Multiple sequence alignment - TraesCS7D01G119100

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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 TraesCS7D01G119100 chr7D 100.000 2560 0 0 1 2560 73953834 73956393 0.000000e+00 4728
1 TraesCS7D01G119100 chrUn 96.397 2276 74 2 1 2268 245706066 245708341 0.000000e+00 3742
2 TraesCS7D01G119100 chrUn 96.355 2277 74 2 1 2268 229310229 229307953 0.000000e+00 3736
3 TraesCS7D01G119100 chrUn 96.355 2277 74 2 1 2268 291535438 291537714 0.000000e+00 3736
4 TraesCS7D01G119100 chrUn 96.311 2277 75 2 1 2268 199874822 199877098 0.000000e+00 3731
5 TraesCS7D01G119100 chrUn 96.135 2277 79 2 1 2268 3845816 3843540 0.000000e+00 3709
6 TraesCS7D01G119100 chrUn 96.135 2277 79 2 1 2268 199904742 199907018 0.000000e+00 3709
7 TraesCS7D01G119100 chr1B 96.355 2277 72 3 1 2268 544593695 544595969 0.000000e+00 3735
8 TraesCS7D01G119100 chr1B 96.223 2277 77 2 1 2268 544623634 544625910 0.000000e+00 3720
9 TraesCS7D01G119100 chr1B 91.409 291 21 3 2271 2558 194081268 194080979 1.850000e-106 396
10 TraesCS7D01G119100 chr5D 96.179 2277 78 2 1 2268 18998922 19001198 0.000000e+00 3714
11 TraesCS7D01G119100 chr3B 91.089 303 18 6 2265 2560 254008096 254008396 3.970000e-108 401
12 TraesCS7D01G119100 chr3B 88.927 289 30 2 2271 2557 584607887 584608175 3.130000e-94 355
13 TraesCS7D01G119100 chr5B 91.349 289 25 0 2269 2557 622433084 622432796 1.850000e-106 396
14 TraesCS7D01G119100 chr5B 90.690 290 26 1 2270 2558 347150796 347151085 4.000000e-103 385
15 TraesCS7D01G119100 chr7B 90.816 294 23 2 2271 2560 136272107 136271814 8.590000e-105 390
16 TraesCS7D01G119100 chr7B 88.776 294 28 4 2271 2560 336884675 336884383 3.130000e-94 355
17 TraesCS7D01G119100 chr4B 90.444 293 24 3 2271 2559 538778399 538778691 1.440000e-102 383
18 TraesCS7D01G119100 chr4B 90.311 289 24 1 2271 2559 40822524 40822240 2.400000e-100 375


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 TraesCS7D01G119100 chr7D 73953834 73956393 2559 False 4728 4728 100.000 1 2560 1 chr7D.!!$F1 2559
1 TraesCS7D01G119100 chrUn 245706066 245708341 2275 False 3742 3742 96.397 1 2268 1 chrUn.!!$F3 2267
2 TraesCS7D01G119100 chrUn 229307953 229310229 2276 True 3736 3736 96.355 1 2268 1 chrUn.!!$R2 2267
3 TraesCS7D01G119100 chrUn 291535438 291537714 2276 False 3736 3736 96.355 1 2268 1 chrUn.!!$F4 2267
4 TraesCS7D01G119100 chrUn 199874822 199877098 2276 False 3731 3731 96.311 1 2268 1 chrUn.!!$F1 2267
5 TraesCS7D01G119100 chrUn 3843540 3845816 2276 True 3709 3709 96.135 1 2268 1 chrUn.!!$R1 2267
6 TraesCS7D01G119100 chrUn 199904742 199907018 2276 False 3709 3709 96.135 1 2268 1 chrUn.!!$F2 2267
7 TraesCS7D01G119100 chr1B 544593695 544595969 2274 False 3735 3735 96.355 1 2268 1 chr1B.!!$F1 2267
8 TraesCS7D01G119100 chr1B 544623634 544625910 2276 False 3720 3720 96.223 1 2268 1 chr1B.!!$F2 2267
9 TraesCS7D01G119100 chr5D 18998922 19001198 2276 False 3714 3714 96.179 1 2268 1 chr5D.!!$F1 2267

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
155 156 0.620556 AGAGTCATTGGGGACGCAAT 59.379 50.000 8.57 8.57 42.62 3.56 F
1034 1037 1.134551 GCAAGGGAAGTTGGCAAAACA 60.135 47.619 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 1219 0.170561 CCGTACCAGTTCTGAGTCGG 59.829 60.0 1.0 7.9 0.00 4.79 R
2517 2527 0.320374 TGGTCGCCTCGATTGTTTCT 59.680 50.0 0.0 0.0 38.42 2.52 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
50 51 4.282703 GGTATAGGGGCGAAAGACTAATCA 59.717 45.833 0.00 0.00 40.87 2.57
53 54 4.028993 AGGGGCGAAAGACTAATCAAAA 57.971 40.909 0.00 0.00 40.87 2.44
75 76 3.052490 ACATCTAGTAGCTGGTTCCCTCT 60.052 47.826 6.01 0.00 0.00 3.69
81 82 2.327325 AGCTGGTTCCCTCTGAAGTA 57.673 50.000 0.00 0.00 32.37 2.24
140 141 6.313519 TCAGGTAAAGCCAATGATTAGAGT 57.686 37.500 0.00 0.00 40.61 3.24
155 156 0.620556 AGAGTCATTGGGGACGCAAT 59.379 50.000 8.57 8.57 42.62 3.56
221 222 1.741401 CTTCGATGAGCCGTGCCAA 60.741 57.895 0.00 0.00 0.00 4.52
361 362 2.089201 TCGATTAAGACAGCAGGACGA 58.911 47.619 0.00 0.00 0.00 4.20
406 407 2.902705 AGGAGTGCGTAACAACTCAA 57.097 45.000 5.29 0.00 31.75 3.02
411 412 1.597663 GTGCGTAACAACTCAACTGCT 59.402 47.619 0.00 0.00 0.00 4.24
590 591 9.688091 TTGGTGGTAGTAGCAAATATTCAAATA 57.312 29.630 3.06 0.00 35.36 1.40
774 775 1.503542 GCGACGTTAGGAAGTCCGA 59.496 57.895 0.00 0.00 42.08 4.55
839 840 1.836604 GCCTGCCAACCCTGGAAAA 60.837 57.895 0.00 0.00 46.92 2.29
1025 1028 3.525800 ACAATGTAGGCAAGGGAAGTT 57.474 42.857 0.00 0.00 0.00 2.66
1034 1037 1.134551 GCAAGGGAAGTTGGCAAAACA 60.135 47.619 0.00 0.00 0.00 2.83
1039 1042 2.893489 GGGAAGTTGGCAAAACAGATCT 59.107 45.455 0.00 0.00 0.00 2.75
