Multiple sequence alignment - TraesCS3D01G335400

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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 TraesCS3D01G335400 chr3D 100.000 2600 0 0 1 2600 447548886 447546287 0.000000e+00 4802
1 TraesCS3D01G335400 chr3D 92.286 350 10 1 2268 2600 447540550 447540201 5.030000e-132 481
2 TraesCS3D01G335400 chr3D 91.277 321 27 1 2267 2587 558872275 558871956 1.100000e-118 436
3 TraesCS3D01G335400 chr3D 86.325 351 30 6 2268 2600 417044510 417044860 1.470000e-97 366
4 TraesCS3D01G335400 chr4D 90.222 2301 166 39 1 2267 474417767 474415492 0.000000e+00 2948
5 TraesCS3D01G335400 chr4D 85.470 351 34 14 2244 2585 190302493 190302835 1.480000e-92 350
6 TraesCS3D01G335400 chr4D 83.041 342 46 10 2268 2600 267168018 267167680 1.510000e-77 300
7 TraesCS3D01G335400 chr7A 89.261 2328 147 51 1 2267 94855307 94857592 0.000000e+00 2819
8 TraesCS3D01G335400 chr5D 90.919 1894 120 28 1 1857 44455327 44457205 0.000000e+00 2497
9 TraesCS3D01G335400 chr6A 88.582 2067 142 42 258 2267 564656823 564654794 0.000000e+00 2423
10 TraesCS3D01G335400 chr2D 94.453 1370 69 2 905 2267 141811245 141812614 0.000000e+00 2102
11 TraesCS3D01G335400 chr2D 94.118 1377 64 8 905 2267 352879358 352880731 0.000000e+00 2078
12 TraesCS3D01G335400 chr2D 91.546 899 43 19 1 872 141810349 141811241 0.000000e+00 1208
13 TraesCS3D01G335400 chr2D 89.241 883 66 20 1 872 352878490 352879354 0.000000e+00 1077
14 TraesCS3D01G335400 chr2D 87.749 351 25 7 2268 2600 295877764 295877414 6.740000e-106 394
15 TraesCS3D01G335400 chr1D 94.263 1377 64 6 905 2267 414577787 414576412 0.000000e+00 2091
16 TraesCS3D01G335400 chr1D 90.066 906 53 18 1 872 414578693 414577791 0.000000e+00 1140
17 TraesCS3D01G335400 chr1D 89.235 353 18 2 2268 2600 204580265 204579913 8.600000e-115 424
18 TraesCS3D01G335400 chr2B 87.751 1845 154 31 226 2030 116476647 116478459 0.000000e+00 2089
19 TraesCS3D01G335400 chr2B 93.478 138 7 2 1 137 116476513 116476649 1.220000e-48 204
20 TraesCS3D01G335400 chr1A 84.214 1704 181 49 1 1662 344114926 344113269 0.000000e+00 1576
21 TraesCS3D01G335400 chr4A 87.736 1378 127 27 906 2267 649676358 649675007 0.000000e+00 1570
22 TraesCS3D01G335400 chr4A 87.373 1378 131 28 906 2267 649712002 649710652 0.000000e+00 1541
23 TraesCS3D01G335400 chr6B 82.057 1867 232 59 176 1984 64970996 64972817 0.000000e+00 1496
24 TraesCS3D01G335400 chr6D 90.313 351 17 1 2267 2600 162892985 162892635 6.600000e-121 444
25 TraesCS3D01G335400 chr7D 90.230 348 16 3 2268 2598 469775239 469775585 3.070000e-119 438
26 TraesCS3D01G335400 chr2A 89.941 338 29 3 2267 2599 388494394 388494731 5.140000e-117 431
27 TraesCS3D01G335400 chr5A 85.757 337 38 5 2268 2599 265560866 265560535 5.330000e-92 348
28 TraesCS3D01G335400 chr5B 84.478 335 45 6 2268 2600 463310419 463310090 8.970000e-85 324


