Multiple sequence alignment - TraesCS6A01G215100

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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 TraesCS6A01G215100 chr6A 100.000 2542 0 0 1 2542 394642542 394645083 0.000000e+00 4695
1 TraesCS6A01G215100 chr6A 96.591 264 9 0 2279 2542 579707703 579707440 3.000000e-119 438
2 TraesCS6A01G215100 chr6A 96.591 264 9 0 2279 2542 591028860 591028597 3.000000e-119 438
3 TraesCS6A01G215100 chr4A 97.060 2279 62 3 1 2278 574767490 574765216 0.000000e+00 3832
4 TraesCS6A01G215100 chr4A 91.182 2302 122 16 1 2279 602465154 602462911 0.000000e+00 3051
5 TraesCS6A01G215100 chr4A 97.338 263 7 0 2279 2541 506115677 506115939 4.990000e-122 448
6 TraesCS6A01G215100 chr4A 96.947 262 8 0 2279 2540 166596950 166596689 8.350000e-120 440
7 TraesCS6A01G215100 chr3A 97.060 2279 58 7 1 2278 224968261 224970531 0.000000e+00 3829
8 TraesCS6A01G215100 chr6B 91.011 2314 124 18 1 2287 617028567 617030823 0.000000e+00 3044
9 TraesCS6A01G215100 chr6B 90.240 2295 134 15 3 2278 399208515 399206292 0.000000e+00 2915
10 TraesCS6A01G215100 chr6B 88.591 894 65 15 1413 2281 101192030 101192911 0.000000e+00 1051
11 TraesCS6A01G215100 chr6B 88.514 888 68 15 1413 2278 423139267 423138392 0.000000e+00 1044
12 TraesCS6A01G215100 chr2B 90.791 2302 169 19 1 2278 622030766 622028484 0.000000e+00 3037
13 TraesCS6A01G215100 chr2B 90.862 2309 126 25 1 2281 435353320 435351069 0.000000e+00 3016
14 TraesCS6A01G215100 chr2B 88.639 889 68 14 1413 2279 760346597 760345720 0.000000e+00 1051
15 TraesCS6A01G215100 chr5A 90.747 2302 131 28 1 2278 692979205 692981448 0.000000e+00 2996
16 TraesCS6A01G215100 chr5A 90.049 2050 121 15 255 2278 693957656 693959648 0.000000e+00 2579
17 TraesCS6A01G215100 chr5A 91.975 947 58 6 1351 2280 516607171 516608116 0.000000e+00 1312
18 TraesCS6A01G215100 chr5A 96.970 264 8 0 2279 2542 483831817 483831554 6.450000e-121 444
19 TraesCS6A01G215100 chr5A 96.591 264 9 0 2279 2542 196271157 196270894 3.000000e-119 438
20 TraesCS6A01G215100 chr5A 96.591 264 9 0 2279 2542 586459331 586459068 3.000000e-119 438
21 TraesCS6A01G215100 chr5A 96.935 261 8 0 2279 2539 663529735 663529995 3.000000e-119 438
22 TraesCS6A01G215100 chr5B 90.433 2310 133 21 1 2280 576501431 576503682 0.000000e+00 2961
23 TraesCS6A01G215100 chr1B 90.083 2299 138 25 1 2279 651732018 651729790 0.000000e+00 2900
24 TraesCS6A01G215100 chr1B 90.474 2068 112 19 1 2041 17134744 17136753 0.000000e+00 2649
25 TraesCS6A01G215100 chr1B 89.471 1947 120 19 358 2278 41212305 41214192 0.000000e+00 2381
26 TraesCS6A01G215100 chr1B 89.374 1948 121 21 358 2278 41174293 41176181 0.000000e+00 2372
27 TraesCS6A01G215100 chr1B 91.701 1458 84 8 210 1658 656439715 656441144 0.000000e+00 1988
28 TraesCS6A01G215100 chr1B 88.015 826 44 7 1479 2280 672837445 672836651 0.000000e+00 926
29 TraesCS6A01G215100 chr1B 88.435 735 55 13 1565 2278 637283646 637282921 0.000000e+00 859
30 TraesCS6A01G215100 chr7B 90.406 2095 118 15 210 2278 709654254 709656291 0.000000e+00 2678
31 TraesCS6A01G215100 chr4B 88.179 736 56 13 1565 2279 11347197 11346472 0.000000e+00 848
32 TraesCS6A01G215100 chr4B 87.224 634 48 14 1413 2025 21166283 21166904 0.000000e+00 691
33 TraesCS6A01G215100 chr1A 97.318 261 7 0 2279 2539 452332514 452332774 6.450000e-121 444


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 TraesCS6A01G215100 chr6A 394642542 394645083 2541 False 4695 4695 100.000 1 2542 1 chr6A.!!$F1 2541
1 TraesCS6A01G215100 chr4A 574765216 574767490 2274 True 3832 3832 97.060 1 2278 1 chr4A.!!$R2 2277
2 TraesCS6A01G215100 chr4A 602462911 602465154 2243 True 3051 3051 91.182 1 2279 1 chr4A.!!$R3 2278
3 TraesCS6A01G215100 chr3A 224968261 224970531 2270 False 3829 3829 97.060 1 2278 1 chr3A.!!$F1 2277
4 TraesCS6A01G215100 chr6B 617028567 617030823 2256 False 3044 3044 91.011 1 2287 1 chr6B.!!$F2 2286
5 TraesCS6A01G215100 chr6B 399206292 399208515 2223 True 2915 2915 90.240 3 2278 1 chr6B.!!$R1 2275
6 TraesCS6A01G215100 chr6B 101192030 101192911 881 False 1051 1051 88.591 1413 2281 1 chr6B.!!$F1 868
7 TraesCS6A01G215100 chr6B 423138392 423139267 875 True 1044 1044 88.514 1413 2278 1 chr6B.!!$R2 865
8 TraesCS6A01G215100 chr2B 622028484 622030766 2282 True 3037 3037 90.791 1 2278 1 chr2B.!!$R2 2277
9 TraesCS6A01G215100 chr2B 435351069 435353320 2251 True 3016 3016 90.862 1 2281 1 chr2B.!!$R1 2280
