGAATATGAAACTTGGCTA 58.337 36.000 0.00 0.00 0.00 3.93
2289 2797 5.513233 AGATGGTGAATATGAAACTTGGCT 58.487 37.500 0.00 0.00 0.00 4.75
2290 2798 5.221126 GGAGATGGTGAATATGAAACTTGGC 60.221 44.000 0.00 0.00 0.00 4.52
2291 2799 6.125029 AGGAGATGGTGAATATGAAACTTGG 58.875 40.000 0.00 0.00 0.00 3.61
2292 2800 8.737168 TTAGGAGATGGTGAATATGAAACTTG 57.263 34.615 0.00 0.00 0.00 3.16
2293 2801 9.566432 GATTAGGAGATGGTGAATATGAAACTT 57.434 33.333 0.00 0.00 0.00 2.66
2294 2802 8.943085 AGATTAGGAGATGGTGAATATGAAACT 58.057 33.333 0.00 0.00 0.00 2.66
2295 2803 9.566432 AAGATTAGGAGATGGTGAATATGAAAC 57.434 33.333 0.00 0.00 0.00 2.78
2298 2806 9.379770 TGTAAGATTAGGAGATGGTGAATATGA 57.620 33.333 0.00 0.00 0.00 2.15
2299 2807 9.429359 GTGTAAGATTAGGAGATGGTGAATATG 57.571 37.037 0.00 0.00 0.00 1.78
2300 2808 8.598041 GGTGTAAGATTAGGAGATGGTGAATAT 58.402 37.037 0.00 0.00 0.00 1.28
2301 2809 7.567250 TGGTGTAAGATTAGGAGATGGTGAATA 59.433 37.037 0.00 0.00 0.00 1.75
2302 2810 6.386927 TGGTGTAAGATTAGGAGATGGTGAAT 59.613 38.462 0.00 0.00 0.00 2.57
2303 2811 5.724370 TGGTGTAAGATTAGGAGATGGTGAA 59.276 40.000 0.00 0.00 0.00 3.18
2304 2812 5.277250 TGGTGTAAGATTAGGAGATGGTGA 58.723 41.667 0.00 0.00 0.00 4.02
2305 2813 5.614324 TGGTGTAAGATTAGGAGATGGTG 57.386 43.478 0.00 0.00 0.00 4.17
2306 2814 5.667626 ACATGGTGTAAGATTAGGAGATGGT 59.332 40.000 0.00 0.00 0.00 3.55
2307 2815 6.042552 AGACATGGTGTAAGATTAGGAGATGG 59.957 42.308 0.00 0.00 0.00 3.51
2308 2816 7.060383 AGACATGGTGTAAGATTAGGAGATG 57.940 40.000 0.00 0.00 0.00 2.90
2309 2817 7.504403 CAAGACATGGTGTAAGATTAGGAGAT 58.496 38.462 0.00 0.00 0.00 2.75
2310 2818 6.630413 GCAAGACATGGTGTAAGATTAGGAGA 60.630 42.308 0.00 0.00 0.00 3.71
2311 2819 5.525378 GCAAGACATGGTGTAAGATTAGGAG 59.475 44.000 0.00 0.00 0.00 3.69
2312 2820 5.189736 AGCAAGACATGGTGTAAGATTAGGA 59.810 40.000 0.00 0.00 38.62 2.94
2313 2821 5.431765 AGCAAGACATGGTGTAAGATTAGG 58.568 41.667 0.00 0.00 38.62 2.69
2314 2822 6.703607 CCTAGCAAGACATGGTGTAAGATTAG 59.296 42.308 0.00 0.00 40.70 1.73
2315 2823 6.582636 CCTAGCAAGACATGGTGTAAGATTA 58.417 40.000 0.00 0.00 40.70 1.75
2316 2824 5.431765 CCTAGCAAGACATGGTGTAAGATT 58.568 41.667 0.00 0.00 40.70 2.40
2317 2825 4.684485 GCCTAGCAAGACATGGTGTAAGAT 60.684 45.833 0.00 0.00 40.70 2.40
2318 2826 3.369471 GCCTAGCAAGACATGGTGTAAGA 60.369 47.826 0.00 0.00 40.70 2.10
2319 2827 2.939103 GCCTAGCAAGACATGGTGTAAG 59.061 50.000 0.00 0.00 40.70 2.34
2320 2828 2.571653 AGCCTAGCAAGACATGGTGTAA 59.428 45.455 0.00 0.00 40.70 2.41
2321 2829 2.093500 CAGCCTAGCAAGACATGGTGTA 60.093 50.000 0.00 0.00 40.70 2.90
2322 2830 0.987294 AGCCTAGCAAGACATGGTGT 59.013 50.000 0.00 0.00 40.70 4.16
2323 2831 1.339438 ACAGCCTAGCAAGACATGGTG 60.339 52.381 0.00 0.00 40.70 4.17
2324 2832 0.987294 ACAGCCTAGCAAGACATGGT 59.013 50.000 0.00 0.00 43.54 3.55
2325 2833 1.065926 TCACAGCCTAGCAAGACATGG 60.066 52.381 0.00 0.00 0.00 3.66