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 TraesCS3D01G335400 chr3D 447546287 447548886 2599 True 4802.0 4802 100.0000 1 2600 1 chr3D.!!$R2 2599
1 TraesCS3D01G335400 chr4D 474415492 474417767 2275 True 2948.0 2948 90.2220 1 2267 1 chr4D.!!$R2 2266
2 TraesCS3D01G335400 chr7A 94855307 94857592 2285 False 2819.0 2819 89.2610 1 2267 1 chr7A.!!$F1 2266
3 TraesCS3D01G335400 chr5D 44455327 44457205 1878 False 2497.0 2497 90.9190 1 1857 1 chr5D.!!$F1 1856
4 TraesCS3D01G335400 chr6A 564654794 564656823 2029 True 2423.0 2423 88.5820 258 2267 1 chr6A.!!$R1 2009
5 TraesCS3D01G335400 chr2D 141810349 141812614 2265 False 1655.0 2102 92.9995 1 2267 2 chr2D.!!$F1 2266
6 TraesCS3D01G335400 chr2D 352878490 352880731 2241 False 1577.5 2078 91.6795 1 2267 2 chr2D.!!$F2 2266
7 TraesCS3D01G335400 chr1D 414576412 414578693 2281 True 1615.5 2091 92.1645 1 2267 2 chr1D.!!$R2 2266
8 TraesCS3D01G335400 chr2B 116476513 116478459 1946 False 1146.5 2089 90.6145 1 2030 2 chr2B.!!$F1 2029
9 TraesCS3D01G335400 chr1A 344113269 344114926 1657 True 1576.0 1576 84.2140 1 1662 1 chr1A.!!$R1 1661
10 TraesCS3D01G335400 chr4A 649675007 649676358 1351 True 1570.0 1570 87.7360 906 2267 1 chr4A.!!$R1 1361
11 TraesCS3D01G335400 chr4A 649710652 649712002 1350 True 1541.0 1541 87.3730 906 2267 1 chr4A.!!$R2 1361
12 TraesCS3D01G335400 chr6B 64970996 64972817 1821 False 1496.0 1496 82.0570 176 1984 1 chr6B.!!$F1 1808

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
412 431 0.322098 ATTGCCGGTTGTTCATCGGA 60.322 50.0 1.9 0.0 45.96 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2402 2565 0.035056 CCACCAAAGCAGGACTAGGG 60.035 60.0 0.0 0.0 0.0 3.53 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
116 119 6.651755 AAACTTCATGTGCTTGAACAAAAG 57.348 33.333 0.00 5.98 35.04 2.27
137 142 8.430063 CAAAAGCATAGCAACTTACATGAAAAG 58.570 33.333 0.00 5.35 0.00 2.27
234 244 4.397420 TCTACTTGCACACAAATCATGGT 58.603 39.130 0.00 0.00 34.74 3.55
282 293 5.239359 TGCATCATAACAGACAAGCAATC 57.761 39.130 0.00 0.00 0.00 2.67
398 417 4.113618 TGGAGCAAAAATGCTTCATTGCC 61.114 43.478 7.69 2.83 44.79 4.52
412 431 0.322098 ATTGCCGGTTGTTCATCGGA 60.322 50.000 1.90 0.00 45.96 4.55
447 466 5.448654 AGCTGCAACCATTATTCTCCATTA 58.551 37.500 1.02 0.00 0.00 1.90
698 758 4.083581 CTTTCAACTAAAGTGCATCCCG 57.916 45.455 0.00 0.00 39.87 5.14
769 862 1.959282 GAATAAGAAGCTGCCCCATGG 59.041 52.381 4.14 4.14 0.00 3.66
807 900 2.665165 TGCTTCAACCTGGTGATTTGT 58.335 42.857 0.00 0.00 0.00 2.83
867 965 9.762933 AATTGTTGTAGCACAAAACTTTCATAT 57.237 25.926 3.74 0.00 40.15 1.78
928 1031 4.882842 ACATTGGTTGTCCCCATTTTAC 57.117 40.909 0.00 0.00 30.89 2.01
956 1059 4.261801 TGTATTAACTGCTTGCCTCTTCC 58.738 43.478 0.00 0.00 0.00 3.46
1177 1292 1.333308 CCACACACAATGCTTCGACAA 59.667 47.619 0.00 0.00 0.00 3.18