10 TraesCS6A01G215100 chr2B 760345720 760346597 877 True 1051 1051 88.639 1413 2279 1 chr2B.!!$R3 866
11 TraesCS6A01G215100 chr5A 692979205 692981448 2243 False 2996 2996 90.747 1 2278 1 chr5A.!!$F3 2277
12 TraesCS6A01G215100 chr5A 693957656 693959648 1992 False 2579 2579 90.049 255 2278 1 chr5A.!!$F4 2023
13 TraesCS6A01G215100 chr5A 516607171 516608116 945 False 1312 1312 91.975 1351 2280 1 chr5A.!!$F1 929
14 TraesCS6A01G215100 chr5B 576501431 576503682 2251 False 2961 2961 90.433 1 2280 1 chr5B.!!$F1 2279
15 TraesCS6A01G215100 chr1B 651729790 651732018 2228 True 2900 2900 90.083 1 2279 1 chr1B.!!$R2 2278
16 TraesCS6A01G215100 chr1B 17134744 17136753 2009 False 2649 2649 90.474 1 2041 1 chr1B.!!$F1 2040
17 TraesCS6A01G215100 chr1B 41212305 41214192 1887 False 2381 2381 89.471 358 2278 1 chr1B.!!$F3 1920
18 TraesCS6A01G215100 chr1B 41174293 41176181 1888 False 2372 2372 89.374 358 2278 1 chr1B.!!$F2 1920
19 TraesCS6A01G215100 chr1B 656439715 656441144 1429 False 1988 1988 91.701 210 1658 1 chr1B.!!$F4 1448
20 TraesCS6A01G215100 chr1B 672836651 672837445 794 True 926 926 88.015 1479 2280 1 chr1B.!!$R3 801
21 TraesCS6A01G215100 chr1B 637282921 637283646 725 True 859 859 88.435 1565 2278 1 chr1B.!!$R1 713
22 TraesCS6A01G215100 chr7B 709654254 709656291 2037 False 2678 2678 90.406 210 2278 1 chr7B.!!$F1 2068
23 TraesCS6A01G215100 chr4B 11346472 11347197 725 True 848 848 88.179 1565 2279 1 chr4B.!!$R1 714
24 TraesCS6A01G215100 chr4B 21166283 21166904 621 False 691 691 87.224 1413 2025 1 chr4B.!!$F1 612

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
138 141 2.507484 CCACAATGGCAAGAAGACTGA 58.493 47.619 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1714 1.130955 GCACAATTTGGCAGTCAACG 58.869 50.0 0.78 0.0 34.67 4.1 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
138 141 2.507484 CCACAATGGCAAGAAGACTGA 58.493 47.619 0.00 0.00 0.00 3.41
472 475 6.107901 AGAGAGAGTGTTGTATGCTCTTTT 57.892 37.500 0.00 0.00 39.43 2.27
527 530 4.894784 TCTTACTTGCTTTCGAAGTGGAT 58.105 39.130 0.00 0.00 35.30 3.41
979 990 9.897744 ACATGTGTACATCTTTCTTTAAATGTG 57.102 29.630 0.00 0.00 33.61 3.21
1118 1129 4.220382 TCAAAATGTTGGCCTTGATTCGAT 59.780 37.500 3.32 0.00 35.29 3.59
1124 1135 1.559219 TGGCCTTGATTCGATCTCCAA 59.441 47.619 3.32 0.00 0.00 3.53
1125 1136 2.216898 GGCCTTGATTCGATCTCCAAG 58.783 52.381 0.00 0.00 36.64 3.61
1126 1137 2.158900 GGCCTTGATTCGATCTCCAAGA 60.159 50.000 14.23 0.00 38.52 3.02
1354 1368 1.858458 GTGATGCTAGATTTGCGCGTA 59.142 47.619 8.43 0.00 0.00 4.42
1471 1487 5.042463 TGAGTTTTGGTTGACTGGACATA 57.958 39.130 0.00 0.00 0.00 2.29
1472 1488 5.063204 TGAGTTTTGGTTGACTGGACATAG 58.937 41.667 0.00 0.00 0.00 2.23
1510 1526 0.890683 GGGATTGGCTGTGGTTTGAG 59.109 55.000 0.00 0.00 0.00 3.02
1596 1625 5.537188 TGTTATTTTGGTTGGTGCATCTTC 58.463 37.500 0.00 0.00 0.00 2.87
1737 1781 6.490040 TCTTTTTGAGCTACTGTTGGCTATTT 59.510 34.615 7.70 0.00 39.05 1.40
1857 1926 0.545646 AGAGAGAAGGGCTGGCATTC 59.454 55.000 19.19 19.19 0.00 2.67
1877 1946 6.314400 GCATTCAATAAATGGACTGCACATTT 59.686 34.615 15.53 15.53 46.76 2.32
2198 2270 3.292460 TGTTGACCTTCCGAATTTGGTT 58.708 40.909 11.68 0.00 32.30 3.67
2283 2359 3.937079 CCGTATTTCTTGTAGTGAACCCC 59.063 47.826 0.00 0.00 0.00 4.95
2284 2360 4.563993 CCGTATTTCTTGTAGTGAACCCCA 60.564 45.833 0.00 0.00 0.00 4.96
2285 2361 5.183228 CGTATTTCTTGTAGTGAACCCCAT 58.817 41.667 0.00 0.00 0.00 4.00
2286 2362 5.064707 CGTATTTCTTGTAGTGAACCCCATG 59.935 44.000 0.00 0.00 0.00 3.66
2287 2363 4.447138 TTTCTTGTAGTGAACCCCATGT 57.553 40.909 0.00 0.00 0.00 3.21
2288 2364 3.417069 TCTTGTAGTGAACCCCATGTG 57.583 47.619 0.00 0.00 0.00 3.21
2289 2365 2.708861 TCTTGTAGTGAACCCCATGTGT 59.291 45.455 0.00 0.00 0.00 3.72
2290 2366 2.851263 TGTAGTGAACCCCATGTGTC 57.149 50.000 0.00 0.00 0.00 3.67
2291 2367 1.349688 TGTAGTGAACCCCATGTGTCC 59.650 52.381 0.00 0.00 0.00 4.02
2292 2368 1.349688 GTAGTGAACCCCATGTGTCCA 59.650 52.381 0.00 0.00 0.00 4.02
2293 2369 0.401738 AGTGAACCCCATGTGTCCAG 59.598 55.000 0.00 0.00 0.00 3.86
2294 2370 0.609131 GTGAACCCCATGTGTCCAGG 60.609 60.000 0.00 0.00 0.00 4.45
2295 2371 1.065410 TGAACCCCATGTGTCCAGGT 61.065 55.000 0.00 0.00 0.00 4.00
2296 2372 0.988832 GAACCCCATGTGTCCAGGTA 59.011 55.000 0.00 0.00 0.00 3.08
2297 2373 0.696501 AACCCCATGTGTCCAGGTAC 59.303 55.000 0.00 0.00 0.00 3.34
2298 2374 1.220749 CCCCATGTGTCCAGGTACG 59.779 63.158 0.00 0.00 0.00 3.67
