Multiple sequence alignment - TraesCS2D01G502800

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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 TraesCS2D01G502800 chr2D 100.000 2585 0 0 1 2585 596268730 596266146 0.000000e+00 4774
1 TraesCS2D01G502800 chr2D 93.034 1895 110 10 447 2334 619798881 619797002 0.000000e+00 2748
2 TraesCS2D01G502800 chr2D 95.540 1390 47 4 1 1377 596306685 596305298 0.000000e+00 2209
3 TraesCS2D01G502800 chr1D 93.826 1895 100 7 447 2335 250223414 250225297 0.000000e+00 2835
4 TraesCS2D01G502800 chr1D 92.993 1898 107 13 447 2335 278102421 278100541 0.000000e+00 2745
5 TraesCS2D01G502800 chr1D 94.222 450 21 3 1 449 482140836 482141281 0.000000e+00 682
6 TraesCS2D01G502800 chr3D 92.884 1897 119 9 447 2334 45865515 45867404 0.000000e+00 2741
7 TraesCS2D01G502800 chr3D 95.067 446 20 2 3 448 490299424 490299867 0.000000e+00 701
8 TraesCS2D01G502800 chr3D 94.235 451 20 6 1 448 471480794 471481241 0.000000e+00 684
9 TraesCS2D01G502800 chr6B 92.563 1896 131 4 447 2334 508826789 508824896 0.000000e+00 2712
10 TraesCS2D01G502800 chr6B 91.715 1895 143 6 447 2335 107818228 107816342 0.000000e+00 2617
11 TraesCS2D01G502800 chr2B 92.198 1897 129 14 447 2332 42139654 42141542 0.000000e+00 2665
12 TraesCS2D01G502800 chr3B 91.355 1874 152 7 447 2317 202921322 202923188 0.000000e+00 2555
13 TraesCS2D01G502800 chr5B 90.986 1886 149 12 447 2326 615401429 615399559 0.000000e+00 2521
14 TraesCS2D01G502800 chr7D 95.089 448 21 1 1 448 532637516 532637962 0.000000e+00 704
15 TraesCS2D01G502800 chr7D 94.444 450 24 1 1 449 461951640 461952089 0.000000e+00 691
16 TraesCS2D01G502800 chr7D 93.973 448 24 3 1 447 521717273 521717718 0.000000e+00 675
17 TraesCS2D01G502800 chr6D 94.855 447 21 2 1 447 118473148 118473592 0.000000e+00 697
18 TraesCS2D01G502800 chr6D 94.407 447 23 2 1 447 329879383 329879827 0.000000e+00 686
19 TraesCS2D01G502800 chr5D 88.699 469 46 4 447 910 563696740 563697206 1.340000e-157 566
20 TraesCS2D01G502800 chr7B 86.902 397 43 6 447 837 35292611 35292218 1.100000e-118 436
21 TraesCS2D01G502800 chr4D 90.040 251 20 1 2340 2585 21755656 21755906 1.150000e-83 320
22 TraesCS2D01G502800 chr4B 88.845 251 21 4 2340 2585 32920179 32919931 4.180000e-78 302
23 TraesCS2D01G502800 chr4A 89.831 236 18 2 2340 2570 580714005 580714239 5.410000e-77 298


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 TraesCS2D01G502800 chr2D 596266146 596268730 2584 True 4774 4774 100.000 1 2585 1 chr2D.!!$R1 2584
1 TraesCS2D01G502800 chr2D 619797002 619798881 1879 True 2748 2748 93.034 447 2334 1 chr2D.!!$R3 1887
2 TraesCS2D01G502800 chr2D 596305298 596306685 1387 True 2209 2209 95.540 1 1377 1 chr2D.!!$R2 1376
3 TraesCS2D01G502800 chr1D 250223414 250225297 1883 False 2835 2835 93.826 447 2335 1 chr1D.!!$F1 1888
4 TraesCS2D01G502800 chr1D 278100541 278102421 1880 True 2745 2745 92.993 447 2335 1 chr1D.!!$R1 1888
5 TraesCS2D01G502800 chr3D 45865515 45867404 1889 False 2741 2741 92.884 447 2334 1 chr3D.!!$F1 1887
6 TraesCS2D01G502800 chr6B 508824896 508826789 1893 True 2712 2712 92.563 447 2334 1 chr6B.!!$R2 1887
7 TraesCS2D01G502800 chr6B 107816342 107818228 1886 True 2617 2617 91.715 447 2335 1 chr6B.!!$R1 1888
8 TraesCS2D01G502800 chr2B 42139654 42141542 1888 False 2665 2665 92.198 447 2332 1 chr2B.!!$F1 1885
9 TraesCS2D01G502800 chr3B 202921322 202923188 1866 False 2555 2555 91.355 447 2317 1 chr3B.!!$F1 1870
10 TraesCS2D01G502800 chr5B 615399559 615401429 1870 True 2521 2521 90.986 447 2326 1 chr5B.!!$R1 1879

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
532 534 0.036577 CAGAGCCTGGTTCACTGGAG 60.037 60.0 13.26 0.0 40.42 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 2575 0.042708 GCGCATCTACGTTGCATCAG 60.043 55.0 11.01 0.0 40.14 2.9 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
28 29 4.158015 CTCCCTCCTTTATATACGTGGGT 58.842 47.826 0.00 0.00 35.20 4.51
35 36 2.236489 TATATACGTGGGTAGGGGGC 57.764 55.000 0.00 0.00 30.81 5.80
99 101 1.056660 CCCTCCACAGTTACACACCT 58.943 55.000 0.00 0.00 0.00 4.00
110 112 3.066342 AGTTACACACCTCGGTCATATCG 59.934 47.826 0.00 0.00 0.00 2.92
159 161 2.858344 CGGTAACTTCATCATCACCGTC 59.142 50.000 2.91 0.00 42.93 4.79
164 166 0.739462 TTCATCATCACCGTCGCCAC 60.739 55.000 0.00 0.00 0.00 5.01
178 180 2.512286 CCACGCCGTCATGCTGAT 60.512 61.111 0.00 0.00 0.00 2.90
194 196 1.330655 TGATGGAACTCTCCCTCGGC 61.331 60.000 0.00 0.00 41.64 5.54
314 316 3.120060 AGACGTACGACTACATCAACCAC 60.120 47.826 24.41 0.00 0.00 4.16
404 406 5.166398 TGCATCACATAGATAGATCTTGCG 58.834 41.667 0.00 0.00 36.48 4.85
532 534 0.036577 CAGAGCCTGGTTCACTGGAG 60.037 60.000 13.26 0.00 40.42 3.86
622 625 4.176752 GGGCGAGGGGTGATGGTC 62.177 72.222 0.00 0.00 0.00 4.02
626 629 2.134287 CGAGGGGTGATGGTCGGAT 61.134 63.158 0.00 0.00 0.00 4.18