1268 1401 1.686587 AGAGACGGATGAACACACACA 59.313 47.619 0.00 0.00 0.00 3.72
1489 1627 2.438021 ACAAGGAGAACTGGCAACACTA 59.562 45.455 0.00 0.00 46.17 2.74
1521 1659 6.036953 TGGTAAAGCAGAAATTTGTTTGCAAG 59.963 34.615 16.62 0.00 38.97 4.01
1597 1737 5.733620 AGACAAAATTGTTGATCAGGCAT 57.266 34.783 0.00 0.00 42.43 4.40
1728 1874 3.517901 TGGTGGTGAAACTAGTAGATGGG 59.482 47.826 3.59 0.00 36.74 4.00
1838 1984 3.385115 GGATACCTCCAGAAGAAAGGGA 58.615 50.000 0.00 0.00 41.64 4.20
1941 2091 6.338214 TGCTCAACACCAATTTAATGCTTA 57.662 33.333 0.00 0.00 0.00 3.09
2015 2169 9.196552 GTTAAGTGATTCAATTCCTTTCCTTTG 57.803 33.333 2.11 0.00 0.00 2.77
2042 2197 6.317893 TGTTCTTGAGGTTTCCTTTGTTACTC 59.682 38.462 0.00 0.00 31.76 2.59
2112 2273 2.543653 GCAGTTGCTCGAAAACATGGTT 60.544 45.455 11.90 0.00 38.21 3.67
2152 2313 1.876156 CTGAGCAAAGTTGGTGGTCTC 59.124 52.381 0.00 0.00 42.63 3.36
2182 2343 1.891150 CTTGCTCAAAGTGAAGGGCAT 59.109 47.619 0.00 0.00 27.64 4.40
2184 2345 3.370840 TGCTCAAAGTGAAGGGCATAT 57.629 42.857 0.00 0.00 0.00 1.78
2231 2394 1.672881 CCCCTTGACGCTCATTGATTC 59.327 52.381 0.00 0.00 0.00 2.52
2252 2415 8.245491 TGATTCGTTAGTGTGCAGTAATTAGTA 58.755 33.333 3.20 0.00 0.00 1.82
2271 2434 5.591643 AGTATTGTTGTGCTAGTTTGTCG 57.408 39.130 0.00 0.00 0.00 4.35
2272 2435 3.896648 ATTGTTGTGCTAGTTTGTCGG 57.103 42.857 0.00 0.00 0.00 4.79
2273 2436 2.319136 TGTTGTGCTAGTTTGTCGGT 57.681 45.000 0.00 0.00 0.00 4.69
2274 2437 1.937223 TGTTGTGCTAGTTTGTCGGTG 59.063 47.619 0.00 0.00 0.00 4.94
2275 2438 2.206750 GTTGTGCTAGTTTGTCGGTGA 58.793 47.619 0.00 0.00 0.00 4.02
2276 2439 2.148916 TGTGCTAGTTTGTCGGTGAG 57.851 50.000 0.00 0.00 0.00 3.51
2277 2440 1.684450 TGTGCTAGTTTGTCGGTGAGA 59.316 47.619 0.00 0.00 0.00 3.27
2278 2441 2.101750 TGTGCTAGTTTGTCGGTGAGAA 59.898 45.455 0.00 0.00 0.00 2.87
2279 2442 2.475487 GTGCTAGTTTGTCGGTGAGAAC 59.525 50.000 0.00 0.00 0.00 3.01
2280 2443 1.719780 GCTAGTTTGTCGGTGAGAACG 59.280 52.381 0.00 0.00 0.00 3.95
2281 2444 2.606308 GCTAGTTTGTCGGTGAGAACGA 60.606 50.000 0.00 0.00 38.13 3.85
2291 2454 2.295253 GTGAGAACGACACCTATGGG 57.705 55.000 0.00 0.00 38.88 4.00
2292 2455 1.822990 GTGAGAACGACACCTATGGGA 59.177 52.381 0.25 0.00 36.25 4.37
2293 2456 2.431057 GTGAGAACGACACCTATGGGAT 59.569 50.000 0.25 0.00 36.25 3.85
2294 2457 2.693591 TGAGAACGACACCTATGGGATC 59.306 50.000 0.25 0.00 36.25 3.36
2295 2458 2.693591 GAGAACGACACCTATGGGATCA 59.306 50.000 0.25 0.00 36.25 2.92
2296 2459 2.431057 AGAACGACACCTATGGGATCAC 59.569 50.000 0.25 0.00 36.25 3.06
2297 2460 2.160721 ACGACACCTATGGGATCACT 57.839 50.000 0.25 0.00 36.25 3.41
2298 2461 1.757118 ACGACACCTATGGGATCACTG 59.243 52.381 0.25 0.00 36.25 3.66
2299 2462 1.069204 CGACACCTATGGGATCACTGG 59.931 57.143 0.25 0.00 36.25 4.00
2300 2463 2.398588 GACACCTATGGGATCACTGGA 58.601 52.381 0.25 0.00 36.25 3.86
2301 2464 2.771943 GACACCTATGGGATCACTGGAA 59.228 50.000 0.25 0.00 36.25 3.53
