Multiple sequence alignment - TraesCS3A01G438100

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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 TraesCS3A01G438100 chr3A 100.000 4005 0 0 1 4005 681445987 681449991 0.000000e+00 7396.0
1 TraesCS3A01G438100 chr3A 88.827 1432 101 15 865 2255 681398958 681400371 0.000000e+00 1703.0
2 TraesCS3A01G438100 chr3A 89.798 892 62 17 2349 3212 681400366 681401256 0.000000e+00 1116.0
3 TraesCS3A01G438100 chr3A 94.400 125 5 2 3783 3905 697840823 697840699 1.470000e-44 191.0
4 TraesCS3A01G438100 chr3D 94.553 1175 47 7 753 1912 544771347 544772519 0.000000e+00 1799.0
5 TraesCS3A01G438100 chr3D 86.602 1433 106 41 865 2255 544444640 544446028 0.000000e+00 1504.0
6 TraesCS3A01G438100 chr3D 90.749 854 63 13 2349 3189 544446023 544446873 0.000000e+00 1125.0
7 TraesCS3A01G438100 chr3D 81.797 846 103 34 2379 3210 544772890 544773698 0.000000e+00 662.0
8 TraesCS3A01G438100 chr3D 83.619 525 56 16 2 508 482183093 482183605 2.180000e-127 466.0
9 TraesCS3A01G438100 chr3D 94.737 209 8 3 546 754 544771018 544771223 4.990000e-84 322.0
10 TraesCS3A01G438100 chr3D 80.347 346 32 17 1912 2241 544772558 544772883 3.110000e-56 230.0
11 TraesCS3A01G438100 chr3D 88.770 187 18 3 2797 2982 544791287 544791471 4.030000e-55 226.0
12 TraesCS3A01G438100 chr3D 82.222 135 22 2 3080 3212 544795892 544796026 9.100000e-22 115.0
13 TraesCS3A01G438100 chr3D 88.235 51 6 0 496 546 173475639 173475689 1.200000e-05 62.1
14 TraesCS3A01G438100 chr3B 94.591 869 41 4 2349 3212 720266919 720267786 0.000000e+00 1339.0
15 TraesCS3A01G438100 chr3B 91.972 872 41 10 865 1711 720265581 720266448 0.000000e+00 1195.0
16 TraesCS3A01G438100 chr3B 87.550 755 59 18 3253 4005 720267771 720268492 0.000000e+00 841.0
17 TraesCS3A01G438100 chr3B 83.709 399 42 12 1863 2255 720266543 720266924 4.920000e-94 355.0
18 TraesCS3A01G438100 chr3B 96.591 88 1 2 2251 2338 126030457 126030372 1.160000e-30 145.0
19 TraesCS3A01G438100 chr3B 89.899 99 9 1 3594 3692 43050408 43050311 4.200000e-25 126.0
20 TraesCS3A01G438100 chr1D 89.927 546 49 4 2 547 317560771 317560232 0.000000e+00 699.0
21 TraesCS3A01G438100 chr1D 95.082 122 4 2 3799 3919 247520958 247521078 1.470000e-44 191.0
22 TraesCS3A01G438100 chr6A 83.009 565 72 13 4 545 103262917 103263480 1.290000e-134 490.0
23 TraesCS3A01G438100 chr6A 100.000 79 0 0 2260 2338 478918942 478918864 3.230000e-31 147.0
24 TraesCS3A01G438100 chr5A 82.979 564 56 17 2 531 622140361 622140918 1.300000e-129 473.0
25 TraesCS3A01G438100 chr5A 82.069 435 53 9 96 507 31282554 31282122 8.240000e-92 348.0
26 TraesCS3A01G438100 chr5A 93.893 131 5 3 3777 3907 547790144 547790017 1.140000e-45 195.0
27 TraesCS3A01G438100 chr5A 95.082 122 4 2 3789 3909 375844483 375844363 1.470000e-44 191.0
28 TraesCS3A01G438100 chr5A 91.579 95 6 2 3590 3683 536863522 536863615 3.250000e-26 130.0
29 TraesCS3A01G438100 chr7B 82.766 470 52 7 96 545 89779495 89779955 3.750000e-105 392.0
30 TraesCS3A01G438100 chr7B 97.674 86 1 1 2253 2338 642366652 642366568 3.230000e-31 147.0
31 TraesCS3A01G438100 chr7B 89.908 109 10 1 2 110 89779369 89779476 5.400000e-29 139.0
32 TraesCS3A01G438100 chr7B 93.617 94 4 2 3595 3687 289427201 289427293 5.400000e-29 139.0
33 TraesCS3A01G438100 chr4B 89.320 309 29 4 2 310 391569615 391569919 6.280000e-103 385.0
34 TraesCS3A01G438100 chr4B 100.000 81 0 0 2258 2338 321732546 321732466 2.490000e-32 150.0
35 TraesCS3A01G438100 chr7A 82.164 342 27 9 2 343 200028928 200028621 3.070000e-66 263.0
36 TraesCS3A01G438100 chr1B 98.230 113 2 0 3796 3908 687254052 687253940 8.780000e-47 198.0
37 TraesCS3A01G438100 chr1B 90.000 110 6 4 3582 3690 322104647 322104542 1.940000e-28 137.0
38 TraesCS3A01G438100 chr7D 97.391 115 3 0 3796 3910 615266607 615266721 3.160000e-46 196.0
39 TraesCS3A01G438100 chr7D 97.222 108 3 0 3799 3906 379324131 379324238 2.460000e-42 183.0
40 TraesCS3A01G438100 chr6D 95.082 122 4 2 3795 3915 435974344 435974464 1.470000e-44 191.0
41 TraesCS3A01G438100 chr1A 93.077 130 5 4 3782 3909 587610167 587610294 1.900000e-43 187.0
42 TraesCS3A01G438100 chr1A 98.795 83 1 0 2256 2338 263537172 263537254 8.970000e-32 148.0
43 TraesCS3A01G438100 chrUn 98.810 84 1 0 2255 2338 87980737 87980820 2.490000e-32 150.0
44 TraesCS3A01G438100 chr2B 100.000 78 0 0 2261 2338 352288497 352288420 1.160000e-30 145.0
45 TraesCS3A01G438100 chr2B 96.552 87 2 1 2252 2338 708208063 708207978 4.170000e-30 143.0