629 632 1.276421 GAGGGGTGATGGTCGGATATG 59.724 57.143 0.00 0.00 0.00 1.78
650 655 4.760047 AATCTGGCGCGCCGTTCT 62.760 61.111 41.73 25.29 39.42 3.01
715 722 0.696501 GCCACTTTCTTCCCTACCCA 59.303 55.000 0.00 0.00 0.00 4.51
842 864 1.098712 TTGTTGTTGGCCACCGTCTC 61.099 55.000 3.88 0.00 0.00 3.36
860 882 1.299850 CGTCGACCTTGTCTGTGCA 60.300 57.895 10.58 0.00 0.00 4.57
897 919 3.209812 CCTCGTCTCCGATGCCGA 61.210 66.667 0.00 0.00 43.27 5.54
1443 1466 3.828451 AGCTTAGAGGAGAGATGATCAGC 59.172 47.826 1.78 1.78 0.00 4.26
1550 1573 4.659111 TTTCATGGCTTGATATGCTTGG 57.341 40.909 3.72 0.00 33.34 3.61
1652 1675 0.173708 GCCAGAGTTCCTAGGTCACG 59.826 60.000 9.08 0.00 0.00 4.35
1659 1682 1.592400 TTCCTAGGTCACGGTCTGCG 61.592 60.000 9.08 0.00 0.00 5.18
1667 1691 2.167219 CACGGTCTGCGGCATACAG 61.167 63.158 18.46 16.70 36.44 2.74
1708 1732 2.093288 AGCTAGAATGTGCTTGCTGCTA 60.093 45.455 0.00 0.00 43.52 3.49
2334 2400 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
2335 2401 8.887036 AAGAAGAAGAAGAAGAAGAAGAAGAC 57.113 34.615 0.00 0.00 0.00 3.01
2336 2402 7.145323 AGAAGAAGAAGAAGAAGAAGAAGACG 58.855 38.462 0.00 0.00 0.00 4.18
2337 2403 5.227152 AGAAGAAGAAGAAGAAGAAGACGC 58.773 41.667 0.00 0.00 0.00 5.19
2338 2404 3.920446 AGAAGAAGAAGAAGAAGACGCC 58.080 45.455 0.00 0.00 0.00 5.68
2339 2405 2.753055 AGAAGAAGAAGAAGACGCCC 57.247 50.000 0.00 0.00 0.00 6.13
2340 2406 2.252714 AGAAGAAGAAGAAGACGCCCT 58.747 47.619 0.00 0.00 0.00 5.19
2341 2407 2.635427 AGAAGAAGAAGAAGACGCCCTT 59.365 45.455 0.00 0.00 37.93 3.95
2342 2408 3.833070 AGAAGAAGAAGAAGACGCCCTTA 59.167 43.478 0.00 0.00 34.68 2.69
2343 2409 3.596310 AGAAGAAGAAGACGCCCTTAC 57.404 47.619 0.00 0.00 34.68 2.34
2344 2410 3.166679 AGAAGAAGAAGACGCCCTTACT 58.833 45.455 0.00 0.00 34.68 2.24
2345 2411 3.056465 AGAAGAAGAAGACGCCCTTACTG 60.056 47.826 0.00 0.00 34.68 2.74
2346 2412 1.550976 AGAAGAAGACGCCCTTACTGG 59.449 52.381 0.00 0.00 34.68 4.00
2347 2413 1.549170 GAAGAAGACGCCCTTACTGGA 59.451 52.381 0.00 0.00 38.35 3.86
2348 2414 1.867363 AGAAGACGCCCTTACTGGAT 58.133 50.000 0.00 0.00 38.35 3.41
2349 2415 2.188817 AGAAGACGCCCTTACTGGATT 58.811 47.619 0.00 0.00 38.35 3.01
2350 2416 2.093447 AGAAGACGCCCTTACTGGATTG 60.093 50.000 0.00 0.00 38.35 2.67
2351 2417 0.541863 AGACGCCCTTACTGGATTGG 59.458 55.000 0.00 0.00 38.35 3.16
2352 2418 0.252197 GACGCCCTTACTGGATTGGT 59.748 55.000 0.00 0.00 38.35 3.67
2353 2419 1.483415 GACGCCCTTACTGGATTGGTA 59.517 52.381 0.00 0.00 38.35 3.25
2354 2420 1.910671 ACGCCCTTACTGGATTGGTAA 59.089 47.619 0.00 0.00 38.35 2.85
2355 2421 2.306512 ACGCCCTTACTGGATTGGTAAA 59.693 45.455 0.00 0.00 38.35 2.01
2356 2422 3.244981 ACGCCCTTACTGGATTGGTAAAA 60.245 43.478 0.00 0.00 38.35 1.52
2357 2423 3.128068 CGCCCTTACTGGATTGGTAAAAC 59.872 47.826 0.00 0.00 38.35 2.43
2358 2424 3.446161 GCCCTTACTGGATTGGTAAAACC 59.554 47.826 0.00 0.00 37.00 3.27
2359 2425 4.813133 GCCCTTACTGGATTGGTAAAACCT 60.813 45.833 0.00 0.00 37.27 3.50
2360 2426 5.574120 GCCCTTACTGGATTGGTAAAACCTA 60.574 44.000 0.00 0.00 37.27 3.08
2361 2427 6.120220 CCCTTACTGGATTGGTAAAACCTAG 58.880 44.000 0.00 0.00 37.27 3.02
2362 2428 6.069847 CCCTTACTGGATTGGTAAAACCTAGA 60.070 42.308 0.00 0.00 37.27 2.43
2363 2429 6.822170 CCTTACTGGATTGGTAAAACCTAGAC 59.178 42.308 0.00 0.00 37.27 2.59
2364 2430 4.828829 ACTGGATTGGTAAAACCTAGACG 58.171 43.478 0.00 0.00 39.58 4.18
2365 2431 4.529377 ACTGGATTGGTAAAACCTAGACGA 59.471 41.667 0.00 0.00 39.58 4.20
2366 2432 5.189145 ACTGGATTGGTAAAACCTAGACGAT 59.811 40.000 0.00 0.00 39.58 3.73
2367 2433 6.057321 TGGATTGGTAAAACCTAGACGATT 57.943 37.500 0.00 0.00 39.58 3.34
2368 2434 7.093201 ACTGGATTGGTAAAACCTAGACGATTA 60.093 37.037 0.00 0.00 39.58 1.75
2369 2435 7.270047 TGGATTGGTAAAACCTAGACGATTAG 58.730 38.462 0.00 0.00 39.58 1.73
2370 2436 7.124599 TGGATTGGTAAAACCTAGACGATTAGA 59.875 37.037 0.00 0.00 39.58 2.10
2371 2437 8.148999 GGATTGGTAAAACCTAGACGATTAGAT 58.851 37.037 0.00 0.00 39.58 1.98
2372 2438 9.543783 GATTGGTAAAACCTAGACGATTAGATT 57.456 33.333 0.00 0.00 39.58 2.40
2373 2439 9.901172 ATTGGTAAAACCTAGACGATTAGATTT 57.099 29.630 0.00 0.00 39.58 2.17
2374 2440 8.712285 TGGTAAAACCTAGACGATTAGATTTG 57.288 34.615 0.00 0.00 39.58 2.32
2375 2441 8.316214 TGGTAAAACCTAGACGATTAGATTTGT 58.684 33.333 0.00 0.00 39.58 2.83
2376 2442 9.159364 GGTAAAACCTAGACGATTAGATTTGTT 57.841 33.333 0.00 0.00 34.73 2.83
2377 2443 9.968743 GTAAAACCTAGACGATTAGATTTGTTG 57.031 33.333 0.00 0.00 0.00 3.33
2378 2444 6.663944 AACCTAGACGATTAGATTTGTTGC 57.336 37.500 0.00 0.00 0.00 4.17
2379 2445 5.730550 ACCTAGACGATTAGATTTGTTGCA 58.269 37.500 0.00 0.00 0.00 4.08
2380 2446 6.170506 ACCTAGACGATTAGATTTGTTGCAA 58.829 36.000 0.00 0.00 0.00 4.08
2381 2447 6.313905 ACCTAGACGATTAGATTTGTTGCAAG 59.686 38.462 0.00 0.00 0.00 4.01
2382 2448 6.313905 CCTAGACGATTAGATTTGTTGCAAGT 59.686 38.462 0.00 0.00 0.00 3.16
