Multiple sequence alignment - TraesCS2D01G384300

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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 TraesCS2D01G384300 chr2D 100.000 2990 0 0 1 2990 488996487 488993498 0.000000e+00 5522.0
1 TraesCS2D01G384300 chr2D 80.825 485 68 14 1015 1493 489009867 489009402 1.020000e-94 357.0
2 TraesCS2D01G384300 chr2D 80.696 316 49 10 12 324 612493343 612493649 4.980000e-58 235.0
3 TraesCS2D01G384300 chr2D 91.837 49 2 2 709 756 488995728 488995681 1.920000e-07 67.6
4 TraesCS2D01G384300 chr2D 91.837 49 2 2 760 807 488995779 488995732 1.920000e-07 67.6
5 TraesCS2D01G384300 chr7B 85.988 1513 96 47 806 2301 19957038 19955625 0.000000e+00 1513.0
6 TraesCS2D01G384300 chr7B 87.176 655 58 15 109 754 19957740 19957103 0.000000e+00 721.0
7 TraesCS2D01G384300 chr7B 84.261 629 66 10 2318 2940 19955640 19955039 1.540000e-162 582.0
8 TraesCS2D01G384300 chr7B 81.899 337 40 11 2643 2975 19960083 19959764 6.360000e-67 265.0
9 TraesCS2D01G384300 chr7B 85.915 71 6 2 2059 2129 19959619 19959553 4.130000e-09 73.1
10 TraesCS2D01G384300 chr1D 85.042 1424 115 48 907 2299 460187756 460186400 0.000000e+00 1360.0
11 TraesCS2D01G384300 chr1D 89.222 334 17 8 2318 2650 393953053 393952738 1.670000e-107 399.0
12 TraesCS2D01G384300 chr1D 86.640 247 20 7 2057 2301 393953273 393953038 8.220000e-66 261.0
13 TraesCS2D01G384300 chr1D 80.714 140 20 5 2857 2990 460185834 460185696 5.270000e-18 102.0
14 TraesCS2D01G384300 chr3B 83.849 1486 123 46 852 2299 733600587 733601993 0.000000e+00 1306.0
15 TraesCS2D01G384300 chr3B 79.588 485 78 19 995 1471 733562550 733563021 7.990000e-86 327.0
16 TraesCS2D01G384300 chr3B 100.000 28 0 0 372 399 411429392 411429419 5.000000e-03 52.8
17 TraesCS2D01G384300 chr3D 83.212 1507 151 49 511 1992 552769543 552770972 0.000000e+00 1288.0
18 TraesCS2D01G384300 chr3D 82.530 332 40 9 2667 2990 552771767 552772088 2.940000e-70 276.0
19 TraesCS2D01G384300 chr3D 82.637 311 26 13 1994 2299 552771102 552771389 1.780000e-62 250.0
20 TraesCS2D01G384300 chr3A 83.848 1424 117 45 913 2299 689073072 689074419 0.000000e+00 1251.0
21 TraesCS2D01G384300 chr3A 86.842 494 54 5 1549 2041 720602767 720602284 2.620000e-150 542.0
22 TraesCS2D01G384300 chr3A 79.958 479 86 9 995 1471 689007216 689007686 7.940000e-91 344.0
23 TraesCS2D01G384300 chr3A 83.974 312 37 7 2667 2975 689074843 689075144 1.360000e-73 287.0
24 TraesCS2D01G384300 chr3A 84.585 253 28 8 532 782 689072385 689072628 1.070000e-59 241.0
25 TraesCS2D01G384300 chr5D 86.220 762 70 22 1550 2301 397474820 397474084 0.000000e+00 793.0
26 TraesCS2D01G384300 chr5D 85.771 759 82 19 1549 2301 397464952 397465690 0.000000e+00 780.0
27 TraesCS2D01G384300 chr5D 83.778 487 42 9 1330 1805 521253778 521254238 7.660000e-116 427.0
28 TraesCS2D01G384300 chr5D 89.489 333 18 6 2318 2650 397474099 397473784 3.590000e-109 405.0
29 TraesCS2D01G384300 chr5D 89.222 334 18 7 2318 2650 375001100 375001416 4.640000e-108 401.0
30 TraesCS2D01G384300 chr5D 87.952 332 23 6 2318 2649 397465675 397465989 2.810000e-100 375.0
31 TraesCS2D01G384300 chr5D 87.449 247 18 7 2057 2301 375000880 375001115 3.800000e-69 272.0
32 TraesCS2D01G384300 chr1A 82.059 981 98 38 1341 2299 551739935 551739011 0.000000e+00 765.0
33 TraesCS2D01G384300 chr1A 84.538 498 53 9 1317 1805 567966427 567965945 3.490000e-129 472.0
34 TraesCS2D01G384300 chr1A 89.333 150 13 2 2504 2650 205552559 205552708 5.090000e-43 185.0
35 TraesCS2D01G384300 chr6B 84.676 757 93 16 1549 2301 666362582 666361845 0.000000e+00 734.0
36 TraesCS2D01G384300 chr6B 88.253 332 21 7 2318 2648 666361860 666361546 6.050000e-102 381.0
37 TraesCS2D01G384300 chr6B 83.631 336 35 10 2319 2654 252551383 252551068 6.270000e-77 298.0
38 TraesCS2D01G384300 chr6B 80.392 102 15 3 7 104 422994228 422994328 4.130000e-09 73.1
39 TraesCS2D01G384300 chr4A 88.347 472 49 5 1571 2041 444375739 444376205 2.010000e-156 562.0
40 TraesCS2D01G384300 chr4A 78.676 136 25 4 6 137 546442389 546442524 1.480000e-13 87.9
41 TraesCS2D01G384300 chr2B 88.288 333 21 7 2318 2650 574051233 574051547 1.680000e-102 383.0
42 TraesCS2D01G384300 chr2B 86.022 186 17 6 2116 2299 574051068 574051246 1.090000e-44 191.0
43 TraesCS2D01G384300 chr2B 84.865 185 15 10 2123 2301 759273328 759273151 1.100000e-39 174.0
44 TraesCS2D01G384300 chr2B 82.353 102 13 3 7 104 109133320 109133420 1.910000e-12 84.2
45 TraesCS2D01G384300 chr2A 89.238 223 19 4 2716 2934 619559879 619560100 1.060000e-69 274.0
46 TraesCS2D01G384300 chr2A 95.935 123 5 0 2528 2650 33473580 33473458 1.820000e-47 200.0
47 TraesCS2D01G384300 chr2A 92.453 53 0 1 2059 2111 619560304 619560352 4.130000e-09 73.1
48 TraesCS2D01G384300 chr7A 96.748 123 4 0 2528 2650 557426169 557426047 3.910000e-49 206.0
49 TraesCS2D01G384300 chr7A 95.238 126 6 0 2525 2650 75694641 75694766 1.820000e-47 200.0