2299 2375 1.550130 CCCCATGTGTCCAGGTACGT 61.550 60.000 0.00 0.00 0.00 3.57
2300 2376 0.391130 CCCATGTGTCCAGGTACGTG 60.391 60.000 8.61 8.61 34.42 4.49
2301 2377 1.019278 CCATGTGTCCAGGTACGTGC 61.019 60.000 10.09 0.00 33.54 5.34
2302 2378 0.320334 CATGTGTCCAGGTACGTGCA 60.320 55.000 10.09 3.32 0.00 4.57
2303 2379 0.394938 ATGTGTCCAGGTACGTGCAA 59.605 50.000 10.09 0.00 0.00 4.08
2304 2380 0.178301 TGTGTCCAGGTACGTGCAAA 59.822 50.000 10.09 0.00 0.00 3.68
2305 2381 1.301423 GTGTCCAGGTACGTGCAAAA 58.699 50.000 10.09 0.00 0.00 2.44
2306 2382 1.877443 GTGTCCAGGTACGTGCAAAAT 59.123 47.619 10.09 0.00 0.00 1.82
2307 2383 2.095919 GTGTCCAGGTACGTGCAAAATC 60.096 50.000 10.09 0.00 0.00 2.17
2308 2384 1.467342 GTCCAGGTACGTGCAAAATCC 59.533 52.381 10.09 0.00 0.00 3.01
2309 2385 1.349688 TCCAGGTACGTGCAAAATCCT 59.650 47.619 10.09 0.00 0.00 3.24
2310 2386 1.468520 CCAGGTACGTGCAAAATCCTG 59.531 52.381 17.07 17.07 41.17 3.86
2311 2387 1.468520 CAGGTACGTGCAAAATCCTGG 59.531 52.381 16.54 0.00 38.81 4.45
2312 2388 0.170339 GGTACGTGCAAAATCCTGGC 59.830 55.000 5.86 0.00 0.00 4.85
2313 2389 0.179200 GTACGTGCAAAATCCTGGCG 60.179 55.000 0.00 0.00 0.00 5.69
2314 2390 0.604243 TACGTGCAAAATCCTGGCGT 60.604 50.000 0.00 0.00 35.29 5.68
2315 2391 1.442520 CGTGCAAAATCCTGGCGTG 60.443 57.895 0.00 0.00 0.00 5.34
2316 2392 1.080569 GTGCAAAATCCTGGCGTGG 60.081 57.895 0.00 0.00 0.00 4.94
2317 2393 2.125952 GCAAAATCCTGGCGTGGC 60.126 61.111 0.00 0.00 0.00 5.01
2333 2409 4.400410 GCCACATGCCAATAACGC 57.600 55.556 0.00 0.00 0.00 4.84
2334 2410 1.226945 GCCACATGCCAATAACGCC 60.227 57.895 0.00 0.00 0.00 5.68
2335 2411 1.943116 GCCACATGCCAATAACGCCA 61.943 55.000 0.00 0.00 0.00 5.69
2336 2412 0.101040 CCACATGCCAATAACGCCAG 59.899 55.000 0.00 0.00 0.00 4.85
2337 2413 0.526096 CACATGCCAATAACGCCAGC 60.526 55.000 0.00 0.00 0.00 4.85
2338 2414 0.964860 ACATGCCAATAACGCCAGCA 60.965 50.000 0.00 0.00 37.94 4.41
2339 2415 0.386476 CATGCCAATAACGCCAGCAT 59.614 50.000 0.00 0.00 44.66 3.79
2340 2416 0.670162 ATGCCAATAACGCCAGCATC 59.330 50.000 0.00 0.00 39.95 3.91
2341 2417 1.360192 GCCAATAACGCCAGCATCC 59.640 57.895 0.00 0.00 0.00 3.51
2342 2418 1.103398 GCCAATAACGCCAGCATCCT 61.103 55.000 0.00 0.00 0.00 3.24
2343 2419 1.392589 CCAATAACGCCAGCATCCTT 58.607 50.000 0.00 0.00 0.00 3.36
2344 2420 1.334869 CCAATAACGCCAGCATCCTTC 59.665 52.381 0.00 0.00 0.00 3.46
2345 2421 2.292267 CAATAACGCCAGCATCCTTCT 58.708 47.619 0.00 0.00 0.00 2.85
2346 2422 2.246719 ATAACGCCAGCATCCTTCTC 57.753 50.000 0.00 0.00 0.00 2.87
2347 2423 0.179111 TAACGCCAGCATCCTTCTCG 60.179 55.000 0.00 0.00 0.00 4.04
2348 2424 2.587194 CGCCAGCATCCTTCTCGG 60.587 66.667 0.00 0.00 0.00 4.63
2349 2425 2.586792 GCCAGCATCCTTCTCGGT 59.413 61.111 0.00 0.00 0.00 4.69
2350 2426 1.078143 GCCAGCATCCTTCTCGGTT 60.078 57.895 0.00 0.00 0.00 4.44
2351 2427 1.372087 GCCAGCATCCTTCTCGGTTG 61.372 60.000 0.00 0.00 35.88 3.77
2352 2428 0.036010 CCAGCATCCTTCTCGGTTGT 60.036 55.000 0.00 0.00 35.34 3.32
2353 2429 1.081892 CAGCATCCTTCTCGGTTGTG 58.918 55.000 0.00 0.00 35.34 3.33
2354 2430 0.687354 AGCATCCTTCTCGGTTGTGT 59.313 50.000 0.00 0.00 35.34 3.72
2355 2431 0.798776 GCATCCTTCTCGGTTGTGTG 59.201 55.000 0.00 0.00 35.34 3.82
2356 2432 1.442769 CATCCTTCTCGGTTGTGTGG 58.557 55.000 0.00 0.00 0.00 4.17
2357 2433 1.001974 CATCCTTCTCGGTTGTGTGGA 59.998 52.381 0.00 0.00 0.00 4.02
2358 2434 0.679505 TCCTTCTCGGTTGTGTGGAG 59.320 55.000 0.00 0.00 0.00 3.86
2359 2435 0.393077 CCTTCTCGGTTGTGTGGAGT 59.607 55.000 0.00 0.00 0.00 3.85
2360 2436 1.616865 CCTTCTCGGTTGTGTGGAGTA 59.383 52.381 0.00 0.00 0.00 2.59
2361 2437 2.233922 CCTTCTCGGTTGTGTGGAGTAT 59.766 50.000 0.00 0.00 0.00 2.12
2362 2438 3.512680 CTTCTCGGTTGTGTGGAGTATC 58.487 50.000 0.00 0.00 0.00 2.24
2381 2457 3.231734 CGGAGGATGTGAGCAACAA 57.768 52.632 0.00 0.00 43.61 2.83
2382 2458 1.081892 CGGAGGATGTGAGCAACAAG 58.918 55.000 0.00 0.00 43.61 3.16
2383 2459 1.338105 CGGAGGATGTGAGCAACAAGA 60.338 52.381 0.00 0.00 43.61 3.02
2384 2460 2.354259 GGAGGATGTGAGCAACAAGAG 58.646 52.381 0.00 0.00 43.61 2.85
2385 2461 2.027745 GGAGGATGTGAGCAACAAGAGA 60.028 50.000 0.00 0.00 43.61 3.10
2386 2462 2.999355 GAGGATGTGAGCAACAAGAGAC 59.001 50.000 0.00 0.00 43.61 3.36
2387 2463 2.369860 AGGATGTGAGCAACAAGAGACA 59.630 45.455 0.00 0.00 43.61 3.41
2388 2464 2.740981 GGATGTGAGCAACAAGAGACAG 59.259 50.000 0.00 0.00 43.61 3.51