2383 2449 5.931532 AGACGATTAGATTTGTTGCAAGTG 58.068 37.500 0.00 0.00 0.00 3.16
2384 2450 5.470098 AGACGATTAGATTTGTTGCAAGTGT 59.530 36.000 0.00 0.00 0.00 3.55
2385 2451 6.017109 AGACGATTAGATTTGTTGCAAGTGTT 60.017 34.615 0.00 0.00 0.00 3.32
2386 2452 6.142817 ACGATTAGATTTGTTGCAAGTGTTC 58.857 36.000 0.00 0.00 0.00 3.18
2387 2453 5.569059 CGATTAGATTTGTTGCAAGTGTTCC 59.431 40.000 0.00 0.00 0.00 3.62
2388 2454 3.733443 AGATTTGTTGCAAGTGTTCCC 57.267 42.857 0.00 0.00 0.00 3.97
2389 2455 3.299503 AGATTTGTTGCAAGTGTTCCCT 58.700 40.909 0.00 0.00 0.00 4.20
2390 2456 2.957491 TTTGTTGCAAGTGTTCCCTG 57.043 45.000 0.00 0.00 0.00 4.45
2391 2457 1.846007 TTGTTGCAAGTGTTCCCTGT 58.154 45.000 0.00 0.00 0.00 4.00
2392 2458 1.846007 TGTTGCAAGTGTTCCCTGTT 58.154 45.000 0.00 0.00 0.00 3.16
2393 2459 3.006112 TGTTGCAAGTGTTCCCTGTTA 57.994 42.857 0.00 0.00 0.00 2.41
2394 2460 3.561143 TGTTGCAAGTGTTCCCTGTTAT 58.439 40.909 0.00 0.00 0.00 1.89
2395 2461 3.957497 TGTTGCAAGTGTTCCCTGTTATT 59.043 39.130 0.00 0.00 0.00 1.40
2396 2462 4.404073 TGTTGCAAGTGTTCCCTGTTATTT 59.596 37.500 0.00 0.00 0.00 1.40
2397 2463 5.594725 TGTTGCAAGTGTTCCCTGTTATTTA 59.405 36.000 0.00 0.00 0.00 1.40
2398 2464 5.957842 TGCAAGTGTTCCCTGTTATTTAG 57.042 39.130 0.00 0.00 0.00 1.85
2399 2465 5.626142 TGCAAGTGTTCCCTGTTATTTAGA 58.374 37.500 0.00 0.00 0.00 2.10
2400 2466 5.705441 TGCAAGTGTTCCCTGTTATTTAGAG 59.295 40.000 0.00 0.00 0.00 2.43
2401 2467 5.938125 GCAAGTGTTCCCTGTTATTTAGAGA 59.062 40.000 0.00 0.00 0.00 3.10
2402 2468 6.599638 GCAAGTGTTCCCTGTTATTTAGAGAT 59.400 38.462 0.00 0.00 0.00 2.75
2403 2469 7.769044 GCAAGTGTTCCCTGTTATTTAGAGATA 59.231 37.037 0.00 0.00 0.00 1.98
2404 2470 9.667107 CAAGTGTTCCCTGTTATTTAGAGATAA 57.333 33.333 0.00 0.00 0.00 1.75
2406 2472 9.668497 AGTGTTCCCTGTTATTTAGAGATAAAC 57.332 33.333 0.00 0.00 0.00 2.01
2407 2473 8.890718 GTGTTCCCTGTTATTTAGAGATAAACC 58.109 37.037 0.00 0.00 0.00 3.27
2408 2474 8.607713 TGTTCCCTGTTATTTAGAGATAAACCA 58.392 33.333 0.00 0.00 0.00 3.67
2409 2475 9.628500 GTTCCCTGTTATTTAGAGATAAACCAT 57.372 33.333 0.00 0.00 0.00 3.55
2410 2476 9.847224 TTCCCTGTTATTTAGAGATAAACCATC 57.153 33.333 0.00 0.00 0.00 3.51
2412 2478 9.853177 CCCTGTTATTTAGAGATAAACCATCTT 57.147 33.333 0.00 0.00 44.41 2.40
2433 2499 4.920640 TTTTTGCCGGTGAGATAAAACA 57.079 36.364 1.90 0.00 0.00 2.83
2434 2500 4.920640 TTTTGCCGGTGAGATAAAACAA 57.079 36.364 1.90 0.00 0.00 2.83
2435 2501 3.907894 TTGCCGGTGAGATAAAACAAC 57.092 42.857 1.90 0.00 0.00 3.32
2436 2502 3.134574 TGCCGGTGAGATAAAACAACT 57.865 42.857 1.90 0.00 0.00 3.16
2437 2503 3.071479 TGCCGGTGAGATAAAACAACTC 58.929 45.455 1.90 0.00 0.00 3.01
2438 2504 2.418976 GCCGGTGAGATAAAACAACTCC 59.581 50.000 1.90 0.00 0.00 3.85
2439 2505 2.671396 CCGGTGAGATAAAACAACTCCG 59.329 50.000 0.00 0.00 37.37 4.63
2440 2506 2.671396 CGGTGAGATAAAACAACTCCGG 59.329 50.000 0.00 0.00 35.14 5.14
2441 2507 3.671716 GGTGAGATAAAACAACTCCGGT 58.328 45.455 0.00 0.00 0.00 5.28
2442 2508 4.618927 CGGTGAGATAAAACAACTCCGGTA 60.619 45.833 0.00 0.00 35.14 4.02
2443 2509 5.240121 GGTGAGATAAAACAACTCCGGTAA 58.760 41.667 0.00 0.00 0.00 2.85
2444 2510 5.121298 GGTGAGATAAAACAACTCCGGTAAC 59.879 44.000 0.00 0.00 0.00 2.50
2445 2511 5.697633 GTGAGATAAAACAACTCCGGTAACA 59.302 40.000 0.00 0.00 0.00 2.41
2446 2512 6.370718 GTGAGATAAAACAACTCCGGTAACAT 59.629 38.462 0.00 0.00 0.00 2.71
2447 2513 7.546667 GTGAGATAAAACAACTCCGGTAACATA 59.453 37.037 0.00 0.00 0.00 2.29
2448 2514 8.095792 TGAGATAAAACAACTCCGGTAACATAA 58.904 33.333 0.00 0.00 0.00 1.90
2449 2515 8.851541 AGATAAAACAACTCCGGTAACATAAA 57.148 30.769 0.00 0.00 0.00 1.40
2450 2516 8.724229 AGATAAAACAACTCCGGTAACATAAAC 58.276 33.333 0.00 0.00 0.00 2.01
2451 2517 6.696441 AAAACAACTCCGGTAACATAAACA 57.304 33.333 0.00 0.00 0.00 2.83
2452 2518 5.934935 AACAACTCCGGTAACATAAACAG 57.065 39.130 0.00 0.00 0.00 3.16
2453 2519 3.749609 ACAACTCCGGTAACATAAACAGC 59.250 43.478 0.00 0.00 0.00 4.40
2454 2520 2.613691 ACTCCGGTAACATAAACAGCG 58.386 47.619 0.00 0.00 0.00 5.18
2455 2521 2.028748 ACTCCGGTAACATAAACAGCGT 60.029 45.455 0.00 0.00 0.00 5.07
2456 2522 3.193267 ACTCCGGTAACATAAACAGCGTA 59.807 43.478 0.00 0.00 0.00 4.42
2457 2523 4.142093 ACTCCGGTAACATAAACAGCGTAT 60.142 41.667 0.00 0.00 0.00 3.06
2458 2524 5.067674 ACTCCGGTAACATAAACAGCGTATA 59.932 40.000 0.00 0.00 0.00 1.47
2459 2525 5.280945 TCCGGTAACATAAACAGCGTATAC 58.719 41.667 0.00 0.00 0.00 1.47
2460 2526 4.445385 CCGGTAACATAAACAGCGTATACC 59.555 45.833 0.00 0.00 0.00 2.73
2461 2527 5.284079 CGGTAACATAAACAGCGTATACCT 58.716 41.667 0.00 0.00 31.52 3.08
2462 2528 6.437928 CGGTAACATAAACAGCGTATACCTA 58.562 40.000 0.00 0.00 31.52 3.08
2463 2529 7.086376 CGGTAACATAAACAGCGTATACCTAT 58.914 38.462 0.00 0.00 31.52 2.57
2464 2530 7.272084 CGGTAACATAAACAGCGTATACCTATC 59.728 40.741 0.00 0.00 31.52 2.08
