Multiple sequence alignment - TraesCS4A01G393800

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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 TraesCS4A01G393800 chr4A 100.000 3626 0 0 1 3626 669382551 669386176 0.000000e+00 6697
1 TraesCS4A01G393800 chr7D 96.654 2331 72 3 1 2328 20460905 20463232 0.000000e+00 3868
2 TraesCS4A01G393800 chr7D 84.672 2290 336 10 1 2281 555195907 555193624 0.000000e+00 2270
3 TraesCS4A01G393800 chr7D 84.428 2299 348 7 2 2293 89532555 89530260 0.000000e+00 2254
4 TraesCS4A01G393800 chr7D 84.426 2273 331 17 1 2260 20404789 20407051 0.000000e+00 2215
5 TraesCS4A01G393800 chr7D 90.411 219 20 1 2788 3005 20463563 20463781 1.650000e-73 287
6 TraesCS4A01G393800 chr7D 84.395 314 17 5 2412 2693 20463248 20463561 2.760000e-71 279
7 TraesCS4A01G393800 chr7D 92.632 95 6 1 2324 2418 93543106 93543013 6.320000e-28 135
8 TraesCS4A01G393800 chr7A 96.353 2331 79 3 1 2328 20780016 20782343 0.000000e+00 3829
9 TraesCS4A01G393800 chr7A 83.905 2305 346 19 1 2291 20660135 20662428 0.000000e+00 2178
10 TraesCS4A01G393800 chr7A 93.013 229 14 2 2786 3012 20782672 20782900 2.090000e-87 333
11 TraesCS4A01G393800 chr7A 83.828 303 14 5 2412 2679 20782359 20782661 4.650000e-64 255
12 TraesCS4A01G393800 chr7A 91.262 103 8 1 2690 2792 735412104 735412205 4.880000e-29 139
13 TraesCS4A01G393800 chr2A 85.150 2303 325 13 1 2293 733088263 733090558 0.000000e+00 2342
14 TraesCS4A01G393800 chr2D 85.000 2300 332 8 1 2292 598814561 598816855 0.000000e+00 2324
15 TraesCS4A01G393800 chr2D 83.252 615 74 9 3013 3626 91228484 91229070 4.120000e-149 538
16 TraesCS4A01G393800 chr2D 90.909 99 9 0 2311 2409 325754002 325754100 2.270000e-27 134
17 TraesCS4A01G393800 chr2B 84.752 2302 336 9 1 2293 727686517 727688812 0.000000e+00 2292
18 TraesCS4A01G393800 chr2B 87.234 470 52 2 3098 3567 36812057 36811596 2.480000e-146 529
19 TraesCS4A01G393800 chr2B 81.270 630 86 15 2998 3626 799853416 799852818 7.040000e-132 481
20 TraesCS4A01G393800 chr2B 90.000 100 9 1 2690 2789 719528660 719528562 1.060000e-25 128
21 TraesCS4A01G393800 chr5B 84.339 613 87 5 3015 3622 673515681 673515073 3.120000e-165 592
22 TraesCS4A01G393800 chr5B 87.740 416 47 1 3012 3423 689912412 689911997 1.960000e-132 483
23 TraesCS4A01G393800 chr5B 90.816 98 8 1 2690 2787 13176058 13175962 2.940000e-26 130
24 TraesCS4A01G393800 chr5B 89.320 103 10 1 2690 2792 296853989 296853888 1.060000e-25 128
25 TraesCS4A01G393800 chr5D 85.662 551 75 2 3013 3562 533535047 533534500 8.730000e-161 577
26 TraesCS4A01G393800 chr5D 87.981 416 46 1 3012 3423 519881215 519880800 4.210000e-134 488
27 TraesCS4A01G393800 chr5D 91.176 102 8 1 2687 2788 65990488 65990588 1.760000e-28 137
28 TraesCS4A01G393800 chr5D 89.320 103 9 2 2690 2792 51073382 51073282 1.060000e-25 128
29 TraesCS4A01G393800 chr1B 90.181 387 36 2 3011 3396 9291551 9291166 1.500000e-138 503
30 TraesCS4A01G393800 chr1B 90.181 387 36 2 3011 3396 9322053 9321668 1.500000e-138 503
31 TraesCS4A01G393800 chr1D 89.922 387 36 3 3011 3396 6977273 6976889 2.510000e-136 496
32 TraesCS4A01G393800 chr4D 88.452 407 43 1 3021 3423 496334369 496333963 4.210000e-134 488
33 TraesCS4A01G393800 chr6B 85.637 369 45 5 3259 3626 682193660 682194021 7.350000e-102 381
34 TraesCS4A01G393800 chr6B 90.909 99 8 1 2325 2423 100361406 100361309 8.170000e-27 132
35 TraesCS4A01G393800 chr6B 89.320 103 8 3 2690 2791 58128461 58128361 3.800000e-25 126
36 TraesCS4A01G393800 chr3B 89.037 301 27 2 3327 3626 736734751 736735046 5.720000e-98 368
37 TraesCS4A01G393800 chr3B 92.632 95 5 2 2319 2413 265853267 265853359 6.320000e-28 135
38 TraesCS4A01G393800 chr3B 91.000 100 6 3 2318 2417 156760441 156760537 8.170000e-27 132
39 TraesCS4A01G393800 chr3B 88.785 107 11 1 2685 2791 256253812 256253707 2.940000e-26 130