46 TraesCS3A01G438100 chr2B 95.349 86 2 2 3598 3683 166044906 166044989 6.980000e-28 135.0
47 TraesCS3A01G438100 chr4A 93.684 95 3 3 2244 2338 446607999 446608090 5.400000e-29 139.0
48 TraesCS3A01G438100 chr4A 95.349 86 3 1 3598 3683 464687280 464687364 6.980000e-28 135.0
49 TraesCS3A01G438100 chr6B 92.473 93 7 0 453 545 132142947 132143039 2.510000e-27 134.0
50 TraesCS3A01G438100 chr5B 91.579 95 6 2 3590 3683 406172670 406172763 3.250000e-26 130.0
51 TraesCS3A01G438100 chr2D 89.216 102 9 2 3595 3696 12630903 12630804 4.200000e-25 126.0


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 TraesCS3A01G438100 chr3A 681445987 681449991 4004 False 7396.00 7396 100.0000 1 4005 1 chr3A.!!$F1 4004
1 TraesCS3A01G438100 chr3A 681398958 681401256 2298 False 1409.50 1703 89.3125 865 3212 2 chr3A.!!$F2 2347
2 TraesCS3A01G438100 chr3D 544444640 544446873 2233 False 1314.50 1504 88.6755 865 3189 2 chr3D.!!$F5 2324
3 TraesCS3A01G438100 chr3D 544771018 544773698 2680 False 753.25 1799 87.8585 546 3210 4 chr3D.!!$F6 2664
4 TraesCS3A01G438100 chr3D 482183093 482183605 512 False 466.00 466 83.6190 2 508 1 chr3D.!!$F2 506
5 TraesCS3A01G438100 chr3B 720265581 720268492 2911 False 932.50 1339 89.4555 865 4005 4 chr3B.!!$F1 3140
6 TraesCS3A01G438100 chr1D 317560232 317560771 539 True 699.00 699 89.9270 2 547 1 chr1D.!!$R1 545
7 TraesCS3A01G438100 chr6A 103262917 103263480 563 False 490.00 490 83.0090 4 545 1 chr6A.!!$F1 541
8 TraesCS3A01G438100 chr5A 622140361 622140918 557 False 473.00 473 82.9790 2 531 1 chr5A.!!$F2 529
9 TraesCS3A01G438100 chr7B 89779369 89779955 586 False 265.50 392 86.3370 2 545 2 chr7B.!!$F2 543

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
605 684 0.246910 TGCGGCTATACAACGGTTGA 59.753 50.0 26.39 11.05 0.00 3.18 F
946 1159 0.530650 TCGTATTAGCAGCAGCAGCC 60.531 55.0 6.10 0.00 45.49 4.85 F
1674 1917 0.960364 ATGCCGGTGTTGCGAAGATT 60.960 50.0 1.90 0.00 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 2044 0.467290 TGGGTTGTGAAACTCCAGGC 60.467 55.0 0.00 0.00 38.04 4.85 R
2310 2648 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.0 23.81 9.51 37.50 3.46 R
3666 4045 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.0 0.00 0.00 0.00 4.12 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
61 67 1.183030 TTTGAGAACCGCCCTCTCGA 61.183 55.000 0.00 0.00 41.95 4.04
150 188 7.437862 GGATTACATCAAGAGACAAAGAGCTAG 59.562 40.741 0.00 0.00 0.00 3.42
237 275 5.867903 TTGAAGCTTGAATCCCTGAAAAA 57.132 34.783 2.10 0.00 0.00 1.94
297 338 2.148768 GTGGGTGTGTACTTGGTTAGC 58.851 52.381 0.00 0.00 0.00 3.09
313 362 0.672091 TAGCGGCTTCGTGCATCAAA 60.672 50.000 8.26 0.00 45.15 2.69
318 367 0.518636 GCTTCGTGCATCAAAGCTCA 59.481 50.000 18.12 0.00 41.66 4.26
394 465 1.095807 GGCCCAGTTATCAGCGAACC 61.096 60.000 0.00 0.00 0.00 3.62
416 487 2.488545 GCCTCTTTCTCTCGTAGTGACA 59.511 50.000 0.00 0.00 0.00 3.58
426 497 1.621317 TCGTAGTGACATTTCCCAGCA 59.379 47.619 0.00 0.00 0.00 4.41
437 508 0.905809 TTCCCAGCATTGCATGGCTT 60.906 50.000 11.91 0.00 38.56 4.35
439 510 1.327690 CCCAGCATTGCATGGCTTCT 61.328 55.000 11.91 0.00 38.56 2.85
450 521 3.008375 TGCATGGCTTCTAGGATATCCAC 59.992 47.826 23.81 5.59 38.89 4.02
465 544 6.062749 GGATATCCACCGATAGCAGTAGATA 58.937 44.000 17.34 0.00 38.82 1.98
471 550 5.414765 CCACCGATAGCAGTAGATACATACA 59.585 44.000 0.00 0.00 0.00 2.29
555 634 3.120304 GCTCCGTCAGTGGTTCATTTTAC 60.120 47.826 0.00 0.00 0.00 2.01
605 684 0.246910 TGCGGCTATACAACGGTTGA 59.753 50.000 26.39 11.05 0.00 3.18
608 687 2.613691 CGGCTATACAACGGTTGAAGT 58.386 47.619 26.39 13.60 0.00 3.01
643 722 4.438336 GCTTATGTACATCGGCTATAGCGA 60.438 45.833 18.30 17.82 43.26 4.93
645 724 1.810755 TGTACATCGGCTATAGCGAGG 59.189 52.381 18.30 20.08 43.26 4.63
800 1004 8.613060 ATGTACTTTACATATTGGAGATGCTG 57.387 34.615 0.00 0.00 46.90 4.41
860 1065 8.012241 GGTAATTTTCGAGCTGCTTATCTTATG 58.988 37.037 2.53 0.00 0.00 1.90
946 1159 0.530650 TCGTATTAGCAGCAGCAGCC 60.531 55.000 6.10 0.00 45.49 4.85
1625 1868 1.617947 AAGGAGATGGGGCTCGTCAC 61.618 60.000 9.69 1.89 35.74 3.67
1674 1917 0.960364 ATGCCGGTGTTGCGAAGATT 60.960 50.000 1.90 0.00 0.00 2.40
1686 1929 2.423185 TGCGAAGATTGCCAAAGGTATG 59.577 45.455 0.00 0.00 0.00 2.39
1698 1941 5.189180 GCCAAAGGTATGATTTCTCTCTGT 58.811 41.667 0.00 0.00 0.00 3.41
1736 1983 2.038952 TGCTGTTGCCTCTGTTCTGTAT 59.961 45.455 0.00 0.00 38.71 2.29