2465 2531 8.302438 GGTAACATAAACAGCGTATACCTATCT 58.698 37.037 0.00 0.00 31.13 1.98
2468 2534 9.856488 AACATAAACAGCGTATACCTATCTATG 57.144 33.333 0.00 6.01 0.00 2.23
2469 2535 9.239551 ACATAAACAGCGTATACCTATCTATGA 57.760 33.333 0.00 0.00 0.00 2.15
2472 2538 7.762588 AACAGCGTATACCTATCTATGAAGT 57.237 36.000 0.00 0.00 0.00 3.01
2473 2539 7.147143 ACAGCGTATACCTATCTATGAAGTG 57.853 40.000 0.00 0.00 0.00 3.16
2474 2540 6.151312 ACAGCGTATACCTATCTATGAAGTGG 59.849 42.308 0.00 0.00 0.00 4.00
2475 2541 6.374613 CAGCGTATACCTATCTATGAAGTGGA 59.625 42.308 0.00 0.00 0.00 4.02
2476 2542 6.946583 AGCGTATACCTATCTATGAAGTGGAA 59.053 38.462 0.00 0.00 0.00 3.53
2477 2543 7.450634 AGCGTATACCTATCTATGAAGTGGAAA 59.549 37.037 0.00 0.00 0.00 3.13
2478 2544 7.541437 GCGTATACCTATCTATGAAGTGGAAAC 59.459 40.741 0.00 0.00 0.00 2.78
2479 2545 8.794553 CGTATACCTATCTATGAAGTGGAAACT 58.205 37.037 0.00 0.00 0.00 2.66
2480 2546 9.915629 GTATACCTATCTATGAAGTGGAAACTG 57.084 37.037 0.00 0.00 0.00 3.16
2481 2547 8.783660 ATACCTATCTATGAAGTGGAAACTGA 57.216 34.615 0.00 0.00 0.00 3.41
2482 2548 7.682787 ACCTATCTATGAAGTGGAAACTGAT 57.317 36.000 0.00 0.00 0.00 2.90
2483 2549 8.783660 ACCTATCTATGAAGTGGAAACTGATA 57.216 34.615 0.00 0.00 0.00 2.15
2484 2550 8.865090 ACCTATCTATGAAGTGGAAACTGATAG 58.135 37.037 0.00 0.00 33.98 2.08
2485 2551 8.310382 CCTATCTATGAAGTGGAAACTGATAGG 58.690 40.741 0.00 0.00 42.16 2.57
2486 2552 7.921041 ATCTATGAAGTGGAAACTGATAGGA 57.079 36.000 0.00 0.00 0.00 2.94
2487 2553 7.733773 TCTATGAAGTGGAAACTGATAGGAA 57.266 36.000 0.00 0.00 0.00 3.36
2488 2554 7.786030 TCTATGAAGTGGAAACTGATAGGAAG 58.214 38.462 0.00 0.00 0.00 3.46
2489 2555 4.579869 TGAAGTGGAAACTGATAGGAAGC 58.420 43.478 0.00 0.00 0.00 3.86
2490 2556 4.287067 TGAAGTGGAAACTGATAGGAAGCT 59.713 41.667 0.00 0.00 0.00 3.74
2491 2557 4.917906 AGTGGAAACTGATAGGAAGCTT 57.082 40.909 0.00 0.00 0.00 3.74
2492 2558 4.583871 AGTGGAAACTGATAGGAAGCTTG 58.416 43.478 2.10 0.00 0.00 4.01
2493 2559 4.287067 AGTGGAAACTGATAGGAAGCTTGA 59.713 41.667 2.10 0.00 0.00 3.02
2494 2560 4.633565 GTGGAAACTGATAGGAAGCTTGAG 59.366 45.833 2.10 0.00 0.00 3.02
2495 2561 4.287067 TGGAAACTGATAGGAAGCTTGAGT 59.713 41.667 2.10 0.00 0.00 3.41
2496 2562 4.873259 GGAAACTGATAGGAAGCTTGAGTC 59.127 45.833 2.10 0.00 0.00 3.36
2497 2563 4.479786 AACTGATAGGAAGCTTGAGTCC 57.520 45.455 2.10 0.00 0.00 3.85
2498 2564 2.769095 ACTGATAGGAAGCTTGAGTCCC 59.231 50.000 2.10 0.00 34.13 4.46
2499 2565 2.103941 CTGATAGGAAGCTTGAGTCCCC 59.896 54.545 2.10 0.00 34.13 4.81
2500 2566 2.293184 TGATAGGAAGCTTGAGTCCCCT 60.293 50.000 2.10 5.42 34.13 4.79
2501 2567 1.867363 TAGGAAGCTTGAGTCCCCTC 58.133 55.000 2.10 0.00 38.27 4.30
2502 2568 0.912006 AGGAAGCTTGAGTCCCCTCC 60.912 60.000 2.10 0.00 36.86 4.30
2503 2569 0.912006 GGAAGCTTGAGTCCCCTCCT 60.912 60.000 2.10 0.00 36.86 3.69
2504 2570 0.251634 GAAGCTTGAGTCCCCTCCTG 59.748 60.000 2.10 0.00 36.86 3.86
2505 2571 0.474660 AAGCTTGAGTCCCCTCCTGT 60.475 55.000 0.00 0.00 36.86 4.00
2506 2572 1.197430 AGCTTGAGTCCCCTCCTGTG 61.197 60.000 0.00 0.00 36.86 3.66
2507 2573 1.194781 GCTTGAGTCCCCTCCTGTGA 61.195 60.000 0.00 0.00 36.86 3.58
2508 2574 1.577736 CTTGAGTCCCCTCCTGTGAT 58.422 55.000 0.00 0.00 36.86 3.06
2509 2575 1.484240 CTTGAGTCCCCTCCTGTGATC 59.516 57.143 0.00 0.00 36.86 2.92
2510 2576 0.712979 TGAGTCCCCTCCTGTGATCT 59.287 55.000 0.00 0.00 36.86 2.75
2511 2577 1.118838 GAGTCCCCTCCTGTGATCTG 58.881 60.000 0.00 0.00 0.00 2.90
2512 2578 0.712979 AGTCCCCTCCTGTGATCTGA 59.287 55.000 0.00 0.00 0.00 3.27
2513 2579 1.293458 AGTCCCCTCCTGTGATCTGAT 59.707 52.381 0.00 0.00 0.00 2.90
2514 2580 1.415659 GTCCCCTCCTGTGATCTGATG 59.584 57.143 0.00 0.00 0.00 3.07
2515 2581 0.108207 CCCCTCCTGTGATCTGATGC 59.892 60.000 0.00 0.00 0.00 3.91
2516 2582 0.835276 CCCTCCTGTGATCTGATGCA 59.165 55.000 0.00 0.00 0.00 3.96
2517 2583 1.211212 CCCTCCTGTGATCTGATGCAA 59.789 52.381 0.00 0.00 0.00 4.08
2518 2584 2.286872 CCTCCTGTGATCTGATGCAAC 58.713 52.381 0.00 0.00 0.00 4.17
2519 2585 1.931841 CTCCTGTGATCTGATGCAACG 59.068 52.381 0.00 0.00 0.00 4.10
2520 2586 1.276138 TCCTGTGATCTGATGCAACGT 59.724 47.619 0.00 0.00 0.00 3.99
2521 2587 2.495669 TCCTGTGATCTGATGCAACGTA 59.504 45.455 0.00 0.00 0.00 3.57
2522 2588 2.862536 CCTGTGATCTGATGCAACGTAG 59.137 50.000 0.00 0.00 0.00 3.51
2523 2589 3.429410 CCTGTGATCTGATGCAACGTAGA 60.429 47.826 0.00 0.00 0.00 2.59
2524 2590 4.366586 CTGTGATCTGATGCAACGTAGAT 58.633 43.478 0.00 0.00 32.87 1.98
2525 2591 4.114794 TGTGATCTGATGCAACGTAGATG 58.885 43.478 1.08 0.00 30.49 2.90
2532 2598 3.299585 CAACGTAGATGCGCCTCG 58.700 61.111 4.18 5.08 34.88 4.63
2533 2599 1.226575 CAACGTAGATGCGCCTCGA 60.227 57.895 4.18 0.00 34.88 4.04
2534 2600 0.800683 CAACGTAGATGCGCCTCGAA 60.801 55.000 4.18 0.00 34.88 3.71
2535 2601 0.525668 AACGTAGATGCGCCTCGAAG 60.526 55.000 4.18 6.03 34.88 3.79
