Multiple sequence alignment - TraesCS6D01G238200

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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 TraesCS6D01G238200 chr6D 100.000 2654 0 0 1 2654 338512999 338515652 0.000000e+00 4902.0
1 TraesCS6D01G238200 chr6D 94.545 55 3 0 377 431 1486551 1486605 4.710000e-13 86.1
2 TraesCS6D01G238200 chr6B 96.880 1827 42 6 373 2187 481845250 481843427 0.000000e+00 3044.0
3 TraesCS6D01G238200 chr6B 94.355 372 20 1 1 372 481845659 481845289 1.070000e-158 569.0
4 TraesCS6D01G238200 chr6B 93.478 46 3 0 374 419 628896644 628896599 4.740000e-08 69.4
5 TraesCS6D01G238200 chr6A 93.077 1950 91 20 453 2396 479042112 479044023 0.000000e+00 2813.0
6 TraesCS6D01G238200 chr6A 83.041 171 27 2 5 174 571018587 571018756 1.270000e-33 154.0
7 TraesCS6D01G238200 chr6A 91.228 57 5 0 375 431 447187386 447187330 7.880000e-11 78.7
8 TraesCS6D01G238200 chr2D 87.435 191 22 2 5 195 372619187 372619375 4.450000e-53 219.0
9 TraesCS6D01G238200 chr2D 83.920 199 30 1 1 199 56293048 56292852 3.490000e-44 189.0
10 TraesCS6D01G238200 chr2D 79.144 187 32 6 2155 2337 61345848 61346031 3.590000e-24 122.0
11 TraesCS6D01G238200 chr2D 92.593 54 3 1 375 428 166605930 166605982 2.830000e-10 76.8
12 TraesCS6D01G238200 chr1D 87.356 174 22 0 1 174 88220063 88220236 1.610000e-47 200.0
13 TraesCS6D01G238200 chr1A 85.128 195 29 0 1 195 84628351 84628545 1.610000e-47 200.0
14 TraesCS6D01G238200 chr7A 83.756 197 28 3 1 195 531069707 531069901 1.620000e-42 183.0
15 TraesCS6D01G238200 chr7A 84.615 78 6 6 2182 2257 269136172 269136245 3.660000e-09 73.1
16 TraesCS6D01G238200 chr7A 86.441 59 8 0 374 432 663369905 663369963 6.130000e-07 65.8
17 TraesCS6D01G238200 chr5B 83.505 194 32 0 2 195 494318375 494318568 5.840000e-42 182.0
18 TraesCS6D01G238200 chr5B 73.897 272 58 10 1107 1367 492619510 492619779 2.170000e-16 97.1
19 TraesCS6D01G238200 chr3D 80.693 202 32 6 2 199 65411720 65411918 1.650000e-32 150.0
20 TraesCS6D01G238200 chr3D 77.917 240 45 4 2160 2393 295261778 295261541 2.750000e-30 143.0
21 TraesCS6D01G238200 chr7B 78.008 241 42 7 2164 2394 671710716 671710477 9.900000e-30 141.0
22 TraesCS6D01G238200 chr7B 96.429 56 2 0 377 432 674592023 674591968 2.810000e-15 93.5
23 TraesCS6D01G238200 chr5A 77.500 160 36 0 2163 2322 687222101 687221942 2.170000e-16 97.1
24 TraesCS6D01G238200 chr2B 89.474 76 8 0 2184 2259 409400312 409400237 2.170000e-16 97.1
25 TraesCS6D01G238200 chr2B 77.692 130 29 0 2494 2623 707373272 707373401 2.190000e-11 80.5
26 TraesCS6D01G238200 chr3A 85.393 89 13 0 2155 2243 737294882 737294794 2.810000e-15 93.5
27 TraesCS6D01G238200 chr4B 91.525 59 3 2 374 431 27124942 27124999 2.190000e-11 80.5
28 TraesCS6D01G238200 chr4B 90.196 51 4 1 2334 2384 648915908 648915859 6.130000e-07 65.8
29 TraesCS6D01G238200 chr4B 91.304 46 4 0 2534 2579 659145308 659145353 2.210000e-06 63.9
30 TraesCS6D01G238200 chr3B 87.879 66 7 1 2157 2222 473684482 473684546 2.830000e-10 76.8


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 TraesCS6D01G238200 chr6D 338512999 338515652 2653 False 4902.0 4902 100.0000 1 2654 1 chr6D.!!$F2 2653
1 TraesCS6D01G238200 chr6B 481843427 481845659 2232 True 1806.5 3044 95.6175 1 2187 2 chr6B.!!$R2 2186
2 TraesCS6D01G238200 chr6A 479042112 479044023 1911 False 2813.0 2813 93.0770 453 2396 1 chr6A.!!$F1 1943

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
665 714 0.868406 CGCGCTTTCTCTTTCAAGGT 59.132 50.0 5.56 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2544 2603 0.035317 GCTGATCGGCACCCATCATA 59.965 55.0 21.88 0.0 0.0 2.15 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
76 77 5.645201 TGGATATAGGGGATCGGATATGAG 58.355 45.833 0.00 0.00 0.00 2.90
103 104 2.542205 CGGATGTGGACGACGCTATTTA 60.542 50.000 0.00 0.00 0.00 1.40
160 161 2.281484 GTGGGCAGGCGTTTGAGA 60.281 61.111 0.00 0.00 0.00 3.27
249 250 8.556589 TGGAGAATGTTAAAAATCTGATCCCTA 58.443 33.333 0.00 0.00 0.00 3.53
287 288 1.210155 GTGCCGAGTGTGCCATTTC 59.790 57.895 0.00 0.00 0.00 2.17
288 289 1.971167 TGCCGAGTGTGCCATTTCC 60.971 57.895 0.00 0.00 0.00 3.13
312 313 3.005050 CCCGAACCGCAGATACTTGTATA 59.995 47.826 0.00 0.00 0.00 1.47
333 334 9.275572 TGTATAAAGAAAGGGTATGACTAGGTT 57.724 33.333 0.00 0.00 0.00 3.50
344 345 7.781693 AGGGTATGACTAGGTTTTAATCGACTA 59.218 37.037 0.00 0.00 0.00 2.59
354 355 8.768957 AGGTTTTAATCGACTAAGACTTAACC 57.231 34.615 8.44 8.44 0.00 2.85