50 TraesCS2D01G384300 chr5A 94.444 126 7 0 2525 2650 580528985 580529110 8.460000e-46 195.0
51 TraesCS2D01G384300 chr5A 74.793 242 48 12 6 239 547794010 547793774 2.450000e-16 97.1
52 TraesCS2D01G384300 chr5A 84.000 75 5 5 2696 2769 450785739 450785671 6.920000e-07 65.8
53 TraesCS2D01G384300 chr5B 78.930 299 20 21 2016 2301 676859163 676858895 2.380000e-36 163.0
54 TraesCS2D01G384300 chr6A 79.259 135 23 5 6 137 575048700 575048568 4.110000e-14 89.8
55 TraesCS2D01G384300 chr6A 84.000 75 5 6 2696 2769 202134099 202134167 6.920000e-07 65.8
56 TraesCS2D01G384300 chrUn 80.342 117 22 1 22 137 53036475 53036591 1.480000e-13 87.9
57 TraesCS2D01G384300 chr7D 78.231 147 17 12 2708 2853 573899627 573899759 2.470000e-11 80.5
58 TraesCS2D01G384300 chr7D 83.529 85 9 5 2010 2090 573898973 573899056 1.150000e-09 75.0
59 TraesCS2D01G384300 chr6D 82.178 101 11 6 2670 2769 257923432 257923526 2.470000e-11 80.5
60 TraesCS2D01G384300 chr1B 77.863 131 24 3 11 137 598676014 598675885 3.200000e-10 76.8
61 TraesCS2D01G384300 chr1B 82.418 91 12 2 7 94 598676105 598676016 3.200000e-10 76.8


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 TraesCS2D01G384300 chr2D 488993498 488996487 2989 True 1885.733333 5522 94.558000 1 2990 3 chr2D.!!$R2 2989
1 TraesCS2D01G384300 chr7B 19955039 19960083 5044 True 630.820000 1513 85.047800 109 2975 5 chr7B.!!$R1 2866
2 TraesCS2D01G384300 chr1D 460185696 460187756 2060 True 731.000000 1360 82.878000 907 2990 2 chr1D.!!$R2 2083
3 TraesCS2D01G384300 chr1D 393952738 393953273 535 True 330.000000 399 87.931000 2057 2650 2 chr1D.!!$R1 593
4 TraesCS2D01G384300 chr3B 733600587 733601993 1406 False 1306.000000 1306 83.849000 852 2299 1 chr3B.!!$F3 1447
5 TraesCS2D01G384300 chr3D 552769543 552772088 2545 False 604.666667 1288 82.793000 511 2990 3 chr3D.!!$F1 2479
6 TraesCS2D01G384300 chr3A 689072385 689075144 2759 False 593.000000 1251 84.135667 532 2975 3 chr3A.!!$F2 2443
7 TraesCS2D01G384300 chr5D 397473784 397474820 1036 True 599.000000 793 87.854500 1550 2650 2 chr5D.!!$R1 1100
8 TraesCS2D01G384300 chr5D 397464952 397465989 1037 False 577.500000 780 86.861500 1549 2649 2 chr5D.!!$F3 1100
9 TraesCS2D01G384300 chr5D 375000880 375001416 536 False 336.500000 401 88.335500 2057 2650 2 chr5D.!!$F2 593
10 TraesCS2D01G384300 chr1A 551739011 551739935 924 True 765.000000 765 82.059000 1341 2299 1 chr1A.!!$R1 958
11 TraesCS2D01G384300 chr6B 666361546 666362582 1036 True 557.500000 734 86.464500 1549 2648 2 chr6B.!!$R2 1099

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
780 3052 0.033504 GTCCTTGTGACGGAGAAGCA 59.966 55.0 0.0 0.0 33.49 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2671 5794 0.239082 CGAGCAGCAATGCAACTCAA 59.761 50.0 21.6 0.0 37.25 3.02 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
17 18 4.357699 GCTCATCTGGAGGCATCG 57.642 61.111 0.00 0.00 44.22 3.84
18 19 1.960250 GCTCATCTGGAGGCATCGC 60.960 63.158 0.00 0.00 44.22 4.58
20 21 0.319727 CTCATCTGGAGGCATCGCTC 60.320 60.000 0.00 0.00 40.13 5.03
22 23 3.512223 ATCTGGAGGCATCGCTCGC 62.512 63.158 0.00 0.00 0.00 5.03
30 31 3.566853 CATCGCTCGCGTGCCAAT 61.567 61.111 25.56 16.82 40.74 3.16
31 32 2.819595 ATCGCTCGCGTGCCAATT 60.820 55.556 25.56 6.76 40.74 2.32
32 33 2.398554 ATCGCTCGCGTGCCAATTT 61.399 52.632 25.56 5.05 40.74 1.82
34 35 2.427765 CGCTCGCGTGCCAATTTTG 61.428 57.895 25.56 7.50 34.35 2.44
35 36 1.081509 GCTCGCGTGCCAATTTTGA 60.082 52.632 21.81 0.00 0.00 2.69
37 38 0.729140 CTCGCGTGCCAATTTTGACC 60.729 55.000 5.77 0.00 0.00 4.02
38 39 1.007964 CGCGTGCCAATTTTGACCA 60.008 52.632 0.00 0.00 0.00 4.02
39 40 1.274798 CGCGTGCCAATTTTGACCAC 61.275 55.000 0.00 0.00 0.00 4.16
40 41 0.943835 GCGTGCCAATTTTGACCACC 60.944 55.000 0.00 0.00 31.22 4.61
42 43 0.319469 GTGCCAATTTTGACCACCCG 60.319 55.000 0.00 0.00 0.00 5.28
43 44 0.468214 TGCCAATTTTGACCACCCGA 60.468 50.000 0.00 0.00 0.00 5.14
44 45 0.894835 GCCAATTTTGACCACCCGAT 59.105 50.000 0.00 0.00 0.00 4.18
45 46 1.135112 GCCAATTTTGACCACCCGATC 60.135 52.381 0.00 0.00 0.00 3.69
47 48 2.080693 CAATTTTGACCACCCGATCGA 58.919 47.619 18.66 0.00 0.00 3.59
49 50 2.018542 TTTTGACCACCCGATCGATC 57.981 50.000 18.66 15.68 0.00 3.69
50 51 1.191535 TTTGACCACCCGATCGATCT 58.808 50.000 22.43 2.98 0.00 2.75
51 52 0.459899 TTGACCACCCGATCGATCTG 59.540 55.000 22.43 16.12 0.00 2.90
52 53 1.300233 GACCACCCGATCGATCTGC 60.300 63.158 22.43 0.00 0.00 4.26
53 54 1.739338 GACCACCCGATCGATCTGCT 61.739 60.000 22.43 1.21 0.00 4.24
56 57 1.239347 CACCCGATCGATCTGCTAGA 58.761 55.000 22.43 0.00 0.00 2.43
57 58 1.198867 CACCCGATCGATCTGCTAGAG 59.801 57.143 22.43 5.62 0.00 2.43
58 59 1.202830 ACCCGATCGATCTGCTAGAGT 60.203 52.381 22.43 6.82 0.00 3.24
59 60 2.038689 ACCCGATCGATCTGCTAGAGTA 59.961 50.000 22.43 0.00 0.00 2.59
60 61 2.675844 CCCGATCGATCTGCTAGAGTAG 59.324 54.545 22.43 3.52 0.00 2.57
61 62 3.331150 CCGATCGATCTGCTAGAGTAGT 58.669 50.000 22.43 0.00 0.00 2.73