1047 1050 6.770785 AGTTGGCAAAACAGATCTGTAACTTA 59.229 34.615 28.10 10.99 44.13 2.24
1055 1058 7.981102 AACAGATCTGTAACTTAGGGAAAAC 57.019 36.000 28.10 0.00 44.13 2.43
1079 1082 1.685421 GCTCTGAGGACTGGGCTCT 60.685 63.158 6.83 0.00 38.22 4.09
1125 1128 3.449227 TCGGCGGATTGCTCGAGT 61.449 61.111 15.13 0.00 45.43 4.18
1216 1219 1.911293 TTCGCCGAGCATGAAACAGC 61.911 55.000 0.00 0.00 0.00 4.40
1328 1331 0.251354 TCTGCCCAGTGCTCTGAATC 59.749 55.000 17.19 6.22 43.76 2.52
1363 1366 0.606944 TCAACCAAGCGCGGGTAAAT 60.607 50.000 23.98 8.85 37.77 1.40
1469 1472 3.373220 CCCACTGTCCCTGTCTACTATCT 60.373 52.174 0.00 0.00 0.00 1.98
1570 1573 5.429957 ACTTTGTGAAATGACTTGAGAGC 57.570 39.130 0.00 0.00 0.00 4.09
1594 1597 1.061033 AGGATAAGTGGGAGCCCTCAT 60.061 52.381 7.16 0.00 36.94 2.90
1755 1765 1.476488 GGGCGGCACATCTGTTAAAAT 59.524 47.619 12.47 0.00 0.00 1.82
1760 1770 6.294508 GGGCGGCACATCTGTTAAAATATAAT 60.295 38.462 12.47 0.00 0.00 1.28
1793 1803 3.667497 AGATGAGCTCAACGAGAACAA 57.333 42.857 22.50 0.00 0.00 2.83
1903 1913 6.765403 TCCTTTAGATCTTCGGAGTTTGAAA 58.235 36.000 0.00 0.00 0.00 2.69
1936 1946 5.875359 GTCAGAAAAGTTACCACAGGGATAG 59.125 44.000 0.00 0.00 38.05 2.08
1939 1949 5.724854 AGAAAAGTTACCACAGGGATAGCTA 59.275 40.000 0.00 0.00 38.05 3.32
1951 1961 1.139853 GGATAGCTAGCTTGTGGCAGT 59.860 52.381 24.88 0.00 44.79 4.40
1968 1978 2.196749 CAGTCAAGCGTTCATAGCGAT 58.803 47.619 0.00 0.00 40.04 4.58
1973 1983 2.293677 AGCGTTCATAGCGATGTTGA 57.706 45.000 6.70 0.00 40.04 3.18
2020 2030 5.877012 TCTTCCTATCATTGTGAAGCAGAAC 59.123 40.000 0.00 0.00 35.35 3.01
2071 2081 1.671379 GGGAACGTGAGCTGGGTTC 60.671 63.158 10.97 10.97 39.38 3.62
2109 2119 6.944096 ACAGGTTAGTTTTACCCTACTGATC 58.056 40.000 0.00 0.00 36.27 2.92
2113 2123 7.016858 AGGTTAGTTTTACCCTACTGATCACAA 59.983 37.037 0.00 0.00 36.27 3.33
2176 2186 2.183478 TCACACAATTGGTCATCGCT 57.817 45.000 10.83 0.00 0.00 4.93
2259 2269 4.500499 AGTCAGAATCCAAGCTAGCATT 57.500 40.909 18.83 7.65 0.00 3.56
2260 2270 4.197750 AGTCAGAATCCAAGCTAGCATTG 58.802 43.478 18.83 16.92 0.00 2.82
2268 2278 0.830648 AAGCTAGCATTGGACGCCTA 59.169 50.000 18.83 0.00 0.00 3.93
2269 2279 0.105039 AGCTAGCATTGGACGCCTAC 59.895 55.000 18.83 0.00 0.00 3.18
2270 2280 0.105039 GCTAGCATTGGACGCCTACT 59.895 55.000 10.63 0.00 0.00 2.57
2271 2281 1.858091 CTAGCATTGGACGCCTACTG 58.142 55.000 0.00 0.00 0.00 2.74
2272 2282 1.409064 CTAGCATTGGACGCCTACTGA 59.591 52.381 0.00 0.00 0.00 3.41
2273 2283 0.833287 AGCATTGGACGCCTACTGAT 59.167 50.000 0.00 0.00 0.00 2.90
2274 2284 2.039418 AGCATTGGACGCCTACTGATA 58.961 47.619 0.00 0.00 0.00 2.15
2275 2285 2.135933 GCATTGGACGCCTACTGATAC 58.864 52.381 0.00 0.00 0.00 2.24
2276 2286 2.394708 CATTGGACGCCTACTGATACG 58.605 52.381 0.00 0.00 0.00 3.06
2277 2287 1.466856 TTGGACGCCTACTGATACGT 58.533 50.000 0.00 0.00 42.27 3.57
2281 2291 1.307097 ACGCCTACTGATACGTCTCC 58.693 55.000 0.00 0.00 32.37 3.71
2282 2292 1.306148 CGCCTACTGATACGTCTCCA 58.694 55.000 0.00 0.00 0.00 3.86
2283 2293 1.674441 CGCCTACTGATACGTCTCCAA 59.326 52.381 0.00 0.00 0.00 3.53
2284 2294 2.541178 CGCCTACTGATACGTCTCCAAC 60.541 54.545 0.00 0.00 0.00 3.77
2299 2309 7.982371 CGTCTCCAACGTATCTATAAGTTTT 57.018 36.000 0.00 0.00 46.42 2.43
2300 2310 7.828604 CGTCTCCAACGTATCTATAAGTTTTG 58.171 38.462 0.00 0.00 46.42 2.44
2301 2311 7.699391 CGTCTCCAACGTATCTATAAGTTTTGA 59.301 37.037 0.00 0.35 46.42 2.69
2302 2312 9.530633 GTCTCCAACGTATCTATAAGTTTTGAT 57.469 33.333 0.00 0.00 33.71 2.57
2305 2315 9.661563 TCCAACGTATCTATAAGTTTTGATTGT 57.338 29.630 0.00 0.00 33.71 2.71
2309 2319 9.661563 ACGTATCTATAAGTTTTGATTGTTCCA 57.338 29.630 0.00 0.00 0.00 3.53
2313 2323 8.579850 TCTATAAGTTTTGATTGTTCCATGCT 57.420 30.769 0.00 0.00 0.00 3.79
2314 2324 9.679661 TCTATAAGTTTTGATTGTTCCATGCTA 57.320 29.630 0.00 0.00 0.00 3.49
2325 2335 9.461312 TGATTGTTCCATGCTATTATATTACCC 57.539 33.333 0.00 0.00 0.00 3.69
2326 2336 7.915293 TTGTTCCATGCTATTATATTACCCG 57.085 36.000 0.00 0.00 0.00 5.28
2327 2337 7.011499 TGTTCCATGCTATTATATTACCCGT 57.989 36.000 0.00 0.00 0.00 5.28
2328 2338 7.455058 TGTTCCATGCTATTATATTACCCGTT 58.545 34.615 0.00 0.00 0.00 4.44
2329 2339 7.940137 TGTTCCATGCTATTATATTACCCGTTT 59.060 33.333 0.00 0.00 0.00 3.60
2330 2340 8.789762 GTTCCATGCTATTATATTACCCGTTTT 58.210 33.333 0.00 0.00 0.00 2.43
2331 2341 8.330466 TCCATGCTATTATATTACCCGTTTTG 57.670 34.615 0.00 0.00 0.00 2.44
2332 2342 7.392113 TCCATGCTATTATATTACCCGTTTTGG 59.608 37.037 0.00 0.00 37.55 3.28
2333 2343 7.392113 CCATGCTATTATATTACCCGTTTTGGA 59.608 37.037 0.00 0.00 42.00 3.53
2334 2344 8.956426 CATGCTATTATATTACCCGTTTTGGAT 58.044 33.333 0.00 0.00 42.00 3.41
2335 2345 8.330466 TGCTATTATATTACCCGTTTTGGATG 57.670 34.615 0.00 0.00 42.00 3.51