2302 2465 3.392616 GACACCTATGGGATCACTGGAAT 59.607 47.826 0.25 0.00 36.25 3.01
2303 2466 3.392616 ACACCTATGGGATCACTGGAATC 59.607 47.826 0.25 0.00 36.25 2.52
2304 2467 2.982488 ACCTATGGGATCACTGGAATCC 59.018 50.000 0.25 0.00 36.25 3.01
2311 2474 4.344359 GGATCACTGGAATCCCTTCTAC 57.656 50.000 0.00 0.00 0.00 2.59
2312 2475 3.243907 GGATCACTGGAATCCCTTCTACG 60.244 52.174 0.00 0.00 0.00 3.51
2313 2476 2.108168 TCACTGGAATCCCTTCTACGG 58.892 52.381 0.00 0.00 0.00 4.02
2314 2477 1.831736 CACTGGAATCCCTTCTACGGT 59.168 52.381 0.00 0.00 0.00 4.83
2315 2478 2.108970 ACTGGAATCCCTTCTACGGTC 58.891 52.381 0.00 0.00 0.00 4.79
2316 2479 1.067212 CTGGAATCCCTTCTACGGTCG 59.933 57.143 0.00 0.00 0.00 4.79
2317 2480 0.388294 GGAATCCCTTCTACGGTCGG 59.612 60.000 0.00 0.00 0.00 4.79
2318 2481 0.249363 GAATCCCTTCTACGGTCGGC 60.249 60.000 0.00 0.00 0.00 5.54
2319 2482 2.012902 AATCCCTTCTACGGTCGGCG 62.013 60.000 0.00 0.00 0.00 6.46
2320 2483 4.203076 CCCTTCTACGGTCGGCGG 62.203 72.222 7.21 0.00 0.00 6.13
2321 2484 4.203076 CCTTCTACGGTCGGCGGG 62.203 72.222 7.21 0.00 0.00 6.13
2322 2485 4.867599 CTTCTACGGTCGGCGGGC 62.868 72.222 7.21 0.00 0.00 6.13
2339 2502 3.691342 CGCGGGGTTGTGAGGAGA 61.691 66.667 0.00 0.00 0.00 3.71
2340 2503 2.266055 GCGGGGTTGTGAGGAGAG 59.734 66.667 0.00 0.00 0.00 3.20
2341 2504 2.266055 CGGGGTTGTGAGGAGAGC 59.734 66.667 0.00 0.00 0.00 4.09
2342 2505 2.583441 CGGGGTTGTGAGGAGAGCA 61.583 63.158 0.00 0.00 0.00 4.26
2343 2506 1.298014 GGGGTTGTGAGGAGAGCAG 59.702 63.158 0.00 0.00 0.00 4.24
2344 2507 1.298014 GGGTTGTGAGGAGAGCAGG 59.702 63.158 0.00 0.00 0.00 4.85
2345 2508 1.484444 GGGTTGTGAGGAGAGCAGGT 61.484 60.000 0.00 0.00 0.00 4.00
2346 2509 0.036858 GGTTGTGAGGAGAGCAGGTC 60.037 60.000 0.00 0.00 0.00 3.85
2347 2510 0.036858 GTTGTGAGGAGAGCAGGTCC 60.037 60.000 0.00 0.00 0.00 4.46
2348 2511 0.471780 TTGTGAGGAGAGCAGGTCCA 60.472 55.000 0.00 0.00 36.43 4.02
2349 2512 0.902048 TGTGAGGAGAGCAGGTCCAG 60.902 60.000 0.00 0.00 36.43 3.86
2350 2513 1.305633 TGAGGAGAGCAGGTCCAGG 60.306 63.158 0.00 0.00 36.43 4.45
2351 2514 1.000993 GAGGAGAGCAGGTCCAGGA 59.999 63.158 0.00 0.00 36.43 3.86
2352 2515 1.001503 AGGAGAGCAGGTCCAGGAG 59.998 63.158 0.00 0.00 36.43 3.69
2353 2516 2.730524 GGAGAGCAGGTCCAGGAGC 61.731 68.421 11.04 11.04 33.84 4.70
2354 2517 2.686835 AGAGCAGGTCCAGGAGCC 60.687 66.667 15.46 7.46 0.00 4.70
2355 2518 3.005539 GAGCAGGTCCAGGAGCCA 61.006 66.667 15.46 0.00 0.00 4.75
2356 2519 3.007920 AGCAGGTCCAGGAGCCAG 61.008 66.667 15.46 9.52 0.00 4.85
2357 2520 4.792804 GCAGGTCCAGGAGCCAGC 62.793 72.222 15.46 15.54 0.00 4.85
2358 2521 3.324930 CAGGTCCAGGAGCCAGCA 61.325 66.667 15.46 0.00 0.00 4.41
2359 2522 3.325753 AGGTCCAGGAGCCAGCAC 61.326 66.667 15.46 0.00 0.00 4.40
2360 2523 3.640407 GGTCCAGGAGCCAGCACA 61.640 66.667 7.50 0.00 0.00 4.57