2389 2465 2.988010 TGTGAGCAACAAGAGACAGT 57.012 45.000 0.00 0.00 35.24 3.55
2390 2466 4.560128 GATGTGAGCAACAAGAGACAGTA 58.440 43.478 0.00 0.00 43.61 2.74
2391 2467 4.400529 TGTGAGCAACAAGAGACAGTAA 57.599 40.909 0.00 0.00 35.24 2.24
2392 2468 4.765273 TGTGAGCAACAAGAGACAGTAAA 58.235 39.130 0.00 0.00 35.24 2.01
2393 2469 5.182487 TGTGAGCAACAAGAGACAGTAAAA 58.818 37.500 0.00 0.00 35.24 1.52
2394 2470 5.645929 TGTGAGCAACAAGAGACAGTAAAAA 59.354 36.000 0.00 0.00 35.24 1.94
2411 2487 2.651382 AAAAGGTTTACGCAGGGTCT 57.349 45.000 0.00 0.00 0.00 3.85
2412 2488 2.651382 AAAGGTTTACGCAGGGTCTT 57.349 45.000 0.00 0.00 0.00 3.01
2413 2489 3.775261 AAAGGTTTACGCAGGGTCTTA 57.225 42.857 0.00 0.00 0.00 2.10
2414 2490 3.775261 AAGGTTTACGCAGGGTCTTAA 57.225 42.857 0.00 0.00 0.00 1.85
2415 2491 3.994931 AGGTTTACGCAGGGTCTTAAT 57.005 42.857 0.00 0.00 0.00 1.40
2416 2492 3.870274 AGGTTTACGCAGGGTCTTAATC 58.130 45.455 0.00 0.00 0.00 1.75
2417 2493 3.518303 AGGTTTACGCAGGGTCTTAATCT 59.482 43.478 0.00 0.00 0.00 2.40
2418 2494 4.713321 AGGTTTACGCAGGGTCTTAATCTA 59.287 41.667 0.00 0.00 0.00 1.98
2419 2495 5.188359 AGGTTTACGCAGGGTCTTAATCTAA 59.812 40.000 0.00 0.00 0.00 2.10
2420 2496 5.876460 GGTTTACGCAGGGTCTTAATCTAAA 59.124 40.000 0.00 0.00 0.00 1.85
2421 2497 6.372381 GGTTTACGCAGGGTCTTAATCTAAAA 59.628 38.462 0.00 0.00 0.00 1.52
2422 2498 7.094677 GGTTTACGCAGGGTCTTAATCTAAAAA 60.095 37.037 0.00 0.00 0.00 1.94
2423 2499 7.605410 TTACGCAGGGTCTTAATCTAAAAAG 57.395 36.000 0.00 0.00 0.00 2.27
2424 2500 5.801380 ACGCAGGGTCTTAATCTAAAAAGA 58.199 37.500 0.00 0.00 0.00 2.52
2425 2501 6.235664 ACGCAGGGTCTTAATCTAAAAAGAA 58.764 36.000 0.00 0.00 33.70 2.52
2426 2502 6.713450 ACGCAGGGTCTTAATCTAAAAAGAAA 59.287 34.615 0.00 0.00 33.70 2.52
2427 2503 7.021790 CGCAGGGTCTTAATCTAAAAAGAAAC 58.978 38.462 0.00 0.00 33.70 2.78
2428 2504 7.313646 GCAGGGTCTTAATCTAAAAAGAAACC 58.686 38.462 0.00 0.00 33.70 3.27
2429 2505 7.176865 GCAGGGTCTTAATCTAAAAAGAAACCT 59.823 37.037 0.00 0.00 39.81 3.50
2430 2506 9.078990 CAGGGTCTTAATCTAAAAAGAAACCTT 57.921 33.333 6.77 0.00 38.39 3.50
2431 2507 9.656323 AGGGTCTTAATCTAAAAAGAAACCTTT 57.344 29.630 0.00 0.00 37.77 3.11
2432 2508 9.692749 GGGTCTTAATCTAAAAAGAAACCTTTG 57.307 33.333 0.00 0.00 34.37 2.77
2433 2509 9.692749 GGTCTTAATCTAAAAAGAAACCTTTGG 57.307 33.333 0.00 0.00 34.37 3.28
2434 2510 9.692749 GTCTTAATCTAAAAAGAAACCTTTGGG 57.307 33.333 0.00 0.00 34.37 4.12
2435 2511 8.364894 TCTTAATCTAAAAAGAAACCTTTGGGC 58.635 33.333 0.00 0.00 34.37 5.36
2436 2512 4.577834 TCTAAAAAGAAACCTTTGGGCG 57.422 40.909 0.00 0.00 34.37 6.13
2437 2513 2.613026 AAAAAGAAACCTTTGGGCGG 57.387 45.000 0.00 0.00 34.37 6.13
2438 2514 0.756294 AAAAGAAACCTTTGGGCGGG 59.244 50.000 0.00 0.00 34.37 6.13
2439 2515 0.397957 AAAGAAACCTTTGGGCGGGT 60.398 50.000 0.00 0.00 37.44 5.28
2440 2516 0.826256 AAGAAACCTTTGGGCGGGTC 60.826 55.000 0.00 0.00 34.35 4.46
2441 2517 2.203582 AAACCTTTGGGCGGGTCC 60.204 61.111 0.00 0.00 34.35 4.46
2454 2530 4.008933 GGTCCCTGCTGCACGTCT 62.009 66.667 0.00 0.00 0.00 4.18
2455 2531 2.740055 GTCCCTGCTGCACGTCTG 60.740 66.667 0.00 0.00 0.00 3.51
2456 2532 4.687215 TCCCTGCTGCACGTCTGC 62.687 66.667 0.00 8.98 44.52 4.26
2465 2541 3.406361 CACGTCTGCGCCTGTGTC 61.406 66.667 4.18 0.00 42.83 3.67
2466 2542 4.664677 ACGTCTGCGCCTGTGTCC 62.665 66.667 4.18 0.00 42.83 4.02
2468 2544 4.008933 GTCTGCGCCTGTGTCCCT 62.009 66.667 4.18 0.00 0.00 4.20
2469 2545 4.007644 TCTGCGCCTGTGTCCCTG 62.008 66.667 4.18 0.00 0.00 4.45
2470 2546 4.320456 CTGCGCCTGTGTCCCTGT 62.320 66.667 4.18 0.00 0.00 4.00
2471 2547 3.832237 CTGCGCCTGTGTCCCTGTT 62.832 63.158 4.18 0.00 0.00 3.16
2472 2548 3.357079 GCGCCTGTGTCCCTGTTG 61.357 66.667 0.00 0.00 0.00 3.33
2473 2549 2.111043 CGCCTGTGTCCCTGTTGT 59.889 61.111 0.00 0.00 0.00 3.32
2474 2550 2.253758 CGCCTGTGTCCCTGTTGTG 61.254 63.158 0.00 0.00 0.00 3.33
2475 2551 2.555547 GCCTGTGTCCCTGTTGTGC 61.556 63.158 0.00 0.00 0.00 4.57
2476 2552 1.898574 CCTGTGTCCCTGTTGTGCC 60.899 63.158 0.00 0.00 0.00 5.01
2477 2553 1.152984 CTGTGTCCCTGTTGTGCCA 60.153 57.895 0.00 0.00 0.00 4.92
2478 2554 0.538057 CTGTGTCCCTGTTGTGCCAT 60.538 55.000 0.00 0.00 0.00 4.40
2479 2555 0.822944 TGTGTCCCTGTTGTGCCATG 60.823 55.000 0.00 0.00 0.00 3.66
2480 2556 0.823356 GTGTCCCTGTTGTGCCATGT 60.823 55.000 0.00 0.00 0.00 3.21
2481 2557 0.537143 TGTCCCTGTTGTGCCATGTC 60.537 55.000 0.00 0.00 0.00 3.06
2482 2558 1.074775 TCCCTGTTGTGCCATGTCC 59.925 57.895 0.00 0.00 0.00 4.02