2336 2346 7.940137 TGCTATTATATTACCCGTTTTGGATGT 59.060 33.333 0.00 0.00 42.00 3.06
2337 2347 8.789762 GCTATTATATTACCCGTTTTGGATGTT 58.210 33.333 0.00 0.00 42.00 2.71
2340 2350 6.844097 ATATTACCCGTTTTGGATGTTTGT 57.156 33.333 0.00 0.00 42.00 2.83
2341 2351 2.880963 ACCCGTTTTGGATGTTTGTG 57.119 45.000 0.00 0.00 42.00 3.33
2342 2352 1.410882 ACCCGTTTTGGATGTTTGTGG 59.589 47.619 0.00 0.00 42.00 4.17
2343 2353 1.270041 CCCGTTTTGGATGTTTGTGGG 60.270 52.381 0.00 0.00 42.00 4.61
2344 2354 1.496934 CGTTTTGGATGTTTGTGGGC 58.503 50.000 0.00 0.00 0.00 5.36
2345 2355 1.068434 CGTTTTGGATGTTTGTGGGCT 59.932 47.619 0.00 0.00 0.00 5.19
2346 2356 2.482839 CGTTTTGGATGTTTGTGGGCTT 60.483 45.455 0.00 0.00 0.00 4.35
2347 2357 3.540617 GTTTTGGATGTTTGTGGGCTTT 58.459 40.909 0.00 0.00 0.00 3.51
2348 2358 4.698575 GTTTTGGATGTTTGTGGGCTTTA 58.301 39.130 0.00 0.00 0.00 1.85
2349 2359 4.329462 TTTGGATGTTTGTGGGCTTTAC 57.671 40.909 0.00 0.00 0.00 2.01
2350 2360 3.237268 TGGATGTTTGTGGGCTTTACT 57.763 42.857 0.00 0.00 0.00 2.24
2351 2361 3.571590 TGGATGTTTGTGGGCTTTACTT 58.428 40.909 0.00 0.00 0.00 2.24
2352 2362 3.964031 TGGATGTTTGTGGGCTTTACTTT 59.036 39.130 0.00 0.00 0.00 2.66
2353 2363 5.141182 TGGATGTTTGTGGGCTTTACTTTA 58.859 37.500 0.00 0.00 0.00 1.85
2354 2364 5.010213 TGGATGTTTGTGGGCTTTACTTTAC 59.990 40.000 0.00 0.00 0.00 2.01
2355 2365 5.010213 GGATGTTTGTGGGCTTTACTTTACA 59.990 40.000 0.00 0.00 0.00 2.41
2356 2366 5.251601 TGTTTGTGGGCTTTACTTTACAC 57.748 39.130 0.00 0.00 0.00 2.90
2357 2367 4.951094 TGTTTGTGGGCTTTACTTTACACT 59.049 37.500 0.00 0.00 0.00 3.55
2358 2368 5.419471 TGTTTGTGGGCTTTACTTTACACTT 59.581 36.000 0.00 0.00 0.00 3.16
2359 2369 6.071278 TGTTTGTGGGCTTTACTTTACACTTT 60.071 34.615 0.00 0.00 0.00 2.66
2360 2370 6.532988 TTGTGGGCTTTACTTTACACTTTT 57.467 33.333 0.00 0.00 0.00 2.27
2361 2371 7.642082 TTGTGGGCTTTACTTTACACTTTTA 57.358 32.000 0.00 0.00 0.00 1.52
2362 2372 7.826918 TGTGGGCTTTACTTTACACTTTTAT 57.173 32.000 0.00 0.00 0.00 1.40
2363 2373 8.921353 TGTGGGCTTTACTTTACACTTTTATA 57.079 30.769 0.00 0.00 0.00 0.98
2364 2374 9.523168 TGTGGGCTTTACTTTACACTTTTATAT 57.477 29.630 0.00 0.00 0.00 0.86
2365 2375 9.999009 GTGGGCTTTACTTTACACTTTTATATC 57.001 33.333 0.00 0.00 0.00 1.63
2366 2376 9.742144 TGGGCTTTACTTTACACTTTTATATCA 57.258 29.630 0.00 0.00 0.00 2.15
2381 2391 9.783256 ACTTTTATATCATTTTTGCGACTAACC 57.217 29.630 0.00 0.00 0.00 2.85
2385 2395 9.826574 TTATATCATTTTTGCGACTAACCTACT 57.173 29.630 0.00 0.00 0.00 2.57
2387 2397 9.826574 ATATCATTTTTGCGACTAACCTACTAA 57.173 29.630 0.00 0.00 0.00 2.24
2388 2398 7.355332 TCATTTTTGCGACTAACCTACTAAC 57.645 36.000 0.00 0.00 0.00 2.34
2389 2399 6.369615 TCATTTTTGCGACTAACCTACTAACC 59.630 38.462 0.00 0.00 0.00 2.85
2390 2400 3.492421 TTGCGACTAACCTACTAACCG 57.508 47.619 0.00 0.00 0.00 4.44
2391 2401 1.745087 TGCGACTAACCTACTAACCGG 59.255 52.381 0.00 0.00 0.00 5.28
2392 2402 2.017049 GCGACTAACCTACTAACCGGA 58.983 52.381 9.46 0.00 0.00 5.14
2393 2403 2.032675 GCGACTAACCTACTAACCGGAG 59.967 54.545 9.46 0.00 0.00 4.63
2419 2429 4.497473 TTTTGCCTATTTCAGTGTTCCG 57.503 40.909 0.00 0.00 0.00 4.30
2420 2430 3.410631 TTGCCTATTTCAGTGTTCCGA 57.589 42.857 0.00 0.00 0.00 4.55
2421 2431 3.410631 TGCCTATTTCAGTGTTCCGAA 57.589 42.857 0.00 0.00 0.00 4.30
2422 2432 3.334691 TGCCTATTTCAGTGTTCCGAAG 58.665 45.455 0.00 0.00 0.00 3.79
2423 2433 3.007506 TGCCTATTTCAGTGTTCCGAAGA 59.992 43.478 0.00 0.00 0.00 2.87
2424 2434 4.000988 GCCTATTTCAGTGTTCCGAAGAA 58.999 43.478 0.00 0.00 0.00 2.52
2425 2435 4.454504 GCCTATTTCAGTGTTCCGAAGAAA 59.545 41.667 0.00 0.00 32.58 2.52
2426 2436 5.048991 GCCTATTTCAGTGTTCCGAAGAAAA 60.049 40.000 0.00 0.00 32.58 2.29
2427 2437 6.603095 CCTATTTCAGTGTTCCGAAGAAAAG 58.397 40.000 0.00 0.00 32.58 2.27
2428 2438 4.893424 TTTCAGTGTTCCGAAGAAAAGG 57.107 40.909 0.00 0.00 32.58 3.11
2429 2439 3.830744 TCAGTGTTCCGAAGAAAAGGA 57.169 42.857 0.00 0.00 32.58 3.36
2430 2440 4.145365 TCAGTGTTCCGAAGAAAAGGAA 57.855 40.909 0.00 0.00 41.75 3.36
2431 2441 4.714632 TCAGTGTTCCGAAGAAAAGGAAT 58.285 39.130 0.01 0.00 41.75 3.01
2432 2442 5.860611 TCAGTGTTCCGAAGAAAAGGAATA 58.139 37.500 0.01 0.00 41.75 1.75
2433 2443 5.699458 TCAGTGTTCCGAAGAAAAGGAATAC 59.301 40.000 13.72 13.72 41.75 1.89
2434 2444 5.001874 AGTGTTCCGAAGAAAAGGAATACC 58.998 41.667 16.65 4.02 41.75 2.73
2435 2445 4.758165 GTGTTCCGAAGAAAAGGAATACCA 59.242 41.667 11.41 0.00 41.75 3.25
2436 2446 5.239963 GTGTTCCGAAGAAAAGGAATACCAA 59.760 40.000 11.41 0.00 41.75 3.67
2437 2447 5.828859 TGTTCCGAAGAAAAGGAATACCAAA 59.171 36.000 0.01 0.00 41.75 3.28
2438 2448 5.952526 TCCGAAGAAAAGGAATACCAAAC 57.047 39.130 0.00 0.00 38.94 2.93