2361 2524 2.431683 GTCCAGGAGCCAGCACAA 59.568 61.111 0.00 0.00 0.00 3.33
2362 2525 1.673665 GTCCAGGAGCCAGCACAAG 60.674 63.158 0.00 0.00 0.00 3.16
2363 2526 2.360852 CCAGGAGCCAGCACAAGG 60.361 66.667 0.00 0.00 0.00 3.61
2364 2527 2.752358 CAGGAGCCAGCACAAGGA 59.248 61.111 0.00 0.00 0.00 3.36
2365 2528 1.302285 CAGGAGCCAGCACAAGGAT 59.698 57.895 0.00 0.00 0.00 3.24
2366 2529 0.747283 CAGGAGCCAGCACAAGGATC 60.747 60.000 0.00 0.00 40.76 3.36
2367 2530 1.817099 GGAGCCAGCACAAGGATCG 60.817 63.158 0.00 0.00 42.37 3.69
2368 2531 1.078848 GAGCCAGCACAAGGATCGT 60.079 57.895 0.00 0.00 31.16 3.73
2369 2532 0.674895 GAGCCAGCACAAGGATCGTT 60.675 55.000 0.00 0.00 31.16 3.85
2370 2533 0.250901 AGCCAGCACAAGGATCGTTT 60.251 50.000 0.00 0.00 0.00 3.60
2371 2534 1.003118 AGCCAGCACAAGGATCGTTTA 59.997 47.619 0.00 0.00 0.00 2.01
2372 2535 1.130561 GCCAGCACAAGGATCGTTTAC 59.869 52.381 0.00 0.00 0.00 2.01
2373 2536 1.737793 CCAGCACAAGGATCGTTTACC 59.262 52.381 0.00 0.00 0.00 2.85
2374 2537 1.737793 CAGCACAAGGATCGTTTACCC 59.262 52.381 0.00 0.00 0.00 3.69
2375 2538 1.349688 AGCACAAGGATCGTTTACCCA 59.650 47.619 0.00 0.00 0.00 4.51
2376 2539 1.737793 GCACAAGGATCGTTTACCCAG 59.262 52.381 0.00 0.00 0.00 4.45
2377 2540 2.356135 CACAAGGATCGTTTACCCAGG 58.644 52.381 0.00 0.00 0.00 4.45
2378 2541 1.982958 ACAAGGATCGTTTACCCAGGT 59.017 47.619 0.00 0.00 0.00 4.00
2379 2542 2.374170 ACAAGGATCGTTTACCCAGGTT 59.626 45.455 0.00 0.00 0.00 3.50
2380 2543 3.007635 CAAGGATCGTTTACCCAGGTTC 58.992 50.000 0.00 0.00 0.00 3.62
2381 2544 1.206371 AGGATCGTTTACCCAGGTTCG 59.794 52.381 0.00 0.00 0.00 3.95
2382 2545 1.648504 GATCGTTTACCCAGGTTCGG 58.351 55.000 0.00 0.00 0.00 4.30
2404 2567 1.719709 GCGAGGATGCGTAAAACCC 59.280 57.895 0.00 0.00 0.00 4.11
2405 2568 0.743345 GCGAGGATGCGTAAAACCCT 60.743 55.000 0.00 0.00 0.00 4.34
2406 2569 1.472026 GCGAGGATGCGTAAAACCCTA 60.472 52.381 0.00 0.00 0.00 3.53
2407 2570 2.470821 CGAGGATGCGTAAAACCCTAG 58.529 52.381 0.00 0.00 0.00 3.02
2408 2571 2.159142 CGAGGATGCGTAAAACCCTAGT 60.159 50.000 0.00 0.00 0.00 2.57
2409 2572 3.455327 GAGGATGCGTAAAACCCTAGTC 58.545 50.000 0.00 0.00 0.00 2.59
2410 2573 2.169978 AGGATGCGTAAAACCCTAGTCC 59.830 50.000 0.00 0.00 0.00 3.85
2411 2574 2.169978 GGATGCGTAAAACCCTAGTCCT 59.830 50.000 0.00 0.00 0.00 3.85
2412 2575 2.754946 TGCGTAAAACCCTAGTCCTG 57.245 50.000 0.00 0.00 0.00 3.86
2413 2576 1.338389 TGCGTAAAACCCTAGTCCTGC 60.338 52.381 0.00 0.00 0.00 4.85
2414 2577 1.066358 GCGTAAAACCCTAGTCCTGCT 60.066 52.381 0.00 0.00 0.00 4.24
2415 2578 2.614734 GCGTAAAACCCTAGTCCTGCTT 60.615 50.000 0.00 0.00 0.00 3.91
2416 2579 3.671716 CGTAAAACCCTAGTCCTGCTTT 58.328 45.455 0.00 0.00 0.00 3.51
2417 2580 3.435671 CGTAAAACCCTAGTCCTGCTTTG 59.564 47.826 0.00 0.00 0.00 2.77
2418 2581 2.586648 AAACCCTAGTCCTGCTTTGG 57.413 50.000 0.00 0.00 0.00 3.28