40 TraesCS4A01G393800 chrUn 84.574 188 14 9 3442 3625 288093625 288093449 4.810000e-39 172
41 TraesCS4A01G393800 chr3A 92.079 101 4 3 2320 2419 720848423 720848326 4.880000e-29 139
42 TraesCS4A01G393800 chr3A 92.708 96 5 2 2325 2419 750351082 750350988 1.760000e-28 137
43 TraesCS4A01G393800 chr5A 92.708 96 5 2 2314 2409 464132857 464132764 1.760000e-28 137
44 TraesCS4A01G393800 chr7B 90.291 103 9 1 2690 2792 744398544 744398443 2.270000e-27 134
45 TraesCS4A01G393800 chr7B 93.590 78 5 0 3548 3625 73607193 73607270 2.290000e-22 117
46 TraesCS4A01G393800 chr1A 89.423 104 9 2 2307 2409 14584405 14584507 2.940000e-26 130
47 TraesCS4A01G393800 chr3D 93.671 79 5 0 3548 3626 38626700 38626778 6.360000e-23 119


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 TraesCS4A01G393800 chr4A 669382551 669386176 3625 False 6697.000000 6697 100.000000 1 3626 1 chr4A.!!$F1 3625
1 TraesCS4A01G393800 chr7D 555193624 555195907 2283 True 2270.000000 2270 84.672000 1 2281 1 chr7D.!!$R3 2280
2 TraesCS4A01G393800 chr7D 89530260 89532555 2295 True 2254.000000 2254 84.428000 2 2293 1 chr7D.!!$R1 2291
3 TraesCS4A01G393800 chr7D 20404789 20407051 2262 False 2215.000000 2215 84.426000 1 2260 1 chr7D.!!$F1 2259
4 TraesCS4A01G393800 chr7D 20460905 20463781 2876 False 1478.000000 3868 90.486667 1 3005 3 chr7D.!!$F2 3004
5 TraesCS4A01G393800 chr7A 20660135 20662428 2293 False 2178.000000 2178 83.905000 1 2291 1 chr7A.!!$F1 2290
6 TraesCS4A01G393800 chr7A 20780016 20782900 2884 False 1472.333333 3829 91.064667 1 3012 3 chr7A.!!$F3 3011
7 TraesCS4A01G393800 chr2A 733088263 733090558 2295 False 2342.000000 2342 85.150000 1 2293 1 chr2A.!!$F1 2292
8 TraesCS4A01G393800 chr2D 598814561 598816855 2294 False 2324.000000 2324 85.000000 1 2292 1 chr2D.!!$F3 2291
9 TraesCS4A01G393800 chr2D 91228484 91229070 586 False 538.000000 538 83.252000 3013 3626 1 chr2D.!!$F1 613
10 TraesCS4A01G393800 chr2B 727686517 727688812 2295 False 2292.000000 2292 84.752000 1 2293 1 chr2B.!!$F1 2292
11 TraesCS4A01G393800 chr2B 799852818 799853416 598 True 481.000000 481 81.270000 2998 3626 1 chr2B.!!$R3 628
12 TraesCS4A01G393800 chr5B 673515073 673515681 608 True 592.000000 592 84.339000 3015 3622 1 chr5B.!!$R3 607
13 TraesCS4A01G393800 chr5D 533534500 533535047 547 True 577.000000 577 85.662000 3013 3562 1 chr5D.!!$R3 549

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
454 455 3.055385 TGACTTGTCTAGGGCGCTTATTT 60.055 43.478 9.23 0.0 0.0 1.40 F
2341 2349 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 2401 0.113776 ACAGTACTTCCTCCGTCCCA 59.886 55.0 0.0 0.0 0.00 4.37 R
3324 3372 0.811281 ATGCCTTTTTGCTAGTCGGC 59.189 50.0 0.0 0.0 38.01 5.54 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
27 28 6.317140 GCTCAAAATACATGGTCAAGAGATCA 59.683 38.462 0.00 0.00 39.67 2.92
112 113 3.999663 CAGAGAAAAACTAGAGCAGTGGG 59.000 47.826 0.00 0.00 37.63 4.61
139 140 5.009310 GCATGTGATGATTTGGAATGCTCTA 59.991 40.000 0.00 0.00 36.78 2.43
454 455 3.055385 TGACTTGTCTAGGGCGCTTATTT 60.055 43.478 9.23 0.00 0.00 1.40
456 457 5.093849 ACTTGTCTAGGGCGCTTATTTAA 57.906 39.130 9.23 0.00 0.00 1.52
593 597 7.934120 TCTCTTTTATAAGAAAGCCTATCCTGC 59.066 37.037 0.00 0.00 39.80 4.85
605 609 4.596643 AGCCTATCCTGCAAGAGATACAAT 59.403 41.667 0.00 0.00 34.07 2.71
621 625 5.533903 AGATACAATTCATGAATGTCCAGCC 59.466 40.000 21.39 8.18 0.00 4.85
869 873 5.484173 TTCCTGTATTGCAGCTTATTTCG 57.516 39.130 0.00 0.00 43.71 3.46
963 967 4.926832 GGTGAAAGCACTCTAGAAGAAGTC 59.073 45.833 0.00 0.00 44.52 3.01
1246 1251 4.180817 TGTCATTACAGTGGACAATAGCG 58.819 43.478 0.00 0.00 38.50 4.26
1248 1253 5.105675 TGTCATTACAGTGGACAATAGCGTA 60.106 40.000 0.00 0.00 38.50 4.42
1340 1345 2.566746 ACCCATTGAGAAGATCCCAGT 58.433 47.619 0.00 0.00 0.00 4.00
1366 1371 7.571919 TGCTATTGGAGATCTTTTCAATCTCT 58.428 34.615 17.38 4.41 45.56 3.10
1575 1580 2.819608 GTGTTCCAGTGGTGTGCATATT 59.180 45.455 9.54 0.00 0.00 1.28