2439 2449 4.453136 TCCGAAGAAAAGGAATACCAAACG 59.547 41.667 0.00 0.00 38.94 3.60
2440 2450 4.379082 CCGAAGAAAAGGAATACCAAACGG 60.379 45.833 0.00 0.00 38.94 4.44
2441 2451 4.453136 CGAAGAAAAGGAATACCAAACGGA 59.547 41.667 0.00 0.00 38.94 4.69
2442 2452 5.390567 CGAAGAAAAGGAATACCAAACGGAG 60.391 44.000 0.00 0.00 38.94 4.63
2443 2453 4.981812 AGAAAAGGAATACCAAACGGAGT 58.018 39.130 0.00 0.00 40.63 3.85
2444 2454 5.001874 AGAAAAGGAATACCAAACGGAGTC 58.998 41.667 0.00 0.00 38.33 3.36
2445 2455 3.345508 AAGGAATACCAAACGGAGTCC 57.654 47.619 0.00 0.00 38.33 3.85
2446 2456 2.262637 AGGAATACCAAACGGAGTCCA 58.737 47.619 10.49 0.00 38.33 4.02
2447 2457 2.640826 AGGAATACCAAACGGAGTCCAA 59.359 45.455 10.49 0.00 38.33 3.53
2448 2458 3.073356 AGGAATACCAAACGGAGTCCAAA 59.927 43.478 10.49 0.00 38.33 3.28
2449 2459 3.189910 GGAATACCAAACGGAGTCCAAAC 59.810 47.826 10.49 0.00 36.19 2.93
2450 2460 1.868469 TACCAAACGGAGTCCAAACG 58.132 50.000 10.49 0.00 45.00 3.60
2451 2461 0.816421 ACCAAACGGAGTCCAAACGG 60.816 55.000 10.49 6.56 45.00 4.44
2452 2462 0.533308 CCAAACGGAGTCCAAACGGA 60.533 55.000 10.49 0.00 45.00 4.69
2453 2463 1.301423 CAAACGGAGTCCAAACGGAA 58.699 50.000 10.49 0.00 45.00 4.30
2454 2464 1.877443 CAAACGGAGTCCAAACGGAAT 59.123 47.619 10.49 0.00 45.00 3.01
2455 2465 1.519408 AACGGAGTCCAAACGGAATG 58.481 50.000 10.49 0.00 45.00 2.67
2456 2466 0.682852 ACGGAGTCCAAACGGAATGA 59.317 50.000 10.49 0.00 29.74 2.57
2457 2467 1.071071 ACGGAGTCCAAACGGAATGAA 59.929 47.619 10.49 0.00 29.74 2.57
2458 2468 2.147958 CGGAGTCCAAACGGAATGAAA 58.852 47.619 10.49 0.00 33.16 2.69
2459 2469 2.095919 CGGAGTCCAAACGGAATGAAAC 60.096 50.000 10.49 0.00 33.16 2.78
2460 2470 2.228103 GGAGTCCAAACGGAATGAAACC 59.772 50.000 3.60 0.00 33.16 3.27
2461 2471 3.146847 GAGTCCAAACGGAATGAAACCT 58.853 45.455 0.00 0.00 33.16 3.50
2462 2472 3.562182 AGTCCAAACGGAATGAAACCTT 58.438 40.909 0.00 0.00 33.16 3.50
2463 2473 3.568430 AGTCCAAACGGAATGAAACCTTC 59.432 43.478 0.00 0.00 33.16 3.46
2464 2474 2.550606 TCCAAACGGAATGAAACCTTCG 59.449 45.455 0.00 0.00 0.00 3.79
2465 2475 2.351350 CCAAACGGAATGAAACCTTCGG 60.351 50.000 0.00 0.00 0.00 4.30
2466 2476 1.530323 AACGGAATGAAACCTTCGGG 58.470 50.000 0.00 0.00 41.87 5.14
2467 2477 0.688487 ACGGAATGAAACCTTCGGGA 59.312 50.000 0.00 0.00 38.77 5.14
2468 2478 1.338769 ACGGAATGAAACCTTCGGGAG 60.339 52.381 0.00 0.00 38.77 4.30
2469 2479 1.095600 GGAATGAAACCTTCGGGAGC 58.904 55.000 0.00 0.00 38.77 4.70
2470 2480 0.727398 GAATGAAACCTTCGGGAGCG 59.273 55.000 0.00 0.00 38.77 5.03
2471 2481 0.323629 AATGAAACCTTCGGGAGCGA 59.676 50.000 0.00 0.00 38.77 4.93
2472 2482 0.541863 ATGAAACCTTCGGGAGCGAT 59.458 50.000 0.00 0.00 38.77 4.58
2473 2483 0.108329 TGAAACCTTCGGGAGCGATC 60.108 55.000 0.00 0.00 38.77 3.69
2474 2484 0.175989 GAAACCTTCGGGAGCGATCT 59.824 55.000 0.00 0.00 38.77 2.75
2475 2485 0.613777 AAACCTTCGGGAGCGATCTT 59.386 50.000 0.00 0.00 38.77 2.40
2476 2486 0.613777 AACCTTCGGGAGCGATCTTT 59.386 50.000 0.00 0.00 38.77 2.52
2477 2487 0.613777 ACCTTCGGGAGCGATCTTTT 59.386 50.000 0.00 0.00 38.77 2.27
2478 2488 1.003233 ACCTTCGGGAGCGATCTTTTT 59.997 47.619 0.00 0.00 38.77 1.94
2479 2489 1.398390 CCTTCGGGAGCGATCTTTTTG 59.602 52.381 0.00 0.00 37.25 2.44
2480 2490 1.398390 CTTCGGGAGCGATCTTTTTGG 59.602 52.381 0.00 0.00 0.00 3.28
2481 2491 0.611200 TCGGGAGCGATCTTTTTGGA 59.389 50.000 0.00 0.00 0.00 3.53
2482 2492 1.002659 TCGGGAGCGATCTTTTTGGAA 59.997 47.619 0.00 0.00 0.00 3.53
2483 2493 1.130561 CGGGAGCGATCTTTTTGGAAC 59.869 52.381 0.00 0.00 0.00 3.62
2484 2494 2.159382 GGGAGCGATCTTTTTGGAACA 58.841 47.619 0.00 0.00 0.00 3.18
2499 2509 2.076863 GGAACAAACGTGATCCAGAGG 58.923 52.381 0.00 0.00 44.27 3.69
2500 2510 2.289444 GGAACAAACGTGATCCAGAGGA 60.289 50.000 0.00 0.00 44.27 3.71
2501 2511 2.457366 ACAAACGTGATCCAGAGGAC 57.543 50.000 0.00 0.00 32.98 3.85
2502 2512 1.971357 ACAAACGTGATCCAGAGGACT 59.029 47.619 0.00 0.00 32.98 3.85
2503 2513 2.368875 ACAAACGTGATCCAGAGGACTT 59.631 45.455 0.00 0.00 32.98 3.01
2504 2514 2.738846 CAAACGTGATCCAGAGGACTTG 59.261 50.000 0.00 0.00 32.98 3.16
2505 2515 0.898320 ACGTGATCCAGAGGACTTGG 59.102 55.000 0.00 0.00 32.98 3.61
2506 2516 1.186200 CGTGATCCAGAGGACTTGGA 58.814 55.000 0.00 0.00 32.98 3.53
2507 2517 1.135915 CGTGATCCAGAGGACTTGGAG 59.864 57.143 0.19 0.00 32.98 3.86
2508 2518 2.183679 GTGATCCAGAGGACTTGGAGT 58.816 52.381 0.19 0.00 32.98 3.85
2509 2519 2.093764 GTGATCCAGAGGACTTGGAGTG 60.094 54.545 0.19 0.00 32.98 3.51
2510 2520 0.908198 ATCCAGAGGACTTGGAGTGC 59.092 55.000 0.19 0.00 36.76 4.40
2511 2521 0.471780 TCCAGAGGACTTGGAGTGCA 60.472 55.000 2.51 0.00 39.19 4.57
2512 2522 0.397941 CCAGAGGACTTGGAGTGCAA 59.602 55.000 0.00 0.00 39.19 4.08