2536 2602 1.355563 CGTAGATGCGCCTCGAAGA 59.644 57.895 4.18 0.00 0.00 2.87
2537 2603 0.248498 CGTAGATGCGCCTCGAAGAA 60.248 55.000 4.18 0.00 34.09 2.52
2538 2604 1.482278 GTAGATGCGCCTCGAAGAAG 58.518 55.000 4.18 0.00 34.09 2.85
2539 2605 1.065701 GTAGATGCGCCTCGAAGAAGA 59.934 52.381 4.18 0.00 34.09 2.87
2540 2606 0.532573 AGATGCGCCTCGAAGAAGAA 59.467 50.000 4.18 0.00 34.09 2.52
2541 2607 1.066858 AGATGCGCCTCGAAGAAGAAA 60.067 47.619 4.18 0.00 34.09 2.52
2542 2608 1.325943 GATGCGCCTCGAAGAAGAAAG 59.674 52.381 4.18 0.00 34.09 2.62
2543 2609 0.670546 TGCGCCTCGAAGAAGAAAGG 60.671 55.000 4.18 0.00 34.09 3.11
2544 2610 0.670854 GCGCCTCGAAGAAGAAAGGT 60.671 55.000 0.00 0.00 34.09 3.50
2545 2611 1.403780 GCGCCTCGAAGAAGAAAGGTA 60.404 52.381 0.00 0.00 34.09 3.08
2546 2612 2.531206 CGCCTCGAAGAAGAAAGGTAG 58.469 52.381 0.00 0.00 34.09 3.18
2547 2613 2.163815 CGCCTCGAAGAAGAAAGGTAGA 59.836 50.000 0.00 0.00 34.09 2.59
2548 2614 3.181485 CGCCTCGAAGAAGAAAGGTAGAT 60.181 47.826 0.00 0.00 34.09 1.98
2549 2615 4.116238 GCCTCGAAGAAGAAAGGTAGATG 58.884 47.826 0.00 0.00 34.09 2.90
2550 2616 4.142138 GCCTCGAAGAAGAAAGGTAGATGA 60.142 45.833 0.00 0.00 34.09 2.92
2551 2617 5.624738 GCCTCGAAGAAGAAAGGTAGATGAA 60.625 44.000 0.00 0.00 34.09 2.57
2552 2618 6.398918 CCTCGAAGAAGAAAGGTAGATGAAA 58.601 40.000 0.00 0.00 34.09 2.69
2553 2619 6.533367 CCTCGAAGAAGAAAGGTAGATGAAAG 59.467 42.308 0.00 0.00 34.09 2.62
2554 2620 6.994221 TCGAAGAAGAAAGGTAGATGAAAGT 58.006 36.000 0.00 0.00 0.00 2.66
2555 2621 6.868864 TCGAAGAAGAAAGGTAGATGAAAGTG 59.131 38.462 0.00 0.00 0.00 3.16
2556 2622 6.868864 CGAAGAAGAAAGGTAGATGAAAGTGA 59.131 38.462 0.00 0.00 0.00 3.41
2557 2623 7.062839 CGAAGAAGAAAGGTAGATGAAAGTGAG 59.937 40.741 0.00 0.00 0.00 3.51
2558 2624 7.546250 AGAAGAAAGGTAGATGAAAGTGAGA 57.454 36.000 0.00 0.00 0.00 3.27
2559 2625 7.967908 AGAAGAAAGGTAGATGAAAGTGAGAA 58.032 34.615 0.00 0.00 0.00 2.87
2560 2626 8.093927 AGAAGAAAGGTAGATGAAAGTGAGAAG 58.906 37.037 0.00 0.00 0.00 2.85
2561 2627 7.546250 AGAAAGGTAGATGAAAGTGAGAAGA 57.454 36.000 0.00 0.00 0.00 2.87
2562 2628 7.967908 AGAAAGGTAGATGAAAGTGAGAAGAA 58.032 34.615 0.00 0.00 0.00 2.52
2563 2629 8.093927 AGAAAGGTAGATGAAAGTGAGAAGAAG 58.906 37.037 0.00 0.00 0.00 2.85
2564 2630 5.729510 AGGTAGATGAAAGTGAGAAGAAGC 58.270 41.667 0.00 0.00 0.00 3.86
2565 2631 4.873259 GGTAGATGAAAGTGAGAAGAAGCC 59.127 45.833 0.00 0.00 0.00 4.35
2566 2632 4.630644 AGATGAAAGTGAGAAGAAGCCA 57.369 40.909 0.00 0.00 0.00 4.75
2567 2633 4.577875 AGATGAAAGTGAGAAGAAGCCAG 58.422 43.478 0.00 0.00 0.00 4.85
2568 2634 4.285517 AGATGAAAGTGAGAAGAAGCCAGA 59.714 41.667 0.00 0.00 0.00 3.86
2569 2635 4.000331 TGAAAGTGAGAAGAAGCCAGAG 58.000 45.455 0.00 0.00 0.00 3.35
2570 2636 3.244353 TGAAAGTGAGAAGAAGCCAGAGG 60.244 47.826 0.00 0.00 0.00 3.69
2581 2647 4.651867 CCAGAGGCATTGGGACTG 57.348 61.111 0.00 0.00 31.94 3.51
2582 2648 1.993653 CCAGAGGCATTGGGACTGA 59.006 57.895 0.00 0.00 31.94 3.41
2583 2649 0.549950 CCAGAGGCATTGGGACTGAT 59.450 55.000 0.00 0.00 31.94 2.90
2584 2650 1.770658 CCAGAGGCATTGGGACTGATA 59.229 52.381 0.00 0.00 31.94 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.152567 TTGGAGTGCCTTTGGGGTG 60.153 57.895 0.00 0.00 37.43 4.61
75 76 0.844661 TGTAACTGTGGAGGGGGCAT 60.845 55.000 0.00 0.00 0.00 4.40
99 101 1.262417 GCACTACGACGATATGACCGA 59.738 52.381 0.00 0.00 0.00 4.69
110 112 1.546834 CTTCGCCTAAGCACTACGAC 58.453 55.000 0.00 0.00 39.83 4.34
178 180 2.683933 GGCCGAGGGAGAGTTCCA 60.684 66.667 0.00 0.00 45.98 3.53
194 196 3.444034 TCGTACTCTTGATCCAGTTGAGG 59.556 47.826 0.00 0.00 0.00 3.86
222 224 0.710567 CACACGTTCAGCTCGATGAC 59.289 55.000 0.00 0.00 0.00 3.06
314 316 3.806316 AGCGGAAGTGTTTTATCAACG 57.194 42.857 0.00 0.00 0.00 4.10
463 465 1.688197 CCAACAGTGAAACCAGGCAAT 59.312 47.619 0.00 0.00 37.80 3.56
532 534 3.701604 AACTGCCGATCCGAGCGTC 62.702 63.158 5.19 0.00 0.00 5.19
622 625 1.442769 CGCCAGATTTCCCATATCCG 58.557 55.000 0.00 0.00 0.00 4.18
626 629 1.891919 GCGCGCCAGATTTCCCATA 60.892 57.895 23.24 0.00 0.00 2.74
650 655 1.119684 TGAGGCTAGATTTGGCGCTA 58.880 50.000 7.64 0.00 35.01 4.26
715 722 1.909986 GAGGCAGTAGGGAAGAAAGGT 59.090 52.381 0.00 0.00 0.00 3.50
842 864 0.874175 TTGCACAGACAAGGTCGACG 60.874 55.000 9.92 0.00 37.67 5.12
897 919 1.615262 GGAAGGGGGTGCTGCTTAT 59.385 57.895 0.00 0.00 0.00 1.73
1049 1071 0.949397 CATGACCCATGCCTGAATCG 59.051 55.000 0.00 0.00 35.02 3.34
1114 1136 3.537580 GGATAAACATTGGACCGTAGCA 58.462 45.455 0.00 0.00 0.00 3.49
1443 1466 0.177604 GAGTCTGGCCAGATGGTCTG 59.822 60.000 37.07 8.51 43.91 3.51
1550 1573 5.909610 GTGTTAGTGCTCAACTTGAACAATC 59.090 40.000 0.00 0.00 38.48 2.67
1652 1675 2.203070 CCCTGTATGCCGCAGACC 60.203 66.667 15.28 0.00 36.12 3.85
1659 1682 1.839894 CTTCCTCCCCCTGTATGCC 59.160 63.158 0.00 0.00 0.00 4.40
1667 1691 1.198759 TGTGTAGTGCTTCCTCCCCC 61.199 60.000 0.00 0.00 0.00 5.40