64 65 5.278071 CCGATCGATCTGCTAGAGTAGTTTT 60.278 44.000 22.43 0.00 0.00 2.43
65 66 6.202937 CGATCGATCTGCTAGAGTAGTTTTT 58.797 40.000 22.43 0.00 0.00 1.94
93 94 4.308458 CGGCTGGTCAACCGTCCA 62.308 66.667 4.79 0.00 44.46 4.02
94 95 2.351276 GGCTGGTCAACCGTCCAT 59.649 61.111 5.06 0.00 39.43 3.41
95 96 1.303317 GGCTGGTCAACCGTCCATT 60.303 57.895 5.06 0.00 39.43 3.16
98 99 1.339929 GCTGGTCAACCGTCCATTTTT 59.660 47.619 0.00 0.00 39.43 1.94
112 113 2.026879 TTTTTGCACTTCCGCGCC 59.973 55.556 0.00 0.00 33.35 6.53
136 2372 1.857965 TCAGGAGAGGATGACAGGTG 58.142 55.000 0.00 0.00 0.00 4.00
137 2373 1.359130 TCAGGAGAGGATGACAGGTGA 59.641 52.381 0.00 0.00 0.00 4.02
139 2375 1.077828 AGGAGAGGATGACAGGTGACA 59.922 52.381 0.00 0.00 0.00 3.58
141 2377 2.175202 GAGAGGATGACAGGTGACACT 58.825 52.381 5.39 0.00 0.00 3.55
142 2378 2.165437 GAGAGGATGACAGGTGACACTC 59.835 54.545 5.39 0.00 0.00 3.51
147 2383 3.130516 GGATGACAGGTGACACTCGATAA 59.869 47.826 5.39 0.00 0.00 1.75
148 2384 4.381612 GGATGACAGGTGACACTCGATAAA 60.382 45.833 5.39 0.00 0.00 1.40
149 2385 4.801330 TGACAGGTGACACTCGATAAAT 57.199 40.909 5.39 0.00 0.00 1.40
180 2416 0.391263 GGGATCGGCGTGAGTTTTCT 60.391 55.000 6.85 0.00 0.00 2.52
191 2427 4.037690 CGTGAGTTTTCTTCAGCTTTTGG 58.962 43.478 0.00 0.00 0.00 3.28
192 2428 4.438744 CGTGAGTTTTCTTCAGCTTTTGGT 60.439 41.667 0.00 0.00 0.00 3.67
193 2429 5.220777 CGTGAGTTTTCTTCAGCTTTTGGTA 60.221 40.000 0.00 0.00 0.00 3.25
196 2432 3.619233 TTTCTTCAGCTTTTGGTACGC 57.381 42.857 0.00 0.00 0.00 4.42
206 2442 3.723835 GCTTTTGGTACGCGAAGTATGTG 60.724 47.826 15.93 0.00 37.69 3.21
217 2453 1.071019 AAGTATGTGTCGCGTGCTCG 61.071 55.000 5.77 3.31 40.37 5.03
242 2478 1.439644 GCGCTCTGGGTAGAAGGAG 59.560 63.158 0.00 0.00 31.21 3.69
254 2490 2.764547 AAGGAGCCCTAGACCCGC 60.765 66.667 0.00 0.00 31.13 6.13
290 2526 2.342279 CCACCGTCGCTTCCTTCA 59.658 61.111 0.00 0.00 0.00 3.02
296 2532 1.673033 CCGTCGCTTCCTTCACAATCT 60.673 52.381 0.00 0.00 0.00 2.40
312 2548 4.162690 CTCGCAGCCACCTACCCC 62.163 72.222 0.00 0.00 0.00 4.95
330 2566 3.528370 GCTTCCTCCGCGCCTCTA 61.528 66.667 0.00 0.00 0.00 2.43
333 2569 0.108329 CTTCCTCCGCGCCTCTAAAA 60.108 55.000 0.00 0.00 0.00 1.52
364 2600 0.478507 CACCAAAGTCCTTGAGGGGT 59.521 55.000 0.00 0.00 37.17 4.95
387 2623 2.029470 TGGTCGGCCAAAATCATTGTTC 60.029 45.455 6.10 0.00 42.83 3.18
417 2653 3.818295 TGGGGTAAGTTTAGCACCATT 57.182 42.857 1.30 0.00 33.77 3.16
418 2654 3.692690 TGGGGTAAGTTTAGCACCATTC 58.307 45.455 1.30 0.00 33.77 2.67
419 2655 3.074687 TGGGGTAAGTTTAGCACCATTCA 59.925 43.478 1.30 0.00 33.77 2.57
420 2656 3.694566 GGGGTAAGTTTAGCACCATTCAG 59.305 47.826 3.80 0.00 33.78 3.02
421 2657 3.694566 GGGTAAGTTTAGCACCATTCAGG 59.305 47.826 3.80 0.00 45.67 3.86
423 2659 1.839424 AGTTTAGCACCATTCAGGCC 58.161 50.000 0.00 0.00 43.14 5.19
424 2660 1.355720 AGTTTAGCACCATTCAGGCCT 59.644 47.619 0.00 0.00 43.14 5.19
425 2661 2.171003 GTTTAGCACCATTCAGGCCTT 58.829 47.619 0.00 0.00 43.14 4.35
451 2687 4.428615 TTTTTGAAACGCCATAGTAGCC 57.571 40.909 0.00 0.00 0.00 3.93
476 2712 0.107263 TGCTGGTGCACTGAGAAACA 60.107 50.000 17.98 3.04 45.31 2.83
477 2713 1.242076 GCTGGTGCACTGAGAAACAT 58.758 50.000 17.98 0.00 39.41 2.71
485 2721 5.412594 GGTGCACTGAGAAACATCAAATCTA 59.587 40.000 17.98 0.00 0.00 1.98
490 2726 7.362401 GCACTGAGAAACATCAAATCTAATGGT 60.362 37.037 0.00 0.00 0.00 3.55
525 2761 0.818040 AACACCAAAGGTCACGGAGC 60.818 55.000 0.00 0.00 31.02 4.70
530 2766 2.357517 AAGGTCACGGAGCTTGCG 60.358 61.111 14.76 0.00 46.56 4.85
559 2795 3.071023 ACCGTCTTCATCCTCTTGAACAA 59.929 43.478 0.00 0.00 32.39 2.83
588 2829 0.904865 TGCCCCTAGGTGTGTCTCTG 60.905 60.000 8.29 0.00 34.57 3.35
591 2832 1.978580 CCCCTAGGTGTGTCTCTGTTT 59.021 52.381 8.29 0.00 0.00 2.83
592 2833 2.372172 CCCCTAGGTGTGTCTCTGTTTT 59.628 50.000 8.29 0.00 0.00 2.43
593 2834 3.181443 CCCCTAGGTGTGTCTCTGTTTTT 60.181 47.826 8.29 0.00 0.00 1.94
595 2836 3.251004 CCTAGGTGTGTCTCTGTTTTTGC 59.749 47.826 0.00 0.00 0.00 3.68
597 2838 1.268539 GGTGTGTCTCTGTTTTTGCGG 60.269 52.381 0.00 0.00 0.00 5.69
598 2839 1.668751 GTGTGTCTCTGTTTTTGCGGA 59.331 47.619 0.00 0.00 0.00 5.54
599 2840 2.290641 GTGTGTCTCTGTTTTTGCGGAT 59.709 45.455 0.00 0.00 0.00 4.18
600 2841 2.290367 TGTGTCTCTGTTTTTGCGGATG 59.710 45.455 0.00 0.00 0.00 3.51
756 3028 5.799213 TCAAATTTCAAAAACCACACCACT 58.201 33.333 0.00 0.00 0.00 4.00
770 3042 2.238646 ACACCACTCTTTGTCCTTGTGA 59.761 45.455 0.00 0.00 0.00 3.58
771 3043 2.614057 CACCACTCTTTGTCCTTGTGAC 59.386 50.000 0.00 0.00 44.72 3.67
779 3051 2.828933 GTCCTTGTGACGGAGAAGC 58.171 57.895 0.00 0.00 33.49 3.86
780 3052 0.033504 GTCCTTGTGACGGAGAAGCA 59.966 55.000 0.00 0.00 33.49 3.91
781 3053 0.976641 TCCTTGTGACGGAGAAGCAT 59.023 50.000 0.00 0.00 0.00 3.79
782 3054 1.347707 TCCTTGTGACGGAGAAGCATT 59.652 47.619 0.00 0.00 0.00 3.56
783 3055 2.154462 CCTTGTGACGGAGAAGCATTT 58.846 47.619 0.00 0.00 0.00 2.32
785 3057 3.365364 CCTTGTGACGGAGAAGCATTTTC 60.365 47.826 0.00 0.00 0.00 2.29