2513 2523 1.610102 CCAGAGGACTTGGAGTGCAAG 60.610 57.143 21.50 21.50 39.19 4.01
2514 2524 1.071385 CAGAGGACTTGGAGTGCAAGT 59.929 52.381 27.72 27.72 44.58 3.16
2520 2530 3.281727 ACTTGGAGTGCAAGTCAAGAA 57.718 42.857 22.87 4.30 38.37 2.52
2521 2531 3.620488 ACTTGGAGTGCAAGTCAAGAAA 58.380 40.909 22.87 3.75 38.37 2.52
2522 2532 3.378427 ACTTGGAGTGCAAGTCAAGAAAC 59.622 43.478 22.87 0.00 38.37 2.78
2523 2533 2.997980 TGGAGTGCAAGTCAAGAAACA 58.002 42.857 0.00 0.00 38.29 2.83
2524 2534 3.351740 TGGAGTGCAAGTCAAGAAACAA 58.648 40.909 0.00 0.00 38.29 2.83
2525 2535 3.953612 TGGAGTGCAAGTCAAGAAACAAT 59.046 39.130 0.00 0.00 38.29 2.71
2526 2536 4.036734 TGGAGTGCAAGTCAAGAAACAATC 59.963 41.667 0.00 0.00 38.29 2.67
2527 2537 4.214437 GAGTGCAAGTCAAGAAACAATCG 58.786 43.478 0.00 0.00 35.94 3.34
2528 2538 3.876914 AGTGCAAGTCAAGAAACAATCGA 59.123 39.130 0.00 0.00 0.00 3.59
2529 2539 4.024556 AGTGCAAGTCAAGAAACAATCGAG 60.025 41.667 0.00 0.00 0.00 4.04
2530 2540 3.250762 TGCAAGTCAAGAAACAATCGAGG 59.749 43.478 0.00 0.00 0.00 4.63
2531 2541 3.814945 CAAGTCAAGAAACAATCGAGGC 58.185 45.455 0.00 0.00 0.00 4.70
2532 2542 2.069273 AGTCAAGAAACAATCGAGGCG 58.931 47.619 0.00 0.00 0.00 5.52
2533 2543 2.066262 GTCAAGAAACAATCGAGGCGA 58.934 47.619 0.00 0.00 41.13 5.54
2534 2544 2.066262 TCAAGAAACAATCGAGGCGAC 58.934 47.619 0.00 0.00 39.18 5.19
2535 2545 1.128692 CAAGAAACAATCGAGGCGACC 59.871 52.381 0.00 0.00 39.18 4.79
2536 2546 0.320374 AGAAACAATCGAGGCGACCA 59.680 50.000 0.00 0.00 39.18 4.02
2537 2547 0.442699 GAAACAATCGAGGCGACCAC 59.557 55.000 0.00 0.00 39.18 4.16
2538 2548 1.289109 AAACAATCGAGGCGACCACG 61.289 55.000 8.83 8.83 39.18 4.94
2539 2549 2.149803 AACAATCGAGGCGACCACGA 62.150 55.000 17.16 17.16 39.18 4.35
2540 2550 1.874019 CAATCGAGGCGACCACGAG 60.874 63.158 18.88 7.29 41.42 4.18
2541 2551 3.064987 AATCGAGGCGACCACGAGG 62.065 63.158 18.88 0.00 41.42 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 156 4.087182 AGTTTGAGAATAGGTCGAGGACA 58.913 43.478 0.00 0.00 33.68 4.02
221 222 1.201429 ACTTGGAGCACCCGATTCCT 61.201 55.000 0.00 0.00 37.93 3.36
305 306 1.141019 TTCTAGGTTAGCGCGCAGG 59.859 57.895 35.10 13.95 0.00 4.85
339 340 2.415491 CGTCCTGCTGTCTTAATCGACA 60.415 50.000 0.00 0.00 41.33 4.35
361 362 3.545703 GGATTTCGACTTCCATGACCAT 58.454 45.455 7.75 0.00 31.99 3.55
394 395 4.211164 TGATTCAGCAGTTGAGTTGTTACG 59.789 41.667 0.00 0.00 37.07 3.18
406 407 1.065126 GGGGCTAGTTGATTCAGCAGT 60.065 52.381 3.25 0.00 37.02 4.40
411 412 3.426787 TTTTCGGGGCTAGTTGATTCA 57.573 42.857 0.00 0.00 0.00 2.57
554 555 3.222173 ACTACCACCAAGATTTGCACA 57.778 42.857 0.00 0.00 0.00 4.57
560 561 8.052748 TGAATATTTGCTACTACCACCAAGATT 58.947 33.333 0.00 0.00 0.00 2.40
590 591 4.010349 CCTCTTCGGCCTTCAAAGTTATT 58.990 43.478 0.00 0.00 0.00 1.40
592 593 2.635915 TCCTCTTCGGCCTTCAAAGTTA 59.364 45.455 0.00 0.00 0.00 2.24
720 721 2.777692 TCCCGGCTCAGGAAATCTTAAT 59.222 45.455 0.00 0.00 0.00 1.40
839 840 1.686110 CCTACCTCCGGCTGAACCT 60.686 63.158 0.00 0.00 35.61 3.50
910 911 2.494059 CTCCGGATTTTCATATGCCGT 58.506 47.619 3.57 0.00 40.33 5.68
942 943 2.182537 GTACGACCGGGCGTGAAT 59.817 61.111 44.48 21.68 45.23 2.57
1003 1006 3.157087 ACTTCCCTTGCCTACATTGTTG 58.843 45.455 0.00 0.00 0.00 3.33
1025 1028 5.705441 CCTAAGTTACAGATCTGTTTTGCCA 59.295 40.000 32.14 11.61 41.83 4.92
1034 1037 6.600882 TCGTTTTCCCTAAGTTACAGATCT 57.399 37.500 0.00 0.00 0.00 2.75
1039 1042 4.456566 GCCAATCGTTTTCCCTAAGTTACA 59.543 41.667 0.00 0.00 0.00 2.41
1047 1050 1.351017 TCAGAGCCAATCGTTTTCCCT 59.649 47.619 0.00 0.00 0.00 4.20
1055 1058 0.179089 CCAGTCCTCAGAGCCAATCG 60.179 60.000 0.00 0.00 0.00 3.34
1200 1203 2.486966 GGCTGTTTCATGCTCGGC 59.513 61.111 6.80 6.80 0.00 5.54
1216 1219 0.170561 CCGTACCAGTTCTGAGTCGG 59.829 60.000 1.00 7.90 0.00 4.79
1328 1331 6.199719 GCTTGGTTGAATTTCTTCACTTTGAG 59.800 38.462 0.00 0.00 41.05 3.02
1363 1366 2.029623 GAGTCATAGTTACTCCCGCCA 58.970 52.381 0.00 0.00 37.91 5.69
1424 1427 5.239306 GGAATCTCGTTAATCCATTCATGCA 59.761 40.000 0.00 0.00 32.08 3.96
1469 1472 0.605319 CCTTGGCTGTGGTTTCGCTA 60.605 55.000 0.00 0.00 0.00 4.26
1503 1506 2.437413 GTCTTCTTTCCCCGCTGATTT 58.563 47.619 0.00 0.00 0.00 2.17
1570 1573 1.694696 GGGCTCCCACTTATCCTACAG 59.305 57.143 0.00 0.00 35.81 2.74
1594 1597 0.250945 TGGTATTTCAGTTGCGCCCA 60.251 50.000 4.18 0.00 0.00 5.36
1603 1606 9.887406 AAGTAAAATAACGTTGTGGTATTTCAG 57.113 29.630 11.99 0.00 0.00 3.02
1755 1765 6.519043 GCTCATCTTAGGACACCTGCATTATA 60.519 42.308 0.00 0.00 34.61 0.98
1760 1770 1.208052 GCTCATCTTAGGACACCTGCA 59.792 52.381 0.00 0.00 34.61 4.41
1793 1803 4.202111 CCCTTTTGTTCCACACGAGATTTT 60.202 41.667 0.00 0.00 0.00 1.82