1708 1732 7.756395 ATGTGAACTTCAGATCAAAGTCAAT 57.244 32.000 12.34 0.26 35.96 2.57
2158 2184 0.466189 CCATGGCCGGAGCTAACAAT 60.466 55.000 5.05 0.00 39.73 2.71
2334 2400 1.575419 TACCAATCCAGTAAGGGCGT 58.425 50.000 0.00 0.00 38.24 5.68
2335 2401 2.702592 TTACCAATCCAGTAAGGGCG 57.297 50.000 0.00 0.00 38.24 6.13
2336 2402 3.446161 GGTTTTACCAATCCAGTAAGGGC 59.554 47.826 0.00 0.00 38.42 5.19
2337 2403 4.930696 AGGTTTTACCAATCCAGTAAGGG 58.069 43.478 0.00 0.00 41.95 3.95
2338 2404 6.822170 GTCTAGGTTTTACCAATCCAGTAAGG 59.178 42.308 0.00 0.00 41.95 2.69
2339 2405 6.534079 CGTCTAGGTTTTACCAATCCAGTAAG 59.466 42.308 0.00 0.00 41.95 2.34
2340 2406 6.211184 TCGTCTAGGTTTTACCAATCCAGTAA 59.789 38.462 0.00 0.00 41.95 2.24
2341 2407 5.716228 TCGTCTAGGTTTTACCAATCCAGTA 59.284 40.000 0.00 0.00 41.95 2.74
2342 2408 4.529377 TCGTCTAGGTTTTACCAATCCAGT 59.471 41.667 0.00 0.00 41.95 4.00
2343 2409 5.080969 TCGTCTAGGTTTTACCAATCCAG 57.919 43.478 0.00 0.00 41.95 3.86
2344 2410 5.687166 ATCGTCTAGGTTTTACCAATCCA 57.313 39.130 0.00 0.00 41.95 3.41
2345 2411 7.495055 TCTAATCGTCTAGGTTTTACCAATCC 58.505 38.462 0.00 0.00 41.95 3.01
2346 2412 9.543783 AATCTAATCGTCTAGGTTTTACCAATC 57.456 33.333 0.00 0.00 41.95 2.67
2347 2413 9.901172 AAATCTAATCGTCTAGGTTTTACCAAT 57.099 29.630 0.00 0.00 41.95 3.16
2348 2414 9.158233 CAAATCTAATCGTCTAGGTTTTACCAA 57.842 33.333 0.00 0.00 41.95 3.67
2349 2415 8.316214 ACAAATCTAATCGTCTAGGTTTTACCA 58.684 33.333 0.00 0.00 41.95 3.25
2350 2416 8.713737 ACAAATCTAATCGTCTAGGTTTTACC 57.286 34.615 3.12 0.00 38.99 2.85
2351 2417 9.968743 CAACAAATCTAATCGTCTAGGTTTTAC 57.031 33.333 3.12 0.00 31.23 2.01
2352 2418 8.662141 GCAACAAATCTAATCGTCTAGGTTTTA 58.338 33.333 3.12 0.00 31.23 1.52
2353 2419 7.174253 TGCAACAAATCTAATCGTCTAGGTTTT 59.826 33.333 3.12 0.00 31.23 2.43
2354 2420 6.653320 TGCAACAAATCTAATCGTCTAGGTTT 59.347 34.615 0.00 0.72 33.39 3.27
2355 2421 6.170506 TGCAACAAATCTAATCGTCTAGGTT 58.829 36.000 0.00 0.00 0.00 3.50
2356 2422 5.730550 TGCAACAAATCTAATCGTCTAGGT 58.269 37.500 0.00 0.00 0.00 3.08
2357 2423 6.313905 ACTTGCAACAAATCTAATCGTCTAGG 59.686 38.462 0.00 0.00 0.00 3.02
2358 2424 7.148573 ACACTTGCAACAAATCTAATCGTCTAG 60.149 37.037 0.00 0.00 0.00 2.43
2359 2425 6.649141 ACACTTGCAACAAATCTAATCGTCTA 59.351 34.615 0.00 0.00 0.00 2.59
2360 2426 5.470098 ACACTTGCAACAAATCTAATCGTCT 59.530 36.000 0.00 0.00 0.00 4.18
2361 2427 5.689819 ACACTTGCAACAAATCTAATCGTC 58.310 37.500 0.00 0.00 0.00 4.20
2362 2428 5.689383 ACACTTGCAACAAATCTAATCGT 57.311 34.783 0.00 0.00 0.00 3.73
2363 2429 5.569059 GGAACACTTGCAACAAATCTAATCG 59.431 40.000 0.00 0.00 0.00 3.34
2364 2430 5.863935 GGGAACACTTGCAACAAATCTAATC 59.136 40.000 0.00 0.00 0.00 1.75
2365 2431 5.539955 AGGGAACACTTGCAACAAATCTAAT 59.460 36.000 0.00 0.00 0.00 1.73
2366 2432 4.892934 AGGGAACACTTGCAACAAATCTAA 59.107 37.500 0.00 0.00 0.00 2.10
2367 2433 4.278170 CAGGGAACACTTGCAACAAATCTA 59.722 41.667 0.00 0.00 0.00 1.98
2368 2434 3.068590 CAGGGAACACTTGCAACAAATCT 59.931 43.478 0.00 0.00 0.00 2.40
2369 2435 3.181476 ACAGGGAACACTTGCAACAAATC 60.181 43.478 0.00 0.00 0.00 2.17
2370 2436 2.765699 ACAGGGAACACTTGCAACAAAT 59.234 40.909 0.00 0.00 0.00 2.32
2371 2437 2.175202 ACAGGGAACACTTGCAACAAA 58.825 42.857 0.00 0.00 0.00 2.83
2372 2438 1.846007 ACAGGGAACACTTGCAACAA 58.154 45.000 0.00 0.00 0.00 2.83
2373 2439 1.846007 AACAGGGAACACTTGCAACA 58.154 45.000 0.00 0.00 0.00 3.33
2374 2440 4.584327 AATAACAGGGAACACTTGCAAC 57.416 40.909 0.00 0.00 0.00 4.17
2375 2441 6.065374 TCTAAATAACAGGGAACACTTGCAA 58.935 36.000 0.00 0.00 0.00 4.08
2376 2442 5.626142 TCTAAATAACAGGGAACACTTGCA 58.374 37.500 0.00 0.00 0.00 4.08
2377 2443 5.938125 TCTCTAAATAACAGGGAACACTTGC 59.062 40.000 0.00 0.00 0.00 4.01
2378 2444 9.667107 TTATCTCTAAATAACAGGGAACACTTG 57.333 33.333 0.00 0.00 0.00 3.16
2380 2446 9.668497 GTTTATCTCTAAATAACAGGGAACACT 57.332 33.333 0.00 0.00 0.00 3.55
2381 2447 8.890718 GGTTTATCTCTAAATAACAGGGAACAC 58.109 37.037 0.00 0.00 0.00 3.32
2382 2448 8.607713 TGGTTTATCTCTAAATAACAGGGAACA 58.392 33.333 0.00 0.00 0.00 3.18
2383 2449 9.628500 ATGGTTTATCTCTAAATAACAGGGAAC 57.372 33.333 0.00 0.00 0.00 3.62
2384 2450 9.847224 GATGGTTTATCTCTAAATAACAGGGAA 57.153 33.333 0.00 0.00 32.83 3.97
2385 2451 9.225682 AGATGGTTTATCTCTAAATAACAGGGA 57.774 33.333 0.00 0.00 42.54 4.20
2386 2452 9.853177 AAGATGGTTTATCTCTAAATAACAGGG 57.147 33.333 0.00 0.00 45.41 4.45
2412 2478 4.920640 TGTTTTATCTCACCGGCAAAAA 57.079 36.364 0.00 0.00 0.00 1.94
2413 2479 4.339814 AGTTGTTTTATCTCACCGGCAAAA 59.660 37.500 0.00 0.00 0.00 2.44
2414 2480 3.886505 AGTTGTTTTATCTCACCGGCAAA 59.113 39.130 0.00 0.00 0.00 3.68
2415 2481 3.482436 AGTTGTTTTATCTCACCGGCAA 58.518 40.909 0.00 0.00 0.00 4.52
2416 2482 3.071479 GAGTTGTTTTATCTCACCGGCA 58.929 45.455 0.00 0.00 0.00 5.69
2417 2483 2.418976 GGAGTTGTTTTATCTCACCGGC 59.581 50.000 0.00 0.00 0.00 6.13