787 3059 3.210227 TGTGACGGAGAAGCATTTTCAA 58.790 40.909 0.00 0.00 0.00 2.69
788 3060 3.629855 TGTGACGGAGAAGCATTTTCAAA 59.370 39.130 0.00 0.00 0.00 2.69
789 3061 4.278170 TGTGACGGAGAAGCATTTTCAAAT 59.722 37.500 0.00 0.00 0.00 2.32
791 3063 5.691754 GTGACGGAGAAGCATTTTCAAATTT 59.308 36.000 0.00 0.00 0.00 1.82
792 3064 5.920273 TGACGGAGAAGCATTTTCAAATTTC 59.080 36.000 0.00 0.00 0.00 2.17
793 3065 5.841810 ACGGAGAAGCATTTTCAAATTTCA 58.158 33.333 0.00 0.00 0.00 2.69
794 3066 6.279882 ACGGAGAAGCATTTTCAAATTTCAA 58.720 32.000 0.00 0.00 0.00 2.69
795 3067 6.760770 ACGGAGAAGCATTTTCAAATTTCAAA 59.239 30.769 0.00 0.00 0.00 2.69
796 3068 7.279758 ACGGAGAAGCATTTTCAAATTTCAAAA 59.720 29.630 2.30 2.30 0.00 2.44
797 3069 8.121708 CGGAGAAGCATTTTCAAATTTCAAAAA 58.878 29.630 4.01 7.15 0.00 1.94
798 3070 9.225201 GGAGAAGCATTTTCAAATTTCAAAAAC 57.775 29.630 4.01 0.58 0.00 2.43
799 3071 9.225201 GAGAAGCATTTTCAAATTTCAAAAACC 57.775 29.630 4.01 0.00 0.00 3.27
803 3075 7.754475 AGCATTTTCAAATTTCAAAAACCACAC 59.246 29.630 4.01 0.00 0.00 3.82
804 3076 7.009083 GCATTTTCAAATTTCAAAAACCACACC 59.991 33.333 4.01 0.00 0.00 4.16
848 3131 3.071206 GCCGAGCCTCTGTCCTCA 61.071 66.667 0.00 0.00 0.00 3.86
876 3167 4.436998 CTCGACACGTGCCCCCTC 62.437 72.222 17.22 4.07 0.00 4.30
895 3187 0.389948 CCGTCCTCTTTTCACCTCCG 60.390 60.000 0.00 0.00 0.00 4.63
902 3194 1.001393 TTTTCACCTCCGGCCATCC 60.001 57.895 2.24 0.00 0.00 3.51
953 3571 0.537653 GTCTCCTTCCTTCCTTCCCG 59.462 60.000 0.00 0.00 0.00 5.14
1031 3669 0.250513 GGGAGCAAGAAGGACATCGT 59.749 55.000 0.00 0.00 0.00 3.73
1166 3810 4.351938 CCCTGACGACGCCGACAA 62.352 66.667 0.00 0.00 39.63 3.18
1167 3811 2.805353 CCTGACGACGCCGACAAG 60.805 66.667 0.00 0.00 39.63 3.16
1168 3812 2.805353 CTGACGACGCCGACAAGG 60.805 66.667 0.00 0.00 39.63 3.61
1169 3813 3.263503 CTGACGACGCCGACAAGGA 62.264 63.158 0.00 0.00 45.00 3.36
1179 3823 2.383527 CGACAAGGACAAGCTCGGC 61.384 63.158 0.00 0.00 0.00 5.54
1206 3850 1.941668 GCCTCCAAACTCTTCGAGGTG 60.942 57.143 4.04 0.00 43.28 4.00
1336 3980 3.973267 GACGAGCAGCTCCACGACC 62.973 68.421 17.16 0.85 0.00 4.79
1428 4072 2.119655 CCTGGCCATCAAGCTGCTC 61.120 63.158 5.51 0.00 0.00 4.26
1429 4073 2.044650 TGGCCATCAAGCTGCTCC 60.045 61.111 0.00 0.00 0.00 4.70
1512 4159 4.717313 GGCAACACCCCCGACTCC 62.717 72.222 0.00 0.00 0.00 3.85
1513 4160 3.637273 GCAACACCCCCGACTCCT 61.637 66.667 0.00 0.00 0.00 3.69
1514 4161 2.663196 CAACACCCCCGACTCCTC 59.337 66.667 0.00 0.00 0.00 3.71
1515 4162 2.606826 AACACCCCCGACTCCTCC 60.607 66.667 0.00 0.00 0.00 4.30
1516 4163 3.175714 AACACCCCCGACTCCTCCT 62.176 63.158 0.00 0.00 0.00 3.69
1517 4164 2.760385 CACCCCCGACTCCTCCTC 60.760 72.222 0.00 0.00 0.00 3.71
1518 4165 4.077180 ACCCCCGACTCCTCCTCC 62.077 72.222 0.00 0.00 0.00 4.30
1519 4166 3.756783 CCCCCGACTCCTCCTCCT 61.757 72.222 0.00 0.00 0.00 3.69
1520 4167 2.123640 CCCCGACTCCTCCTCCTC 60.124 72.222 0.00 0.00 0.00 3.71
1521 4168 2.123640 CCCGACTCCTCCTCCTCC 60.124 72.222 0.00 0.00 0.00 4.30
1633 4318 4.020617 CCAAGTCCGGCTCCAGCA 62.021 66.667 0.00 0.00 44.36 4.41
1634 4319 2.032528 CAAGTCCGGCTCCAGCAA 59.967 61.111 0.00 0.00 44.36 3.91
1635 4320 2.032681 AAGTCCGGCTCCAGCAAC 59.967 61.111 0.00 0.00 44.36 4.17
1636 4321 2.818169 AAGTCCGGCTCCAGCAACA 61.818 57.895 0.00 0.00 44.36 3.33
1637 4322 2.738213 AAGTCCGGCTCCAGCAACAG 62.738 60.000 0.00 0.00 44.36 3.16
1645 4330 2.599578 CCAGCAACAGCAAGCCCT 60.600 61.111 0.00 0.00 0.00 5.19
1652 4343 1.999634 AACAGCAAGCCCTGTCAGGT 62.000 55.000 17.85 0.00 44.86 4.00
1689 4386 3.414700 GACGTGGGCAAGTCGCTG 61.415 66.667 0.00 0.00 41.91 5.18
1746 4448 1.412226 CGTGAAGCACATCGACGTG 59.588 57.895 7.37 7.37 40.00 4.49
1859 4584 3.070748 GTCTCTCCAAACCTTGCTCTTC 58.929 50.000 0.00 0.00 0.00 2.87
1863 4588 3.072944 CTCCAAACCTTGCTCTTCTCTG 58.927 50.000 0.00 0.00 0.00 3.35
1866 4591 3.557898 CCAAACCTTGCTCTTCTCTGCTA 60.558 47.826 0.00 0.00 0.00 3.49
1870 4595 3.260740 CCTTGCTCTTCTCTGCTACTTG 58.739 50.000 0.00 0.00 0.00 3.16
1874 4599 2.166254 GCTCTTCTCTGCTACTTGCTCT 59.834 50.000 0.00 0.00 43.37 4.09
1876 4601 4.423732 CTCTTCTCTGCTACTTGCTCTTC 58.576 47.826 0.00 0.00 43.37 2.87
1877 4602 3.829026 TCTTCTCTGCTACTTGCTCTTCA 59.171 43.478 0.00 0.00 43.37 3.02
1878 4603 4.465660 TCTTCTCTGCTACTTGCTCTTCAT 59.534 41.667 0.00 0.00 43.37 2.57
1879 4604 4.120792 TCTCTGCTACTTGCTCTTCATG 57.879 45.455 0.00 0.00 43.37 3.07
1880 4605 3.118847 TCTCTGCTACTTGCTCTTCATGG 60.119 47.826 0.00 0.00 43.37 3.66
1935 4660 0.384309 TGGATGGATCTGACGTACGC 59.616 55.000 16.72 8.98 0.00 4.42
1952 4679 2.699954 ACGCTCGAATCCATTTGTTCT 58.300 42.857 0.00 0.00 0.00 3.01
1974 4713 0.833287 TGCTGCAGGAGGGATTCTAC 59.167 55.000 17.12 0.00 0.00 2.59
2040 4907 9.692325 ATGCTCTCCTTATCAGTCTTTTATTTT 57.308 29.630 0.00 0.00 0.00 1.82
2091 4970 7.201785 GGTTTCAGTTCAGTTTGGTCAGATTTA 60.202 37.037 0.00 0.00 0.00 1.40