2483 2559 1.075482 CCCTGTTGTGCCATGTCCT 59.925 57.895 0.00 0.00 0.00 3.85
2484 2560 1.246056 CCCTGTTGTGCCATGTCCTG 61.246 60.000 0.00 0.00 0.00 3.86
2493 2569 2.436646 CATGTCCTGGACGGGTGC 60.437 66.667 21.15 0.00 34.95 5.01
2494 2570 2.927856 ATGTCCTGGACGGGTGCA 60.928 61.111 21.15 3.64 34.95 4.57
2495 2571 2.959484 ATGTCCTGGACGGGTGCAG 61.959 63.158 21.15 12.73 46.77 4.41
2505 2581 2.870372 GGGTGCAGCACGATTGTC 59.130 61.111 19.42 4.08 34.83 3.18
2506 2582 1.965930 GGGTGCAGCACGATTGTCA 60.966 57.895 19.42 0.00 34.83 3.58
2507 2583 1.308069 GGGTGCAGCACGATTGTCAT 61.308 55.000 19.42 0.00 34.83 3.06
2508 2584 0.097674 GGTGCAGCACGATTGTCATC 59.902 55.000 19.42 0.00 34.83 2.92
2509 2585 1.081892 GTGCAGCACGATTGTCATCT 58.918 50.000 10.47 0.00 0.00 2.90
2510 2586 1.081094 TGCAGCACGATTGTCATCTG 58.919 50.000 0.00 3.33 0.00 2.90
2511 2587 1.081892 GCAGCACGATTGTCATCTGT 58.918 50.000 0.00 0.00 0.00 3.41
2512 2588 2.270923 GCAGCACGATTGTCATCTGTA 58.729 47.619 0.00 0.00 0.00 2.74
2513 2589 2.672874 GCAGCACGATTGTCATCTGTAA 59.327 45.455 0.00 0.00 0.00 2.41
2514 2590 3.125146 GCAGCACGATTGTCATCTGTAAA 59.875 43.478 0.00 0.00 0.00 2.01
2515 2591 4.378356 GCAGCACGATTGTCATCTGTAAAA 60.378 41.667 0.00 0.00 0.00 1.52
2516 2592 5.319139 CAGCACGATTGTCATCTGTAAAAG 58.681 41.667 0.00 0.00 0.00 2.27
2517 2593 4.393062 AGCACGATTGTCATCTGTAAAAGG 59.607 41.667 0.00 0.00 0.00 3.11
2518 2594 4.391830 GCACGATTGTCATCTGTAAAAGGA 59.608 41.667 0.00 0.00 0.00 3.36
2519 2595 5.106712 GCACGATTGTCATCTGTAAAAGGAA 60.107 40.000 0.00 0.00 0.00 3.36
2520 2596 6.567701 GCACGATTGTCATCTGTAAAAGGAAA 60.568 38.462 0.00 0.00 0.00 3.13
2521 2597 7.017645 CACGATTGTCATCTGTAAAAGGAAAG 58.982 38.462 0.00 0.00 0.00 2.62
2522 2598 6.934645 ACGATTGTCATCTGTAAAAGGAAAGA 59.065 34.615 0.00 0.00 0.00 2.52
2523 2599 7.444183 ACGATTGTCATCTGTAAAAGGAAAGAA 59.556 33.333 0.00 0.00 0.00 2.52
2524 2600 7.746475 CGATTGTCATCTGTAAAAGGAAAGAAC 59.254 37.037 0.00 0.00 0.00 3.01
2525 2601 8.697507 ATTGTCATCTGTAAAAGGAAAGAACT 57.302 30.769 0.00 0.00 0.00 3.01
2526 2602 8.519799 TTGTCATCTGTAAAAGGAAAGAACTT 57.480 30.769 0.00 0.00 0.00 2.66
2527 2603 9.621629 TTGTCATCTGTAAAAGGAAAGAACTTA 57.378 29.630 0.00 0.00 0.00 2.24
2528 2604 9.273016 TGTCATCTGTAAAAGGAAAGAACTTAG 57.727 33.333 0.00 0.00 0.00 2.18
2529 2605 8.722394 GTCATCTGTAAAAGGAAAGAACTTAGG 58.278 37.037 0.00 0.00 0.00 2.69
2530 2606 8.437575 TCATCTGTAAAAGGAAAGAACTTAGGT 58.562 33.333 0.00 0.00 0.00 3.08
2531 2607 8.507249 CATCTGTAAAAGGAAAGAACTTAGGTG 58.493 37.037 0.00 0.00 0.00 4.00
2532 2608 7.798071 TCTGTAAAAGGAAAGAACTTAGGTGA 58.202 34.615 0.00 0.00 0.00 4.02
2533 2609 8.269317 TCTGTAAAAGGAAAGAACTTAGGTGAA 58.731 33.333 0.00 0.00 0.00 3.18
2534 2610 8.810990 TGTAAAAGGAAAGAACTTAGGTGAAA 57.189 30.769 0.00 0.00 0.00 2.69
2535 2611 8.899771 TGTAAAAGGAAAGAACTTAGGTGAAAG 58.100 33.333 0.00 0.00 0.00 2.62
2536 2612 7.956328 AAAAGGAAAGAACTTAGGTGAAAGT 57.044 32.000 0.00 0.00 41.46 2.66
2538 2614 6.944234 AGGAAAGAACTTAGGTGAAAGTTG 57.056 37.500 6.71 0.00 46.92 3.16
2539 2615 6.424032 AGGAAAGAACTTAGGTGAAAGTTGT 58.576 36.000 6.71 0.40 46.92 3.32
2540 2616 6.542735 AGGAAAGAACTTAGGTGAAAGTTGTC 59.457 38.462 6.71 2.51 46.92 3.18
2541 2617 5.986004 AAGAACTTAGGTGAAAGTTGTCG 57.014 39.130 6.71 0.00 46.92 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 141 5.495640 CCTTCTTAACTGGCTCAGAGAAAT 58.504 41.667 0.00 0.00 35.18 2.17
250 253 5.541868 ACCCATCTCTATCAAATCTGTCGAT 59.458 40.000 0.00 0.00 0.00 3.59
979 990 5.220931 CCATAGCTTTTTACATGTCAGCCTC 60.221 44.000 0.00 0.00 0.00 4.70
1118 1129 4.164221 ACCTGTTGAACTTCTTCTTGGAGA 59.836 41.667 0.00 0.00 0.00 3.71
1124 1135 3.118261 TGCAGACCTGTTGAACTTCTTCT 60.118 43.478 0.00 0.00 0.00 2.85
1125 1136 3.206150 TGCAGACCTGTTGAACTTCTTC 58.794 45.455 0.00 0.00 0.00 2.87
1126 1137 3.281727 TGCAGACCTGTTGAACTTCTT 57.718 42.857 0.00 0.00 0.00 2.52
1207 1221 2.099921 GCTCCTCTCGCATCAACTTAGA 59.900 50.000 0.00 0.00 0.00 2.10
1245 1259 2.569404 AGCTTCGGTCTCCTCTGATTTT 59.431 45.455 0.00 0.00 0.00 1.82
1391 1405 2.299582 CCAAAGCCAACATCAACCATGA 59.700 45.455 0.00 0.00 40.57 3.07
1471 1487 3.139025 CCCTGGTCCATATTGTGATTCCT 59.861 47.826 0.00 0.00 0.00 3.36
1472 1488 3.138283 TCCCTGGTCCATATTGTGATTCC 59.862 47.826 0.00 0.00 0.00 3.01
1510 1526 2.100749 CACCAACCAAAACAGAACCTCC 59.899 50.000 0.00 0.00 0.00 4.30