405 444 9.850628 TCTTCATGCAAAATCAAAGAAAGATAG 57.149 29.630 0.00 0.00 0.00 2.08
432 471 6.513180 TCAACTGAGACATAACGAAGTCTTT 58.487 36.000 0.00 0.00 45.00 2.52
433 472 6.984474 TCAACTGAGACATAACGAAGTCTTTT 59.016 34.615 0.00 0.00 45.00 2.27
665 714 0.868406 CGCGCTTTCTCTTTCAAGGT 59.132 50.000 5.56 0.00 0.00 3.50
988 1037 1.272781 CAGCTTACACTCGCAGCTAC 58.727 55.000 0.00 0.00 42.15 3.58
1398 1447 2.048127 GATGAGATACGGCGGGCC 60.048 66.667 13.24 0.00 0.00 5.80
1497 1546 3.112709 GAGCAGTTCGCCGGTGAC 61.113 66.667 19.40 13.05 44.04 3.67
1614 1663 1.135731 GTCAGCGACTGTCGGAGAG 59.864 63.158 28.92 0.00 40.84 3.20
1674 1723 4.331443 TGATTACGCGCATTTGAGTTATGT 59.669 37.500 5.73 0.00 0.00 2.29
1680 1729 3.848019 GCGCATTTGAGTTATGTCTTGTG 59.152 43.478 0.30 0.00 0.00 3.33
1681 1730 4.613622 GCGCATTTGAGTTATGTCTTGTGT 60.614 41.667 0.30 0.00 0.00 3.72
1705 1754 1.327764 GGCGCGAAGAACTTCTAATGG 59.672 52.381 12.10 0.00 37.44 3.16
1707 1756 2.029365 GCGCGAAGAACTTCTAATGGAC 59.971 50.000 12.10 0.00 37.44 4.02
1722 1771 6.288294 TCTAATGGACGTGCAGCTTTATATT 58.712 36.000 16.77 4.72 0.00 1.28
1857 1906 5.413309 AGGTCTGATCTTGAGTTTGGTAG 57.587 43.478 0.00 0.00 0.00 3.18
2066 2119 5.277345 CCGATCCCTTACAAAGCTTAATTCG 60.277 44.000 0.00 0.00 0.00 3.34
2167 2226 7.012421 AGAGTACAACTTTGGAAGTGCTAAAAG 59.988 37.037 0.00 0.00 41.91 2.27
2180 2239 6.283161 AGTGCTAAAAGTCTGACGTTAAAC 57.717 37.500 9.33 9.37 0.00 2.01
2192 2251 5.992829 TCTGACGTTAAACTTTTAGGCATGA 59.007 36.000 0.00 0.00 0.00 3.07
2214 2273 6.957150 TGACAAATCAAACATTTTTCATGGC 58.043 32.000 0.00 0.00 0.00 4.40
2224 2283 9.332301 CAAACATTTTTCATGGCAATTTATGTC 57.668 29.630 0.00 0.00 0.00 3.06
2226 2285 7.095910 ACATTTTTCATGGCAATTTATGTCGA 58.904 30.769 0.00 0.00 36.00 4.20
2228 2287 3.942539 TCATGGCAATTTATGTCGACG 57.057 42.857 11.62 0.00 36.00 5.12
2229 2288 2.031560 TCATGGCAATTTATGTCGACGC 59.968 45.455 11.62 5.93 36.00 5.19
2250 2309 4.858692 CGCAAGGATGACAAATTTAGTTGG 59.141 41.667 0.00 0.00 32.50 3.77
2252 2311 4.701956 AGGATGACAAATTTAGTTGGCG 57.298 40.909 0.00 0.00 39.58 5.69
2267 2326 2.853914 GCGAGCACGACACTTTCC 59.146 61.111 8.01 0.00 42.66 3.13
2303 2362 2.043652 AGCCGGATTTGCCATGCT 60.044 55.556 5.05 0.00 39.02 3.79
2312 2371 3.555586 GGATTTGCCATGCTTGTCAACTT 60.556 43.478 0.00 0.00 36.34 2.66
2320 2379 3.708563 TGCTTGTCAACTTAACTTGCC 57.291 42.857 0.00 0.00 0.00 4.52
2323 2382 3.795488 GCTTGTCAACTTAACTTGCCACC 60.795 47.826 0.00 0.00 0.00 4.61
2329 2388 1.216930 ACTTAACTTGCCACCCTTGGT 59.783 47.619 0.00 0.00 45.98 3.67
2332 2391 2.463047 AACTTGCCACCCTTGGTAAA 57.537 45.000 0.00 0.00 45.83 2.01
2346 2405 7.812669 CACCCTTGGTAAACATAGAAAATGTTC 59.187 37.037 4.01 0.00 36.02 3.18
2347 2406 7.507616 ACCCTTGGTAAACATAGAAAATGTTCA 59.492 33.333 4.01 0.00 40.94 3.18
2368 2427 9.921637 TGTTCAATTTGTCATACCTAAAAATCC 57.078 29.630 0.00 0.00 0.00 3.01
2375 2434 5.577945 TGTCATACCTAAAAATCCGACGTTC 59.422 40.000 0.00 0.00 0.00 3.95
2384 2443 3.539431 AATCCGACGTTCGCTAGATAG 57.461 47.619 0.00 0.00 38.82 2.08
2387 2446 1.596260 CCGACGTTCGCTAGATAGTCA 59.404 52.381 0.00 0.00 38.82 3.41
2388 2447 2.348685 CCGACGTTCGCTAGATAGTCAG 60.349 54.545 0.00 0.00 38.82 3.51
2396 2455 4.643463 TCGCTAGATAGTCAGGTCCTAAG 58.357 47.826 0.00 0.00 0.00 2.18
2397 2456 4.347292 TCGCTAGATAGTCAGGTCCTAAGA 59.653 45.833 0.00 0.00 0.00 2.10
2398 2457 5.013287 TCGCTAGATAGTCAGGTCCTAAGAT 59.987 44.000 0.00 0.00 0.00 2.40
2399 2458 6.212993 TCGCTAGATAGTCAGGTCCTAAGATA 59.787 42.308 0.00 0.00 0.00 1.98
2400 2459 6.537301 CGCTAGATAGTCAGGTCCTAAGATAG 59.463 46.154 0.00 0.00 0.00 2.08
2401 2460 7.399634 GCTAGATAGTCAGGTCCTAAGATAGT 58.600 42.308 0.00 0.00 0.00 2.12
2402 2461 7.551617 GCTAGATAGTCAGGTCCTAAGATAGTC 59.448 44.444 0.00 0.00 0.00 2.59
2403 2462 6.469410 AGATAGTCAGGTCCTAAGATAGTCG 58.531 44.000 0.00 0.00 0.00 4.18
2404 2463 3.822940 AGTCAGGTCCTAAGATAGTCGG 58.177 50.000 0.00 0.00 0.00 4.79
2405 2464 2.885894 GTCAGGTCCTAAGATAGTCGGG 59.114 54.545 0.00 0.00 0.00 5.14
2406 2465 2.512896 TCAGGTCCTAAGATAGTCGGGT 59.487 50.000 0.00 0.00 0.00 5.28
2407 2466 2.885894 CAGGTCCTAAGATAGTCGGGTC 59.114 54.545 0.00 0.00 0.00 4.46
2408 2467 2.158490 AGGTCCTAAGATAGTCGGGTCC 60.158 54.545 0.00 0.00 0.00 4.46
2409 2468 2.158490 GGTCCTAAGATAGTCGGGTCCT 60.158 54.545 0.00 0.00 0.00 3.85
2410 2469 3.073650 GGTCCTAAGATAGTCGGGTCCTA 59.926 52.174 0.00 0.00 0.00 2.94
2411 2470 4.446889 GGTCCTAAGATAGTCGGGTCCTAA 60.447 50.000 0.00 0.00 0.00 2.69