2092 4971 6.861065 TCAGTTCAGTTTGGTCAGATTTAC 57.139 37.500 0.00 0.00 0.00 2.01
2093 4972 5.465390 TCAGTTCAGTTTGGTCAGATTTACG 59.535 40.000 0.00 0.00 0.00 3.18
2114 4993 0.255033 ATCTGCTGCCATGCTCTTCA 59.745 50.000 0.00 0.00 0.00 3.02
2120 4999 2.268298 CTGCCATGCTCTTCAATTTGC 58.732 47.619 0.00 0.00 0.00 3.68
2161 5045 3.235481 TTCCTGGACGGCCGTGAA 61.235 61.111 39.65 28.69 36.79 3.18
2210 5097 8.154856 TCAATTAGGGGTAATCAATGTAGTAGC 58.845 37.037 0.00 0.00 0.00 3.58
2211 5098 7.626999 ATTAGGGGTAATCAATGTAGTAGCA 57.373 36.000 0.00 0.00 0.00 3.49
2212 5099 5.552870 AGGGGTAATCAATGTAGTAGCAG 57.447 43.478 0.00 0.00 0.00 4.24
2301 5191 8.531146 AGGAGCTATCTTAATTAGCTTCATCTC 58.469 37.037 20.15 9.45 46.03 2.75
2302 5192 7.763985 GGAGCTATCTTAATTAGCTTCATCTCC 59.236 40.741 16.81 11.03 46.03 3.71
2303 5193 8.434589 AGCTATCTTAATTAGCTTCATCTCCT 57.565 34.615 12.15 0.00 43.90 3.69
2304 5194 8.879227 AGCTATCTTAATTAGCTTCATCTCCTT 58.121 33.333 12.15 0.00 43.90 3.36
2308 5198 8.425577 TCTTAATTAGCTTCATCTCCTTTTCG 57.574 34.615 0.00 0.00 0.00 3.46
2310 5200 8.786826 TTAATTAGCTTCATCTCCTTTTCGAA 57.213 30.769 0.00 0.00 0.00 3.71
2311 5201 7.687941 AATTAGCTTCATCTCCTTTTCGAAA 57.312 32.000 6.47 6.47 0.00 3.46
2312 5202 7.687941 ATTAGCTTCATCTCCTTTTCGAAAA 57.312 32.000 21.35 21.35 0.00 2.29
2313 5203 7.504924 TTAGCTTCATCTCCTTTTCGAAAAA 57.495 32.000 22.67 9.71 0.00 1.94
2385 5341 6.318628 TGTGATGCCATTTTTATGTTCGTAC 58.681 36.000 0.00 0.00 0.00 3.67
2441 5447 6.416455 TGTGAATCATGTTTTCTTTTACGTGC 59.584 34.615 0.00 0.00 32.59 5.34
2578 5671 6.012113 TCCAGATTCCAGAATGTTTGATTGT 58.988 36.000 0.00 0.00 0.00 2.71
2650 5773 3.243367 CCTTTTGGTTTCGATCAGTTGCA 60.243 43.478 0.00 0.00 34.07 4.08
2651 5774 4.549458 CTTTTGGTTTCGATCAGTTGCAT 58.451 39.130 0.00 0.00 0.00 3.96
2652 5775 4.582701 TTTGGTTTCGATCAGTTGCATT 57.417 36.364 0.00 0.00 0.00 3.56
2653 5776 3.557577 TGGTTTCGATCAGTTGCATTG 57.442 42.857 0.00 0.00 0.00 2.82
2654 5777 2.884012 TGGTTTCGATCAGTTGCATTGT 59.116 40.909 0.00 0.00 0.00 2.71
2655 5778 3.317711 TGGTTTCGATCAGTTGCATTGTT 59.682 39.130 0.00 0.00 0.00 2.83
2656 5779 4.202101 TGGTTTCGATCAGTTGCATTGTTT 60.202 37.500 0.00 0.00 0.00 2.83
2657 5780 4.744631 GGTTTCGATCAGTTGCATTGTTTT 59.255 37.500 0.00 0.00 0.00 2.43
2658 5781 5.234116 GGTTTCGATCAGTTGCATTGTTTTT 59.766 36.000 0.00 0.00 0.00 1.94
2724 5849 5.009110 TCCTATCAGTCGCTTAGTTCATCTG 59.991 44.000 0.00 0.00 0.00 2.90
2726 5851 4.098055 TCAGTCGCTTAGTTCATCTGTC 57.902 45.455 0.00 0.00 0.00 3.51
2761 5886 6.624423 AGTTCATGCAACCTTTTGATATCAC 58.376 36.000 4.48 0.00 35.28 3.06
2775 5900 3.118149 TGATATCACTGCAGTTGGCTCAT 60.118 43.478 18.94 4.76 45.15 2.90
2832 5957 3.741830 TTTCTGCACGACCGTGGCA 62.742 57.895 21.80 17.92 45.49 4.92
2838 5963 1.497278 CACGACCGTGGCAATCTTG 59.503 57.895 14.12 0.00 42.00 3.02
2840 5965 0.036388 ACGACCGTGGCAATCTTGAT 60.036 50.000 0.00 0.00 0.00 2.57
2853 5978 6.830324 TGGCAATCTTGATTAGCTTCATTAGT 59.170 34.615 0.00 0.00 0.00 2.24
2855 5980 7.012704 GGCAATCTTGATTAGCTTCATTAGTGA 59.987 37.037 0.00 0.00 0.00 3.41
2856 5981 8.068977 GCAATCTTGATTAGCTTCATTAGTGAG 58.931 37.037 0.00 0.00 35.39 3.51
2860 5985 9.376075 TCTTGATTAGCTTCATTAGTGAGAAAG 57.624 33.333 0.00 0.00 35.39 2.62
2883 6008 4.517453 GGTTGTAGGCAGTGTAATGTTGAA 59.483 41.667 0.00 0.00 0.00 2.69
2898 6026 7.914871 TGTAATGTTGAACTGCATGTTATATGC 59.085 33.333 6.99 6.99 44.76 3.14
2928 6056 3.795101 CCGAATCAGATTCAAATTGCAGC 59.205 43.478 20.87 0.00 39.22 5.25
2934 6062 6.822667 TCAGATTCAAATTGCAGCTTTAGA 57.177 33.333 0.00 0.00 0.00 2.10
2936 6064 6.432162 TCAGATTCAAATTGCAGCTTTAGACT 59.568 34.615 0.00 0.00 0.00 3.24
2940 6068 9.410556 GATTCAAATTGCAGCTTTAGACTTTTA 57.589 29.630 0.00 0.00 0.00 1.52
2941 6069 9.762933 ATTCAAATTGCAGCTTTAGACTTTTAA 57.237 25.926 0.00 0.00 0.00 1.52
2942 6070 8.574196 TCAAATTGCAGCTTTAGACTTTTAAC 57.426 30.769 0.00 0.00 0.00 2.01
2943 6071 7.378461 TCAAATTGCAGCTTTAGACTTTTAACG 59.622 33.333 0.00 0.00 0.00 3.18
2944 6072 4.141855 TGCAGCTTTAGACTTTTAACGC 57.858 40.909 0.00 0.00 0.00 4.84
2945 6073 3.562141 TGCAGCTTTAGACTTTTAACGCA 59.438 39.130 0.00 0.00 32.13 5.24
2946 6074 3.906601 GCAGCTTTAGACTTTTAACGCAC 59.093 43.478 0.00 0.00 32.13 5.34
2947 6075 4.141680 CAGCTTTAGACTTTTAACGCACG 58.858 43.478 0.00 0.00 32.13 5.34
2948 6076 3.805971 AGCTTTAGACTTTTAACGCACGT 59.194 39.130 0.00 0.00 32.13 4.49
2949 6077 4.084693 AGCTTTAGACTTTTAACGCACGTC 60.085 41.667 0.00 0.00 32.13 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.960250 GCGATGCCTCCAGATGAGC 60.960 63.158 0.00 0.00 39.98 4.26
2 3 1.744639 GAGCGATGCCTCCAGATGA 59.255 57.895 0.00 0.00 0.00 2.92
3 4 1.664017 CGAGCGATGCCTCCAGATG 60.664 63.158 0.00 0.00 0.00 2.90
4 5 2.733301 CGAGCGATGCCTCCAGAT 59.267 61.111 0.00 0.00 0.00 2.90
13 14 2.582202 AAATTGGCACGCGAGCGATG 62.582 55.000 24.72 17.76 42.83 3.84
14 15 1.922135 AAAATTGGCACGCGAGCGAT 61.922 50.000 24.72 15.14 42.83 4.58
16 17 2.126888 AAAATTGGCACGCGAGCG 60.127 55.556 21.88 16.38 46.03 5.03