1596 1625 6.312918 ACAGTATCATTACGCCACAGTTTTAG 59.687 38.462 0.00 0.00 33.32 1.85
1674 1708 4.518970 ACAATTTGGCAGTCAACGAATACT 59.481 37.500 0.78 0.00 34.67 2.12
1680 1714 1.130955 GCACAATTTGGCAGTCAACG 58.869 50.000 0.78 0.00 34.67 4.10
1711 1747 4.207165 AGCCAACAGTAGCTCAAAAAGAA 58.793 39.130 0.00 0.00 32.71 2.52
1835 1890 1.656587 TGCCAGCCCTTCTCTCTAAA 58.343 50.000 0.00 0.00 0.00 1.85
1857 1926 5.808540 CAGGAAATGTGCAGTCCATTTATTG 59.191 40.000 12.28 10.20 41.34 1.90
1877 1946 2.334977 TGTTAGTTCTTGGGCTCAGGA 58.665 47.619 0.00 0.00 0.00 3.86
2118 2190 1.898330 ATTTTTGTCATGGCCGCCCC 61.898 55.000 7.03 0.00 0.00 5.80
2235 2311 4.666412 TTATGACTCCCCATTTTGGTCA 57.334 40.909 0.00 0.00 40.43 4.02
2283 2359 0.320334 TGCACGTACCTGGACACATG 60.320 55.000 0.00 0.00 0.00 3.21
2284 2360 0.394938 TTGCACGTACCTGGACACAT 59.605 50.000 0.00 0.00 0.00 3.21
2285 2361 0.178301 TTTGCACGTACCTGGACACA 59.822 50.000 0.00 0.00 0.00 3.72
2286 2362 1.301423 TTTTGCACGTACCTGGACAC 58.699 50.000 0.00 0.00 0.00 3.67
2287 2363 2.147958 GATTTTGCACGTACCTGGACA 58.852 47.619 0.00 0.00 0.00 4.02
2288 2364 1.467342 GGATTTTGCACGTACCTGGAC 59.533 52.381 0.00 0.00 0.00 4.02
2289 2365 1.349688 AGGATTTTGCACGTACCTGGA 59.650 47.619 0.00 0.00 0.00 3.86
2290 2366 1.468520 CAGGATTTTGCACGTACCTGG 59.531 52.381 16.57 0.00 40.50 4.45
2291 2367 1.468520 CCAGGATTTTGCACGTACCTG 59.531 52.381 17.11 17.11 42.82 4.00
2292 2368 1.821216 CCAGGATTTTGCACGTACCT 58.179 50.000 0.00 0.00 0.00 3.08
2293 2369 0.170339 GCCAGGATTTTGCACGTACC 59.830 55.000 0.00 0.00 0.00 3.34
2294 2370 0.179200 CGCCAGGATTTTGCACGTAC 60.179 55.000 0.00 0.00 0.00 3.67
2295 2371 0.604243 ACGCCAGGATTTTGCACGTA 60.604 50.000 0.00 0.00 30.79 3.57
2296 2372 1.896660 ACGCCAGGATTTTGCACGT 60.897 52.632 0.00 0.00 0.00 4.49
2297 2373 1.442520 CACGCCAGGATTTTGCACG 60.443 57.895 0.00 0.00 0.00 5.34
2298 2374 1.080569 CCACGCCAGGATTTTGCAC 60.081 57.895 0.00 0.00 0.00 4.57
2299 2375 2.929903 GCCACGCCAGGATTTTGCA 61.930 57.895 0.00 0.00 0.00 4.08
2300 2376 2.125952 GCCACGCCAGGATTTTGC 60.126 61.111 0.00 0.00 0.00 3.68
2316 2392 1.226945 GGCGTTATTGGCATGTGGC 60.227 57.895 0.00 0.00 43.74 5.01
2317 2393 0.101040 CTGGCGTTATTGGCATGTGG 59.899 55.000 0.00 0.00 44.06 4.17
2318 2394 0.526096 GCTGGCGTTATTGGCATGTG 60.526 55.000 0.00 0.00 44.06 3.21
2319 2395 0.964860 TGCTGGCGTTATTGGCATGT 60.965 50.000 0.00 0.00 44.06 3.21
2320 2396 0.386476 ATGCTGGCGTTATTGGCATG 59.614 50.000 0.00 0.00 44.06 4.06
2321 2397 0.670162 GATGCTGGCGTTATTGGCAT 59.330 50.000 0.00 0.00 44.06 4.40
2322 2398 1.383456 GGATGCTGGCGTTATTGGCA 61.383 55.000 0.00 0.00 42.76 4.92
2323 2399 1.103398 AGGATGCTGGCGTTATTGGC 61.103 55.000 0.00 0.00 0.00 4.52
2324 2400 1.334869 GAAGGATGCTGGCGTTATTGG 59.665 52.381 0.00 0.00 0.00 3.16
2325 2401 2.289002 GAGAAGGATGCTGGCGTTATTG 59.711 50.000 0.00 0.00 0.00 1.90
2326 2402 2.565841 GAGAAGGATGCTGGCGTTATT 58.434 47.619 0.00 0.00 0.00 1.40
2327 2403 1.539065 CGAGAAGGATGCTGGCGTTAT 60.539 52.381 0.00 0.00 0.00 1.89
2328 2404 0.179111 CGAGAAGGATGCTGGCGTTA 60.179 55.000 0.00 0.00 0.00 3.18
2329 2405 1.448540 CGAGAAGGATGCTGGCGTT 60.449 57.895 0.00 0.00 0.00 4.84
2330 2406 2.185350 CGAGAAGGATGCTGGCGT 59.815 61.111 0.00 0.00 0.00 5.68
2331 2407 2.587194 CCGAGAAGGATGCTGGCG 60.587 66.667 0.00 0.00 45.00 5.69
2332 2408 1.078143 AACCGAGAAGGATGCTGGC 60.078 57.895 0.00 0.00 45.00 4.85
2333 2409 0.036010 ACAACCGAGAAGGATGCTGG 60.036 55.000 0.00 0.00 45.69 4.85
2334 2410 1.081892 CACAACCGAGAAGGATGCTG 58.918 55.000 0.00 0.00 45.69 4.41
2335 2411 0.687354 ACACAACCGAGAAGGATGCT 59.313 50.000 0.00 0.00 45.69 3.79
2336 2412 0.798776 CACACAACCGAGAAGGATGC 59.201 55.000 0.00 0.00 45.69 3.91
2337 2413 1.001974 TCCACACAACCGAGAAGGATG 59.998 52.381 0.00 0.00 46.99 3.51
2338 2414 1.276421 CTCCACACAACCGAGAAGGAT 59.724 52.381 0.00 0.00 45.00 3.24
2339 2415 0.679505 CTCCACACAACCGAGAAGGA 59.320 55.000 0.00 0.00 45.00 3.36
2340 2416 6.704394 GGATACTCCACACAACCGAGAAGG 62.704 54.167 0.00 0.00 40.63 3.46
2341 2417 3.512680 GATACTCCACACAACCGAGAAG 58.487 50.000 0.00 0.00 0.00 2.85
2342 2418 2.232941 GGATACTCCACACAACCGAGAA 59.767 50.000 0.00 0.00 36.28 2.87
2343 2419 1.822990 GGATACTCCACACAACCGAGA 59.177 52.381 0.00 0.00 36.28 4.04
2344 2420 1.469251 CGGATACTCCACACAACCGAG 60.469 57.143 0.00 0.00 41.09 4.63
2345 2421 0.528924 CGGATACTCCACACAACCGA 59.471 55.000 0.00 0.00 41.09 4.69
2346 2422 0.459585 CCGGATACTCCACACAACCG 60.460 60.000 0.00 0.00 35.91 4.44