2326 2834 2.277969 CTCACAGCCTAGCAAGACATG 58.722 52.381 0.00 0.00 0.00 3.21
2327 2835 1.406614 GCTCACAGCCTAGCAAGACAT 60.407 52.381 0.00 0.00 38.63 3.06
2328 2836 0.036952 GCTCACAGCCTAGCAAGACA 60.037 55.000 0.00 0.00 38.63 3.41
2329 2837 0.248843 AGCTCACAGCCTAGCAAGAC 59.751 55.000 0.00 0.00 43.77 3.01
2330 2838 0.248565 CAGCTCACAGCCTAGCAAGA 59.751 55.000 0.00 0.00 43.77 3.02
2331 2839 1.367599 GCAGCTCACAGCCTAGCAAG 61.368 60.000 0.00 0.00 43.77 4.01
2332 2840 1.376424 GCAGCTCACAGCCTAGCAA 60.376 57.895 0.00 0.00 43.77 3.91
2333 2841 0.972471 TAGCAGCTCACAGCCTAGCA 60.972 55.000 0.00 0.00 43.77 3.49
2334 2842 0.529555 GTAGCAGCTCACAGCCTAGC 60.530 60.000 0.00 0.00 43.77 3.42
2335 2843 0.820226 TGTAGCAGCTCACAGCCTAG 59.180 55.000 0.00 0.00 43.77 3.02
2336 2844 1.489481 ATGTAGCAGCTCACAGCCTA 58.511 50.000 0.00 0.00 43.77 3.93
2337 2845 0.617413 AATGTAGCAGCTCACAGCCT 59.383 50.000 0.00 0.00 43.77 4.58
2338 2846 1.936547 GTAATGTAGCAGCTCACAGCC 59.063 52.381 0.00 0.00 43.77 4.85
2339 2847 2.621338 TGTAATGTAGCAGCTCACAGC 58.379 47.619 0.00 0.00 42.84 4.40
2340 2848 4.498241 TCTTGTAATGTAGCAGCTCACAG 58.502 43.478 0.00 0.00 0.00 3.66
2341 2849 4.535526 TCTTGTAATGTAGCAGCTCACA 57.464 40.909 0.00 2.48 0.00 3.58
2342 2850 5.355596 AGATCTTGTAATGTAGCAGCTCAC 58.644 41.667 0.00 0.00 0.00 3.51
2343 2851 5.604758 AGATCTTGTAATGTAGCAGCTCA 57.395 39.130 0.00 0.00 0.00 4.26
2344 2852 5.236047 CCAAGATCTTGTAATGTAGCAGCTC 59.764 44.000 29.03 0.00 38.85 4.09
2345 2853 5.104776 TCCAAGATCTTGTAATGTAGCAGCT 60.105 40.000 29.03 0.00 38.85 4.24
2346 2854 5.007136 GTCCAAGATCTTGTAATGTAGCAGC 59.993 44.000 29.03 7.04 38.85 5.25
2347 2855 6.108687 TGTCCAAGATCTTGTAATGTAGCAG 58.891 40.000 29.03 13.07 38.85 4.24
2348 2856 6.048732 TGTCCAAGATCTTGTAATGTAGCA 57.951 37.500 29.03 14.73 38.85 3.49
2349 2857 6.985188 TTGTCCAAGATCTTGTAATGTAGC 57.015 37.500 29.03 12.81 38.85 3.58
2350 2858 8.230486 GTGTTTGTCCAAGATCTTGTAATGTAG 58.770 37.037 29.03 14.96 38.85 2.74
2351 2859 7.936847 AGTGTTTGTCCAAGATCTTGTAATGTA 59.063 33.333 29.03 10.89 38.85 2.29
2352 2860 6.772716 AGTGTTTGTCCAAGATCTTGTAATGT 59.227 34.615 29.03 6.42 38.85 2.71
2353 2861 7.206981 AGTGTTTGTCCAAGATCTTGTAATG 57.793 36.000 29.03 16.55 38.85 1.90
2354 2862 8.784043 GTTAGTGTTTGTCCAAGATCTTGTAAT 58.216 33.333 29.03 11.85 38.85 1.89
2355 2863 7.771361 TGTTAGTGTTTGTCCAAGATCTTGTAA 59.229 33.333 29.03 19.36 38.85 2.41
2356 2864 7.276658 TGTTAGTGTTTGTCCAAGATCTTGTA 58.723 34.615 29.03 15.17 38.85 2.41
2357 2865 6.119536 TGTTAGTGTTTGTCCAAGATCTTGT 58.880 36.000 29.03 13.18 38.85 3.16
2358 2866 6.618287 TGTTAGTGTTTGTCCAAGATCTTG 57.382 37.500 25.75 25.75 40.13 3.02
2359 2867 7.823745 AATGTTAGTGTTTGTCCAAGATCTT 57.176 32.000 0.88 0.88 0.00 2.40
2360 2868 7.823745 AAATGTTAGTGTTTGTCCAAGATCT 57.176 32.000 0.00 0.00 0.00 2.75
2361 2869 8.950403 GTAAATGTTAGTGTTTGTCCAAGATC 57.050 34.615 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.