1595 1600 1.177401 GCCAGTGGTCTTGGAAATCC 58.823 55.000 11.74 0.00 0.00 3.01
1737 1742 4.098044 CGCATTAGGGACTCTCTAGTTCAA 59.902 45.833 0.00 0.00 41.75 2.69
1770 1775 1.576421 CAACCTTTCTGTGAGCGCC 59.424 57.895 2.29 0.00 0.00 6.53
2051 2059 2.155279 GTTTCCCAAGCTGAAGACTCC 58.845 52.381 0.00 0.00 0.00 3.85
2059 2067 1.622811 AGCTGAAGACTCCTCAGTTGG 59.377 52.381 6.54 0.00 34.27 3.77
2096 2104 4.033990 TGAAGCAGCTAGAGATACAACG 57.966 45.455 0.00 0.00 0.00 4.10
2281 2289 0.982704 ACAGTGGCAGCATTCTCTCT 59.017 50.000 0.00 0.00 0.00 3.10
2305 2313 5.819379 TGAGAATGACCTATCAGAAATGTGC 59.181 40.000 0.00 0.00 38.57 4.57
2334 2342 3.896317 GCAATAGCTACTCCCTCCG 57.104 57.895 0.00 0.00 37.91 4.63
2335 2343 1.041437 GCAATAGCTACTCCCTCCGT 58.959 55.000 0.00 0.00 37.91 4.69
2336 2344 1.000052 GCAATAGCTACTCCCTCCGTC 60.000 57.143 0.00 0.00 37.91 4.79
2337 2345 1.614413 CAATAGCTACTCCCTCCGTCC 59.386 57.143 0.00 0.00 0.00 4.79
2339 2347 1.284111 TAGCTACTCCCTCCGTCCCA 61.284 60.000 0.00 0.00 0.00 4.37
2340 2348 1.457831 GCTACTCCCTCCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
2341 2349 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
2343 2351 2.890814 CTACTCCCTCCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
2344 2352 3.816842 GCTACTCCCTCCGTCCCATAATA 60.817 52.174 0.00 0.00 0.00 0.98
2345 2353 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2346 2354 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2347 2355 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2348 2356 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2349 2357 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2350 2358 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2351 2359 6.269194 TCCCTCCGTCCCATAATATAAGAAT 58.731 40.000 0.00 0.00 0.00 2.40
2352 2360 6.156256 TCCCTCCGTCCCATAATATAAGAATG 59.844 42.308 0.00 0.00 0.00 2.67
2353 2361 5.817816 CCTCCGTCCCATAATATAAGAATGC 59.182 44.000 0.00 0.00 0.00 3.56
2354 2362 6.352222 CCTCCGTCCCATAATATAAGAATGCT 60.352 42.308 0.00 0.00 0.00 3.79
2355 2363 7.016153 TCCGTCCCATAATATAAGAATGCTT 57.984 36.000 0.00 0.00 38.15 3.91
2356 2364 7.458397 TCCGTCCCATAATATAAGAATGCTTT 58.542 34.615 0.00 0.00 35.56 3.51
2357 2365 7.942341 TCCGTCCCATAATATAAGAATGCTTTT 59.058 33.333 0.00 0.00 35.56 2.27
2358 2366 8.023128 CCGTCCCATAATATAAGAATGCTTTTG 58.977 37.037 0.00 0.00 35.56 2.44
2359 2367 8.783093 CGTCCCATAATATAAGAATGCTTTTGA 58.217 33.333 0.00 0.00 35.56 2.69
2360 2368 9.899226 GTCCCATAATATAAGAATGCTTTTGAC 57.101 33.333 0.00 0.00 35.56 3.18
2361 2369 9.639563 TCCCATAATATAAGAATGCTTTTGACA 57.360 29.630 0.00 0.00 35.56 3.58
2362 2370 9.683069 CCCATAATATAAGAATGCTTTTGACAC 57.317 33.333 0.00 0.00 35.56 3.67
2368 2376 7.986085 ATAAGAATGCTTTTGACACTACACT 57.014 32.000 0.00 0.00 35.56 3.55
2370 2378 7.426929 AAGAATGCTTTTGACACTACACTAG 57.573 36.000 0.00 0.00 0.00 2.57
2371 2379 6.525629 AGAATGCTTTTGACACTACACTAGT 58.474 36.000 0.00 0.00 40.28 2.57
2372 2380 7.667557 AGAATGCTTTTGACACTACACTAGTA 58.332 34.615 0.00 0.00 37.23 1.82
2373 2381 8.314751 AGAATGCTTTTGACACTACACTAGTAT 58.685 33.333 0.00 0.00 37.23 2.12
2374 2382 9.582431 GAATGCTTTTGACACTACACTAGTATA 57.418 33.333 0.00 0.00 37.23 1.47
2375 2383 9.938280 AATGCTTTTGACACTACACTAGTATAA 57.062 29.630 0.00 0.00 37.23 0.98
2376 2384 9.938280 ATGCTTTTGACACTACACTAGTATAAA 57.062 29.630 0.00 0.00 37.23 1.40
2377 2385 9.767228 TGCTTTTGACACTACACTAGTATAAAA 57.233 29.630 0.00 0.00 37.23 1.52
2400 2408 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
2401 2409 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
2402 2410 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
2403 2411 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
2404 2412 5.184479 CGTTCTTATATTATGGGACGGAGGA 59.816 44.000 0.00 0.00 0.00 3.71