2347 2423 0.899720 TCCGGATACTCCACACAACC 59.100 55.000 0.00 0.00 35.91 3.77
2348 2424 1.134788 CCTCCGGATACTCCACACAAC 60.135 57.143 3.57 0.00 35.91 3.32
2349 2425 1.191535 CCTCCGGATACTCCACACAA 58.808 55.000 3.57 0.00 35.91 3.33
2350 2426 0.333652 TCCTCCGGATACTCCACACA 59.666 55.000 3.57 0.00 35.91 3.72
2351 2427 1.341531 CATCCTCCGGATACTCCACAC 59.658 57.143 3.57 0.00 40.98 3.82
2352 2428 1.063190 ACATCCTCCGGATACTCCACA 60.063 52.381 3.57 0.00 40.98 4.17
2353 2429 1.341531 CACATCCTCCGGATACTCCAC 59.658 57.143 3.57 0.00 40.98 4.02
2354 2430 1.216930 TCACATCCTCCGGATACTCCA 59.783 52.381 3.57 0.00 40.98 3.86
2355 2431 1.889829 CTCACATCCTCCGGATACTCC 59.110 57.143 3.57 0.00 40.98 3.85
2356 2432 1.271102 GCTCACATCCTCCGGATACTC 59.729 57.143 3.57 0.00 40.98 2.59
2357 2433 1.333177 GCTCACATCCTCCGGATACT 58.667 55.000 3.57 0.00 40.98 2.12
2358 2434 1.040646 TGCTCACATCCTCCGGATAC 58.959 55.000 3.57 0.00 40.98 2.24
2359 2435 1.412710 GTTGCTCACATCCTCCGGATA 59.587 52.381 3.57 0.00 40.98 2.59
2360 2436 0.179000 GTTGCTCACATCCTCCGGAT 59.821 55.000 3.57 0.00 44.21 4.18
2361 2437 1.191489 TGTTGCTCACATCCTCCGGA 61.191 55.000 2.93 2.93 35.55 5.14
2362 2438 0.321564 TTGTTGCTCACATCCTCCGG 60.322 55.000 0.00 0.00 34.43 5.14
2363 2439 1.081892 CTTGTTGCTCACATCCTCCG 58.918 55.000 0.00 0.00 34.43 4.63
2364 2440 2.027745 TCTCTTGTTGCTCACATCCTCC 60.028 50.000 0.00 0.00 34.43 4.30
2365 2441 2.999355 GTCTCTTGTTGCTCACATCCTC 59.001 50.000 0.00 0.00 34.43 3.71
2366 2442 2.369860 TGTCTCTTGTTGCTCACATCCT 59.630 45.455 0.00 0.00 34.43 3.24
2367 2443 2.740981 CTGTCTCTTGTTGCTCACATCC 59.259 50.000 0.00 0.00 34.43 3.51
2368 2444 3.397482 ACTGTCTCTTGTTGCTCACATC 58.603 45.455 0.00 0.00 34.43 3.06
2369 2445 3.482156 ACTGTCTCTTGTTGCTCACAT 57.518 42.857 0.00 0.00 34.43 3.21
2370 2446 2.988010 ACTGTCTCTTGTTGCTCACA 57.012 45.000 0.00 0.00 0.00 3.58
2371 2447 5.734855 TTTTACTGTCTCTTGTTGCTCAC 57.265 39.130 0.00 0.00 0.00 3.51
2391 2467 2.940158 AGACCCTGCGTAAACCTTTTT 58.060 42.857 0.00 0.00 0.00 1.94
2392 2468 2.651382 AGACCCTGCGTAAACCTTTT 57.349 45.000 0.00 0.00 0.00 2.27
2393 2469 2.651382 AAGACCCTGCGTAAACCTTT 57.349 45.000 0.00 0.00 0.00 3.11
2394 2470 3.775261 TTAAGACCCTGCGTAAACCTT 57.225 42.857 0.00 0.00 0.00 3.50
2395 2471 3.518303 AGATTAAGACCCTGCGTAAACCT 59.482 43.478 0.00 0.00 0.00 3.50
2396 2472 3.870274 AGATTAAGACCCTGCGTAAACC 58.130 45.455 0.00 0.00 0.00 3.27
2397 2473 6.973229 TTTAGATTAAGACCCTGCGTAAAC 57.027 37.500 0.00 0.00 0.00 2.01
2398 2474 7.879160 TCTTTTTAGATTAAGACCCTGCGTAAA 59.121 33.333 0.00 0.00 0.00 2.01
2399 2475 7.388437 TCTTTTTAGATTAAGACCCTGCGTAA 58.612 34.615 0.00 0.00 0.00 3.18
2400 2476 6.938507 TCTTTTTAGATTAAGACCCTGCGTA 58.061 36.000 0.00 0.00 0.00 4.42
2401 2477 5.801380 TCTTTTTAGATTAAGACCCTGCGT 58.199 37.500 0.00 0.00 0.00 5.24
2402 2478 6.737254 TTCTTTTTAGATTAAGACCCTGCG 57.263 37.500 0.00 0.00 30.53 5.18
2403 2479 7.176865 AGGTTTCTTTTTAGATTAAGACCCTGC 59.823 37.037 0.00 0.00 33.76 4.85
2404 2480 8.637196 AGGTTTCTTTTTAGATTAAGACCCTG 57.363 34.615 0.00 0.00 33.76 4.45
2405 2481 9.656323 AAAGGTTTCTTTTTAGATTAAGACCCT 57.344 29.630 0.00 0.00 40.01 4.34
2406 2482 9.692749 CAAAGGTTTCTTTTTAGATTAAGACCC 57.307 33.333 0.00 0.00 40.92 4.46
2407 2483 9.692749 CCAAAGGTTTCTTTTTAGATTAAGACC 57.307 33.333 0.00 0.00 40.92 3.85
2408 2484 9.692749 CCCAAAGGTTTCTTTTTAGATTAAGAC 57.307 33.333 0.00 0.00 40.92 3.01
2409 2485 8.364894 GCCCAAAGGTTTCTTTTTAGATTAAGA 58.635 33.333 0.00 0.00 40.92 2.10
2410 2486 7.328493 CGCCCAAAGGTTTCTTTTTAGATTAAG 59.672 37.037 0.00 0.00 40.92 1.85
2411 2487 7.149307 CGCCCAAAGGTTTCTTTTTAGATTAA 58.851 34.615 0.00 0.00 40.92 1.40
2412 2488 6.294843 CCGCCCAAAGGTTTCTTTTTAGATTA 60.295 38.462 0.00 0.00 40.92 1.75
2413 2489 5.510690 CCGCCCAAAGGTTTCTTTTTAGATT 60.511 40.000 0.00 0.00 40.92 2.40
2414 2490 4.021456 CCGCCCAAAGGTTTCTTTTTAGAT 60.021 41.667 0.00 0.00 40.92 1.98
2415 2491 3.319689 CCGCCCAAAGGTTTCTTTTTAGA 59.680 43.478 0.00 0.00 40.92 2.10
2416 2492 3.554129 CCCGCCCAAAGGTTTCTTTTTAG 60.554 47.826 0.00 0.00 40.92 1.85
2417 2493 2.365941 CCCGCCCAAAGGTTTCTTTTTA 59.634 45.455 0.00 0.00 40.92 1.52
2418 2494 1.140052 CCCGCCCAAAGGTTTCTTTTT 59.860 47.619 0.00 0.00 40.92 1.94
2419 2495 0.756294 CCCGCCCAAAGGTTTCTTTT 59.244 50.000 0.00 0.00 40.92 2.27
2420 2496 0.397957 ACCCGCCCAAAGGTTTCTTT 60.398 50.000 0.00 0.00 43.41 2.52