1796 2044 9.410556 CAAAGTTCAAACTAATAAGGGATGTTG 57.589 33.333 0.00 0.00 38.57 3.33
1803 2051 3.303351 AATAAGGGATGTTGCCTGGAG 57.697 47.619 0.00 0.00 37.13 3.86
1826 2074 3.358111 TCACAACCCACAAAAGAGTCA 57.642 42.857 0.00 0.00 0.00 3.41
1834 2082 3.803778 CCCACAAAAGAGTCATTGTTTGC 59.196 43.478 10.59 0.00 37.66 3.68
1842 2095 6.942532 AAGAGTCATTGTTTGCAGAACTTA 57.057 33.333 11.34 3.08 0.00 2.24
2011 2328 8.632679 TGGCTGGATAATCTTTGATTTTATGTC 58.367 33.333 0.00 0.00 0.00 3.06
2181 2519 6.448369 TTTCTAGAATTCCAACTCTCCCAA 57.552 37.500 5.89 0.00 0.00 4.12
2224 2562 8.686334 TCTATATTCTCATTTCCTGGTTTTTGC 58.314 33.333 0.00 0.00 0.00 3.68
2254 2592 5.833667 TGCTATAGTGTGCTTAGTGTCCTAT 59.166 40.000 0.84 0.00 0.00 2.57
2255 2593 6.016192 TGCTATAGTGTGCTTAGTGTCCTATC 60.016 42.308 0.84 0.00 0.00 2.08
2256 2594 5.793030 ATAGTGTGCTTAGTGTCCTATCC 57.207 43.478 0.00 0.00 0.00 2.59
2257 2595 3.714144 AGTGTGCTTAGTGTCCTATCCT 58.286 45.455 0.00 0.00 0.00 3.24
2258 2596 3.449018 AGTGTGCTTAGTGTCCTATCCTG 59.551 47.826 0.00 0.00 0.00 3.86
2259 2597 3.195825 GTGTGCTTAGTGTCCTATCCTGT 59.804 47.826 0.00 0.00 0.00 4.00
2260 2598 4.401519 GTGTGCTTAGTGTCCTATCCTGTA 59.598 45.833 0.00 0.00 0.00 2.74
2261 2599 5.020795 TGTGCTTAGTGTCCTATCCTGTAA 58.979 41.667 0.00 0.00 0.00 2.41
2262 2600 5.482526 TGTGCTTAGTGTCCTATCCTGTAAA 59.517 40.000 0.00 0.00 0.00 2.01
2263 2601 6.014070 TGTGCTTAGTGTCCTATCCTGTAAAA 60.014 38.462 0.00 0.00 0.00 1.52
2264 2602 6.877322 GTGCTTAGTGTCCTATCCTGTAAAAA 59.123 38.462 0.00 0.00 0.00 1.94
2286 2624 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2287 2625 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2288 2626 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2289 2627 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
2290 2628 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2296 2634 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2297 2635 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2298 2636 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2299 2637 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2302 2640 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2314 2652 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
2315 2653 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2316 2654 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2317 2655 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2318 2656 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2319 2657 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2320 2658 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2321 2659 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2322 2660 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2323 2661 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2324 2662 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
2325 2663 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
2326 2664 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2327 2665 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2328 2666 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2329 2667 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2330 2668 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2331 2669 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2332 2670 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2344 2682 6.481434 ACCACTTTGGGTCTATATAGTGTC 57.519 41.667 9.58 2.56 43.37 3.67
2345 2683 5.365895 ACCACTTTGGGTCTATATAGTGTCC 59.634 44.000 9.58 10.19 43.37 4.02
2346 2684 5.602978 CCACTTTGGGTCTATATAGTGTCCT 59.397 44.000 9.58 0.00 32.67 3.85
2347 2685 6.781014 CCACTTTGGGTCTATATAGTGTCCTA 59.219 42.308 9.58 6.52 32.67 2.94
2348 2686 7.455008 CCACTTTGGGTCTATATAGTGTCCTAT 59.545 40.741 9.58 0.00 34.42 2.57
2349 2687 8.524487 CACTTTGGGTCTATATAGTGTCCTATC 58.476 40.741 9.58 0.00 35.49 2.08
2350 2688 7.674772 ACTTTGGGTCTATATAGTGTCCTATCC 59.325 40.741 9.58 0.00 35.49 2.59
2351 2689 6.989709 TGGGTCTATATAGTGTCCTATCCT 57.010 41.667 9.58 0.00 35.49 3.24
2352 2690 6.732487 TGGGTCTATATAGTGTCCTATCCTG 58.268 44.000 9.58 0.00 35.49 3.86
2360 2698 3.714144 AGTGTCCTATCCTGTAAGTGCT 58.286 45.455 0.00 0.00 0.00 4.40
2491 2832 4.955811 TGGGTCATATAGTTAGTGCTGG 57.044 45.455 0.00 0.00 0.00 4.85
2505 2846 4.150897 AGTGCTGGTAGTTTGAAGTCAA 57.849 40.909 0.00 0.00 0.00 3.18
2525 2866 5.575606 GTCAAATGCACTTGAATCAATCCAG 59.424 40.000 12.86 0.00 37.08 3.86