17 18 1.081509 TCAAAATTGGCACGCGAGC 60.082 52.632 20.70 20.70 0.00 5.03
18 19 0.729140 GGTCAAAATTGGCACGCGAG 60.729 55.000 15.93 5.97 33.59 5.03
20 21 1.007964 TGGTCAAAATTGGCACGCG 60.008 52.632 3.53 3.53 33.59 6.01
22 23 0.319469 GGGTGGTCAAAATTGGCACG 60.319 55.000 0.00 0.00 33.59 5.34
23 24 0.319469 CGGGTGGTCAAAATTGGCAC 60.319 55.000 0.00 0.00 33.59 5.01
25 26 0.894835 ATCGGGTGGTCAAAATTGGC 59.105 50.000 0.00 0.00 0.00 4.52
26 27 1.132262 CGATCGGGTGGTCAAAATTGG 59.868 52.381 7.38 0.00 0.00 3.16
27 28 2.080693 TCGATCGGGTGGTCAAAATTG 58.919 47.619 16.41 0.00 0.00 2.32
28 29 2.483014 TCGATCGGGTGGTCAAAATT 57.517 45.000 16.41 0.00 0.00 1.82
29 30 2.170607 AGATCGATCGGGTGGTCAAAAT 59.829 45.455 19.33 0.00 0.00 1.82
30 31 1.553248 AGATCGATCGGGTGGTCAAAA 59.447 47.619 19.33 0.00 0.00 2.44
31 32 1.134818 CAGATCGATCGGGTGGTCAAA 60.135 52.381 19.33 0.00 0.00 2.69
32 33 0.459899 CAGATCGATCGGGTGGTCAA 59.540 55.000 19.33 0.00 0.00 3.18
34 35 1.300233 GCAGATCGATCGGGTGGTC 60.300 63.158 24.00 6.10 0.00 4.02
35 36 0.467474 TAGCAGATCGATCGGGTGGT 60.467 55.000 31.54 24.71 34.69 4.16
37 38 1.198867 CTCTAGCAGATCGATCGGGTG 59.801 57.143 31.54 22.78 34.69 4.61
38 39 1.202830 ACTCTAGCAGATCGATCGGGT 60.203 52.381 28.33 28.33 36.69 5.28
39 40 1.529226 ACTCTAGCAGATCGATCGGG 58.471 55.000 24.00 18.67 0.00 5.14
40 41 3.331150 ACTACTCTAGCAGATCGATCGG 58.669 50.000 19.66 19.66 0.00 4.18
77 78 0.893727 AAATGGACGGTTGACCAGCC 60.894 55.000 0.51 1.53 43.10 4.85
78 79 0.958822 AAAATGGACGGTTGACCAGC 59.041 50.000 0.51 0.00 43.10 4.85
101 102 1.078759 CTGAAGTAGGCGCGGAAGTG 61.079 60.000 8.83 0.00 46.39 3.16
102 103 1.215647 CTGAAGTAGGCGCGGAAGT 59.784 57.895 8.83 0.00 0.00 3.01
103 104 1.519455 CCTGAAGTAGGCGCGGAAG 60.519 63.158 8.83 0.00 40.38 3.46
104 105 1.945354 CTCCTGAAGTAGGCGCGGAA 61.945 60.000 8.83 0.00 46.87 4.30
105 106 2.361992 TCCTGAAGTAGGCGCGGA 60.362 61.111 8.83 0.00 46.87 5.54
107 108 1.064946 CTCTCCTGAAGTAGGCGCG 59.935 63.158 0.00 0.00 46.87 6.86
108 109 1.038130 TCCTCTCCTGAAGTAGGCGC 61.038 60.000 0.00 0.00 46.87 6.53
109 110 1.339610 CATCCTCTCCTGAAGTAGGCG 59.660 57.143 0.00 0.00 46.87 5.52
110 111 2.364002 GTCATCCTCTCCTGAAGTAGGC 59.636 54.545 0.00 0.00 46.87 3.93
112 113 3.636300 CCTGTCATCCTCTCCTGAAGTAG 59.364 52.174 0.00 0.00 0.00 2.57
126 2362 2.949451 ATCGAGTGTCACCTGTCATC 57.051 50.000 0.00 0.00 0.00 2.92
168 2404 3.340337 AAAGCTGAAGAAAACTCACGC 57.660 42.857 0.00 0.00 0.00 5.34
170 2406 4.998788 ACCAAAAGCTGAAGAAAACTCAC 58.001 39.130 0.00 0.00 0.00 3.51
180 2416 1.529438 CTTCGCGTACCAAAAGCTGAA 59.471 47.619 5.77 0.00 0.00 3.02
196 2432 1.071019 AGCACGCGACACATACTTCG 61.071 55.000 15.93 0.00 38.31 3.79
217 2453 3.733344 TACCCAGAGCGCGATTGGC 62.733 63.158 12.10 0.00 38.69 4.52
227 2463 0.031616 AGGGCTCCTTCTACCCAGAG 60.032 60.000 0.00 0.00 46.88 3.35
272 2508 3.119096 GAAGGAAGCGACGGTGGC 61.119 66.667 7.06 7.06 0.00 5.01
275 2511 0.034896 ATTGTGAAGGAAGCGACGGT 59.965 50.000 0.00 0.00 0.00 4.83
278 2514 1.656095 CGAGATTGTGAAGGAAGCGAC 59.344 52.381 0.00 0.00 0.00 5.19
290 2526 0.108138 GTAGGTGGCTGCGAGATTGT 60.108 55.000 0.00 0.00 0.00 2.71
333 2569 8.973182 TCAAGGACTTTGGTGTAACTTTTATTT 58.027 29.630 0.00 0.00 37.39 1.40
347 2583 2.357154 CCATACCCCTCAAGGACTTTGG 60.357 54.545 0.00 0.00 38.24 3.28
354 2590 1.830145 CCGACCATACCCCTCAAGG 59.170 63.158 0.00 0.00 0.00 3.61
441 2677 2.244651 GCAACGCCGGCTACTATGG 61.245 63.158 26.68 9.51 0.00 2.74
490 2726 3.265791 GGTGTTGCCAAAATGTGAAACA 58.734 40.909 0.00 0.00 45.10 2.83
516 2752 0.179215 CAAATCGCAAGCTCCGTGAC 60.179 55.000 6.63 0.00 37.18 3.67
525 2761 1.128692 GAAGACGGTCCAAATCGCAAG 59.871 52.381 4.14 0.00 0.00 4.01
530 2766 3.118592 AGAGGATGAAGACGGTCCAAATC 60.119 47.826 4.14 5.40 34.42 2.17
770 3042 5.841810 TGAAATTTGAAAATGCTTCTCCGT 58.158 33.333 0.00 0.00 0.00 4.69
771 3043 6.768029 TTGAAATTTGAAAATGCTTCTCCG 57.232 33.333 0.00 0.00 0.00 4.63
772 3044 9.225201 GTTTTTGAAATTTGAAAATGCTTCTCC 57.775 29.630 14.91 0.00 0.00 3.71
774 3046 8.738106 TGGTTTTTGAAATTTGAAAATGCTTCT 58.262 25.926 14.91 0.00 0.00 2.85
775 3047 8.797215 GTGGTTTTTGAAATTTGAAAATGCTTC 58.203 29.630 14.91 5.77 0.00 3.86
776 3048 8.302438 TGTGGTTTTTGAAATTTGAAAATGCTT 58.698 25.926 14.91 0.00 0.00 3.91
777 3049 7.754475 GTGTGGTTTTTGAAATTTGAAAATGCT 59.246 29.630 14.91 0.00 0.00 3.79
779 3051 8.025445 TGGTGTGGTTTTTGAAATTTGAAAATG 58.975 29.630 14.91 0.00 0.00 2.32
780 3052 8.026026 GTGGTGTGGTTTTTGAAATTTGAAAAT 58.974 29.630 14.91 0.00 0.00 1.82
781 3053 7.363431 GTGGTGTGGTTTTTGAAATTTGAAAA 58.637 30.769 10.93 10.93 0.00 2.29
782 3054 6.072452 GGTGGTGTGGTTTTTGAAATTTGAAA 60.072 34.615 0.00 0.00 0.00 2.69
783 3055 5.412904 GGTGGTGTGGTTTTTGAAATTTGAA 59.587 36.000 0.00 0.00 0.00 2.69
785 3057 4.095632 GGGTGGTGTGGTTTTTGAAATTTG 59.904 41.667 0.00 0.00 0.00 2.32
787 3059 3.371059 GGGGTGGTGTGGTTTTTGAAATT 60.371 43.478 0.00 0.00 0.00 1.82