2412 2471 5.136105 GTCCTAAGATAGTCGGGTCCTAAA 58.864 45.833 0.00 0.00 0.00 1.85
2413 2472 5.774184 GTCCTAAGATAGTCGGGTCCTAAAT 59.226 44.000 0.00 0.00 0.00 1.40
2414 2473 6.267242 GTCCTAAGATAGTCGGGTCCTAAATT 59.733 42.308 0.00 0.00 0.00 1.82
2415 2474 6.842807 TCCTAAGATAGTCGGGTCCTAAATTT 59.157 38.462 0.00 0.00 0.00 1.82
2416 2475 7.346436 TCCTAAGATAGTCGGGTCCTAAATTTT 59.654 37.037 0.00 0.00 0.00 1.82
2417 2476 7.991460 CCTAAGATAGTCGGGTCCTAAATTTTT 59.009 37.037 0.00 0.00 0.00 1.94
2434 2493 1.588674 TTTTACTCCACTGTGCACCG 58.411 50.000 15.69 11.05 0.00 4.94
2435 2494 0.250124 TTTACTCCACTGTGCACCGG 60.250 55.000 15.69 12.44 0.00 5.28
2436 2495 1.116536 TTACTCCACTGTGCACCGGA 61.117 55.000 15.69 16.08 0.00 5.14
2437 2496 0.902984 TACTCCACTGTGCACCGGAT 60.903 55.000 15.69 9.92 0.00 4.18
2438 2497 1.742880 CTCCACTGTGCACCGGATG 60.743 63.158 15.69 3.68 0.00 3.51
2439 2498 2.747460 CCACTGTGCACCGGATGG 60.747 66.667 15.69 12.45 42.84 3.51
2440 2499 2.747460 CACTGTGCACCGGATGGG 60.747 66.667 15.69 0.00 40.75 4.00
2466 2525 5.703730 TTTTGGGATAGTTGTAGGGTAGG 57.296 43.478 0.00 0.00 0.00 3.18
2467 2526 2.686119 TGGGATAGTTGTAGGGTAGGC 58.314 52.381 0.00 0.00 0.00 3.93
2468 2527 1.617357 GGGATAGTTGTAGGGTAGGCG 59.383 57.143 0.00 0.00 0.00 5.52
2469 2528 1.617357 GGATAGTTGTAGGGTAGGCGG 59.383 57.143 0.00 0.00 0.00 6.13
2470 2529 2.314246 GATAGTTGTAGGGTAGGCGGT 58.686 52.381 0.00 0.00 0.00 5.68
2471 2530 1.477553 TAGTTGTAGGGTAGGCGGTG 58.522 55.000 0.00 0.00 0.00 4.94
2472 2531 1.219935 GTTGTAGGGTAGGCGGTGG 59.780 63.158 0.00 0.00 0.00 4.61
2473 2532 1.991167 TTGTAGGGTAGGCGGTGGG 60.991 63.158 0.00 0.00 0.00 4.61
2474 2533 2.364710 GTAGGGTAGGCGGTGGGT 60.365 66.667 0.00 0.00 0.00 4.51
2475 2534 2.042639 TAGGGTAGGCGGTGGGTC 60.043 66.667 0.00 0.00 0.00 4.46
2480 2539 4.468769 TAGGCGGTGGGTCGGGAT 62.469 66.667 0.00 0.00 0.00 3.85
2481 2540 3.988050 TAGGCGGTGGGTCGGGATT 62.988 63.158 0.00 0.00 0.00 3.01
2483 2542 4.404098 GCGGTGGGTCGGGATTGT 62.404 66.667 0.00 0.00 0.00 2.71
2484 2543 2.125269 CGGTGGGTCGGGATTGTC 60.125 66.667 0.00 0.00 0.00 3.18
2485 2544 2.949909 CGGTGGGTCGGGATTGTCA 61.950 63.158 0.00 0.00 0.00 3.58
2486 2545 1.078426 GGTGGGTCGGGATTGTCAG 60.078 63.158 0.00 0.00 0.00 3.51
2487 2546 1.078426 GTGGGTCGGGATTGTCAGG 60.078 63.158 0.00 0.00 0.00 3.86
2488 2547 2.124695 GGGTCGGGATTGTCAGGC 60.125 66.667 0.00 0.00 0.00 4.85
2489 2548 2.511600 GGTCGGGATTGTCAGGCG 60.512 66.667 0.00 0.00 0.00 5.52
2490 2549 2.511600 GTCGGGATTGTCAGGCGG 60.512 66.667 0.00 0.00 0.00 6.13
2491 2550 2.682136 TCGGGATTGTCAGGCGGA 60.682 61.111 0.00 0.00 0.00 5.54
2492 2551 2.063979 TCGGGATTGTCAGGCGGAT 61.064 57.895 0.00 0.00 0.00 4.18
2493 2552 0.757561 TCGGGATTGTCAGGCGGATA 60.758 55.000 0.00 0.00 0.00 2.59
2494 2553 0.321671 CGGGATTGTCAGGCGGATAT 59.678 55.000 0.00 0.00 0.00 1.63
2495 2554 1.813513 GGGATTGTCAGGCGGATATG 58.186 55.000 0.00 0.00 0.00 1.78
2496 2555 1.160137 GGATTGTCAGGCGGATATGC 58.840 55.000 0.00 0.00 0.00 3.14
2520 2579 3.420482 GTGCCCTGGCCACCCTAT 61.420 66.667 0.00 0.00 41.09 2.57
2521 2580 2.076184 GTGCCCTGGCCACCCTATA 61.076 63.158 0.00 0.00 41.09 1.31
2522 2581 1.073008 TGCCCTGGCCACCCTATAT 60.073 57.895 0.00 0.00 41.09 0.86
2523 2582 1.133809 TGCCCTGGCCACCCTATATC 61.134 60.000 0.00 0.00 41.09 1.63
2524 2583 0.842467 GCCCTGGCCACCCTATATCT 60.842 60.000 0.00 0.00 34.56 1.98
2525 2584 0.987294 CCCTGGCCACCCTATATCTG 59.013 60.000 0.00 0.00 0.00 2.90
2526 2585 1.734655 CCTGGCCACCCTATATCTGT 58.265 55.000 0.00 0.00 0.00 3.41
2527 2586 1.625818 CCTGGCCACCCTATATCTGTC 59.374 57.143 0.00 0.00 0.00 3.51
2528 2587 2.614259 CTGGCCACCCTATATCTGTCT 58.386 52.381 0.00 0.00 0.00 3.41
2529 2588 2.975489 CTGGCCACCCTATATCTGTCTT 59.025 50.000 0.00 0.00 0.00 3.01
2530 2589 3.392616 CTGGCCACCCTATATCTGTCTTT 59.607 47.826 0.00 0.00 0.00 2.52
2531 2590 3.785887 TGGCCACCCTATATCTGTCTTTT 59.214 43.478 0.00 0.00 0.00 2.27
2532 2591 4.972568 TGGCCACCCTATATCTGTCTTTTA 59.027 41.667 0.00 0.00 0.00 1.52
2533 2592 5.610982 TGGCCACCCTATATCTGTCTTTTAT 59.389 40.000 0.00 0.00 0.00 1.40
2534 2593 6.102615 TGGCCACCCTATATCTGTCTTTTATT 59.897 38.462 0.00 0.00 0.00 1.40
2535 2594 7.004691 GGCCACCCTATATCTGTCTTTTATTT 58.995 38.462 0.00 0.00 0.00 1.40
2536 2595 7.505923 GGCCACCCTATATCTGTCTTTTATTTT 59.494 37.037 0.00 0.00 0.00 1.82
2537 2596 8.352942 GCCACCCTATATCTGTCTTTTATTTTG 58.647 37.037 0.00 0.00 0.00 2.44