2583 2925 5.461516 TTACTAGTGTCACCCCTCTATCA 57.538 43.478 5.39 0.00 0.00 2.15
2705 3047 0.541392 TGCATAAGATGTCCCTGCGT 59.459 50.000 0.00 0.00 35.63 5.24
2768 3122 5.470098 CCAGCAACTATGTAACTCAACAAGT 59.530 40.000 0.00 0.00 41.10 3.16
2782 3136 5.643348 ACTCAACAAGTTGCGATCAATGATA 59.357 36.000 9.64 0.00 40.24 2.15
2793 3148 7.043961 TGCGATCAATGATAACTAAGAGACT 57.956 36.000 0.00 0.00 0.00 3.24
2796 3151 8.272176 GCGATCAATGATAACTAAGAGACTTTG 58.728 37.037 0.00 0.00 0.00 2.77
2851 3207 0.950836 CAAACGCAGTGATGGGAACA 59.049 50.000 0.00 0.00 45.00 3.18
2866 3222 3.075148 GGGAACAAAGGCAGTTCTACTC 58.925 50.000 14.25 2.03 43.67 2.59
2884 3240 6.600388 TCTACTCAGAAGCAGAGATATCACT 58.400 40.000 5.32 0.42 36.91 3.41
2939 3295 3.823281 ACTCTGGAATGCTGAGATCTG 57.177 47.619 14.81 0.00 0.00 2.90
3012 3368 8.045507 TGTTTTCTCTAAGCTCTGATGATCAAT 58.954 33.333 0.00 0.00 0.00 2.57
3022 3378 5.548406 CTCTGATGATCAATATCACAGGCA 58.452 41.667 0.00 0.00 44.79 4.75
3205 3584 8.928448 ACTACTGATGTCCATATTGATTAGTGT 58.072 33.333 0.00 0.00 0.00 3.55
3286 3665 4.397420 TGTTGTGATGCCTGTAGAATGTT 58.603 39.130 0.00 0.00 0.00 2.71
3291 3670 6.413892 TGTGATGCCTGTAGAATGTTGATTA 58.586 36.000 0.00 0.00 0.00 1.75
3296 3675 5.414454 TGCCTGTAGAATGTTGATTAACCAC 59.586 40.000 0.00 0.00 35.92 4.16
3361 3740 5.869579 TCAAGCTTATATCTGGATTGGGTC 58.130 41.667 0.00 0.00 0.00 4.46
3412 3791 0.250510 GCCCCATAGCTTGTCTAGGC 60.251 60.000 0.00 0.00 31.59 3.93
3427 3806 7.148171 GCTTGTCTAGGCATAAGTTGAATTTCT 60.148 37.037 0.00 0.00 0.00 2.52
3477 3856 2.579410 ATTCACACTACCACAACCCC 57.421 50.000 0.00 0.00 0.00 4.95
3478 3857 1.513858 TTCACACTACCACAACCCCT 58.486 50.000 0.00 0.00 0.00 4.79
3499 3878 7.179516 ACCCCTTTTGGTTACTATGTTAATTGG 59.820 37.037 0.00 0.00 33.91 3.16
3540 3919 7.549488 TCCTAGCTCTTATGTGCTTTAAGTTTC 59.451 37.037 10.05 0.00 42.24 2.78
3607 3986 9.898152 AAAGAATCTTTAGAAATACTCCCTCTG 57.102 33.333 6.43 0.00 0.00 3.35
3609 3988 8.700973 AGAATCTTTAGAAATACTCCCTCTGTC 58.299 37.037 0.00 0.00 0.00 3.51
3610 3989 6.793505 TCTTTAGAAATACTCCCTCTGTCC 57.206 41.667 0.00 0.00 0.00 4.02
3611 3990 5.661759 TCTTTAGAAATACTCCCTCTGTCCC 59.338 44.000 0.00 0.00 0.00 4.46
3613 3992 4.014273 AGAAATACTCCCTCTGTCCCAT 57.986 45.455 0.00 0.00 0.00 4.00
3615 3994 5.538877 AGAAATACTCCCTCTGTCCCATAA 58.461 41.667 0.00 0.00 0.00 1.90
3616 3995 6.153924 AGAAATACTCCCTCTGTCCCATAAT 58.846 40.000 0.00 0.00 0.00 1.28
3617 3996 5.832539 AATACTCCCTCTGTCCCATAATG 57.167 43.478 0.00 0.00 0.00 1.90
3618 3997 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
3619 3998 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
3620 3999 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
3621 4000 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
3622 4001 4.631234 TCCCTCTGTCCCATAATGTAAGT 58.369 43.478 0.00 0.00 0.00 2.24
3623 4002 5.036916 TCCCTCTGTCCCATAATGTAAGTT 58.963 41.667 0.00 0.00 0.00 2.66
3624 4003 5.104527 TCCCTCTGTCCCATAATGTAAGTTG 60.105 44.000 0.00 0.00 0.00 3.16
3702 4081 7.932491 GGGAGTAGTATTCAAAGATAACCCTTC 59.068 40.741 0.00 0.00 0.00 3.46
3792 4171 4.252878 CCATTGCCTTAATTGTTGGGTTC 58.747 43.478 0.00 0.00 0.00 3.62
3807 4186 5.191426 GTTGGGTTCTTAAATACTCCCTCC 58.809 45.833 0.00 0.00 36.23 4.30
3810 4189 4.080695 GGGTTCTTAAATACTCCCTCCGTT 60.081 45.833 0.00 0.00 32.89 4.44
3813 4192 3.382546 TCTTAAATACTCCCTCCGTTCCG 59.617 47.826 0.00 0.00 0.00 4.30
3816 4195 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
3819 4198 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3820 4199 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3824 4203 3.332034 CCTCCGTTCCGAATTACTTGTT 58.668 45.455 0.00 0.00 0.00 2.83
3825 4204 3.124636 CCTCCGTTCCGAATTACTTGTTG 59.875 47.826 0.00 0.00 0.00 3.33
3830 4209 4.553938 CGTTCCGAATTACTTGTTGCAAGT 60.554 41.667 17.05 17.05 0.00 3.16
3831 4210 5.333492 CGTTCCGAATTACTTGTTGCAAGTA 60.333 40.000 15.26 15.26 0.00 2.24
3833 4212 6.176975 TCCGAATTACTTGTTGCAAGTATG 57.823 37.500 18.60 11.03 33.27 2.39
3835 4214 5.123186 CCGAATTACTTGTTGCAAGTATGGA 59.877 40.000 18.60 8.01 33.27 3.41
3836 4215 6.183360 CCGAATTACTTGTTGCAAGTATGGAT 60.183 38.462 18.60 9.59 33.27 3.41
3837 4216 6.688385 CGAATTACTTGTTGCAAGTATGGATG 59.312 38.462 18.60 7.89 33.27 3.51
3838 4217 7.466746 AATTACTTGTTGCAAGTATGGATGT 57.533 32.000 18.60 0.00 33.27 3.06
3841 4220 6.683974 ACTTGTTGCAAGTATGGATGTATC 57.316 37.500 12.20 0.00 0.00 2.24