2418 2484 2.671396 CGGAGTTGTTTTATCTCACCGG 59.329 50.000 0.00 0.00 35.24 5.28
2419 2485 2.671396 CCGGAGTTGTTTTATCTCACCG 59.329 50.000 0.00 0.00 37.98 4.94
2420 2486 3.671716 ACCGGAGTTGTTTTATCTCACC 58.328 45.455 9.46 0.00 0.00 4.02
2421 2487 5.697633 TGTTACCGGAGTTGTTTTATCTCAC 59.302 40.000 9.46 0.00 0.00 3.51
2422 2488 5.856156 TGTTACCGGAGTTGTTTTATCTCA 58.144 37.500 9.46 0.00 0.00 3.27
2423 2489 6.980051 ATGTTACCGGAGTTGTTTTATCTC 57.020 37.500 9.46 0.00 0.00 2.75
2424 2490 8.724229 GTTTATGTTACCGGAGTTGTTTTATCT 58.276 33.333 9.46 0.00 0.00 1.98
2425 2491 8.505625 TGTTTATGTTACCGGAGTTGTTTTATC 58.494 33.333 9.46 0.00 0.00 1.75
2426 2492 8.393671 TGTTTATGTTACCGGAGTTGTTTTAT 57.606 30.769 9.46 0.00 0.00 1.40
2427 2493 7.520292 GCTGTTTATGTTACCGGAGTTGTTTTA 60.520 37.037 9.46 0.00 0.00 1.52
2428 2494 6.696441 TGTTTATGTTACCGGAGTTGTTTT 57.304 33.333 9.46 0.00 0.00 2.43
2429 2495 5.278120 GCTGTTTATGTTACCGGAGTTGTTT 60.278 40.000 9.46 0.00 0.00 2.83
2430 2496 4.214758 GCTGTTTATGTTACCGGAGTTGTT 59.785 41.667 9.46 0.00 0.00 2.83
2431 2497 3.749609 GCTGTTTATGTTACCGGAGTTGT 59.250 43.478 9.46 0.00 0.00 3.32
2432 2498 3.181524 CGCTGTTTATGTTACCGGAGTTG 60.182 47.826 9.46 0.00 0.00 3.16
2433 2499 2.997986 CGCTGTTTATGTTACCGGAGTT 59.002 45.455 9.46 0.00 0.00 3.01
2434 2500 2.028748 ACGCTGTTTATGTTACCGGAGT 60.029 45.455 9.46 0.00 0.00 3.85
2435 2501 2.613691 ACGCTGTTTATGTTACCGGAG 58.386 47.619 9.46 0.00 0.00 4.63
2436 2502 2.747396 ACGCTGTTTATGTTACCGGA 57.253 45.000 9.46 0.00 0.00 5.14
2437 2503 4.445385 GGTATACGCTGTTTATGTTACCGG 59.555 45.833 0.00 0.00 0.00 5.28
2438 2504 5.284079 AGGTATACGCTGTTTATGTTACCG 58.716 41.667 0.00 0.00 34.43 4.02
2439 2505 8.302438 AGATAGGTATACGCTGTTTATGTTACC 58.698 37.037 0.00 0.00 0.00 2.85
2442 2508 9.856488 CATAGATAGGTATACGCTGTTTATGTT 57.144 33.333 13.83 0.00 0.00 2.71
2443 2509 9.239551 TCATAGATAGGTATACGCTGTTTATGT 57.760 33.333 17.50 5.57 0.00 2.29
2446 2512 9.293404 ACTTCATAGATAGGTATACGCTGTTTA 57.707 33.333 0.00 0.00 0.00 2.01
2447 2513 8.082852 CACTTCATAGATAGGTATACGCTGTTT 58.917 37.037 0.00 0.00 0.00 2.83
2448 2514 7.309255 CCACTTCATAGATAGGTATACGCTGTT 60.309 40.741 0.00 0.00 0.00 3.16
2449 2515 6.151312 CCACTTCATAGATAGGTATACGCTGT 59.849 42.308 0.00 0.00 0.00 4.40
2450 2516 6.374613 TCCACTTCATAGATAGGTATACGCTG 59.625 42.308 0.00 0.00 0.00 5.18
2451 2517 6.482524 TCCACTTCATAGATAGGTATACGCT 58.517 40.000 0.00 0.00 0.00 5.07
2452 2518 6.754702 TCCACTTCATAGATAGGTATACGC 57.245 41.667 0.00 0.00 0.00 4.42
2453 2519 8.794553 AGTTTCCACTTCATAGATAGGTATACG 58.205 37.037 0.00 0.00 0.00 3.06
2454 2520 9.915629 CAGTTTCCACTTCATAGATAGGTATAC 57.084 37.037 0.00 0.00 0.00 1.47
2455 2521 9.877222 TCAGTTTCCACTTCATAGATAGGTATA 57.123 33.333 0.00 0.00 0.00 1.47
2456 2522 8.783660 TCAGTTTCCACTTCATAGATAGGTAT 57.216 34.615 0.00 0.00 0.00 2.73
2457 2523 8.783660 ATCAGTTTCCACTTCATAGATAGGTA 57.216 34.615 0.00 0.00 0.00 3.08
2458 2524 7.682787 ATCAGTTTCCACTTCATAGATAGGT 57.317 36.000 0.00 0.00 0.00 3.08
2459 2525 8.310382 CCTATCAGTTTCCACTTCATAGATAGG 58.690 40.741 0.00 0.00 40.90 2.57
2460 2526 9.083422 TCCTATCAGTTTCCACTTCATAGATAG 57.917 37.037 0.00 0.00 34.09 2.08
2461 2527 9.434275 TTCCTATCAGTTTCCACTTCATAGATA 57.566 33.333 0.00 0.00 0.00 1.98
2462 2528 7.921041 TCCTATCAGTTTCCACTTCATAGAT 57.079 36.000 0.00 0.00 0.00 1.98
2463 2529 7.633772 GCTTCCTATCAGTTTCCACTTCATAGA 60.634 40.741 0.00 0.00 0.00 1.98
2464 2530 6.481644 GCTTCCTATCAGTTTCCACTTCATAG 59.518 42.308 0.00 0.00 0.00 2.23
2465 2531 6.156949 AGCTTCCTATCAGTTTCCACTTCATA 59.843 38.462 0.00 0.00 0.00 2.15
2466 2532 5.045286 AGCTTCCTATCAGTTTCCACTTCAT 60.045 40.000 0.00 0.00 0.00 2.57
2467 2533 4.287067 AGCTTCCTATCAGTTTCCACTTCA 59.713 41.667 0.00 0.00 0.00 3.02
2468 2534 4.837972 AGCTTCCTATCAGTTTCCACTTC 58.162 43.478 0.00 0.00 0.00 3.01
2469 2535 4.917906 AGCTTCCTATCAGTTTCCACTT 57.082 40.909 0.00 0.00 0.00 3.16
2470 2536 4.287067 TCAAGCTTCCTATCAGTTTCCACT 59.713 41.667 0.00 0.00 0.00 4.00
2471 2537 4.579869 TCAAGCTTCCTATCAGTTTCCAC 58.420 43.478 0.00 0.00 0.00 4.02
2472 2538 4.287067 ACTCAAGCTTCCTATCAGTTTCCA 59.713 41.667 0.00 0.00 0.00 3.53
2473 2539 4.837972 ACTCAAGCTTCCTATCAGTTTCC 58.162 43.478 0.00 0.00 0.00 3.13
2474 2540 4.873259 GGACTCAAGCTTCCTATCAGTTTC 59.127 45.833 0.00 0.00 0.00 2.78
2475 2541 4.323868 GGGACTCAAGCTTCCTATCAGTTT 60.324 45.833 0.00 0.00 31.90 2.66
2476 2542 3.198853 GGGACTCAAGCTTCCTATCAGTT 59.801 47.826 0.00 0.00 31.90 3.16
2477 2543 2.769095 GGGACTCAAGCTTCCTATCAGT 59.231 50.000 0.00 0.00 31.90 3.41
2478 2544 2.103941 GGGGACTCAAGCTTCCTATCAG 59.896 54.545 0.00 0.00 31.90 2.90
2479 2545 2.119495 GGGGACTCAAGCTTCCTATCA 58.881 52.381 0.00 0.00 31.90 2.15
2480 2546 2.403561 AGGGGACTCAAGCTTCCTATC 58.596 52.381 0.00 0.00 32.90 2.08
2481 2547 2.577772 AGGGGACTCAAGCTTCCTAT 57.422 50.000 0.00 0.00 32.90 2.57