2538 2597 8.850156 CCACCCTATATCTGTCTTTTATTTTGG 58.150 37.037 0.00 0.00 0.00 3.28
2539 2598 8.352942 CACCCTATATCTGTCTTTTATTTTGGC 58.647 37.037 0.00 0.00 0.00 4.52
2540 2599 8.282256 ACCCTATATCTGTCTTTTATTTTGGCT 58.718 33.333 0.00 0.00 0.00 4.75
2541 2600 8.571336 CCCTATATCTGTCTTTTATTTTGGCTG 58.429 37.037 0.00 0.00 0.00 4.85
2542 2601 8.571336 CCTATATCTGTCTTTTATTTTGGCTGG 58.429 37.037 0.00 0.00 0.00 4.85
2543 2602 9.342308 CTATATCTGTCTTTTATTTTGGCTGGA 57.658 33.333 0.00 0.00 0.00 3.86
2544 2603 8.773033 ATATCTGTCTTTTATTTTGGCTGGAT 57.227 30.769 0.00 0.00 0.00 3.41
2545 2604 9.866655 ATATCTGTCTTTTATTTTGGCTGGATA 57.133 29.630 0.00 0.00 0.00 2.59
2546 2605 8.773033 ATCTGTCTTTTATTTTGGCTGGATAT 57.227 30.769 0.00 0.00 0.00 1.63
2547 2606 7.999679 TCTGTCTTTTATTTTGGCTGGATATG 58.000 34.615 0.00 0.00 0.00 1.78
2548 2607 7.833682 TCTGTCTTTTATTTTGGCTGGATATGA 59.166 33.333 0.00 0.00 0.00 2.15
2549 2608 8.537728 TGTCTTTTATTTTGGCTGGATATGAT 57.462 30.769 0.00 0.00 0.00 2.45
2550 2609 8.415553 TGTCTTTTATTTTGGCTGGATATGATG 58.584 33.333 0.00 0.00 0.00 3.07
2551 2610 7.869429 GTCTTTTATTTTGGCTGGATATGATGG 59.131 37.037 0.00 0.00 0.00 3.51
2552 2611 6.669125 TTTATTTTGGCTGGATATGATGGG 57.331 37.500 0.00 0.00 0.00 4.00
2553 2612 3.686227 TTTTGGCTGGATATGATGGGT 57.314 42.857 0.00 0.00 0.00 4.51
2554 2613 2.662535 TTGGCTGGATATGATGGGTG 57.337 50.000 0.00 0.00 0.00 4.61
2555 2614 0.111061 TGGCTGGATATGATGGGTGC 59.889 55.000 0.00 0.00 0.00 5.01
2556 2615 0.610232 GGCTGGATATGATGGGTGCC 60.610 60.000 0.00 0.00 0.00 5.01
2557 2616 0.957395 GCTGGATATGATGGGTGCCG 60.957 60.000 0.00 0.00 0.00 5.69
2558 2617 0.686789 CTGGATATGATGGGTGCCGA 59.313 55.000 0.00 0.00 0.00 5.54
2559 2618 1.280133 CTGGATATGATGGGTGCCGAT 59.720 52.381 0.00 0.00 0.00 4.18
2560 2619 1.278985 TGGATATGATGGGTGCCGATC 59.721 52.381 6.32 6.32 0.00 3.69
2561 2620 1.278985 GGATATGATGGGTGCCGATCA 59.721 52.381 16.25 16.25 33.20 2.92
2562 2621 2.625737 GATATGATGGGTGCCGATCAG 58.374 52.381 18.21 0.00 32.20 2.90
2563 2622 0.035317 TATGATGGGTGCCGATCAGC 59.965 55.000 18.21 0.00 42.24 4.26
2568 2627 3.785859 GGTGCCGATCAGCCTGGA 61.786 66.667 0.00 0.00 37.22 3.86
2569 2628 2.507944 GTGCCGATCAGCCTGGAT 59.492 61.111 0.00 0.00 0.00 3.41
2570 2629 1.890979 GTGCCGATCAGCCTGGATG 60.891 63.158 5.38 5.38 0.00 3.51
2571 2630 2.369633 TGCCGATCAGCCTGGATGT 61.370 57.895 12.27 0.00 0.00 3.06
2572 2631 1.153086 GCCGATCAGCCTGGATGTT 60.153 57.895 12.27 3.13 0.00 2.71
2573 2632 0.749454 GCCGATCAGCCTGGATGTTT 60.749 55.000 12.27 0.65 0.00 2.83
2574 2633 1.019673 CCGATCAGCCTGGATGTTTG 58.980 55.000 12.27 7.53 0.00 2.93
2575 2634 1.407299 CCGATCAGCCTGGATGTTTGA 60.407 52.381 12.27 0.22 0.00 2.69
2576 2635 1.938577 CGATCAGCCTGGATGTTTGAG 59.061 52.381 12.27 0.00 0.00 3.02
2577 2636 2.295885 GATCAGCCTGGATGTTTGAGG 58.704 52.381 12.27 0.00 0.00 3.86
2579 2638 3.608432 GCCTGGATGTTTGAGGCC 58.392 61.111 0.00 0.00 45.69 5.19
2580 2639 1.000396 GCCTGGATGTTTGAGGCCT 60.000 57.895 3.86 3.86 45.69 5.19
2581 2640 1.318158 GCCTGGATGTTTGAGGCCTG 61.318 60.000 12.00 0.00 45.69 4.85
2582 2641 0.038744 CCTGGATGTTTGAGGCCTGT 59.961 55.000 12.00 0.00 0.00 4.00
2583 2642 1.548582 CCTGGATGTTTGAGGCCTGTT 60.549 52.381 12.00 0.00 0.00 3.16
2584 2643 2.242043 CTGGATGTTTGAGGCCTGTTT 58.758 47.619 12.00 0.00 0.00 2.83
2585 2644 2.629617 CTGGATGTTTGAGGCCTGTTTT 59.370 45.455 12.00 0.00 0.00 2.43
2586 2645 3.826157 CTGGATGTTTGAGGCCTGTTTTA 59.174 43.478 12.00 0.00 0.00 1.52
2587 2646 3.826157 TGGATGTTTGAGGCCTGTTTTAG 59.174 43.478 12.00 0.00 0.00 1.85
2595 2654 4.687464 CCTGTTTTAGGCGTCGGT 57.313 55.556 0.00 0.00 40.38 4.69
2596 2655 2.452767 CCTGTTTTAGGCGTCGGTC 58.547 57.895 0.00 0.00 40.38 4.79
2597 2656 0.037605 CCTGTTTTAGGCGTCGGTCT 60.038 55.000 0.00 0.00 40.38 3.85
2598 2657 1.068474 CTGTTTTAGGCGTCGGTCTG 58.932 55.000 0.00 0.00 0.00 3.51
2599 2658 0.675083 TGTTTTAGGCGTCGGTCTGA 59.325 50.000 0.00 0.00 0.00 3.27
2600 2659 1.068895 TGTTTTAGGCGTCGGTCTGAA 59.931 47.619 0.00 0.00 0.00 3.02
2601 2660 2.289195 TGTTTTAGGCGTCGGTCTGAAT 60.289 45.455 0.00 0.00 0.00 2.57
2602 2661 2.740447 GTTTTAGGCGTCGGTCTGAATT 59.260 45.455 0.00 0.00 0.00 2.17
2603 2662 2.004583 TTAGGCGTCGGTCTGAATTG 57.995 50.000 0.00 0.00 0.00 2.32
2604 2663 1.179152 TAGGCGTCGGTCTGAATTGA 58.821 50.000 0.00 0.00 0.00 2.57
2605 2664 0.320374 AGGCGTCGGTCTGAATTGAA 59.680 50.000 0.00 0.00 0.00 2.69
2606 2665 1.153353 GGCGTCGGTCTGAATTGAAA 58.847 50.000 0.00 0.00 0.00 2.69