2405 2413 6.294899 CGTTCTTATATTATGGGACGGAGGAA 60.295 42.308 0.00 0.00 0.00 3.36
2406 2414 6.852420 TCTTATATTATGGGACGGAGGAAG 57.148 41.667 0.00 0.00 0.00 3.46
2407 2415 6.320518 TCTTATATTATGGGACGGAGGAAGT 58.679 40.000 0.00 0.00 0.00 3.01
2408 2416 7.472741 TCTTATATTATGGGACGGAGGAAGTA 58.527 38.462 0.00 0.00 0.00 2.24
2409 2417 5.997384 ATATTATGGGACGGAGGAAGTAC 57.003 43.478 0.00 0.00 0.00 2.73
2410 2418 3.393426 TTATGGGACGGAGGAAGTACT 57.607 47.619 0.00 0.00 0.00 2.73
2548 2567 4.335037 GCAGATCAAGGAAAAGGACAGATC 59.665 45.833 0.00 0.00 0.00 2.75
2583 2626 1.066502 GTCTGGGACTCCTCTGCTTTC 60.067 57.143 0.00 0.00 0.00 2.62
2585 2628 1.627834 CTGGGACTCCTCTGCTTTCTT 59.372 52.381 0.00 0.00 0.00 2.52
2640 2683 3.223435 ACGGTGATGCTACTGCTACTAT 58.777 45.455 0.00 0.00 40.48 2.12
2654 2697 5.159273 TGCTACTATTGTTGGTGTCATCA 57.841 39.130 0.00 0.00 0.00 3.07
2669 2712 5.284079 GTGTCATCATGTGCTTTTTCTTGT 58.716 37.500 0.00 0.00 0.00 3.16
2679 2722 5.105797 TGTGCTTTTTCTTGTCAAGTGTGAT 60.106 36.000 12.30 0.00 35.80 3.06
2681 2724 7.141363 GTGCTTTTTCTTGTCAAGTGTGATAT 58.859 34.615 12.30 0.00 35.80 1.63
2683 2726 7.862372 TGCTTTTTCTTGTCAAGTGTGATATTC 59.138 33.333 12.30 0.00 35.80 1.75
2685 2728 9.604626 CTTTTTCTTGTCAAGTGTGATATTCTC 57.395 33.333 12.30 0.00 35.80 2.87
2689 2732 7.901029 TCTTGTCAAGTGTGATATTCTCTTCT 58.099 34.615 12.30 0.00 35.80 2.85
2690 2733 9.025041 TCTTGTCAAGTGTGATATTCTCTTCTA 57.975 33.333 12.30 0.00 35.80 2.10
2691 2734 8.988064 TTGTCAAGTGTGATATTCTCTTCTAC 57.012 34.615 0.00 0.00 35.80 2.59
2692 2735 8.354711 TGTCAAGTGTGATATTCTCTTCTACT 57.645 34.615 0.00 0.00 35.80 2.57
2693 2736 8.462811 TGTCAAGTGTGATATTCTCTTCTACTC 58.537 37.037 0.00 0.00 35.80 2.59
2694 2737 7.918562 GTCAAGTGTGATATTCTCTTCTACTCC 59.081 40.741 0.00 0.00 35.80 3.85
2695 2738 6.969993 AGTGTGATATTCTCTTCTACTCCC 57.030 41.667 0.00 0.00 0.00 4.30
2696 2739 6.678547 AGTGTGATATTCTCTTCTACTCCCT 58.321 40.000 0.00 0.00 0.00 4.20
2697 2740 6.775629 AGTGTGATATTCTCTTCTACTCCCTC 59.224 42.308 0.00 0.00 0.00 4.30
2698 2741 6.775629 GTGTGATATTCTCTTCTACTCCCTCT 59.224 42.308 0.00 0.00 0.00 3.69
2699 2742 6.775142 TGTGATATTCTCTTCTACTCCCTCTG 59.225 42.308 0.00 0.00 0.00 3.35
2700 2743 6.775629 GTGATATTCTCTTCTACTCCCTCTGT 59.224 42.308 0.00 0.00 0.00 3.41
2701 2744 7.001674 TGATATTCTCTTCTACTCCCTCTGTC 58.998 42.308 0.00 0.00 0.00 3.51
2702 2745 3.655615 TCTCTTCTACTCCCTCTGTCC 57.344 52.381 0.00 0.00 0.00 4.02
2703 2746 2.242708 TCTCTTCTACTCCCTCTGTCCC 59.757 54.545 0.00 0.00 0.00 4.46
2704 2747 2.000803 TCTTCTACTCCCTCTGTCCCA 58.999 52.381 0.00 0.00 0.00 4.37
2705 2748 2.382305 TCTTCTACTCCCTCTGTCCCAA 59.618 50.000 0.00 0.00 0.00 4.12
2706 2749 3.173965 CTTCTACTCCCTCTGTCCCAAA 58.826 50.000 0.00 0.00 0.00 3.28
2707 2750 3.269592 TCTACTCCCTCTGTCCCAAAA 57.730 47.619 0.00 0.00 0.00 2.44
2708 2751 3.593942 TCTACTCCCTCTGTCCCAAAAA 58.406 45.455 0.00 0.00 0.00 1.94
2709 2752 4.175962 TCTACTCCCTCTGTCCCAAAAAT 58.824 43.478 0.00 0.00 0.00 1.82
2710 2753 5.347124 TCTACTCCCTCTGTCCCAAAAATA 58.653 41.667 0.00 0.00 0.00 1.40
2711 2754 5.788533 TCTACTCCCTCTGTCCCAAAAATAA 59.211 40.000 0.00 0.00 0.00 1.40
2712 2755 4.923415 ACTCCCTCTGTCCCAAAAATAAG 58.077 43.478 0.00 0.00 0.00 1.73
2713 2756 4.354087 ACTCCCTCTGTCCCAAAAATAAGT 59.646 41.667 0.00 0.00 0.00 2.24
2714 2757 5.162980 ACTCCCTCTGTCCCAAAAATAAGTT 60.163 40.000 0.00 0.00 0.00 2.66
2715 2758 5.711698 TCCCTCTGTCCCAAAAATAAGTTT 58.288 37.500 0.00 0.00 0.00 2.66
2716 2759 5.773176 TCCCTCTGTCCCAAAAATAAGTTTC 59.227 40.000 0.00 0.00 0.00 2.78
2717 2760 5.775195 CCCTCTGTCCCAAAAATAAGTTTCT 59.225 40.000 0.00 0.00 0.00 2.52
2718 2761 6.267699 CCCTCTGTCCCAAAAATAAGTTTCTT 59.732 38.462 0.00 0.00 0.00 2.52
2719 2762 7.450323 CCCTCTGTCCCAAAAATAAGTTTCTTA 59.550 37.037 0.00 0.00 0.00 2.10
2720 2763 8.856103 CCTCTGTCCCAAAAATAAGTTTCTTAA 58.144 33.333 0.00 0.00 0.00 1.85