1903 1913 5.601313 TGGTAACTTTTCTGACACCTCTAGT 59.399 40.000 0.00 0.00 37.61 2.57
1936 1946 0.801251 CTTGACTGCCACAAGCTAGC 59.199 55.000 6.62 6.62 44.23 3.42
1951 1961 2.293677 ACATCGCTATGAACGCTTGA 57.706 45.000 5.05 0.00 36.54 3.02
1968 1978 6.573664 ACATCGAAGGATCAAAAATCAACA 57.426 33.333 0.00 0.00 0.00 3.33
1973 1983 3.065371 GCCGACATCGAAGGATCAAAAAT 59.935 43.478 2.09 0.00 43.02 1.82
2071 2081 1.210413 CCTGTCTCACGACGGTCTG 59.790 63.158 6.57 4.17 43.59 3.51
2109 2119 5.635549 TGAATTACTATCGCGACATTGTG 57.364 39.130 12.93 0.28 0.00 3.33
2113 2123 4.945246 AGGTTGAATTACTATCGCGACAT 58.055 39.130 12.93 0.00 0.00 3.06
2150 2160 5.562501 CGATGACCAATTGTGTGAATCAACA 60.563 40.000 4.43 0.00 0.00 3.33
2176 2186 2.031120 CCACTGGCTTTTCAACCAAGA 58.969 47.619 0.00 0.00 34.96 3.02
2199 2209 2.261671 CGGCACACGGTAGCTTCT 59.738 61.111 0.00 0.00 39.42 2.85
2259 2269 1.019673 GACGTATCAGTAGGCGTCCA 58.980 55.000 4.82 0.00 45.24 4.02
2260 2270 3.841642 GACGTATCAGTAGGCGTCC 57.158 57.895 4.82 0.00 45.24 4.79
2276 2286 8.922058 TCAAAACTTATAGATACGTTGGAGAC 57.078 34.615 0.00 0.00 0.00 3.36
2279 2289 9.661563 ACAATCAAAACTTATAGATACGTTGGA 57.338 29.630 0.00 0.00 0.00 3.53
2283 2293 9.661563 TGGAACAATCAAAACTTATAGATACGT 57.338 29.630 0.00 0.00 31.92 3.57
2304 2314 7.916914 AACGGGTAATATAATAGCATGGAAC 57.083 36.000 0.00 0.00 0.00 3.62
2305 2315 8.788806 CAAAACGGGTAATATAATAGCATGGAA 58.211 33.333 0.00 0.00 0.00 3.53
2306 2316 7.392113 CCAAAACGGGTAATATAATAGCATGGA 59.608 37.037 0.00 0.00 0.00 3.41
2307 2317 7.392113 TCCAAAACGGGTAATATAATAGCATGG 59.608 37.037 0.00 0.00 34.36 3.66
2308 2318 8.330466 TCCAAAACGGGTAATATAATAGCATG 57.670 34.615 0.00 0.00 34.36 4.06
2309 2319 8.956426 CATCCAAAACGGGTAATATAATAGCAT 58.044 33.333 0.00 0.00 34.36 3.79
2310 2320 7.940137 ACATCCAAAACGGGTAATATAATAGCA 59.060 33.333 0.00 0.00 34.36 3.49
2311 2321 8.331730 ACATCCAAAACGGGTAATATAATAGC 57.668 34.615 0.00 0.00 34.36 2.97
2314 2324 8.973182 ACAAACATCCAAAACGGGTAATATAAT 58.027 29.630 0.00 0.00 34.36 1.28
2315 2325 8.244802 CACAAACATCCAAAACGGGTAATATAA 58.755 33.333 0.00 0.00 34.36 0.98
2316 2326 7.148052 CCACAAACATCCAAAACGGGTAATATA 60.148 37.037 0.00 0.00 34.36 0.86
2317 2327 6.350612 CCACAAACATCCAAAACGGGTAATAT 60.351 38.462 0.00 0.00 34.36 1.28
2318 2328 5.047943 CCACAAACATCCAAAACGGGTAATA 60.048 40.000 0.00 0.00 34.36 0.98
2319 2329 4.262249 CCACAAACATCCAAAACGGGTAAT 60.262 41.667 0.00 0.00 34.36 1.89
2320 2330 3.068307 CCACAAACATCCAAAACGGGTAA 59.932 43.478 0.00 0.00 34.36 2.85
2321 2331 2.623889 CCACAAACATCCAAAACGGGTA 59.376 45.455 0.00 0.00 34.36 3.69
2322 2332 1.410882 CCACAAACATCCAAAACGGGT 59.589 47.619 0.00 0.00 34.36 5.28
2323 2333 1.270041 CCCACAAACATCCAAAACGGG 60.270 52.381 0.00 0.00 34.36 5.28
2324 2334 1.871822 GCCCACAAACATCCAAAACGG 60.872 52.381 0.00 0.00 0.00 4.44
2325 2335 1.068434 AGCCCACAAACATCCAAAACG 59.932 47.619 0.00 0.00 0.00 3.60
2326 2336 2.908688 AGCCCACAAACATCCAAAAC 57.091 45.000 0.00 0.00 0.00 2.43
2327 2337 3.922171 AAAGCCCACAAACATCCAAAA 57.078 38.095 0.00 0.00 0.00 2.44
2328 2338 3.964031 AGTAAAGCCCACAAACATCCAAA 59.036 39.130 0.00 0.00 0.00 3.28
2329 2339 3.571590 AGTAAAGCCCACAAACATCCAA 58.428 40.909 0.00 0.00 0.00 3.53
2330 2340 3.237268 AGTAAAGCCCACAAACATCCA 57.763 42.857 0.00 0.00 0.00 3.41
2331 2341 4.600692 AAAGTAAAGCCCACAAACATCC 57.399 40.909 0.00 0.00 0.00 3.51
2332 2342 5.918576 GTGTAAAGTAAAGCCCACAAACATC 59.081 40.000 0.00 0.00 0.00 3.06
2333 2343 5.596772 AGTGTAAAGTAAAGCCCACAAACAT 59.403 36.000 0.00 0.00 0.00 2.71
2334 2344 4.951094 AGTGTAAAGTAAAGCCCACAAACA 59.049 37.500 0.00 0.00 0.00 2.83
2335 2345 5.509716 AGTGTAAAGTAAAGCCCACAAAC 57.490 39.130 0.00 0.00 0.00 2.93
2336 2346 6.532988 AAAGTGTAAAGTAAAGCCCACAAA 57.467 33.333 0.00 0.00 0.00 2.83
2337 2347 6.532988 AAAAGTGTAAAGTAAAGCCCACAA 57.467 33.333 0.00 0.00 0.00 3.33
2338 2348 7.826918 ATAAAAGTGTAAAGTAAAGCCCACA 57.173 32.000 0.00 0.00 0.00 4.17
2339 2349 9.999009 GATATAAAAGTGTAAAGTAAAGCCCAC 57.001 33.333 0.00 0.00 0.00 4.61
2340 2350 9.742144 TGATATAAAAGTGTAAAGTAAAGCCCA 57.258 29.630 0.00 0.00 0.00 5.36
2355 2365 9.783256 GGTTAGTCGCAAAAATGATATAAAAGT 57.217 29.630 0.00 0.00 0.00 2.66
2359 2369 9.826574 AGTAGGTTAGTCGCAAAAATGATATAA 57.173 29.630 0.00 0.00 0.00 0.98
2361 2371 9.826574 TTAGTAGGTTAGTCGCAAAAATGATAT 57.173 29.630 0.00 0.00 0.00 1.63
2362 2372 9.090692 GTTAGTAGGTTAGTCGCAAAAATGATA 57.909 33.333 0.00 0.00 0.00 2.15
2363 2373 7.065443 GGTTAGTAGGTTAGTCGCAAAAATGAT 59.935 37.037 0.00 0.00 0.00 2.45
2364 2374 6.369615 GGTTAGTAGGTTAGTCGCAAAAATGA 59.630 38.462 0.00 0.00 0.00 2.57
2365 2375 6.540205 GGTTAGTAGGTTAGTCGCAAAAATG 58.460 40.000 0.00 0.00 0.00 2.32