2607 2666 1.533731 GGCGTCGGTCTGAATTGAAAA 59.466 47.619 0.00 0.00 0.00 2.29
2608 2667 2.031508 GGCGTCGGTCTGAATTGAAAAA 60.032 45.455 0.00 0.00 0.00 1.94
2609 2668 3.365969 GGCGTCGGTCTGAATTGAAAAAT 60.366 43.478 0.00 0.00 0.00 1.82
2610 2669 3.846335 GCGTCGGTCTGAATTGAAAAATC 59.154 43.478 0.00 0.00 0.00 2.17
2611 2670 4.081761 CGTCGGTCTGAATTGAAAAATCG 58.918 43.478 0.00 0.00 0.00 3.34
2612 2671 4.377022 CGTCGGTCTGAATTGAAAAATCGT 60.377 41.667 0.00 0.00 0.00 3.73
2613 2672 4.846137 GTCGGTCTGAATTGAAAAATCGTG 59.154 41.667 0.00 0.00 0.00 4.35
2614 2673 4.752604 TCGGTCTGAATTGAAAAATCGTGA 59.247 37.500 0.00 0.00 0.00 4.35
2615 2674 4.846137 CGGTCTGAATTGAAAAATCGTGAC 59.154 41.667 0.00 0.00 0.00 3.67
2616 2675 5.154222 GGTCTGAATTGAAAAATCGTGACC 58.846 41.667 0.00 0.00 34.56 4.02
2617 2676 4.846137 GTCTGAATTGAAAAATCGTGACCG 59.154 41.667 0.00 0.00 0.00 4.79
2629 2688 3.313012 TCGTGACCGATCAAATGACTT 57.687 42.857 0.00 0.00 38.40 3.01
2630 2689 2.993220 TCGTGACCGATCAAATGACTTG 59.007 45.455 0.00 0.00 38.40 3.16
2641 2700 5.545658 TCAAATGACTTGATAAGCCGTTC 57.454 39.130 0.00 0.00 39.20 3.95
2642 2701 4.092821 TCAAATGACTTGATAAGCCGTTCG 59.907 41.667 0.00 0.00 39.20 3.95
2643 2702 3.520290 ATGACTTGATAAGCCGTTCGA 57.480 42.857 0.00 0.00 0.00 3.71
2644 2703 3.306917 TGACTTGATAAGCCGTTCGAA 57.693 42.857 0.00 0.00 0.00 3.71
2645 2704 3.857052 TGACTTGATAAGCCGTTCGAAT 58.143 40.909 0.00 0.00 0.00 3.34
2646 2705 3.616821 TGACTTGATAAGCCGTTCGAATG 59.383 43.478 10.53 10.53 0.00 2.67
2647 2706 3.857052 ACTTGATAAGCCGTTCGAATGA 58.143 40.909 18.97 0.00 0.00 2.57
2648 2707 4.442706 ACTTGATAAGCCGTTCGAATGAT 58.557 39.130 18.97 4.00 0.00 2.45
2649 2708 4.271049 ACTTGATAAGCCGTTCGAATGATG 59.729 41.667 18.97 4.17 0.00 3.07
2650 2709 2.543848 TGATAAGCCGTTCGAATGATGC 59.456 45.455 18.97 13.86 0.00 3.91
2651 2710 1.295792 TAAGCCGTTCGAATGATGCC 58.704 50.000 18.97 4.38 0.00 4.40
2652 2711 1.705337 AAGCCGTTCGAATGATGCCG 61.705 55.000 18.97 7.74 0.00 5.69
2653 2712 3.014036 CCGTTCGAATGATGCCGG 58.986 61.111 18.97 13.15 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.552104 CGTCGATCAAACTACGTAAATCAGC 60.552 44.000 0.00 0.00 0.00 4.26
76 77 1.836383 GTCGTCCACATCCGTGTATC 58.164 55.000 0.00 0.00 41.93 2.24
95 96 3.079960 TCGAGCACTCCTTAAATAGCG 57.920 47.619 0.00 0.00 0.00 4.26
103 104 0.108424 GCAGTGATCGAGCACTCCTT 60.108 55.000 32.02 10.52 45.54 3.36
145 146 2.747855 CCTCTCAAACGCCTGCCC 60.748 66.667 0.00 0.00 0.00 5.36
160 161 2.456989 CGCGTACGACAAATATGACCT 58.543 47.619 21.65 0.00 43.93 3.85
211 212 1.466167 CATTCTCCAGCAAACACTCCG 59.534 52.381 0.00 0.00 0.00 4.63
213 214 5.689383 TTAACATTCTCCAGCAAACACTC 57.311 39.130 0.00 0.00 0.00 3.51
216 217 7.652909 CAGATTTTTAACATTCTCCAGCAAACA 59.347 33.333 0.00 0.00 0.00 2.83
249 250 5.254115 GCACCTAGGACCTGTTTCTTTAAT 58.746 41.667 17.98 0.00 0.00 1.40
288 289 1.968050 AAGTATCTGCGGTTCGGGGG 61.968 60.000 0.00 0.00 0.00 5.40
294 295 7.280205 CCTTTCTTTATACAAGTATCTGCGGTT 59.720 37.037 0.00 0.00 0.00 4.44
351 352 4.192317 GTTCACTTGACAGAGACTTGGTT 58.808 43.478 0.00 0.00 0.00 3.67
354 355 5.052481 TCATGTTCACTTGACAGAGACTTG 58.948 41.667 0.00 0.00 0.00 3.16
405 444 7.251994 AGACTTCGTTATGTCTCAGTTGATAC 58.748 38.462 0.00 0.00 39.04 2.24
410 449 7.494625 TCAAAAAGACTTCGTTATGTCTCAGTT 59.505 33.333 0.00 0.00 42.02 3.16
648 697 1.398960 CGCACCTTGAAAGAGAAAGCG 60.399 52.381 0.00 0.00 36.62 4.68
665 714 0.179086 TCTCTTGTGACAGCAACGCA 60.179 50.000 0.00 0.00 0.00 5.24
1254 1303 2.895680 GCCATCTCTGCGGTCTCA 59.104 61.111 0.00 0.00 0.00 3.27
1326 1375 3.179939 GGCGAGTCGGCGAAGTTC 61.180 66.667 23.96 9.22 43.33 3.01
1497 1546 1.958579 TCGTCCATTCCATAGTACGGG 59.041 52.381 0.00 0.00 0.00 5.28
1509 1558 1.511613 AGTCCATCCCATCGTCCATT 58.488 50.000 0.00 0.00 0.00 3.16
1680 1729 4.699522 AGTTCTTCGCGCCCCCAC 62.700 66.667 0.00 0.00 0.00 4.61
1681 1730 3.894547 GAAGTTCTTCGCGCCCCCA 62.895 63.158 0.00 0.00 0.00 4.96
1705 1754 3.673746 TGCAATATAAAGCTGCACGTC 57.326 42.857 1.02 0.00 41.01 4.34
1707 1756 3.976942 GGATTGCAATATAAAGCTGCACG 59.023 43.478 12.97 0.00 45.31 5.34
1722 1771 2.371841 ACACTTCCTGTACTGGATTGCA 59.628 45.455 20.84 6.53 35.83 4.08
1857 1906 2.476051 CGACAAGCGTGCACCATC 59.524 61.111 12.15 0.41 34.64 3.51
2033 2082 5.786264 TTGTAAGGGATCGGTTAGAGATC 57.214 43.478 0.00 0.00 42.68 2.75
2053 2106 5.888412 ACTTTGCAACGAATTAAGCTTTG 57.112 34.783 10.27 0.00 0.00 2.77