2419 2582 1.446016 AACCCTAGTCCTGCTTTGGT 58.554 50.000 0.00 0.00 33.13 3.67
2420 2583 0.693049 ACCCTAGTCCTGCTTTGGTG 59.307 55.000 0.00 0.00 31.34 4.17
2421 2584 0.035056 CCCTAGTCCTGCTTTGGTGG 60.035 60.000 0.00 0.00 0.00 4.61
2422 2585 0.984230 CCTAGTCCTGCTTTGGTGGA 59.016 55.000 0.00 0.00 0.00 4.02
2423 2586 1.561542 CCTAGTCCTGCTTTGGTGGAT 59.438 52.381 0.00 0.00 32.03 3.41
2424 2587 2.636830 CTAGTCCTGCTTTGGTGGATG 58.363 52.381 0.00 0.00 32.03 3.51
2425 2588 0.773644 AGTCCTGCTTTGGTGGATGT 59.226 50.000 0.00 0.00 32.03 3.06
2426 2589 1.985159 AGTCCTGCTTTGGTGGATGTA 59.015 47.619 0.00 0.00 32.03 2.29
2427 2590 2.578021 AGTCCTGCTTTGGTGGATGTAT 59.422 45.455 0.00 0.00 32.03 2.29
2428 2591 3.010584 AGTCCTGCTTTGGTGGATGTATT 59.989 43.478 0.00 0.00 32.03 1.89
2429 2592 3.129287 GTCCTGCTTTGGTGGATGTATTG 59.871 47.826 0.00 0.00 32.03 1.90
2430 2593 3.010027 TCCTGCTTTGGTGGATGTATTGA 59.990 43.478 0.00 0.00 0.00 2.57
2431 2594 3.379372 CCTGCTTTGGTGGATGTATTGAG 59.621 47.826 0.00 0.00 0.00 3.02
2432 2595 4.012374 CTGCTTTGGTGGATGTATTGAGT 58.988 43.478 0.00 0.00 0.00 3.41
2433 2596 3.758023 TGCTTTGGTGGATGTATTGAGTG 59.242 43.478 0.00 0.00 0.00 3.51
2434 2597 3.758554 GCTTTGGTGGATGTATTGAGTGT 59.241 43.478 0.00 0.00 0.00 3.55
2435 2598 4.218417 GCTTTGGTGGATGTATTGAGTGTT 59.782 41.667 0.00 0.00 0.00 3.32
2436 2599 5.619981 GCTTTGGTGGATGTATTGAGTGTTC 60.620 44.000 0.00 0.00 0.00 3.18
2437 2600 4.908601 TGGTGGATGTATTGAGTGTTCT 57.091 40.909 0.00 0.00 0.00 3.01
2438 2601 5.241403 TGGTGGATGTATTGAGTGTTCTT 57.759 39.130 0.00 0.00 0.00 2.52
2439 2602 5.003160 TGGTGGATGTATTGAGTGTTCTTG 58.997 41.667 0.00 0.00 0.00 3.02
2440 2603 5.221823 TGGTGGATGTATTGAGTGTTCTTGA 60.222 40.000 0.00 0.00 0.00 3.02
2441 2604 5.352569 GGTGGATGTATTGAGTGTTCTTGAG 59.647 44.000 0.00 0.00 0.00 3.02
2442 2605 4.937620 TGGATGTATTGAGTGTTCTTGAGC 59.062 41.667 0.00 0.00 0.00 4.26
2443 2606 5.181748 GGATGTATTGAGTGTTCTTGAGCT 58.818 41.667 0.00 0.00 0.00 4.09
2444 2607 5.645497 GGATGTATTGAGTGTTCTTGAGCTT 59.355 40.000 0.00 0.00 0.00 3.74
2445 2608 6.150140 GGATGTATTGAGTGTTCTTGAGCTTT 59.850 38.462 0.00 0.00 0.00 3.51
2446 2609 6.545504 TGTATTGAGTGTTCTTGAGCTTTC 57.454 37.500 0.00 0.00 0.00 2.62
2447 2610 4.739046 ATTGAGTGTTCTTGAGCTTTCG 57.261 40.909 0.00 0.00 0.00 3.46
2448 2611 3.452755 TGAGTGTTCTTGAGCTTTCGA 57.547 42.857 0.00 0.00 0.00 3.71
2449 2612 3.792401 TGAGTGTTCTTGAGCTTTCGAA 58.208 40.909 0.00 0.00 0.00 3.71
2450 2613 3.555956 TGAGTGTTCTTGAGCTTTCGAAC 59.444 43.478 0.00 13.02 37.02 3.95
2451 2614 3.798202 AGTGTTCTTGAGCTTTCGAACT 58.202 40.909 17.85 0.00 37.31 3.01
2452 2615 4.945246 AGTGTTCTTGAGCTTTCGAACTA 58.055 39.130 17.85 7.33 37.31 2.24
2453 2616 4.985409 AGTGTTCTTGAGCTTTCGAACTAG 59.015 41.667 17.85 0.00 37.31 2.57
2454 2617 3.741344 TGTTCTTGAGCTTTCGAACTAGC 59.259 43.478 12.90 12.90 37.31 3.42
2461 2624 3.851098 AGCTTTCGAACTAGCTAAGGTG 58.149 45.455 20.15 0.00 45.46 4.00