3843 4222 7.564793 ACTTGTTGCAAGTATGGATGTATCTA 58.435 34.615 12.20 0.00 0.00 1.98
3845 4224 7.360113 TGTTGCAAGTATGGATGTATCTAGA 57.640 36.000 0.00 0.00 0.00 2.43
3846 4225 7.966812 TGTTGCAAGTATGGATGTATCTAGAT 58.033 34.615 10.73 10.73 0.00 1.98
3847 4226 7.874528 TGTTGCAAGTATGGATGTATCTAGATG 59.125 37.037 15.79 0.00 0.00 2.90
3850 4229 9.259832 TGCAAGTATGGATGTATCTAGATGTAT 57.740 33.333 15.79 9.11 0.00 2.29
3877 4256 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
3879 4258 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
3880 4259 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3881 4260 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
3882 4261 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
3883 4262 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
3884 4263 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
3885 4264 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
3886 4265 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
3887 4266 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
3888 4267 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
3889 4268 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
3890 4269 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
3891 4270 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
3892 4271 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
3893 4272 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
3894 4273 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
3895 4274 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3896 4275 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
3897 4276 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
3898 4277 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
3899 4278 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3900 4279 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3901 4280 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
3905 4284 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
3927 4306 7.785506 AGTAGTATGGTTAGCACTTCCTAAGAT 59.214 37.037 0.00 0.00 0.00 2.40
3969 4348 3.868619 TGTAAACTTGGTGGTAGCCTT 57.131 42.857 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.950309 CAGCAGCAATCCTAGAAAGCAT 59.050 45.455 0.00 0.00 0.00 3.79
25 26 8.984764 GGTTCTCAAAACAAAAACTACACTTTT 58.015 29.630 0.00 0.00 0.00 2.27
26 27 7.327518 CGGTTCTCAAAACAAAAACTACACTTT 59.672 33.333 0.00 0.00 0.00 2.66
27 28 6.804783 CGGTTCTCAAAACAAAAACTACACTT 59.195 34.615 0.00 0.00 0.00 3.16
80 86 0.107017 CAGTCGGATGCAAATCCCCT 60.107 55.000 0.65 0.00 37.43 4.79
121 159 7.633772 GCTCTTTGTCTCTTGATGTAATCCCTA 60.634 40.741 0.00 0.00 44.73 3.53
150 188 1.333791 GGACGCGCTTAATATTGGTGC 60.334 52.381 5.73 14.61 0.00 5.01
297 338 4.751539 CTTTGATGCACGAAGCCG 57.248 55.556 0.00 0.00 44.83 5.52
318 367 2.434884 CGATGCACGAACCAGCCT 60.435 61.111 0.00 0.00 45.77 4.58
394 465 1.738350 TCACTACGAGAGAAAGAGGCG 59.262 52.381 0.00 0.00 0.00 5.52
401 472 3.830178 TGGGAAATGTCACTACGAGAGAA 59.170 43.478 0.00 0.00 0.00 2.87
402 473 3.427573 TGGGAAATGTCACTACGAGAGA 58.572 45.455 0.00 0.00 0.00 3.10
416 487 0.179468 GCCATGCAATGCTGGGAAAT 59.821 50.000 19.83 0.00 44.97 2.17
426 497 4.290459 TGGATATCCTAGAAGCCATGCAAT 59.710 41.667 22.35 0.00 36.82 3.56
437 508 4.018324 ACTGCTATCGGTGGATATCCTAGA 60.018 45.833 22.35 17.49 34.71 2.43
439 510 4.317530 ACTGCTATCGGTGGATATCCTA 57.682 45.455 22.35 6.56 34.71 2.94
487 566 1.408127 CGCCATACCTTGATTGGGTGA 60.408 52.381 0.00 0.00 37.65 4.02
539 618 9.559732 CCATAGATATGTAAAATGAACCACTGA 57.440 33.333 0.00 0.00 31.82 3.41
605 684 1.533625 TAAGCATTTCAGCCGCACTT 58.466 45.000 0.00 0.00 34.23 3.16
608 687 1.462616 ACATAAGCATTTCAGCCGCA 58.537 45.000 0.00 0.00 34.23 5.69
645 724 7.562138 ACAAATAATGTAAAACGGCCAATGGC 61.562 38.462 17.42 17.42 44.43 4.40
839 1044 4.875536 TGCATAAGATAAGCAGCTCGAAAA 59.124 37.500 0.00 0.00 33.75 2.29
860 1065 5.877012 TCCTCTCTTGTTGTTCTTATGATGC 59.123 40.000 0.00 0.00 0.00 3.91
946 1159 1.957695 TGCTGCTCTGTTGACTGCG 60.958 57.895 0.00 0.00 0.00 5.18
1086 1329 4.710695 CGCACCTCGTACACCGCA 62.711 66.667 0.00 0.00 36.19 5.69
1419 1662 4.980805 GCCACCAGTTCGACGCCA 62.981 66.667 0.00 0.00 0.00 5.69
1454 1697 4.704833 TGGCGTCCTTGGAGCAGC 62.705 66.667 11.23 7.82 0.00 5.25
1625 1868 1.453155 CTTGGAATCGAACACCCTGG 58.547 55.000 0.00 0.00 0.00 4.45
1674 1917 5.188434 CAGAGAGAAATCATACCTTTGGCA 58.812 41.667 0.00 0.00 0.00 4.92