2494 2560 1.415659 CATCAGATCACAGGAGGGGAC 59.584 57.143 0.00 0.00 0.00 4.46
2495 2561 1.798626 CATCAGATCACAGGAGGGGA 58.201 55.000 0.00 0.00 0.00 4.81
2496 2562 0.108207 GCATCAGATCACAGGAGGGG 59.892 60.000 0.00 0.00 0.00 4.79
2497 2563 0.835276 TGCATCAGATCACAGGAGGG 59.165 55.000 0.00 0.00 0.00 4.30
2498 2564 2.286872 GTTGCATCAGATCACAGGAGG 58.713 52.381 0.00 0.00 0.00 4.30
2499 2565 1.931841 CGTTGCATCAGATCACAGGAG 59.068 52.381 0.00 0.00 0.00 3.69
2500 2566 1.276138 ACGTTGCATCAGATCACAGGA 59.724 47.619 0.00 0.00 0.00 3.86
2501 2567 1.730501 ACGTTGCATCAGATCACAGG 58.269 50.000 0.00 0.00 0.00 4.00
2502 2568 3.774066 TCTACGTTGCATCAGATCACAG 58.226 45.455 0.00 0.00 0.00 3.66
2503 2569 3.866883 TCTACGTTGCATCAGATCACA 57.133 42.857 0.00 0.00 0.00 3.58
2504 2570 3.060003 GCATCTACGTTGCATCAGATCAC 60.060 47.826 5.84 0.00 39.90 3.06
2505 2571 3.126073 GCATCTACGTTGCATCAGATCA 58.874 45.455 5.84 0.00 39.90 2.92
2506 2572 2.154580 CGCATCTACGTTGCATCAGATC 59.845 50.000 11.01 0.00 40.14 2.75
2507 2573 2.130395 CGCATCTACGTTGCATCAGAT 58.870 47.619 11.01 1.21 40.14 2.90
2508 2574 1.559831 CGCATCTACGTTGCATCAGA 58.440 50.000 11.01 0.00 40.14 3.27
2509 2575 0.042708 GCGCATCTACGTTGCATCAG 60.043 55.000 11.01 0.00 40.14 2.90
2510 2576 1.428370 GGCGCATCTACGTTGCATCA 61.428 55.000 10.83 0.00 40.14 3.07
2511 2577 1.154205 AGGCGCATCTACGTTGCATC 61.154 55.000 10.83 2.58 40.14 3.91
2512 2578 1.153369 AGGCGCATCTACGTTGCAT 60.153 52.632 10.83 0.00 40.14 3.96
2513 2579 1.809619 GAGGCGCATCTACGTTGCA 60.810 57.895 16.00 0.00 40.14 4.08
2514 2580 2.860628 CGAGGCGCATCTACGTTGC 61.861 63.158 20.86 0.00 36.74 4.17
2515 2581 0.800683 TTCGAGGCGCATCTACGTTG 60.801 55.000 20.86 3.12 34.88 4.10
2516 2582 0.525668 CTTCGAGGCGCATCTACGTT 60.526 55.000 20.86 0.00 34.88 3.99
2517 2583 1.064296 CTTCGAGGCGCATCTACGT 59.936 57.895 20.86 0.00 34.88 3.57
2518 2584 0.248498 TTCTTCGAGGCGCATCTACG 60.248 55.000 20.86 7.97 0.00 3.51
2519 2585 1.065701 TCTTCTTCGAGGCGCATCTAC 59.934 52.381 20.86 0.00 0.00 2.59
2520 2586 1.389555 TCTTCTTCGAGGCGCATCTA 58.610 50.000 20.86 6.29 0.00 1.98
2521 2587 0.532573 TTCTTCTTCGAGGCGCATCT 59.467 50.000 20.86 2.60 0.00 2.90
2522 2588 1.325943 CTTTCTTCTTCGAGGCGCATC 59.674 52.381 12.96 12.96 0.00 3.91
2523 2589 1.363744 CTTTCTTCTTCGAGGCGCAT 58.636 50.000 10.83 0.00 0.00 4.73
2524 2590 0.670546 CCTTTCTTCTTCGAGGCGCA 60.671 55.000 10.83 0.00 0.00 6.09
2525 2591 0.670854 ACCTTTCTTCTTCGAGGCGC 60.671 55.000 0.00 0.00 32.42 6.53
2526 2592 2.163815 TCTACCTTTCTTCTTCGAGGCG 59.836 50.000 0.00 0.00 32.42 5.52
2527 2593 3.870633 TCTACCTTTCTTCTTCGAGGC 57.129 47.619 0.00 0.00 32.42 4.70
2528 2594 5.584253 TCATCTACCTTTCTTCTTCGAGG 57.416 43.478 0.00 0.00 35.39 4.63
2529 2595 7.062839 CACTTTCATCTACCTTTCTTCTTCGAG 59.937 40.741 0.00 0.00 0.00 4.04
2530 2596 6.868864 CACTTTCATCTACCTTTCTTCTTCGA 59.131 38.462 0.00 0.00 0.00 3.71
2531 2597 6.868864 TCACTTTCATCTACCTTTCTTCTTCG 59.131 38.462 0.00 0.00 0.00 3.79
2532 2598 8.091449 TCTCACTTTCATCTACCTTTCTTCTTC 58.909 37.037 0.00 0.00 0.00 2.87
2533 2599 7.967908 TCTCACTTTCATCTACCTTTCTTCTT 58.032 34.615 0.00 0.00 0.00 2.52
2534 2600 7.546250 TCTCACTTTCATCTACCTTTCTTCT 57.454 36.000 0.00 0.00 0.00 2.85
2535 2601 8.091449 TCTTCTCACTTTCATCTACCTTTCTTC 58.909 37.037 0.00 0.00 0.00 2.87
2536 2602 7.967908 TCTTCTCACTTTCATCTACCTTTCTT 58.032 34.615 0.00 0.00 0.00 2.52
2537 2603 7.546250 TCTTCTCACTTTCATCTACCTTTCT 57.454 36.000 0.00 0.00 0.00 2.52
2538 2604 7.148490 GCTTCTTCTCACTTTCATCTACCTTTC 60.148 40.741 0.00 0.00 0.00 2.62
2539 2605 6.652900 GCTTCTTCTCACTTTCATCTACCTTT 59.347 38.462 0.00 0.00 0.00 3.11
2540 2606 6.169800 GCTTCTTCTCACTTTCATCTACCTT 58.830 40.000 0.00 0.00 0.00 3.50
2541 2607 5.337975 GGCTTCTTCTCACTTTCATCTACCT 60.338 44.000 0.00 0.00 0.00 3.08
2542 2608 4.873259 GGCTTCTTCTCACTTTCATCTACC 59.127 45.833 0.00 0.00 0.00 3.18
2543 2609 5.482908 TGGCTTCTTCTCACTTTCATCTAC 58.517 41.667 0.00 0.00 0.00 2.59
2544 2610 5.481824 TCTGGCTTCTTCTCACTTTCATCTA 59.518 40.000 0.00 0.00 0.00 1.98
2545 2611 4.285517 TCTGGCTTCTTCTCACTTTCATCT 59.714 41.667 0.00 0.00 0.00 2.90
2546 2612 4.573900 TCTGGCTTCTTCTCACTTTCATC 58.426 43.478 0.00 0.00 0.00 2.92
2547 2613 4.565236 CCTCTGGCTTCTTCTCACTTTCAT 60.565 45.833 0.00 0.00 0.00 2.57
2548 2614 3.244353 CCTCTGGCTTCTTCTCACTTTCA 60.244 47.826 0.00 0.00 0.00 2.69
2549 2615 3.333804 CCTCTGGCTTCTTCTCACTTTC 58.666 50.000 0.00 0.00 0.00 2.62
2550 2616 2.551938 GCCTCTGGCTTCTTCTCACTTT 60.552 50.000 0.73 0.00 46.69 2.66
2551 2617 1.003003 GCCTCTGGCTTCTTCTCACTT 59.997 52.381 0.73 0.00 46.69 3.16
2552 2618 0.612744 GCCTCTGGCTTCTTCTCACT 59.387 55.000 0.73 0.00 46.69 3.41
2553 2619 3.151461 GCCTCTGGCTTCTTCTCAC 57.849 57.895 0.73 0.00 46.69 3.51
2564 2630 0.549950 ATCAGTCCCAATGCCTCTGG 59.450 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.