2462 2625 2.930682 GCTTTCGAACTAGCTAAGGTGG 59.069 50.000 13.41 0.00 34.57 4.61
2463 2626 2.667473 TTCGAACTAGCTAAGGTGGC 57.333 50.000 0.00 0.00 0.00 5.01
2464 2627 1.848652 TCGAACTAGCTAAGGTGGCT 58.151 50.000 0.00 0.00 43.02 4.75
2465 2628 1.476891 TCGAACTAGCTAAGGTGGCTG 59.523 52.381 0.00 0.00 40.52 4.85
2466 2629 1.471676 CGAACTAGCTAAGGTGGCTGG 60.472 57.143 0.00 0.00 42.63 4.85
2467 2630 1.831736 GAACTAGCTAAGGTGGCTGGA 59.168 52.381 4.04 0.00 40.03 3.86
2468 2631 1.952621 ACTAGCTAAGGTGGCTGGAA 58.047 50.000 4.04 0.00 40.03 3.53
2469 2632 2.482494 ACTAGCTAAGGTGGCTGGAAT 58.518 47.619 4.04 0.00 40.03 3.01
2470 2633 2.436173 ACTAGCTAAGGTGGCTGGAATC 59.564 50.000 4.04 0.00 40.03 2.52
2471 2634 0.548510 AGCTAAGGTGGCTGGAATCC 59.451 55.000 0.00 0.00 38.73 3.01
2472 2635 0.466372 GCTAAGGTGGCTGGAATCCC 60.466 60.000 0.00 0.00 0.00 3.85
2473 2636 1.216990 CTAAGGTGGCTGGAATCCCT 58.783 55.000 0.00 0.00 0.00 4.20
2474 2637 1.141858 CTAAGGTGGCTGGAATCCCTC 59.858 57.143 0.00 0.00 0.00 4.30
2475 2638 0.551131 AAGGTGGCTGGAATCCCTCT 60.551 55.000 0.00 0.00 0.00 3.69
2476 2639 0.985490 AGGTGGCTGGAATCCCTCTC 60.985 60.000 0.00 0.00 0.00 3.20
2477 2640 1.529309 GTGGCTGGAATCCCTCTCC 59.471 63.158 0.00 0.00 0.00 3.71
2478 2641 0.985490 GTGGCTGGAATCCCTCTCCT 60.985 60.000 0.00 0.00 33.77 3.69
2479 2642 0.984961 TGGCTGGAATCCCTCTCCTG 60.985 60.000 0.00 0.00 35.56 3.86
2480 2643 1.704007 GGCTGGAATCCCTCTCCTGG 61.704 65.000 0.00 0.00 33.65 4.45
2481 2644 0.985490 GCTGGAATCCCTCTCCTGGT 60.985 60.000 0.00 0.00 33.65 4.00
2482 2645 1.127343 CTGGAATCCCTCTCCTGGTC 58.873 60.000 0.00 0.00 33.77 4.02
2483 2646 0.687757 TGGAATCCCTCTCCTGGTCG 60.688 60.000 0.00 0.00 33.77 4.79
2484 2647 1.443828 GAATCCCTCTCCTGGTCGC 59.556 63.158 0.00 0.00 0.00 5.19
2485 2648 2.034048 GAATCCCTCTCCTGGTCGCC 62.034 65.000 0.00 0.00 0.00 5.54
2486 2649 2.537714 AATCCCTCTCCTGGTCGCCT 62.538 60.000 0.00 0.00 0.00 5.52
2487 2650 2.937959 ATCCCTCTCCTGGTCGCCTC 62.938 65.000 0.00 0.00 0.00 4.70
2488 2651 3.522731 CCTCTCCTGGTCGCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
2489 2652 3.522731 CTCTCCTGGTCGCCTCGG 61.523 72.222 0.00 0.00 0.00 4.63
2500 2663 2.995547 GCCTCGGGCCTCCTTTTA 59.004 61.111 0.84 0.00 44.06 1.52
2501 2664 1.532238 GCCTCGGGCCTCCTTTTAT 59.468 57.895 0.84 0.00 44.06 1.40
2502 2665 0.763035 GCCTCGGGCCTCCTTTTATA 59.237 55.000 0.84 0.00 44.06 0.98
2503 2666 1.270893 GCCTCGGGCCTCCTTTTATAG 60.271 57.143 0.84 0.00 44.06 1.31
2504 2667 2.047830 CCTCGGGCCTCCTTTTATAGT 58.952 52.381 0.84 0.00 0.00 2.12
2505 2668 2.224305 CCTCGGGCCTCCTTTTATAGTG 60.224 54.545 0.84 0.00 0.00 2.74
2506 2669 2.698797 CTCGGGCCTCCTTTTATAGTGA 59.301 50.000 0.84 0.00 0.00 3.41
2507 2670 3.109151 TCGGGCCTCCTTTTATAGTGAA 58.891 45.455 0.84 0.00 0.00 3.18
2508 2671 3.520317 TCGGGCCTCCTTTTATAGTGAAA 59.480 43.478 0.84 0.00 0.00 2.69