1686 1929 9.444534 GAAAAGAAAGAACAACAGAGAGAAATC 57.555 33.333 0.00 0.00 0.00 2.17
1698 1941 5.643379 ACAGCACTGAAAAGAAAGAACAA 57.357 34.783 4.31 0.00 0.00 2.83
1796 2044 0.467290 TGGGTTGTGAAACTCCAGGC 60.467 55.000 0.00 0.00 38.04 4.85
1803 2051 4.082463 TGACTCTTTTGTGGGTTGTGAAAC 60.082 41.667 0.00 0.00 37.35 2.78
1826 2074 7.288810 TGGAATCTTAAGTTCTGCAAACAAT 57.711 32.000 1.63 5.46 0.00 2.71
1870 2146 6.211785 ACCCTTGTTCTTTTTCTTACCAACAA 59.788 34.615 0.00 0.00 33.76 2.83
1874 2150 5.265989 ACACCCTTGTTCTTTTTCTTACCA 58.734 37.500 0.00 0.00 28.43 3.25
1885 2161 2.370189 CCAAGAGAGACACCCTTGTTCT 59.630 50.000 0.00 0.00 35.47 3.01
1967 2283 3.392616 AGCCAAATGGATCTACGGATTCT 59.607 43.478 2.98 0.00 37.39 2.40
1973 2289 2.620251 TCCAGCCAAATGGATCTACG 57.380 50.000 2.98 0.00 44.56 3.51
2147 2485 5.473504 TGGAATTCTAGAAAGCCTGTGAAAC 59.526 40.000 21.00 1.34 37.35 2.78
2263 2601 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
2264 2602 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
2265 2603 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
2266 2604 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
2267 2605 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
2268 2606 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2269 2607 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2270 2608 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2271 2609 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2272 2610 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2297 2635 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2298 2636 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2299 2637 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2300 2638 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2301 2639 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2302 2640 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2303 2641 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2304 2642 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2305 2643 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
2306 2644 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2307 2645 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2308 2646 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2309 2647 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2310 2648 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2311 2649 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2312 2650 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2313 2651 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2314 2652 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2315 2653 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2316 2654 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2321 2659 5.365895 GGACACTATATAGACCCAAAGTGGT 59.634 44.000 16.79 0.00 42.79 4.16
2322 2660 5.602978 AGGACACTATATAGACCCAAAGTGG 59.397 44.000 16.79 0.00 38.87 4.00
2323 2661 6.732896 AGGACACTATATAGACCCAAAGTG 57.267 41.667 16.79 6.61 40.08 3.16
2324 2662 7.674772 GGATAGGACACTATATAGACCCAAAGT 59.325 40.741 16.79 3.38 39.97 2.66
2325 2663 7.896496 AGGATAGGACACTATATAGACCCAAAG 59.104 40.741 16.79 0.53 39.97 2.77
2326 2664 7.674348 CAGGATAGGACACTATATAGACCCAAA 59.326 40.741 16.79 6.94 39.97 3.28
2327 2665 7.182760 CAGGATAGGACACTATATAGACCCAA 58.817 42.308 16.79 8.10 39.97 4.12
2328 2666 6.277283 ACAGGATAGGACACTATATAGACCCA 59.723 42.308 16.79 6.41 39.97 4.51
2329 2667 6.733509 ACAGGATAGGACACTATATAGACCC 58.266 44.000 16.79 12.70 39.97 4.46
2330 2668 9.398538 CTTACAGGATAGGACACTATATAGACC 57.601 40.741 16.79 14.69 39.97 3.85
2331 2669 9.962809 ACTTACAGGATAGGACACTATATAGAC 57.037 37.037 16.79 7.17 39.97 2.59
2332 2670 9.961264 CACTTACAGGATAGGACACTATATAGA 57.039 37.037 16.79 0.00 39.97 1.98
2333 2671 8.679100 GCACTTACAGGATAGGACACTATATAG 58.321 40.741 8.27 8.27 39.97 1.31
2334 2672 8.391699 AGCACTTACAGGATAGGACACTATATA 58.608 37.037 0.00 0.00 39.97 0.86
2335 2673 7.177568 CAGCACTTACAGGATAGGACACTATAT 59.822 40.741 0.00 0.00 39.97 0.86
2336 2674 6.490381 CAGCACTTACAGGATAGGACACTATA 59.510 42.308 0.00 0.00 39.97 1.31
2337 2675 5.303078 CAGCACTTACAGGATAGGACACTAT 59.697 44.000 0.00 0.00 42.53 2.12
2338 2676 4.645136 CAGCACTTACAGGATAGGACACTA 59.355 45.833 0.00 0.00 0.00 2.74
2339 2677 3.449018 CAGCACTTACAGGATAGGACACT 59.551 47.826 0.00 0.00 0.00 3.55