2066 2119 8.920509 TTTTTACTCCTCTAAAACTTTGCAAC 57.079 30.769 0.00 0.00 0.00 4.17
2108 2161 0.725117 GATCGGTTAGGTGCGGTTTG 59.275 55.000 0.00 0.00 0.00 2.93
2167 2226 5.662211 TGCCTAAAAGTTTAACGTCAGAC 57.338 39.130 0.00 0.00 0.00 3.51
2180 2239 7.894376 ATGTTTGATTTGTCATGCCTAAAAG 57.106 32.000 0.00 0.00 0.00 2.27
2192 2251 6.939132 TGCCATGAAAAATGTTTGATTTGT 57.061 29.167 0.00 0.00 0.00 2.83
2214 2273 4.033932 TCATCCTTGCGTCGACATAAATTG 59.966 41.667 17.16 4.80 0.00 2.32
2222 2281 1.144969 TTTGTCATCCTTGCGTCGAC 58.855 50.000 5.18 5.18 0.00 4.20
2224 2283 2.900122 AATTTGTCATCCTTGCGTCG 57.100 45.000 0.00 0.00 0.00 5.12
2226 2285 5.460646 CAACTAAATTTGTCATCCTTGCGT 58.539 37.500 0.00 0.00 0.00 5.24
2228 2287 4.627035 GCCAACTAAATTTGTCATCCTTGC 59.373 41.667 0.00 0.00 0.00 4.01
2229 2288 4.858692 CGCCAACTAAATTTGTCATCCTTG 59.141 41.667 0.00 0.00 0.00 3.61
2250 2309 1.664965 AGGAAAGTGTCGTGCTCGC 60.665 57.895 2.69 0.00 36.96 5.03
2252 2311 1.569479 GCCAGGAAAGTGTCGTGCTC 61.569 60.000 0.00 0.00 40.19 4.26
2280 2339 1.212751 GGCAAATCCGGCTCACAAC 59.787 57.895 0.00 0.00 0.00 3.32
2281 2340 0.611618 ATGGCAAATCCGGCTCACAA 60.612 50.000 0.00 0.00 37.80 3.33
2283 2342 1.434696 CATGGCAAATCCGGCTCAC 59.565 57.895 0.00 0.00 37.80 3.51
2284 2343 2.417257 GCATGGCAAATCCGGCTCA 61.417 57.895 0.00 0.00 37.80 4.26
2285 2344 1.669999 AAGCATGGCAAATCCGGCTC 61.670 55.000 0.00 0.00 44.28 4.70
2286 2345 1.683365 AAGCATGGCAAATCCGGCT 60.683 52.632 0.00 0.00 46.17 5.52
2287 2346 1.519898 CAAGCATGGCAAATCCGGC 60.520 57.895 0.00 0.00 37.80 6.13
2288 2347 0.179129 GACAAGCATGGCAAATCCGG 60.179 55.000 0.00 0.00 37.80 5.14
2320 2379 7.227049 ACATTTTCTATGTTTACCAAGGGTG 57.773 36.000 0.00 0.00 36.19 4.61
2323 2382 9.927668 ATTGAACATTTTCTATGTTTACCAAGG 57.072 29.630 4.79 0.00 41.76 3.61
2346 2405 7.428183 CGTCGGATTTTTAGGTATGACAAATTG 59.572 37.037 0.00 0.00 0.00 2.32
2347 2406 7.120138 ACGTCGGATTTTTAGGTATGACAAATT 59.880 33.333 0.00 0.00 0.00 1.82
2357 2416 1.728425 GCGAACGTCGGATTTTTAGGT 59.272 47.619 8.96 0.00 40.84 3.08
2358 2417 1.997606 AGCGAACGTCGGATTTTTAGG 59.002 47.619 8.96 0.00 40.84 2.69
2368 2427 2.348685 CCTGACTATCTAGCGAACGTCG 60.349 54.545 0.00 0.00 43.89 5.12
2375 2434 4.643463 TCTTAGGACCTGACTATCTAGCG 58.357 47.826 3.53 0.00 0.00 4.26
2384 2443 2.885894 CCCGACTATCTTAGGACCTGAC 59.114 54.545 3.53 0.00 0.00 3.51
2387 2446 2.158490 GGACCCGACTATCTTAGGACCT 60.158 54.545 0.00 0.00 0.00 3.85
2388 2447 2.158490 AGGACCCGACTATCTTAGGACC 60.158 54.545 0.00 0.00 0.00 4.46
2414 2473 1.944024 CGGTGCACAGTGGAGTAAAAA 59.056 47.619 20.43 0.00 0.00 1.94
2415 2474 1.588674 CGGTGCACAGTGGAGTAAAA 58.411 50.000 20.43 0.00 0.00 1.52
2416 2475 0.250124 CCGGTGCACAGTGGAGTAAA 60.250 55.000 20.43 0.00 0.00 2.01
2417 2476 1.116536 TCCGGTGCACAGTGGAGTAA 61.117 55.000 20.43 0.00 0.00 2.24
2418 2477 0.902984 ATCCGGTGCACAGTGGAGTA 60.903 55.000 23.45 7.37 33.21 2.59
2419 2478 2.217038 ATCCGGTGCACAGTGGAGT 61.217 57.895 23.45 12.88 33.21 3.85
2420 2479 1.742880 CATCCGGTGCACAGTGGAG 60.743 63.158 23.45 14.70 33.21 3.86
2421 2480 2.347114 CATCCGGTGCACAGTGGA 59.653 61.111 22.08 22.08 34.45 4.02
2422 2481 2.747460 CCATCCGGTGCACAGTGG 60.747 66.667 20.43 15.19 0.00 4.00
2423 2482 2.747460 CCCATCCGGTGCACAGTG 60.747 66.667 20.43 9.81 0.00 3.66
2424 2483 3.249189 ACCCATCCGGTGCACAGT 61.249 61.111 20.43 0.00 46.09 3.55
2443 2502 5.574120 GCCTACCCTACAACTATCCCAAAAA 60.574 44.000 0.00 0.00 0.00 1.94
2444 2503 4.080186 GCCTACCCTACAACTATCCCAAAA 60.080 45.833 0.00 0.00 0.00 2.44
2445 2504 3.457012 GCCTACCCTACAACTATCCCAAA 59.543 47.826 0.00 0.00 0.00 3.28
2446 2505 3.043418 GCCTACCCTACAACTATCCCAA 58.957 50.000 0.00 0.00 0.00 4.12
2447 2506 2.686119 GCCTACCCTACAACTATCCCA 58.314 52.381 0.00 0.00 0.00 4.37
2448 2507 1.617357 CGCCTACCCTACAACTATCCC 59.383 57.143 0.00 0.00 0.00 3.85
2449 2508 1.617357 CCGCCTACCCTACAACTATCC 59.383 57.143 0.00 0.00 0.00 2.59
2450 2509 2.035576 CACCGCCTACCCTACAACTATC 59.964 54.545 0.00 0.00 0.00 2.08
2451 2510 2.037144 CACCGCCTACCCTACAACTAT 58.963 52.381 0.00 0.00 0.00 2.12
2452 2511 1.477553 CACCGCCTACCCTACAACTA 58.522 55.000 0.00 0.00 0.00 2.24
2453 2512 1.262640 CCACCGCCTACCCTACAACT 61.263 60.000 0.00 0.00 0.00 3.16
2454 2513 1.219935 CCACCGCCTACCCTACAAC 59.780 63.158 0.00 0.00 0.00 3.32
2455 2514 1.991167 CCCACCGCCTACCCTACAA 60.991 63.158 0.00 0.00 0.00 2.41
2456 2515 2.364579 CCCACCGCCTACCCTACA 60.365 66.667 0.00 0.00 0.00 2.74