2366 2376 5.349543 CGGTTAGTAGGTTAGTCGCAAAAAT 59.650 40.000 0.00 0.00 0.00 1.82
2367 2377 4.685628 CGGTTAGTAGGTTAGTCGCAAAAA 59.314 41.667 0.00 0.00 0.00 1.94
2368 2378 4.236935 CGGTTAGTAGGTTAGTCGCAAAA 58.763 43.478 0.00 0.00 0.00 2.44
2369 2379 3.367292 CCGGTTAGTAGGTTAGTCGCAAA 60.367 47.826 0.00 0.00 0.00 3.68
2370 2380 2.164219 CCGGTTAGTAGGTTAGTCGCAA 59.836 50.000 0.00 0.00 0.00 4.85
2371 2381 1.745087 CCGGTTAGTAGGTTAGTCGCA 59.255 52.381 0.00 0.00 0.00 5.10
2372 2382 2.017049 TCCGGTTAGTAGGTTAGTCGC 58.983 52.381 0.00 0.00 0.00 5.19
2373 2383 2.615912 CCTCCGGTTAGTAGGTTAGTCG 59.384 54.545 0.00 0.00 0.00 4.18
2374 2384 2.360483 GCCTCCGGTTAGTAGGTTAGTC 59.640 54.545 0.00 0.00 32.67 2.59
2375 2385 2.024560 AGCCTCCGGTTAGTAGGTTAGT 60.025 50.000 0.00 0.00 32.67 2.24
2376 2386 2.664015 AGCCTCCGGTTAGTAGGTTAG 58.336 52.381 0.00 0.00 32.67 2.34
2377 2387 2.834638 AGCCTCCGGTTAGTAGGTTA 57.165 50.000 0.00 0.00 32.67 2.85
2378 2388 1.948391 AAGCCTCCGGTTAGTAGGTT 58.052 50.000 0.00 0.00 32.67 3.50
2379 2389 1.948391 AAAGCCTCCGGTTAGTAGGT 58.052 50.000 0.00 0.00 32.67 3.08
2380 2390 3.345508 AAAAAGCCTCCGGTTAGTAGG 57.654 47.619 0.00 0.51 0.00 3.18
2397 2407 4.580995 TCGGAACACTGAAATAGGCAAAAA 59.419 37.500 0.00 0.00 0.00 1.94
2398 2408 4.138290 TCGGAACACTGAAATAGGCAAAA 58.862 39.130 0.00 0.00 0.00 2.44
2399 2409 3.745799 TCGGAACACTGAAATAGGCAAA 58.254 40.909 0.00 0.00 0.00 3.68
2400 2410 3.410631 TCGGAACACTGAAATAGGCAA 57.589 42.857 0.00 0.00 0.00 4.52
2401 2411 3.007506 TCTTCGGAACACTGAAATAGGCA 59.992 43.478 0.00 0.00 0.00 4.75
2402 2412 3.596214 TCTTCGGAACACTGAAATAGGC 58.404 45.455 0.00 0.00 0.00 3.93
2403 2413 6.348540 CCTTTTCTTCGGAACACTGAAATAGG 60.349 42.308 4.40 8.90 33.18 2.57
2404 2414 6.426937 TCCTTTTCTTCGGAACACTGAAATAG 59.573 38.462 4.40 5.33 33.18 1.73
2405 2415 6.292923 TCCTTTTCTTCGGAACACTGAAATA 58.707 36.000 4.40 0.00 33.18 1.40
2406 2416 5.130350 TCCTTTTCTTCGGAACACTGAAAT 58.870 37.500 4.40 0.00 33.18 2.17
2407 2417 4.519213 TCCTTTTCTTCGGAACACTGAAA 58.481 39.130 0.00 0.37 33.18 2.69
2408 2418 4.145365 TCCTTTTCTTCGGAACACTGAA 57.855 40.909 0.00 0.00 33.18 3.02
2409 2419 3.830744 TCCTTTTCTTCGGAACACTGA 57.169 42.857 0.00 0.00 33.18 3.41
2410 2420 5.106673 GGTATTCCTTTTCTTCGGAACACTG 60.107 44.000 0.00 0.00 41.71 3.66
2411 2421 5.001874 GGTATTCCTTTTCTTCGGAACACT 58.998 41.667 0.00 0.00 41.71 3.55
2412 2422 4.758165 TGGTATTCCTTTTCTTCGGAACAC 59.242 41.667 0.00 0.00 41.71 3.32
2413 2423 4.975631 TGGTATTCCTTTTCTTCGGAACA 58.024 39.130 0.00 0.00 41.71 3.18
2414 2424 5.952526 TTGGTATTCCTTTTCTTCGGAAC 57.047 39.130 0.00 0.00 41.71 3.62
2415 2425 5.049267 CGTTTGGTATTCCTTTTCTTCGGAA 60.049 40.000 0.00 0.00 42.96 4.30
2416 2426 4.453136 CGTTTGGTATTCCTTTTCTTCGGA 59.547 41.667 0.00 0.00 34.23 4.55
2417 2427 4.379082 CCGTTTGGTATTCCTTTTCTTCGG 60.379 45.833 0.00 0.00 34.23 4.30
2418 2428 4.453136 TCCGTTTGGTATTCCTTTTCTTCG 59.547 41.667 0.00 0.00 36.30 3.79
2419 2429 5.472478 ACTCCGTTTGGTATTCCTTTTCTTC 59.528 40.000 0.00 0.00 36.30 2.87
2420 2430 5.382616 ACTCCGTTTGGTATTCCTTTTCTT 58.617 37.500 0.00 0.00 36.30 2.52
2421 2431 4.981812 ACTCCGTTTGGTATTCCTTTTCT 58.018 39.130 0.00 0.00 36.30 2.52
2422 2432 4.155462 GGACTCCGTTTGGTATTCCTTTTC 59.845 45.833 0.00 0.00 36.30 2.29
2423 2433 4.077108 GGACTCCGTTTGGTATTCCTTTT 58.923 43.478 0.00 0.00 36.30 2.27
2424 2434 3.073356 TGGACTCCGTTTGGTATTCCTTT 59.927 43.478 0.00 0.00 36.30 3.11
2425 2435 2.640826 TGGACTCCGTTTGGTATTCCTT 59.359 45.455 0.00 0.00 36.30 3.36
2426 2436 2.262637 TGGACTCCGTTTGGTATTCCT 58.737 47.619 0.00 0.00 36.30 3.36
2427 2437 2.773993 TGGACTCCGTTTGGTATTCC 57.226 50.000 0.00 0.00 36.30 3.01
2428 2438 3.120442 CGTTTGGACTCCGTTTGGTATTC 60.120 47.826 0.00 0.00 36.30 1.75
2429 2439 2.809696 CGTTTGGACTCCGTTTGGTATT 59.190 45.455 0.00 0.00 36.30 1.89
2430 2440 2.419667 CGTTTGGACTCCGTTTGGTAT 58.580 47.619 0.00 0.00 36.30 2.73
2431 2441 1.540797 CCGTTTGGACTCCGTTTGGTA 60.541 52.381 0.00 0.00 37.49 3.25
2432 2442 0.816421 CCGTTTGGACTCCGTTTGGT 60.816 55.000 0.00 0.00 37.49 3.67
2433 2443 0.533308 TCCGTTTGGACTCCGTTTGG 60.533 55.000 0.00 0.00 40.17 3.28
2434 2444 1.301423 TTCCGTTTGGACTCCGTTTG 58.699 50.000 0.00 0.00 46.45 2.93
2435 2445 1.877443 CATTCCGTTTGGACTCCGTTT 59.123 47.619 0.00 0.00 46.45 3.60
2436 2446 1.071071 TCATTCCGTTTGGACTCCGTT 59.929 47.619 0.00 0.00 46.45 4.44
2437 2447 0.682852 TCATTCCGTTTGGACTCCGT 59.317 50.000 0.00 0.00 46.45 4.69
2438 2448 1.803334 TTCATTCCGTTTGGACTCCG 58.197 50.000 0.00 0.00 46.45 4.63
2439 2449 2.228103 GGTTTCATTCCGTTTGGACTCC 59.772 50.000 0.00 0.00 46.45 3.85
2440 2450 3.146847 AGGTTTCATTCCGTTTGGACTC 58.853 45.455 0.00 0.00 46.45 3.36