2421 2497 0.826256 GACCCGCCCAAAGGTTTCTT 60.826 55.000 0.00 0.00 36.17 2.52
2422 2498 1.228459 GACCCGCCCAAAGGTTTCT 60.228 57.895 0.00 0.00 36.17 2.52
2423 2499 2.273179 GGACCCGCCCAAAGGTTTC 61.273 63.158 0.00 0.00 36.17 2.78
2424 2500 2.203582 GGACCCGCCCAAAGGTTT 60.204 61.111 0.00 0.00 36.17 3.27
2437 2513 4.008933 AGACGTGCAGCAGGGACC 62.009 66.667 19.03 7.94 33.68 4.46
2438 2514 2.740055 CAGACGTGCAGCAGGGAC 60.740 66.667 19.03 12.15 33.95 4.46
2451 2527 4.008933 AGGGACACAGGCGCAGAC 62.009 66.667 10.83 0.00 0.00 3.51
2452 2528 4.007644 CAGGGACACAGGCGCAGA 62.008 66.667 10.83 0.00 0.00 4.26
2453 2529 3.832237 AACAGGGACACAGGCGCAG 62.832 63.158 10.83 3.04 0.00 5.18
2454 2530 3.872603 AACAGGGACACAGGCGCA 61.873 61.111 10.83 0.00 0.00 6.09
2455 2531 3.357079 CAACAGGGACACAGGCGC 61.357 66.667 0.00 0.00 0.00 6.53
2456 2532 2.111043 ACAACAGGGACACAGGCG 59.889 61.111 0.00 0.00 0.00 5.52
2457 2533 2.555547 GCACAACAGGGACACAGGC 61.556 63.158 0.00 0.00 0.00 4.85
2458 2534 1.898574 GGCACAACAGGGACACAGG 60.899 63.158 0.00 0.00 0.00 4.00
2459 2535 1.152984 TGGCACAACAGGGACACAG 60.153 57.895 0.00 0.00 31.92 3.66
2460 2536 3.002371 TGGCACAACAGGGACACA 58.998 55.556 0.00 0.00 31.92 3.72
2476 2552 2.436646 GCACCCGTCCAGGACATG 60.437 66.667 20.13 14.51 45.00 3.21
2477 2553 2.927856 TGCACCCGTCCAGGACAT 60.928 61.111 20.13 1.14 45.00 3.06
2478 2554 3.625897 CTGCACCCGTCCAGGACA 61.626 66.667 20.13 0.00 45.00 4.02
2484 2560 4.760047 ATCGTGCTGCACCCGTCC 62.760 66.667 25.61 1.27 0.00 4.79
2485 2561 2.742372 AATCGTGCTGCACCCGTC 60.742 61.111 25.61 2.04 0.00 4.79
2486 2562 3.049674 CAATCGTGCTGCACCCGT 61.050 61.111 25.61 9.97 0.00 5.28
2487 2563 3.027170 GACAATCGTGCTGCACCCG 62.027 63.158 25.61 15.99 0.00 5.28
2488 2564 1.308069 ATGACAATCGTGCTGCACCC 61.308 55.000 25.61 3.59 0.00 4.61
2489 2565 0.097674 GATGACAATCGTGCTGCACC 59.902 55.000 25.61 11.78 0.00 5.01
2490 2566 1.081892 AGATGACAATCGTGCTGCAC 58.918 50.000 22.38 22.38 37.92 4.57
2491 2567 1.081094 CAGATGACAATCGTGCTGCA 58.919 50.000 0.00 0.00 37.92 4.41
2492 2568 1.081892 ACAGATGACAATCGTGCTGC 58.918 50.000 0.00 0.00 37.92 5.25
2493 2569 4.926860 TTTACAGATGACAATCGTGCTG 57.073 40.909 0.00 0.00 37.92 4.41
2494 2570 4.393062 CCTTTTACAGATGACAATCGTGCT 59.607 41.667 0.00 0.00 37.92 4.40
2495 2571 4.391830 TCCTTTTACAGATGACAATCGTGC 59.608 41.667 0.00 0.00 37.92 5.34
2496 2572 6.480524 TTCCTTTTACAGATGACAATCGTG 57.519 37.500 0.00 0.00 37.92 4.35
2497 2573 6.934645 TCTTTCCTTTTACAGATGACAATCGT 59.065 34.615 0.00 0.00 37.92 3.73
2498 2574 7.364522 TCTTTCCTTTTACAGATGACAATCG 57.635 36.000 0.00 0.00 37.92 3.34
2499 2575 8.787852 AGTTCTTTCCTTTTACAGATGACAATC 58.212 33.333 0.00 0.00 0.00 2.67
2500 2576 8.697507 AGTTCTTTCCTTTTACAGATGACAAT 57.302 30.769 0.00 0.00 0.00 2.71
2501 2577 8.519799 AAGTTCTTTCCTTTTACAGATGACAA 57.480 30.769 0.00 0.00 0.00 3.18
2502 2578 9.273016 CTAAGTTCTTTCCTTTTACAGATGACA 57.727 33.333 0.00 0.00 0.00 3.58
2503 2579 8.722394 CCTAAGTTCTTTCCTTTTACAGATGAC 58.278 37.037 0.00 0.00 0.00 3.06
2504 2580 8.437575 ACCTAAGTTCTTTCCTTTTACAGATGA 58.562 33.333 0.00 0.00 0.00 2.92
2505 2581 8.507249 CACCTAAGTTCTTTCCTTTTACAGATG 58.493 37.037 0.00 0.00 0.00 2.90
2506 2582 8.437575 TCACCTAAGTTCTTTCCTTTTACAGAT 58.562 33.333 0.00 0.00 0.00 2.90
2507 2583 7.798071 TCACCTAAGTTCTTTCCTTTTACAGA 58.202 34.615 0.00 0.00 0.00 3.41
2508 2584 8.446599 TTCACCTAAGTTCTTTCCTTTTACAG 57.553 34.615 0.00 0.00 0.00 2.74
2509 2585 8.810990 TTTCACCTAAGTTCTTTCCTTTTACA 57.189 30.769 0.00 0.00 0.00 2.41
2510 2586 8.900781 ACTTTCACCTAAGTTCTTTCCTTTTAC 58.099 33.333 0.00 0.00 34.81 2.01
2511 2587 9.470399 AACTTTCACCTAAGTTCTTTCCTTTTA 57.530 29.630 0.00 0.00 43.04 1.52
2512 2588 7.956328 ACTTTCACCTAAGTTCTTTCCTTTT 57.044 32.000 0.00 0.00 34.81 2.27
2513 2589 7.396339 ACAACTTTCACCTAAGTTCTTTCCTTT 59.604 33.333 0.00 0.00 44.33 3.11
2514 2590 6.890268 ACAACTTTCACCTAAGTTCTTTCCTT 59.110 34.615 0.00 0.00 44.33 3.36
2515 2591 6.424032 ACAACTTTCACCTAAGTTCTTTCCT 58.576 36.000 0.00 0.00 44.33 3.36
2516 2592 6.511282 CGACAACTTTCACCTAAGTTCTTTCC 60.511 42.308 0.00 0.00 44.33 3.13
2517 2593 6.419771 CGACAACTTTCACCTAAGTTCTTTC 58.580 40.000 0.00 0.00 44.33 2.62
2518 2594 6.359480 CGACAACTTTCACCTAAGTTCTTT 57.641 37.500 0.00 0.00 44.33 2.52
2519 2595 5.986004 CGACAACTTTCACCTAAGTTCTT 57.014 39.130 0.00 0.00 44.33 2.52


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

AutoCloner maintained by Alex Coulton.