2457 2516 2.364710 ACCCACCGCCTACCCTAC 60.365 66.667 0.00 0.00 0.00 3.18
2458 2517 2.042639 GACCCACCGCCTACCCTA 60.043 66.667 0.00 0.00 0.00 3.53
2463 2522 3.988050 AATCCCGACCCACCGCCTA 62.988 63.158 0.00 0.00 0.00 3.93
2466 2525 4.404098 ACAATCCCGACCCACCGC 62.404 66.667 0.00 0.00 0.00 5.68
2467 2526 2.125269 GACAATCCCGACCCACCG 60.125 66.667 0.00 0.00 0.00 4.94
2468 2527 1.078426 CTGACAATCCCGACCCACC 60.078 63.158 0.00 0.00 0.00 4.61
2469 2528 1.078426 CCTGACAATCCCGACCCAC 60.078 63.158 0.00 0.00 0.00 4.61
2470 2529 2.966732 GCCTGACAATCCCGACCCA 61.967 63.158 0.00 0.00 0.00 4.51
2471 2530 2.124695 GCCTGACAATCCCGACCC 60.125 66.667 0.00 0.00 0.00 4.46
2472 2531 2.511600 CGCCTGACAATCCCGACC 60.512 66.667 0.00 0.00 0.00 4.79
2473 2532 2.311688 ATCCGCCTGACAATCCCGAC 62.312 60.000 0.00 0.00 0.00 4.79
2474 2533 0.757561 TATCCGCCTGACAATCCCGA 60.758 55.000 0.00 0.00 0.00 5.14
2475 2534 0.321671 ATATCCGCCTGACAATCCCG 59.678 55.000 0.00 0.00 0.00 5.14
2476 2535 1.813513 CATATCCGCCTGACAATCCC 58.186 55.000 0.00 0.00 0.00 3.85
2477 2536 1.160137 GCATATCCGCCTGACAATCC 58.840 55.000 0.00 0.00 0.00 3.01
2504 2563 1.073008 ATATAGGGTGGCCAGGGCA 60.073 57.895 12.83 12.83 44.11 5.36
2505 2564 0.842467 AGATATAGGGTGGCCAGGGC 60.842 60.000 5.11 5.91 41.06 5.19
2506 2565 0.987294 CAGATATAGGGTGGCCAGGG 59.013 60.000 5.11 0.00 0.00 4.45
2507 2566 1.625818 GACAGATATAGGGTGGCCAGG 59.374 57.143 5.11 0.00 0.00 4.45
2508 2567 2.614259 AGACAGATATAGGGTGGCCAG 58.386 52.381 5.11 0.00 0.00 4.85
2509 2568 2.795291 AGACAGATATAGGGTGGCCA 57.205 50.000 0.00 0.00 0.00 5.36
2510 2569 4.439253 AAAAGACAGATATAGGGTGGCC 57.561 45.455 0.00 0.00 0.00 5.36
2511 2570 8.352942 CAAAATAAAAGACAGATATAGGGTGGC 58.647 37.037 0.00 0.00 0.00 5.01
2512 2571 8.850156 CCAAAATAAAAGACAGATATAGGGTGG 58.150 37.037 0.00 0.00 0.00 4.61
2513 2572 8.352942 GCCAAAATAAAAGACAGATATAGGGTG 58.647 37.037 0.00 0.00 0.00 4.61
2514 2573 8.282256 AGCCAAAATAAAAGACAGATATAGGGT 58.718 33.333 0.00 0.00 0.00 4.34
2515 2574 8.571336 CAGCCAAAATAAAAGACAGATATAGGG 58.429 37.037 0.00 0.00 0.00 3.53
2516 2575 8.571336 CCAGCCAAAATAAAAGACAGATATAGG 58.429 37.037 0.00 0.00 0.00 2.57
2517 2576 9.342308 TCCAGCCAAAATAAAAGACAGATATAG 57.658 33.333 0.00 0.00 0.00 1.31
2518 2577 9.866655 ATCCAGCCAAAATAAAAGACAGATATA 57.133 29.630 0.00 0.00 0.00 0.86
2519 2578 8.773033 ATCCAGCCAAAATAAAAGACAGATAT 57.227 30.769 0.00 0.00 0.00 1.63
2520 2579 9.866655 ATATCCAGCCAAAATAAAAGACAGATA 57.133 29.630 0.00 0.00 0.00 1.98
2521 2580 8.636213 CATATCCAGCCAAAATAAAAGACAGAT 58.364 33.333 0.00 0.00 0.00 2.90
2522 2581 7.833682 TCATATCCAGCCAAAATAAAAGACAGA 59.166 33.333 0.00 0.00 0.00 3.41
2523 2582 7.999679 TCATATCCAGCCAAAATAAAAGACAG 58.000 34.615 0.00 0.00 0.00 3.51
2524 2583 7.953005 TCATATCCAGCCAAAATAAAAGACA 57.047 32.000 0.00 0.00 0.00 3.41
2525 2584 7.869429 CCATCATATCCAGCCAAAATAAAAGAC 59.131 37.037 0.00 0.00 0.00 3.01
2526 2585 7.015487 CCCATCATATCCAGCCAAAATAAAAGA 59.985 37.037 0.00 0.00 0.00 2.52
2527 2586 7.156673 CCCATCATATCCAGCCAAAATAAAAG 58.843 38.462 0.00 0.00 0.00 2.27
2528 2587 6.614906 ACCCATCATATCCAGCCAAAATAAAA 59.385 34.615 0.00 0.00 0.00 1.52
2529 2588 6.041865 CACCCATCATATCCAGCCAAAATAAA 59.958 38.462 0.00 0.00 0.00 1.40
2530 2589 5.539574 CACCCATCATATCCAGCCAAAATAA 59.460 40.000 0.00 0.00 0.00 1.40
2531 2590 5.078949 CACCCATCATATCCAGCCAAAATA 58.921 41.667 0.00 0.00 0.00 1.40
2532 2591 3.899360 CACCCATCATATCCAGCCAAAAT 59.101 43.478 0.00 0.00 0.00 1.82
2533 2592 3.298619 CACCCATCATATCCAGCCAAAA 58.701 45.455 0.00 0.00 0.00 2.44
2534 2593 2.948115 CACCCATCATATCCAGCCAAA 58.052 47.619 0.00 0.00 0.00 3.28
2535 2594 1.479205 GCACCCATCATATCCAGCCAA 60.479 52.381 0.00 0.00 0.00 4.52
2536 2595 0.111061 GCACCCATCATATCCAGCCA 59.889 55.000 0.00 0.00 0.00 4.75
2537 2596 0.610232 GGCACCCATCATATCCAGCC 60.610 60.000 0.00 0.00 0.00 4.85
2538 2597 0.957395 CGGCACCCATCATATCCAGC 60.957 60.000 0.00 0.00 0.00 4.85
2539 2598 0.686789 TCGGCACCCATCATATCCAG 59.313 55.000 0.00 0.00 0.00 3.86
2540 2599 1.278985 GATCGGCACCCATCATATCCA 59.721 52.381 0.00 0.00 0.00 3.41
2541 2600 1.278985 TGATCGGCACCCATCATATCC 59.721 52.381 0.00 0.00 0.00 2.59
2542 2601 2.625737 CTGATCGGCACCCATCATATC 58.374 52.381 0.00 0.00 0.00 1.63
2543 2602 1.339438 GCTGATCGGCACCCATCATAT 60.339 52.381 21.88 0.00 0.00 1.78
2544 2603 0.035317 GCTGATCGGCACCCATCATA 59.965 55.000 21.88 0.00 0.00 2.15
2545 2604 1.228063 GCTGATCGGCACCCATCAT 60.228 57.895 21.88 0.00 0.00 2.45