2721 2764 9.678941 CTCTGTCCCAAAAATAAGTTTCTTAAC 57.321 33.333 0.00 0.00 34.36 2.01
2722 2765 9.416284 TCTGTCCCAAAAATAAGTTTCTTAACT 57.584 29.630 0.00 0.00 46.44 2.24
2775 2818 8.754991 TTAAACTTGAGACACTTATTTTGGGA 57.245 30.769 0.00 0.00 0.00 4.37
2776 2819 6.635030 AACTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 0.00 4.46
2777 2820 4.755123 ACTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
2778 2821 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
2779 2822 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
2780 2823 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
2781 2824 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2782 2825 2.640826 ACACTTATTTTGGGACGGAGGA 59.359 45.455 0.00 0.00 0.00 3.71
2783 2826 3.073356 ACACTTATTTTGGGACGGAGGAA 59.927 43.478 0.00 0.00 0.00 3.36
2784 2827 3.689649 CACTTATTTTGGGACGGAGGAAG 59.310 47.826 0.00 0.00 0.00 3.46
2803 2849 9.569122 GGAGGAAGTATTATTGTGGCTTATTAA 57.431 33.333 0.00 0.00 0.00 1.40
2814 2860 7.915293 TTGTGGCTTATTAAGAGATCGAAAA 57.085 32.000 7.63 0.00 0.00 2.29
2849 2895 9.326339 GTTTCCGTGTTCAGACTTAATTATTTC 57.674 33.333 0.00 0.00 0.00 2.17
2850 2896 8.610248 TTCCGTGTTCAGACTTAATTATTTCA 57.390 30.769 0.00 0.00 0.00 2.69
2877 2924 4.981794 ACTTGTAGTTGTTTCAACTGTGC 58.018 39.130 20.71 12.94 0.00 4.57
2892 2940 0.387112 TGTGCACTGCTATTTTGCGC 60.387 50.000 19.41 0.00 45.11 6.09
2917 2965 5.231991 GTGTGCTTGTTGTTGAACCTATTTG 59.768 40.000 0.00 0.00 0.00 2.32
2920 2968 5.359576 TGCTTGTTGTTGAACCTATTTGAGT 59.640 36.000 0.00 0.00 0.00 3.41
2926 2974 4.582656 TGTTGAACCTATTTGAGTTGTGGG 59.417 41.667 0.00 0.00 0.00 4.61
2960 3008 5.757850 AGAAGACTTGGTTTGTGATTCAC 57.242 39.130 9.93 9.93 34.56 3.18
3019 3067 2.159179 TGATGCCTGGCTCACTACTA 57.841 50.000 21.03 0.00 0.00 1.82
3043 3091 0.246086 TTTCGTATACGCCGGGTGTT 59.754 50.000 19.71 9.31 39.60 3.32
3046 3094 1.516892 GTATACGCCGGGTGTTGGA 59.483 57.895 19.71 0.69 0.00 3.53
3053 3101 1.752198 CCGGGTGTTGGAGTCTTCA 59.248 57.895 0.00 0.00 0.00 3.02
3080 3128 1.504359 CTAAAACACGGGCACTCGAA 58.496 50.000 0.00 0.00 0.00 3.71
3083 3131 1.314730 AAACACGGGCACTCGAAAAT 58.685 45.000 0.00 0.00 0.00 1.82
3087 3135 2.006888 CACGGGCACTCGAAAATGTAT 58.993 47.619 0.00 0.00 0.00 2.29
3093 3141 4.873827 GGGCACTCGAAAATGTATAGAACA 59.126 41.667 0.00 0.00 43.86 3.18
3103 3151 5.435686 AATGTATAGAACACCAAGAGCCA 57.564 39.130 0.00 0.00 42.09 4.75
3148 3196 3.243501 GGCAAACACATGATAATGCCGAT 60.244 43.478 16.99 0.00 43.26 4.18
3222 3270 0.884704 ATCTGGTCACACACGGCAAC 60.885 55.000 0.00 0.00 0.00 4.17
3247 3295 3.049674 CACGTGGCACATTCGGCT 61.050 61.111 19.09 0.00 44.52 5.52
3324 3372 0.541863 ATTTAGTCCCACCTCGCCTG 59.458 55.000 0.00 0.00 0.00 4.85
3340 3388 0.804989 CCTGCCGACTAGCAAAAAGG 59.195 55.000 0.00 0.00 43.52 3.11
3344 3392 1.202348 GCCGACTAGCAAAAAGGCATT 59.798 47.619 7.50 0.00 43.65 3.56
3397 3445 5.662674 AGCTTCGGTCTTCATTAGTAAGT 57.337 39.130 0.00 0.00 0.00 2.24
3423 3471 5.067413 TCCGTACAGTCACTATGAATCTTCC 59.933 44.000 0.00 0.00 0.00 3.46
3432 3480 2.717639 ATGAATCTTCCTGTTCCGGG 57.282 50.000 0.00 0.00 0.00 5.73
3433 3481 1.358152 TGAATCTTCCTGTTCCGGGT 58.642 50.000 0.00 0.00 0.00 5.28
3480 3530 2.136298 TCTAAAAATGGATGCCGGCA 57.864 45.000 34.80 34.80 0.00 5.69
3552 3605 1.760613 TGGAGCAATAGTTACCCGAGG 59.239 52.381 0.00 0.00 0.00 4.63
3595 3648 3.421844 GCCACCATCAAAGTTTAGTCCT 58.578 45.455 0.00 0.00 0.00 3.85
3601 3654 5.546499 ACCATCAAAGTTTAGTCCTACCTCA 59.454 40.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.849804 ACGTGAAATATTTGCTAGATCTTGT 57.150 32.000 5.17 0.00 0.00 3.16
112 113 3.872511 TTCCAAATCATCACATGCCAC 57.127 42.857 0.00 0.00 0.00 5.01
139 140 3.228453 CCATTCCAAGCAAGGCTATGAT 58.772 45.455 0.00 0.00 38.25 2.45
456 457 8.643324 GTGATTATCAATCTACTACCCTTGTCT 58.357 37.037 0.00 0.00 38.72 3.41
591 595 7.201758 GGACATTCATGAATTGTATCTCTTGCA 60.202 37.037 18.41 0.00 0.00 4.08