788 3060 2.171659 GGGGTGGTGTGGTTTTTGAAAT 59.828 45.455 0.00 0.00 0.00 2.17
789 3061 1.555533 GGGGTGGTGTGGTTTTTGAAA 59.444 47.619 0.00 0.00 0.00 2.69
791 3063 1.038130 CGGGGTGGTGTGGTTTTTGA 61.038 55.000 0.00 0.00 0.00 2.69
792 3064 1.439644 CGGGGTGGTGTGGTTTTTG 59.560 57.895 0.00 0.00 0.00 2.44
793 3065 1.758906 CCGGGGTGGTGTGGTTTTT 60.759 57.895 0.00 0.00 0.00 1.94
794 3066 2.123640 CCGGGGTGGTGTGGTTTT 60.124 61.111 0.00 0.00 0.00 2.43
803 3075 2.908015 CACCTATGACCGGGGTGG 59.092 66.667 16.64 8.85 44.63 4.61
833 3115 0.820226 TTGATGAGGACAGAGGCTCG 59.180 55.000 9.22 6.83 0.00 5.03
848 3131 0.595053 CGTGTCGAGCGGCTATTGAT 60.595 55.000 0.60 0.00 0.00 2.57
875 3166 0.974383 GGAGGTGAAAAGAGGACGGA 59.026 55.000 0.00 0.00 0.00 4.69
876 3167 0.389948 CGGAGGTGAAAAGAGGACGG 60.390 60.000 0.00 0.00 0.00 4.79
895 3187 4.222847 GACGACGGAGGGATGGCC 62.223 72.222 0.00 0.00 0.00 5.36
902 3194 0.100861 GGAGCTTTAGACGACGGAGG 59.899 60.000 0.00 0.00 0.00 4.30
983 3601 2.430610 ATGGCCGCTCTCTCTGTCC 61.431 63.158 0.00 0.00 0.00 4.02
986 3612 2.108566 CCATGGCCGCTCTCTCTG 59.891 66.667 0.00 0.00 0.00 3.35
1031 3669 1.748403 GCCTGCATGAGGACGGATA 59.252 57.895 13.48 0.00 46.33 2.59
1150 3788 2.805353 CTTGTCGGCGTCGTCAGG 60.805 66.667 10.18 6.89 36.03 3.86
1151 3789 2.805353 CCTTGTCGGCGTCGTCAG 60.805 66.667 10.18 3.67 36.03 3.51
1152 3790 3.289062 TCCTTGTCGGCGTCGTCA 61.289 61.111 10.18 7.45 37.69 4.35
1154 3792 3.141522 TTGTCCTTGTCGGCGTCGT 62.142 57.895 10.18 0.00 37.69 4.34
1165 3809 2.262915 CTCGCCGAGCTTGTCCTT 59.737 61.111 0.00 0.00 0.00 3.36
1179 3823 1.807573 GAGTTTGGAGGCGAGCTCG 60.808 63.158 31.37 31.37 43.27 5.03
1206 3850 0.674534 CCTCCAGCCCGATGTAGTAC 59.325 60.000 0.00 0.00 0.00 2.73
1236 3880 4.651867 ATGCAGGTGGTGAGCATC 57.348 55.556 0.00 0.00 45.11 3.91
1245 3889 1.953138 GGCGATCTCGATGCAGGTG 60.953 63.158 3.33 0.00 43.02 4.00
1495 4139 4.717313 GGAGTCGGGGGTGTTGCC 62.717 72.222 0.00 0.00 0.00 4.52
1496 4140 3.607370 GAGGAGTCGGGGGTGTTGC 62.607 68.421 0.00 0.00 0.00 4.17
1497 4141 2.663196 GAGGAGTCGGGGGTGTTG 59.337 66.667 0.00 0.00 0.00 3.33
1498 4142 2.606826 GGAGGAGTCGGGGGTGTT 60.607 66.667 0.00 0.00 0.00 3.32
1499 4143 3.602030 AGGAGGAGTCGGGGGTGT 61.602 66.667 0.00 0.00 0.00 4.16
1500 4144 2.760385 GAGGAGGAGTCGGGGGTG 60.760 72.222 0.00 0.00 0.00 4.61
1512 4159 2.520741 GGCGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1513 4160 4.144727 GGGCGAGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1515 4162 4.507916 TCGGGCGAGGAGGAGGAG 62.508 72.222 0.00 0.00 0.00 3.69
1516 4163 4.816984 GTCGGGCGAGGAGGAGGA 62.817 72.222 0.00 0.00 0.00 3.71
1518 4165 3.522731 CTGTCGGGCGAGGAGGAG 61.523 72.222 0.00 0.00 0.00 3.69
1521 4168 4.504916 CTGCTGTCGGGCGAGGAG 62.505 72.222 0.00 0.00 34.52 3.69
1632 4317 1.521450 CCTGACAGGGCTTGCTGTTG 61.521 60.000 14.26 0.00 33.50 3.33
1633 4318 1.228367 CCTGACAGGGCTTGCTGTT 60.228 57.895 14.26 0.00 33.50 3.16
1634 4319 1.127567 TACCTGACAGGGCTTGCTGT 61.128 55.000 25.34 4.38 40.58 4.40
1635 4320 0.392193 CTACCTGACAGGGCTTGCTG 60.392 60.000 25.34 3.75 40.58 4.41
1636 4321 1.986413 CTACCTGACAGGGCTTGCT 59.014 57.895 25.34 5.87 40.58 3.91
1637 4322 1.746991 GCTACCTGACAGGGCTTGC 60.747 63.158 25.34 17.84 40.58 4.01
1645 4330 3.713650 GCCTCTGGCTACCTGACA 58.286 61.111 0.73 0.00 46.69 3.58
1689 4386 2.103736 GCGCGGTACAGGTAGTCC 59.896 66.667 8.83 0.00 0.00 3.85
1758 4460 4.785575 TCCATGAAGCGGGAGAGA 57.214 55.556 0.00 0.00 0.00 3.10
1863 4588 3.194062 GACTCCATGAAGAGCAAGTAGC 58.806 50.000 0.00 0.00 46.19 3.58
1866 4591 2.264455 AGGACTCCATGAAGAGCAAGT 58.736 47.619 0.00 0.00 37.39 3.16
1870 4595 3.894427 TCATCTAGGACTCCATGAAGAGC 59.106 47.826 0.00 0.00 37.39 4.09
1874 4599 7.733773 TTAGTTTCATCTAGGACTCCATGAA 57.266 36.000 0.00 5.56 34.23 2.57
1876 4601 8.834465 CATTTTAGTTTCATCTAGGACTCCATG 58.166 37.037 0.00 0.00 0.00 3.66
1877 4602 8.772250 TCATTTTAGTTTCATCTAGGACTCCAT 58.228 33.333 0.00 0.00 0.00 3.41
1878 4603 8.146053 TCATTTTAGTTTCATCTAGGACTCCA 57.854 34.615 0.00 0.00 0.00 3.86
1879 4604 9.050601 CATCATTTTAGTTTCATCTAGGACTCC 57.949 37.037 0.00 0.00 0.00 3.85
1880 4605 9.823647 TCATCATTTTAGTTTCATCTAGGACTC 57.176 33.333 0.00 0.00 0.00 3.36
1935 4660 4.394300 AGCAAGAGAACAAATGGATTCGAG 59.606 41.667 0.00 0.00 0.00 4.04
1952 4679 0.254178 GAATCCCTCCTGCAGCAAGA 59.746 55.000 8.66 2.13 0.00 3.02
1974 4713 2.928334 AGCAGTCAATTGGATGCTAGG 58.072 47.619 26.69 4.24 46.70 3.02
2040 4907 6.591448 CACAAGTCTGCATGATGAACTAACTA 59.409 38.462 0.00 0.00 0.00 2.24
2042 4909 5.391310 CCACAAGTCTGCATGATGAACTAAC 60.391 44.000 0.00 0.00 0.00 2.34
2049 4916 3.253921 TGAAACCACAAGTCTGCATGATG 59.746 43.478 0.00 0.00 0.00 3.07
2091 4970 0.531532 GAGCATGGCAGCAGATACGT 60.532 55.000 10.71 0.00 36.85 3.57
2092 4971 0.249784 AGAGCATGGCAGCAGATACG 60.250 55.000 10.71 0.00 36.85 3.06
2093 4972 1.872313 GAAGAGCATGGCAGCAGATAC 59.128 52.381 10.71 0.00 36.85 2.24