2441 2451 3.223674 AGGTTTCATTCCGTTTGGACT 57.776 42.857 0.00 0.00 46.45 3.85
2442 2452 3.608474 CGAAGGTTTCATTCCGTTTGGAC 60.608 47.826 0.00 0.00 46.45 4.02
2443 2453 2.550606 CGAAGGTTTCATTCCGTTTGGA 59.449 45.455 0.00 0.00 44.61 3.53
2444 2454 2.928694 CGAAGGTTTCATTCCGTTTGG 58.071 47.619 0.00 0.00 0.00 3.28
2463 2473 1.130561 GTTCCAAAAAGATCGCTCCCG 59.869 52.381 0.00 0.00 0.00 5.14
2464 2474 2.159382 TGTTCCAAAAAGATCGCTCCC 58.841 47.619 0.00 0.00 0.00 4.30
2465 2475 3.915437 TTGTTCCAAAAAGATCGCTCC 57.085 42.857 0.00 0.00 0.00 4.70
2466 2476 3.664025 CGTTTGTTCCAAAAAGATCGCTC 59.336 43.478 0.00 0.00 0.00 5.03
2467 2477 3.066203 ACGTTTGTTCCAAAAAGATCGCT 59.934 39.130 0.00 0.00 0.00 4.93
2468 2478 3.179599 CACGTTTGTTCCAAAAAGATCGC 59.820 43.478 0.00 0.00 0.00 4.58
2469 2479 4.593157 TCACGTTTGTTCCAAAAAGATCG 58.407 39.130 0.00 0.00 0.00 3.69
2470 2480 5.629435 GGATCACGTTTGTTCCAAAAAGATC 59.371 40.000 13.34 13.34 40.26 2.75
2471 2481 5.068460 TGGATCACGTTTGTTCCAAAAAGAT 59.932 36.000 3.91 0.00 45.09 2.40
2472 2482 4.399618 TGGATCACGTTTGTTCCAAAAAGA 59.600 37.500 3.91 0.00 45.09 2.52
2473 2483 4.677584 TGGATCACGTTTGTTCCAAAAAG 58.322 39.130 3.91 0.00 45.09 2.27
2474 2484 4.399618 TCTGGATCACGTTTGTTCCAAAAA 59.600 37.500 7.12 0.00 46.56 1.94
2475 2485 3.948473 TCTGGATCACGTTTGTTCCAAAA 59.052 39.130 7.12 0.00 46.56 2.44
2476 2486 3.546724 TCTGGATCACGTTTGTTCCAAA 58.453 40.909 7.12 0.00 46.56 3.28
2477 2487 3.138304 CTCTGGATCACGTTTGTTCCAA 58.862 45.455 7.12 0.42 46.56 3.53
2478 2488 2.549992 CCTCTGGATCACGTTTGTTCCA 60.550 50.000 5.88 5.88 45.62 3.53
2479 2489 2.076863 CCTCTGGATCACGTTTGTTCC 58.923 52.381 0.00 0.00 40.74 3.62
2480 2490 2.737252 GTCCTCTGGATCACGTTTGTTC 59.263 50.000 0.00 0.00 32.73 3.18
2481 2491 2.368875 AGTCCTCTGGATCACGTTTGTT 59.631 45.455 0.00 0.00 32.73 2.83
2482 2492 1.971357 AGTCCTCTGGATCACGTTTGT 59.029 47.619 0.00 0.00 32.73 2.83
2483 2493 2.738846 CAAGTCCTCTGGATCACGTTTG 59.261 50.000 0.00 0.00 32.73 2.93
2484 2494 2.289694 CCAAGTCCTCTGGATCACGTTT 60.290 50.000 0.00 0.00 32.73 3.60
2485 2495 1.276421 CCAAGTCCTCTGGATCACGTT 59.724 52.381 0.00 0.00 32.73 3.99
2486 2496 0.898320 CCAAGTCCTCTGGATCACGT 59.102 55.000 0.00 0.00 32.73 4.49
2487 2497 1.135915 CTCCAAGTCCTCTGGATCACG 59.864 57.143 0.00 0.00 32.73 4.35
2488 2498 2.093764 CACTCCAAGTCCTCTGGATCAC 60.094 54.545 0.00 0.00 32.73 3.06
2489 2499 2.182827 CACTCCAAGTCCTCTGGATCA 58.817 52.381 0.00 0.00 32.73 2.92
2490 2500 1.134551 GCACTCCAAGTCCTCTGGATC 60.135 57.143 0.00 0.00 32.73 3.36
2491 2501 0.908198 GCACTCCAAGTCCTCTGGAT 59.092 55.000 0.00 0.00 32.73 3.41
2492 2502 0.471780 TGCACTCCAAGTCCTCTGGA 60.472 55.000 0.00 0.00 0.00 3.86
2493 2503 0.397941 TTGCACTCCAAGTCCTCTGG 59.602 55.000 0.00 0.00 0.00 3.86
2494 2504 1.805869 CTTGCACTCCAAGTCCTCTG 58.194 55.000 0.00 0.00 44.74 3.35
2502 2512 3.351740 TGTTTCTTGACTTGCACTCCAA 58.648 40.909 0.00 0.00 0.00 3.53
2503 2513 2.997980 TGTTTCTTGACTTGCACTCCA 58.002 42.857 0.00 0.00 0.00 3.86
2504 2514 4.540824 GATTGTTTCTTGACTTGCACTCC 58.459 43.478 0.00 0.00 0.00 3.85
2505 2515 4.024893 TCGATTGTTTCTTGACTTGCACTC 60.025 41.667 0.00 0.00 0.00 3.51
2506 2516 3.876914 TCGATTGTTTCTTGACTTGCACT 59.123 39.130 0.00 0.00 0.00 4.40
2507 2517 4.209452 TCGATTGTTTCTTGACTTGCAC 57.791 40.909 0.00 0.00 0.00 4.57
2508 2518 3.250762 CCTCGATTGTTTCTTGACTTGCA 59.749 43.478 0.00 0.00 0.00 4.08
2509 2519 3.814945 CCTCGATTGTTTCTTGACTTGC 58.185 45.455 0.00 0.00 0.00 4.01
2510 2520 3.665323 CGCCTCGATTGTTTCTTGACTTG 60.665 47.826 0.00 0.00 0.00 3.16
2511 2521 2.480419 CGCCTCGATTGTTTCTTGACTT 59.520 45.455 0.00 0.00 0.00 3.01
2512 2522 2.069273 CGCCTCGATTGTTTCTTGACT 58.931 47.619 0.00 0.00 0.00 3.41
2513 2523 2.066262 TCGCCTCGATTGTTTCTTGAC 58.934 47.619 0.00 0.00 0.00 3.18
2514 2524 2.066262 GTCGCCTCGATTGTTTCTTGA 58.934 47.619 0.00 0.00 38.42 3.02
2515 2525 1.128692 GGTCGCCTCGATTGTTTCTTG 59.871 52.381 0.00 0.00 38.42 3.02
2516 2526 1.270625 TGGTCGCCTCGATTGTTTCTT 60.271 47.619 0.00 0.00 38.42 2.52
2517 2527 0.320374 TGGTCGCCTCGATTGTTTCT 59.680 50.000 0.00 0.00 38.42 2.52
2518 2528 0.442699 GTGGTCGCCTCGATTGTTTC 59.557 55.000 0.00 0.00 38.42 2.78
2519 2529 1.289109 CGTGGTCGCCTCGATTGTTT 61.289 55.000 12.82 0.00 42.19 2.83
2520 2530 1.736645 CGTGGTCGCCTCGATTGTT 60.737 57.895 12.82 0.00 42.19 2.83
2521 2531 2.126071 CGTGGTCGCCTCGATTGT 60.126 61.111 12.82 0.00 42.19 2.71
2522 2532 1.874019 CTCGTGGTCGCCTCGATTG 60.874 63.158 18.45 8.51 46.01 2.67
2523 2533 2.490217 CTCGTGGTCGCCTCGATT 59.510 61.111 18.45 0.00 46.01 3.34
2524 2534 3.518998 CCTCGTGGTCGCCTCGAT 61.519 66.667 18.45 0.00 46.01 3.59


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

AutoCloner maintained by Alex Coulton.