592 596 7.137426 GGACATTCATGAATTGTATCTCTTGC 58.863 38.462 18.41 6.05 0.00 4.01
593 597 8.217131 TGGACATTCATGAATTGTATCTCTTG 57.783 34.615 18.41 7.43 0.00 3.02
605 609 1.278985 ACTCGGCTGGACATTCATGAA 59.721 47.619 11.26 11.26 0.00 2.57
621 625 1.522668 TGGACAATGGCTTCAACTCG 58.477 50.000 0.00 0.00 0.00 4.18
783 787 5.324409 TGCAAAACATTCCTTATCTGACCT 58.676 37.500 0.00 0.00 0.00 3.85
869 873 7.653767 TTCCGTTTGAAAAGATAGTCTTCTC 57.346 36.000 0.00 0.00 35.27 2.87
1246 1251 6.317391 AGAGGTAGTATAGTGAACGTTGGTAC 59.683 42.308 5.00 1.86 0.00 3.34
1248 1253 5.125097 CAGAGGTAGTATAGTGAACGTTGGT 59.875 44.000 5.00 0.00 0.00 3.67
1340 1345 8.051535 AGAGATTGAAAAGATCTCCAATAGCAA 58.948 33.333 14.20 6.01 46.88 3.91
1366 1371 3.637911 ATTACGTAGACCCAAATGGCA 57.362 42.857 0.00 0.00 37.83 4.92
1575 1580 1.547675 GGATTTCCAAGACCACTGGCA 60.548 52.381 0.00 0.00 35.64 4.92
1595 1600 1.891060 GAGCGTCTGCAGGTTTGTCG 61.891 60.000 15.13 10.27 46.23 4.35
1671 1676 3.297134 TTCCACAACCTCAAGCTTCTT 57.703 42.857 0.00 0.00 0.00 2.52
1737 1742 2.802719 AGGTTGGACAAATACCGCATT 58.197 42.857 0.00 0.00 37.04 3.56
2051 2059 1.197430 AGGCAGGTCTCCCAACTGAG 61.197 60.000 0.00 0.00 34.21 3.35
2059 2067 2.484594 GCTTCAGATTAGGCAGGTCTCC 60.485 54.545 0.00 0.00 0.00 3.71
2111 2119 9.190317 GGTTGATTAAGAATAATCTTTCCAGGT 57.810 33.333 0.00 0.00 43.43 4.00
2281 2289 5.819379 GCACATTTCTGATAGGTCATTCTCA 59.181 40.000 0.00 0.00 32.98 3.27
2294 2302 4.788201 GCTTACAAACGTGCACATTTCTGA 60.788 41.667 18.64 0.00 0.00 3.27
2328 2336 6.349300 CATTCTTATATTATGGGACGGAGGG 58.651 44.000 0.00 0.00 0.00 4.30
2329 2337 5.817816 GCATTCTTATATTATGGGACGGAGG 59.182 44.000 0.00 0.00 0.00 4.30
2332 2340 7.687941 AAAGCATTCTTATATTATGGGACGG 57.312 36.000 0.00 0.00 31.02 4.79
2333 2341 8.783093 TCAAAAGCATTCTTATATTATGGGACG 58.217 33.333 0.00 0.00 31.02 4.79
2334 2342 9.899226 GTCAAAAGCATTCTTATATTATGGGAC 57.101 33.333 0.00 0.00 31.02 4.46
2335 2343 9.639563 TGTCAAAAGCATTCTTATATTATGGGA 57.360 29.630 0.00 0.00 31.02 4.37
2336 2344 9.683069 GTGTCAAAAGCATTCTTATATTATGGG 57.317 33.333 0.00 0.00 31.02 4.00
2344 2352 7.986085 AGTGTAGTGTCAAAAGCATTCTTAT 57.014 32.000 0.00 0.00 31.02 1.73
2345 2353 8.148351 ACTAGTGTAGTGTCAAAAGCATTCTTA 58.852 33.333 0.00 0.00 37.69 2.10
2346 2354 6.992715 ACTAGTGTAGTGTCAAAAGCATTCTT 59.007 34.615 0.00 0.00 37.69 2.52
2347 2355 6.525629 ACTAGTGTAGTGTCAAAAGCATTCT 58.474 36.000 0.00 0.00 37.69 2.40
2348 2356 6.787085 ACTAGTGTAGTGTCAAAAGCATTC 57.213 37.500 0.00 0.00 37.69 2.67
2349 2357 9.938280 TTATACTAGTGTAGTGTCAAAAGCATT 57.062 29.630 5.39 0.00 39.81 3.56
2350 2358 9.938280 TTTATACTAGTGTAGTGTCAAAAGCAT 57.062 29.630 5.39 0.00 39.81 3.79
2351 2359 9.767228 TTTTATACTAGTGTAGTGTCAAAAGCA 57.233 29.630 5.39 0.00 39.81 3.91
2375 2383 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
2376 2384 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
2377 2385 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
2378 2386 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
2379 2387 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
2380 2388 5.184479 TCCTCCGTCCCATAATATAAGAACG 59.816 44.000 0.00 0.00 0.00 3.95
2381 2389 6.600882 TCCTCCGTCCCATAATATAAGAAC 57.399 41.667 0.00 0.00 0.00 3.01
2382 2390 6.785963 ACTTCCTCCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
2383 2391 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
2384 2392 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
2385 2393 7.177921 CAGTACTTCCTCCGTCCCATAATATAA 59.822 40.741 0.00 0.00 0.00 0.98
2386 2394 6.662234 CAGTACTTCCTCCGTCCCATAATATA 59.338 42.308 0.00 0.00 0.00 0.86
2387 2395 5.480772 CAGTACTTCCTCCGTCCCATAATAT 59.519 44.000 0.00 0.00 0.00 1.28
2388 2396 4.831155 CAGTACTTCCTCCGTCCCATAATA 59.169 45.833 0.00 0.00 0.00 0.98
2389 2397 3.641906 CAGTACTTCCTCCGTCCCATAAT 59.358 47.826 0.00 0.00 0.00 1.28