2114 4993 5.069516 AGTCTGACCAAACTGAATGCAAATT 59.930 36.000 3.76 0.00 0.00 1.82
2120 4999 4.261322 CCACAAGTCTGACCAAACTGAATG 60.261 45.833 3.76 0.00 0.00 2.67
2210 5097 9.229784 GATAAGATGCAAATCAACATTACACTG 57.770 33.333 0.00 0.00 0.00 3.66
2211 5098 9.182214 AGATAAGATGCAAATCAACATTACACT 57.818 29.630 0.00 0.00 0.00 3.55
2212 5099 9.793252 AAGATAAGATGCAAATCAACATTACAC 57.207 29.630 0.00 0.00 0.00 2.90
2243 5133 5.806654 TTCGATCATTCATCCCACAGATA 57.193 39.130 0.00 0.00 32.37 1.98
2244 5134 4.694760 TTCGATCATTCATCCCACAGAT 57.305 40.909 0.00 0.00 34.66 2.90
2245 5135 4.635223 GATTCGATCATTCATCCCACAGA 58.365 43.478 0.00 0.00 0.00 3.41
2246 5136 3.431233 CGATTCGATCATTCATCCCACAG 59.569 47.826 0.00 0.00 0.00 3.66
2247 5137 3.069443 TCGATTCGATCATTCATCCCACA 59.931 43.478 4.29 0.00 0.00 4.17
2254 5144 4.024641 CCTGCAATTCGATTCGATCATTCA 60.025 41.667 9.96 7.29 35.23 2.57
2312 5202 9.573133 CCGAACAGATGAAGCTAATTAATTTTT 57.427 29.630 5.91 0.00 0.00 1.94
2313 5203 8.956426 TCCGAACAGATGAAGCTAATTAATTTT 58.044 29.630 5.91 0.00 0.00 1.82
2318 5208 6.816136 TGATCCGAACAGATGAAGCTAATTA 58.184 36.000 0.00 0.00 0.00 1.40
2319 5209 5.674525 TGATCCGAACAGATGAAGCTAATT 58.325 37.500 0.00 0.00 0.00 1.40
2320 5210 5.282055 TGATCCGAACAGATGAAGCTAAT 57.718 39.130 0.00 0.00 0.00 1.73
2321 5211 4.736126 TGATCCGAACAGATGAAGCTAA 57.264 40.909 0.00 0.00 0.00 3.09
2327 5217 4.831107 TGAAACATGATCCGAACAGATGA 58.169 39.130 0.00 0.00 0.00 2.92
2385 5341 6.261118 GGAAACACAAATAAGATGCAGCTAG 58.739 40.000 4.15 0.00 0.00 3.42
2441 5447 7.254455 CGATTACCAAATACAGCCTTCTTACAG 60.254 40.741 0.00 0.00 0.00 2.74
2504 5534 6.983307 TGCTTGCTTGAAAATACAGCTAAAAA 59.017 30.769 0.00 0.00 0.00 1.94
2506 5536 5.920273 GTGCTTGCTTGAAAATACAGCTAAA 59.080 36.000 0.00 0.00 0.00 1.85
2507 5537 5.009510 TGTGCTTGCTTGAAAATACAGCTAA 59.990 36.000 0.00 0.00 0.00 3.09
2508 5538 4.518590 TGTGCTTGCTTGAAAATACAGCTA 59.481 37.500 0.00 0.00 0.00 3.32
2509 5539 3.318839 TGTGCTTGCTTGAAAATACAGCT 59.681 39.130 0.00 0.00 0.00 4.24
2510 5540 3.641648 TGTGCTTGCTTGAAAATACAGC 58.358 40.909 0.00 0.00 0.00 4.40
2511 5541 4.863491 ACTGTGCTTGCTTGAAAATACAG 58.137 39.130 0.00 0.00 39.94 2.74
2512 5542 4.916983 ACTGTGCTTGCTTGAAAATACA 57.083 36.364 0.00 0.00 0.00 2.29
2513 5543 5.966335 CAAACTGTGCTTGCTTGAAAATAC 58.034 37.500 0.00 0.00 0.00 1.89
2545 5590 7.405292 ACATTCTGGAATCTGGATAAACAAGA 58.595 34.615 0.00 0.00 0.00 3.02
2547 5592 8.306038 CAAACATTCTGGAATCTGGATAAACAA 58.694 33.333 0.00 0.00 0.00 2.83
2659 5782 9.709495 AGCAATGCAACTCAAATTAATCTAAAA 57.291 25.926 8.35 0.00 0.00 1.52
2660 5783 9.142515 CAGCAATGCAACTCAAATTAATCTAAA 57.857 29.630 8.35 0.00 0.00 1.85
2661 5784 7.276218 GCAGCAATGCAACTCAAATTAATCTAA 59.724 33.333 8.35 0.00 34.41 2.10
2662 5785 6.753279 GCAGCAATGCAACTCAAATTAATCTA 59.247 34.615 8.35 0.00 34.41 1.98
2663 5786 5.579511 GCAGCAATGCAACTCAAATTAATCT 59.420 36.000 8.35 0.00 34.41 2.40
2664 5787 5.579511 AGCAGCAATGCAACTCAAATTAATC 59.420 36.000 8.35 0.00 37.25 1.75
2665 5788 5.484715 AGCAGCAATGCAACTCAAATTAAT 58.515 33.333 8.35 0.00 37.25 1.40
2666 5789 4.885413 AGCAGCAATGCAACTCAAATTAA 58.115 34.783 8.35 0.00 37.25 1.40
2667 5790 4.487948 GAGCAGCAATGCAACTCAAATTA 58.512 39.130 18.50 0.00 37.25 1.40
2668 5791 3.323243 GAGCAGCAATGCAACTCAAATT 58.677 40.909 18.50 0.00 37.25 1.82
2669 5792 2.670229 CGAGCAGCAATGCAACTCAAAT 60.670 45.455 21.60 0.00 37.25 2.32
2670 5793 1.335233 CGAGCAGCAATGCAACTCAAA 60.335 47.619 21.60 0.00 37.25 2.69
2671 5794 0.239082 CGAGCAGCAATGCAACTCAA 59.761 50.000 21.60 0.00 37.25 3.02
2672 5795 0.886043 ACGAGCAGCAATGCAACTCA 60.886 50.000 21.60 0.00 37.25 3.41
2673 5796 1.061711 CTACGAGCAGCAATGCAACTC 59.938 52.381 8.35 12.41 37.25 3.01
2724 5849 5.193663 TGCATGAACTAGAGAGCATAGAC 57.806 43.478 0.00 0.00 0.00 2.59
2726 5851 4.749099 GGTTGCATGAACTAGAGAGCATAG 59.251 45.833 0.00 0.00 34.66 2.23
2761 5886 4.510711 CAGAGTAATATGAGCCAACTGCAG 59.489 45.833 13.48 13.48 44.83 4.41
2820 5945 0.948623 TCAAGATTGCCACGGTCGTG 60.949 55.000 15.62 15.62 45.02 4.35
2832 5957 9.896645 TTCTCACTAATGAAGCTAATCAAGATT 57.103 29.630 0.52 0.52 36.24 2.40
2838 5963 8.394121 CAACCTTTCTCACTAATGAAGCTAATC 58.606 37.037 0.00 0.00 33.30 1.75
2840 5965 7.224297 ACAACCTTTCTCACTAATGAAGCTAA 58.776 34.615 0.00 0.00 33.30 3.09
2853 5978 2.438021 ACACTGCCTACAACCTTTCTCA 59.562 45.455 0.00 0.00 0.00 3.27
2855 5980 4.699925 TTACACTGCCTACAACCTTTCT 57.300 40.909 0.00 0.00 0.00 2.52
2856 5981 4.760204 ACATTACACTGCCTACAACCTTTC 59.240 41.667 0.00 0.00 0.00 2.62
2860 5985 4.069304 TCAACATTACACTGCCTACAACC 58.931 43.478 0.00 0.00 0.00 3.77
2883 6008 4.058721 TGTCTCGCATATAACATGCAGT 57.941 40.909 9.65 0.00 44.75 4.40
2898 6026 3.511699 TGAATCTGATTCGGTTGTCTCG 58.488 45.455 21.70 0.00 42.15 4.04
2928 6056 4.209703 TGGACGTGCGTTAAAAGTCTAAAG 59.790 41.667 1.60 0.00 32.86 1.85
2934 6062 3.761311 TTTTGGACGTGCGTTAAAAGT 57.239 38.095 1.60 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.