2546 2605 2.190313 GCTGATCGGCACCCATCA 59.810 61.111 21.88 0.00 0.00 3.07
2547 2606 2.592861 GGCTGATCGGCACCCATC 60.593 66.667 27.26 5.67 38.25 3.51
2548 2607 3.092511 AGGCTGATCGGCACCCAT 61.093 61.111 27.26 5.33 41.46 4.00
2549 2608 4.100084 CAGGCTGATCGGCACCCA 62.100 66.667 27.26 0.00 41.46 4.51
2550 2609 4.864334 CCAGGCTGATCGGCACCC 62.864 72.222 27.26 10.80 41.46 4.61
2551 2610 3.112205 ATCCAGGCTGATCGGCACC 62.112 63.158 27.26 11.54 41.46 5.01
2552 2611 1.890979 CATCCAGGCTGATCGGCAC 60.891 63.158 27.26 16.45 41.46 5.01
2553 2612 1.913951 AACATCCAGGCTGATCGGCA 61.914 55.000 27.26 7.82 41.46 5.69
2554 2613 0.749454 AAACATCCAGGCTGATCGGC 60.749 55.000 18.73 18.73 38.75 5.54
2555 2614 1.019673 CAAACATCCAGGCTGATCGG 58.980 55.000 17.94 4.99 0.00 4.18
2556 2615 1.938577 CTCAAACATCCAGGCTGATCG 59.061 52.381 17.94 5.76 0.00 3.69
2557 2616 2.295885 CCTCAAACATCCAGGCTGATC 58.704 52.381 17.94 0.00 0.00 2.92
2558 2617 2.431954 CCTCAAACATCCAGGCTGAT 57.568 50.000 17.94 4.81 0.00 2.90
2559 2618 3.963733 CCTCAAACATCCAGGCTGA 57.036 52.632 17.94 2.24 0.00 4.26
2563 2622 0.038744 ACAGGCCTCAAACATCCAGG 59.961 55.000 0.00 0.00 0.00 4.45
2564 2623 1.915141 AACAGGCCTCAAACATCCAG 58.085 50.000 0.00 0.00 0.00 3.86
2565 2624 2.380064 AAACAGGCCTCAAACATCCA 57.620 45.000 0.00 0.00 0.00 3.41
2566 2625 3.193479 CCTAAAACAGGCCTCAAACATCC 59.807 47.826 0.00 0.00 37.70 3.51
2567 2626 4.440839 CCTAAAACAGGCCTCAAACATC 57.559 45.455 0.00 0.00 37.70 3.06
2579 2638 1.068474 CAGACCGACGCCTAAAACAG 58.932 55.000 0.00 0.00 0.00 3.16
2580 2639 0.675083 TCAGACCGACGCCTAAAACA 59.325 50.000 0.00 0.00 0.00 2.83
2581 2640 1.787012 TTCAGACCGACGCCTAAAAC 58.213 50.000 0.00 0.00 0.00 2.43
2582 2641 2.739913 CAATTCAGACCGACGCCTAAAA 59.260 45.455 0.00 0.00 0.00 1.52
2583 2642 2.028839 TCAATTCAGACCGACGCCTAAA 60.029 45.455 0.00 0.00 0.00 1.85
2584 2643 1.546923 TCAATTCAGACCGACGCCTAA 59.453 47.619 0.00 0.00 0.00 2.69
2585 2644 1.179152 TCAATTCAGACCGACGCCTA 58.821 50.000 0.00 0.00 0.00 3.93
2586 2645 0.320374 TTCAATTCAGACCGACGCCT 59.680 50.000 0.00 0.00 0.00 5.52
2587 2646 1.153353 TTTCAATTCAGACCGACGCC 58.847 50.000 0.00 0.00 0.00 5.68
2588 2647 2.961522 TTTTCAATTCAGACCGACGC 57.038 45.000 0.00 0.00 0.00 5.19
2589 2648 4.081761 CGATTTTTCAATTCAGACCGACG 58.918 43.478 0.00 0.00 0.00 5.12
2590 2649 4.846137 CACGATTTTTCAATTCAGACCGAC 59.154 41.667 0.00 0.00 0.00 4.79
2591 2650 4.752604 TCACGATTTTTCAATTCAGACCGA 59.247 37.500 0.00 0.00 0.00 4.69
2592 2651 4.846137 GTCACGATTTTTCAATTCAGACCG 59.154 41.667 0.00 0.00 0.00 4.79
2593 2652 5.154222 GGTCACGATTTTTCAATTCAGACC 58.846 41.667 0.00 0.00 33.34 3.85
2594 2653 4.846137 CGGTCACGATTTTTCAATTCAGAC 59.154 41.667 0.00 0.00 44.60 3.51
2595 2654 4.752604 TCGGTCACGATTTTTCAATTCAGA 59.247 37.500 0.00 0.00 45.59 3.27
2596 2655 5.029650 TCGGTCACGATTTTTCAATTCAG 57.970 39.130 0.00 0.00 45.59 3.02
2609 2668 3.305744 TCAAGTCATTTGATCGGTCACGA 60.306 43.478 0.00 0.00 42.96 4.35
2610 2669 2.993220 TCAAGTCATTTGATCGGTCACG 59.007 45.455 0.00 0.00 40.82 4.35
2620 2679 4.092821 TCGAACGGCTTATCAAGTCATTTG 59.907 41.667 0.00 0.00 38.17 2.32
2621 2680 4.250464 TCGAACGGCTTATCAAGTCATTT 58.750 39.130 0.00 0.00 30.88 2.32
2622 2681 3.857052 TCGAACGGCTTATCAAGTCATT 58.143 40.909 0.00 0.00 30.88 2.57
2623 2682 3.520290 TCGAACGGCTTATCAAGTCAT 57.480 42.857 0.00 0.00 30.88 3.06
2624 2683 3.306917 TTCGAACGGCTTATCAAGTCA 57.693 42.857 0.00 0.00 30.88 3.41
2625 2684 3.863424 TCATTCGAACGGCTTATCAAGTC 59.137 43.478 0.00 0.00 0.00 3.01
2626 2685 3.857052 TCATTCGAACGGCTTATCAAGT 58.143 40.909 0.00 0.00 0.00 3.16
2627 2686 4.766007 CATCATTCGAACGGCTTATCAAG 58.234 43.478 0.00 0.00 0.00 3.02
2628 2687 3.002246 GCATCATTCGAACGGCTTATCAA 59.998 43.478 0.00 0.00 0.00 2.57
2629 2688 2.543848 GCATCATTCGAACGGCTTATCA 59.456 45.455 0.00 0.00 0.00 2.15
2630 2689 2.096218 GGCATCATTCGAACGGCTTATC 60.096 50.000 0.00 0.00 0.00 1.75
2631 2690 1.873591 GGCATCATTCGAACGGCTTAT 59.126 47.619 0.00 0.00 0.00 1.73
2632 2691 1.295792 GGCATCATTCGAACGGCTTA 58.704 50.000 0.00 0.00 0.00 3.09
2633 2692 1.705337 CGGCATCATTCGAACGGCTT 61.705 55.000 0.00 0.00 0.00 4.35
2634 2693 2.173669 CGGCATCATTCGAACGGCT 61.174 57.895 0.00 0.00 0.00 5.52
2635 2694 2.324477 CGGCATCATTCGAACGGC 59.676 61.111 0.00 1.56 0.00 5.68
2636 2695 3.014036 CCGGCATCATTCGAACGG 58.986 61.111 0.00 3.83 32.93 4.44


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

AutoCloner maintained by Alex Coulton.