2390 2398 3.028850 CAGTACTTCCTCCGTCCCATAA 58.971 50.000 0.00 0.00 0.00 1.90
2391 2399 2.024655 ACAGTACTTCCTCCGTCCCATA 60.025 50.000 0.00 0.00 0.00 2.74
2392 2400 1.273098 ACAGTACTTCCTCCGTCCCAT 60.273 52.381 0.00 0.00 0.00 4.00
2393 2401 0.113776 ACAGTACTTCCTCCGTCCCA 59.886 55.000 0.00 0.00 0.00 4.37
2394 2402 1.747924 GTACAGTACTTCCTCCGTCCC 59.252 57.143 3.19 0.00 0.00 4.46
2395 2403 2.720915 AGTACAGTACTTCCTCCGTCC 58.279 52.381 7.48 0.00 34.86 4.79
2396 2404 3.312146 GCTAGTACAGTACTTCCTCCGTC 59.688 52.174 18.56 0.00 40.14 4.79
2397 2405 3.054508 AGCTAGTACAGTACTTCCTCCGT 60.055 47.826 18.56 0.00 40.14 4.69
2398 2406 3.543665 AGCTAGTACAGTACTTCCTCCG 58.456 50.000 18.56 2.82 40.14 4.63
2399 2407 5.503662 GAAGCTAGTACAGTACTTCCTCC 57.496 47.826 18.56 0.13 40.14 4.30
2403 2411 5.648960 AGTGAGGAAGCTAGTACAGTACTTC 59.351 44.000 18.56 9.70 40.14 3.01
2404 2412 5.572252 AGTGAGGAAGCTAGTACAGTACTT 58.428 41.667 18.56 0.15 40.14 2.24
2405 2413 5.182169 AGTGAGGAAGCTAGTACAGTACT 57.818 43.478 17.51 17.51 42.68 2.73
2406 2414 4.034279 CGAGTGAGGAAGCTAGTACAGTAC 59.966 50.000 2.05 2.05 0.00 2.73
2407 2415 4.190001 CGAGTGAGGAAGCTAGTACAGTA 58.810 47.826 0.00 0.00 0.00 2.74
2408 2416 3.011119 CGAGTGAGGAAGCTAGTACAGT 58.989 50.000 0.00 0.00 0.00 3.55
2409 2417 3.011119 ACGAGTGAGGAAGCTAGTACAG 58.989 50.000 0.00 0.00 0.00 2.74
2410 2418 3.008330 GACGAGTGAGGAAGCTAGTACA 58.992 50.000 0.00 0.00 0.00 2.90
2448 2456 4.632688 TCATGTCACATCAGCATGTTGTAG 59.367 41.667 9.54 6.02 46.50 2.74
2548 2567 0.578683 CAGACACTATGCGCAATCGG 59.421 55.000 17.11 7.64 35.95 4.18
2640 2683 2.585330 AGCACATGATGACACCAACAA 58.415 42.857 0.00 0.00 0.00 2.83
2654 2697 5.104374 CACACTTGACAAGAAAAAGCACAT 58.896 37.500 21.95 0.00 0.00 3.21
2669 2712 7.068839 GGGAGTAGAAGAGAATATCACACTTGA 59.931 40.741 0.00 0.00 35.73 3.02
2679 2722 5.399267 GGGACAGAGGGAGTAGAAGAGAATA 60.399 48.000 0.00 0.00 0.00 1.75
2681 2724 3.309265 GGGACAGAGGGAGTAGAAGAGAA 60.309 52.174 0.00 0.00 0.00 2.87
2683 2726 2.024846 TGGGACAGAGGGAGTAGAAGAG 60.025 54.545 0.00 0.00 0.00 2.85
2685 2728 2.534042 TGGGACAGAGGGAGTAGAAG 57.466 55.000 0.00 0.00 0.00 2.85
2689 2732 5.550403 ACTTATTTTTGGGACAGAGGGAGTA 59.450 40.000 0.00 0.00 42.39 2.59
2690 2733 4.354087 ACTTATTTTTGGGACAGAGGGAGT 59.646 41.667 0.00 0.00 42.39 3.85
2691 2734 4.923415 ACTTATTTTTGGGACAGAGGGAG 58.077 43.478 0.00 0.00 42.39 4.30
2692 2735 5.333566 AACTTATTTTTGGGACAGAGGGA 57.666 39.130 0.00 0.00 42.39 4.20
2693 2736 5.775195 AGAAACTTATTTTTGGGACAGAGGG 59.225 40.000 0.00 0.00 42.39 4.30
2694 2737 6.901081 AGAAACTTATTTTTGGGACAGAGG 57.099 37.500 0.00 0.00 42.39 3.69
2695 2738 9.678941 GTTAAGAAACTTATTTTTGGGACAGAG 57.321 33.333 0.00 0.00 33.88 3.35
2696 2739 9.416284 AGTTAAGAAACTTATTTTTGGGACAGA 57.584 29.630 0.00 0.00 43.60 3.41
2749 2792 9.362151 TCCCAAAATAAGTGTCTCAAGTTTAAT 57.638 29.630 0.00 0.00 0.00 1.40
2750 2793 8.626526 GTCCCAAAATAAGTGTCTCAAGTTTAA 58.373 33.333 0.00 0.00 0.00 1.52
2751 2794 7.041644 CGTCCCAAAATAAGTGTCTCAAGTTTA 60.042 37.037 0.00 0.00 0.00 2.01
2752 2795 6.238648 CGTCCCAAAATAAGTGTCTCAAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
2753 2796 5.238650 CGTCCCAAAATAAGTGTCTCAAGTT 59.761 40.000 0.00 0.00 0.00 2.66
2754 2797 4.755123 CGTCCCAAAATAAGTGTCTCAAGT 59.245 41.667 0.00 0.00 0.00 3.16
2755 2798 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
2756 2799 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2757 2800 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
2758 2801 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
2759 2802 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2760 2803 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2761 2804 2.640826 TCCTCCGTCCCAAAATAAGTGT 59.359 45.455 0.00 0.00 0.00 3.55
2762 2805 3.343941 TCCTCCGTCCCAAAATAAGTG 57.656 47.619 0.00 0.00 0.00 3.16