2340 2678 3.430929 CCAGCACTTACAGGATAGGACAC 60.431 52.174 0.00 0.00 0.00 3.67
2341 2679 2.766263 CCAGCACTTACAGGATAGGACA 59.234 50.000 0.00 0.00 0.00 4.02
2342 2680 2.483889 GCCAGCACTTACAGGATAGGAC 60.484 54.545 0.00 0.00 0.00 3.85
2343 2681 1.762957 GCCAGCACTTACAGGATAGGA 59.237 52.381 0.00 0.00 0.00 2.94
2344 2682 1.765314 AGCCAGCACTTACAGGATAGG 59.235 52.381 0.00 0.00 0.00 2.57
2345 2683 3.550437 AAGCCAGCACTTACAGGATAG 57.450 47.619 0.00 0.00 0.00 2.08
2346 2684 5.429681 TTTAAGCCAGCACTTACAGGATA 57.570 39.130 0.00 0.00 31.94 2.59
2347 2685 4.301072 TTTAAGCCAGCACTTACAGGAT 57.699 40.909 0.00 0.00 31.94 3.24
2348 2686 3.780804 TTTAAGCCAGCACTTACAGGA 57.219 42.857 0.00 0.00 31.94 3.86
2349 2687 3.758554 ACATTTAAGCCAGCACTTACAGG 59.241 43.478 0.00 0.00 31.94 4.00
2350 2688 5.376854 AACATTTAAGCCAGCACTTACAG 57.623 39.130 0.00 0.00 31.94 2.74
2351 2689 5.534654 AGAAACATTTAAGCCAGCACTTACA 59.465 36.000 0.00 0.00 31.94 2.41
2352 2690 6.013842 AGAAACATTTAAGCCAGCACTTAC 57.986 37.500 0.00 0.00 31.94 2.34
2360 2698 9.515226 AATGTAGTAAGAGAAACATTTAAGCCA 57.485 29.630 0.00 0.00 38.98 4.75
2390 2728 4.041567 TCAAGAGAGTGGTGGATTTTGCTA 59.958 41.667 0.00 0.00 0.00 3.49
2432 2770 1.462616 TCATGTTGGGAAATGGAGCG 58.537 50.000 0.00 0.00 0.00 5.03
2505 2846 3.512329 TGCTGGATTGATTCAAGTGCATT 59.488 39.130 5.21 0.00 0.00 3.56
2525 2866 8.603181 CCTTTAAACCATTATACAATGCTTTGC 58.397 33.333 11.96 0.00 40.28 3.68
2555 2897 3.681593 GGGGTGACACTAGTAAATTGCA 58.318 45.455 5.39 0.00 0.00 4.08
2583 2925 4.646492 ACAAATCCAACTTGCTTCTGACTT 59.354 37.500 0.00 0.00 0.00 3.01
2705 3047 7.722285 AGGCATAGTTAACAAGAAACTGGTTTA 59.278 33.333 8.61 0.00 37.71 2.01
2768 3122 7.492524 AGTCTCTTAGTTATCATTGATCGCAA 58.507 34.615 1.55 0.00 38.60 4.85
2805 3161 7.009999 CCGACTTCTCTGATATTTCTGAAACAG 59.990 40.741 4.73 8.66 30.48 3.16
2851 3207 3.071602 TGCTTCTGAGTAGAACTGCCTTT 59.928 43.478 0.00 0.00 37.99 3.11
2866 3222 6.631971 TCTACAGTGATATCTCTGCTTCTG 57.368 41.667 26.96 15.81 40.14 3.02
2884 3240 1.687146 CTCCAGGCCCTGCTCTACA 60.687 63.158 4.81 0.00 0.00 2.74
3012 3368 9.797642 ATTCACATATAAATTCTGCCTGTGATA 57.202 29.630 3.61 0.00 40.59 2.15
3022 3378 8.664079 AGTGGCTAGGATTCACATATAAATTCT 58.336 33.333 0.00 0.00 34.17 2.40
3164 3533 6.820656 ACATCAGTAGTGCTAAGGAATTTCTG 59.179 38.462 0.00 0.00 0.00 3.02
3169 3548 4.716784 TGGACATCAGTAGTGCTAAGGAAT 59.283 41.667 0.00 0.00 0.00 3.01
3244 3623 9.676195 CACAACATAACACTAATCATTTCACAA 57.324 29.630 0.00 0.00 0.00 3.33
3245 3624 9.061435 TCACAACATAACACTAATCATTTCACA 57.939 29.630 0.00 0.00 0.00 3.58
3248 3627 9.013490 GCATCACAACATAACACTAATCATTTC 57.987 33.333 0.00 0.00 0.00 2.17
3249 3628 7.975616 GGCATCACAACATAACACTAATCATTT 59.024 33.333 0.00 0.00 0.00 2.32
3250 3629 7.340232 AGGCATCACAACATAACACTAATCATT 59.660 33.333 0.00 0.00 0.00 2.57
3251 3630 6.830324 AGGCATCACAACATAACACTAATCAT 59.170 34.615 0.00 0.00 0.00 2.45
3252 3631 6.093909 CAGGCATCACAACATAACACTAATCA 59.906 38.462 0.00 0.00 0.00 2.57
3253 3632 6.094048 ACAGGCATCACAACATAACACTAATC 59.906 38.462 0.00 0.00 0.00 1.75
3254 3633 5.945784 ACAGGCATCACAACATAACACTAAT 59.054 36.000 0.00 0.00 0.00 1.73
3255 3634 5.312895 ACAGGCATCACAACATAACACTAA 58.687 37.500 0.00 0.00 0.00 2.24
3256 3635 4.905429 ACAGGCATCACAACATAACACTA 58.095 39.130 0.00 0.00 0.00 2.74
3257 3636 3.754965 ACAGGCATCACAACATAACACT 58.245 40.909 0.00 0.00 0.00 3.55
3258 3637 4.935205 TCTACAGGCATCACAACATAACAC 59.065 41.667 0.00 0.00 0.00 3.32
3286 3665 5.072600 ACTTGTAAGTGGGAGTGGTTAATCA 59.927 40.000 0.00 0.00 37.98 2.57
3322 3701 2.874701 GCTTGAGTGAACTTCTCTGCAA 59.125 45.455 0.00 3.10 34.81 4.08
3361 3740 1.949525 CACTGGACCAAGGTCTTGTTG 59.050 52.381 18.03 7.52 44.04 3.33
3370 3749 4.709840 CAGGCTCACTGGACCAAG 57.290 61.111 0.00 0.00 43.70 3.61
3412 3791 7.587629 TCTTCAGCACAGAAATTCAACTTATG 58.412 34.615 0.00 0.00 0.00 1.90
3427 3806 1.342496 CAGACTCACCTCTTCAGCACA 59.658 52.381 0.00 0.00 0.00 4.57
3513 3892 6.578023 ACTTAAAGCACATAAGAGCTAGGAG 58.422 40.000 9.35 0.00 40.96 3.69
3514 3893 6.546428 ACTTAAAGCACATAAGAGCTAGGA 57.454 37.500 9.35 0.00 40.96 2.94
3515 3894 7.334421 TGAAACTTAAAGCACATAAGAGCTAGG 59.666 37.037 9.35 0.00 40.96 3.02
3516 3895 8.171840 GTGAAACTTAAAGCACATAAGAGCTAG 58.828 37.037 9.35 0.00 40.96 3.42
3517 3896 7.659799 TGTGAAACTTAAAGCACATAAGAGCTA 59.340 33.333 9.35 0.00 38.12 3.32
3518 3897 6.486657 TGTGAAACTTAAAGCACATAAGAGCT 59.513 34.615 9.35 0.00 39.87 4.09