2763 2806 3.329814 ACTTCCTCCGTCCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
2764 2807 3.951663 ACTTCCTCCGTCCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
2765 2808 5.703730 ATACTTCCTCCGTCCCAAAATAA 57.296 39.130 0.00 0.00 0.00 1.40
2766 2809 5.703730 AATACTTCCTCCGTCCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
2767 2810 4.586306 AATACTTCCTCCGTCCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
2768 2811 5.703730 ATAATACTTCCTCCGTCCCAAAA 57.296 39.130 0.00 0.00 0.00 2.44
2769 2812 5.045432 ACAATAATACTTCCTCCGTCCCAAA 60.045 40.000 0.00 0.00 0.00 3.28
2770 2813 4.472108 ACAATAATACTTCCTCCGTCCCAA 59.528 41.667 0.00 0.00 0.00 4.12
2771 2814 4.035112 ACAATAATACTTCCTCCGTCCCA 58.965 43.478 0.00 0.00 0.00 4.37
2772 2815 4.377897 CACAATAATACTTCCTCCGTCCC 58.622 47.826 0.00 0.00 0.00 4.46
2773 2816 4.377897 CCACAATAATACTTCCTCCGTCC 58.622 47.826 0.00 0.00 0.00 4.79
2774 2817 3.808174 GCCACAATAATACTTCCTCCGTC 59.192 47.826 0.00 0.00 0.00 4.79
2775 2818 3.454812 AGCCACAATAATACTTCCTCCGT 59.545 43.478 0.00 0.00 0.00 4.69
2776 2819 4.073293 AGCCACAATAATACTTCCTCCG 57.927 45.455 0.00 0.00 0.00 4.63
2777 2820 9.569122 TTAATAAGCCACAATAATACTTCCTCC 57.431 33.333 0.00 0.00 0.00 4.30
2814 2860 1.662122 GAACACGGAAACACAACTCGT 59.338 47.619 0.00 0.00 34.19 4.18
2849 2895 8.181573 ACAGTTGAAACAACTACAAGTAACATG 58.818 33.333 15.17 0.00 0.00 3.21
2850 2896 8.181573 CACAGTTGAAACAACTACAAGTAACAT 58.818 33.333 15.17 0.00 0.00 2.71
2877 2924 0.110238 ACACGCGCAAAATAGCAGTG 60.110 50.000 5.73 6.47 43.70 3.66
2892 2940 1.132262 AGGTTCAACAACAAGCACACG 59.868 47.619 0.00 0.00 33.70 4.49
2917 2965 0.465460 TGAACAGCCACCCACAACTC 60.465 55.000 0.00 0.00 0.00 3.01
2920 2968 1.702401 TCTATGAACAGCCACCCACAA 59.298 47.619 0.00 0.00 0.00 3.33
2926 2974 3.686726 CCAAGTCTTCTATGAACAGCCAC 59.313 47.826 0.00 0.00 0.00 5.01
3019 3067 2.159057 ACCCGGCGTATACGAAAATTCT 60.159 45.455 28.66 1.30 43.02 2.40
3043 3091 0.251386 AGCTCTCGGTGAAGACTCCA 60.251 55.000 0.00 0.00 0.00 3.86
3046 3094 3.321111 TGTTTTAGCTCTCGGTGAAGACT 59.679 43.478 0.00 0.00 0.00 3.24
3053 3101 0.037605 CCCGTGTTTTAGCTCTCGGT 60.038 55.000 11.30 0.00 38.50 4.69
3080 3128 5.648092 GTGGCTCTTGGTGTTCTATACATTT 59.352 40.000 0.00 0.00 39.39 2.32
3083 3131 3.580895 TGTGGCTCTTGGTGTTCTATACA 59.419 43.478 0.00 0.00 0.00 2.29
3087 3135 2.037251 GAGTGTGGCTCTTGGTGTTCTA 59.963 50.000 0.00 0.00 40.98 2.10
3093 3141 2.743718 CCGAGTGTGGCTCTTGGT 59.256 61.111 0.00 0.00 41.98 3.67
3103 3151 5.460646 CAATTTATTCACTTTGCCGAGTGT 58.539 37.500 14.08 2.00 45.64 3.55
3125 3173 3.523606 GGCATTATCATGTGTTTGCCA 57.476 42.857 20.07 0.00 46.87 4.92
3247 3295 3.980989 ACCGTGCCGTTAGTCGCA 61.981 61.111 0.00 0.00 38.35 5.10
3265 3313 1.659098 CGGCAAAGAGTATCAACCGTC 59.341 52.381 0.00 0.00 37.82 4.79
3297 3345 2.378547 AGGTGGGACTAAATCTTTGCCA 59.621 45.455 0.00 0.00 0.00 4.92
3324 3372 0.811281 ATGCCTTTTTGCTAGTCGGC 59.189 50.000 0.00 0.00 38.01 5.54
3344 3392 8.238631 GCGGTTGGAGTATTGAACTATTTAAAA 58.761 33.333 0.00 0.00 39.07 1.52
3397 3445 4.948004 AGATTCATAGTGACTGTACGGACA 59.052 41.667 9.17 5.61 0.00 4.02
3423 3471 3.447586 TGAATCTTCTCTACCCGGAACAG 59.552 47.826 0.73 0.00 0.00 3.16
3432 3480 6.155475 ACAGCCACTATGAATCTTCTCTAC 57.845 41.667 0.00 0.00 0.00 2.59
3433 3481 5.009110 CGACAGCCACTATGAATCTTCTCTA 59.991 44.000 0.00 0.00 0.00 2.43
3530 3580 2.431057 CTCGGGTAACTATTGCTCCACT 59.569 50.000 0.00 0.00 0.00 4.00
3533 3583 1.070289 CCCTCGGGTAACTATTGCTCC 59.930 57.143 0.00 0.00 0.00 4.70
3552 3605 4.499183 CCTTATCATTATCGAGAGCCACC 58.501 47.826 0.00 0.00 0.00 4.61
3563 3616 6.376248 ACTTTGATGGTGGCCTTATCATTAT 58.624 36.000 14.85 4.48 31.54 1.28
3595 3648 3.451402 TGCTTGTCTCTAGGTGAGGTA 57.549 47.619 0.00 0.00 42.86 3.08
3601 3654 3.883489 GGTTTTGTTGCTTGTCTCTAGGT 59.117 43.478 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.