3655 4034 5.482878 TCCCTCCGTCCCAATAATATAAGAC 59.517 44.000 0.00 0.00 0.00 3.01
3661 4040 3.339713 ACTCCCTCCGTCCCAATAATA 57.660 47.619 0.00 0.00 0.00 0.98
3666 4045 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3702 4081 8.041323 AGAGTGTACCATTTACCTCACTTATTG 58.959 37.037 0.00 0.00 36.49 1.90
3753 4132 0.107703 TGGCCTGAACGATCATGGAC 60.108 55.000 3.32 11.11 34.37 4.02
3755 4134 1.335810 CAATGGCCTGAACGATCATGG 59.664 52.381 3.32 1.58 34.37 3.66
3782 4161 6.208840 AGGGAGTATTTAAGAACCCAACAA 57.791 37.500 0.00 0.00 39.73 2.83
3807 4186 5.333492 TACTTGCAACAAGTAATTCGGAACG 60.333 40.000 15.81 0.00 40.66 3.95
3810 4189 5.123186 CCATACTTGCAACAAGTAATTCGGA 59.877 40.000 20.49 2.49 36.45 4.55
3813 4192 7.538575 ACATCCATACTTGCAACAAGTAATTC 58.461 34.615 20.49 0.00 36.45 2.17
3816 4195 8.046708 AGATACATCCATACTTGCAACAAGTAA 58.953 33.333 20.49 8.15 36.45 2.24
3819 4198 6.932356 AGATACATCCATACTTGCAACAAG 57.068 37.500 5.80 5.80 0.00 3.16
3820 4199 7.791029 TCTAGATACATCCATACTTGCAACAA 58.209 34.615 0.00 0.00 0.00 2.83
3824 4203 7.544804 ACATCTAGATACATCCATACTTGCA 57.455 36.000 4.54 0.00 0.00 4.08
3851 4230 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
3853 4232 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3854 4233 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3855 4234 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
3856 4235 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
3858 4237 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
3861 4240 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
3863 4242 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
3864 4243 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
3865 4244 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
3866 4245 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
3867 4246 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
3868 4247 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
3869 4248 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
3870 4249 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3871 4250 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
3872 4251 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
3874 4253 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
3875 4254 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
3877 4256 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
3879 4258 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3880 4259 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3881 4260 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3882 4261 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3883 4262 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3884 4263 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
3885 4264 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
3886 4265 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
3887 4266 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
3888 4267 2.905415 TACTACTCCCTCCGTTCCAA 57.095 50.000 0.00 0.00 0.00 3.53
3889 4268 2.662866 CATACTACTCCCTCCGTTCCA 58.337 52.381 0.00 0.00 0.00 3.53
3890 4269 1.962100 CCATACTACTCCCTCCGTTCC 59.038 57.143 0.00 0.00 0.00 3.62
3891 4270 2.664015 ACCATACTACTCCCTCCGTTC 58.336 52.381 0.00 0.00 0.00 3.95
3892 4271 2.842645 ACCATACTACTCCCTCCGTT 57.157 50.000 0.00 0.00 0.00 4.44
3893 4272 2.842645 AACCATACTACTCCCTCCGT 57.157 50.000 0.00 0.00 0.00 4.69
3894 4273 2.557490 GCTAACCATACTACTCCCTCCG 59.443 54.545 0.00 0.00 0.00 4.63
3895 4274 3.321396 GTGCTAACCATACTACTCCCTCC 59.679 52.174 0.00 0.00 0.00 4.30
3896 4275 4.216708 AGTGCTAACCATACTACTCCCTC 58.783 47.826 0.00 0.00 0.00 4.30
3897 4276 4.267341 AGTGCTAACCATACTACTCCCT 57.733 45.455 0.00 0.00 0.00 4.20
3898 4277 4.202233 GGAAGTGCTAACCATACTACTCCC 60.202 50.000 0.00 0.00 0.00 4.30
3899 4278 4.650131 AGGAAGTGCTAACCATACTACTCC 59.350 45.833 0.00 0.00 0.00 3.85
3900 4279 5.855740 AGGAAGTGCTAACCATACTACTC 57.144 43.478 0.00 0.00 0.00 2.59
3901 4280 7.124052 TCTTAGGAAGTGCTAACCATACTACT 58.876 38.462 0.00 0.00 0.00 2.57
3905 4284 8.179509 TCTATCTTAGGAAGTGCTAACCATAC 57.820 38.462 0.00 0.00 0.00 2.39
3927 4306 2.912956 AGGGACATTTTGGTGAGCTCTA 59.087 45.455 16.19 0.00 0.00 2.43
3969 4348 3.290948 AGCTTGGTAAAGTCAACCACA 57.709 42.857 0.00 0.00 46.56 4.17


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

AutoCloner maintained by Alex Coulton.