2509 2672 4.019141 TCGGGCCTCCTTTTATAGTGAAAA 60.019 41.667 0.84 0.00 0.00 2.29
2510 2673 4.335594 CGGGCCTCCTTTTATAGTGAAAAG 59.664 45.833 0.84 2.35 43.25 2.27
2517 2680 4.998788 CTTTTATAGTGAAAAGGGGCTGC 58.001 43.478 0.00 0.00 41.00 5.25
2518 2681 2.729028 TATAGTGAAAAGGGGCTGCC 57.271 50.000 11.05 11.05 0.00 4.85
2519 2682 0.704076 ATAGTGAAAAGGGGCTGCCA 59.296 50.000 22.05 0.00 0.00 4.92
2520 2683 0.251165 TAGTGAAAAGGGGCTGCCAC 60.251 55.000 22.05 18.62 0.00 5.01
2521 2684 1.832167 GTGAAAAGGGGCTGCCACA 60.832 57.895 25.12 8.56 0.00 4.17
2522 2685 1.531365 TGAAAAGGGGCTGCCACAG 60.531 57.895 25.12 0.00 34.12 3.66
2523 2686 1.531602 GAAAAGGGGCTGCCACAGT 60.532 57.895 25.12 7.62 33.43 3.55
2524 2687 1.809567 GAAAAGGGGCTGCCACAGTG 61.810 60.000 25.12 0.00 33.43 3.66
2525 2688 3.815407 AAAGGGGCTGCCACAGTGG 62.815 63.158 25.12 16.16 41.55 4.00
2546 2709 3.329300 CACAGGAGGTGGAAAGGTG 57.671 57.895 0.00 0.00 44.04 4.00
2547 2710 0.474184 CACAGGAGGTGGAAAGGTGT 59.526 55.000 0.00 0.00 44.04 4.16
2548 2711 1.697432 CACAGGAGGTGGAAAGGTGTA 59.303 52.381 0.00 0.00 44.04 2.90
2549 2712 1.697982 ACAGGAGGTGGAAAGGTGTAC 59.302 52.381 0.00 0.00 0.00 2.90
2550 2713 1.697432 CAGGAGGTGGAAAGGTGTACA 59.303 52.381 0.00 0.00 0.00 2.90
2551 2714 1.978580 AGGAGGTGGAAAGGTGTACAG 59.021 52.381 0.00 0.00 0.00 2.74
2552 2715 1.697982 GGAGGTGGAAAGGTGTACAGT 59.302 52.381 0.00 0.00 0.00 3.55
2553 2716 2.550208 GGAGGTGGAAAGGTGTACAGTG 60.550 54.545 0.00 0.00 0.00 3.66
2554 2717 1.202770 AGGTGGAAAGGTGTACAGTGC 60.203 52.381 0.00 0.00 0.00 4.40
2555 2718 0.865769 GTGGAAAGGTGTACAGTGCG 59.134 55.000 0.00 0.00 0.00 5.34
2556 2719 0.882927 TGGAAAGGTGTACAGTGCGC 60.883 55.000 0.00 0.00 0.00 6.09
2557 2720 1.491563 GAAAGGTGTACAGTGCGCG 59.508 57.895 0.00 0.00 0.00 6.86
2558 2721 0.942410 GAAAGGTGTACAGTGCGCGA 60.942 55.000 12.10 0.00 0.00 5.87
2559 2722 0.944311 AAAGGTGTACAGTGCGCGAG 60.944 55.000 12.10 0.00 0.00 5.03
2573 2736 4.585526 CGAGCTTATCGCCCGGCA 62.586 66.667 10.77 0.00 45.98 5.69
2574 2737 2.031163 GAGCTTATCGCCCGGCAT 59.969 61.111 10.77 4.97 40.39 4.40
2575 2738 1.598130 GAGCTTATCGCCCGGCATT 60.598 57.895 10.77 0.00 40.39 3.56
2576 2739 0.320421 GAGCTTATCGCCCGGCATTA 60.320 55.000 10.77 0.00 40.39 1.90
2577 2740 0.602905 AGCTTATCGCCCGGCATTAC 60.603 55.000 10.77 0.00 40.39 1.89
2578 2741 1.897398 GCTTATCGCCCGGCATTACG 61.897 60.000 10.77 0.00 0.00 3.18
2587 2750 2.849081 CGGCATTACGGGACAAAGT 58.151 52.632 0.00 0.00 0.00 2.66
2588 2751 0.446222 CGGCATTACGGGACAAAGTG 59.554 55.000 0.00 0.00 0.00 3.16
2589 2752 0.170339 GGCATTACGGGACAAAGTGC 59.830 55.000 0.00 0.00 0.00 4.40
2590 2753 0.878416 GCATTACGGGACAAAGTGCA 59.122 50.000 0.00 0.00 0.00 4.57
2591 2754 1.472480 GCATTACGGGACAAAGTGCAT 59.528 47.619 0.00 0.00 0.00 3.96
2592 2755 2.094752 GCATTACGGGACAAAGTGCATT 60.095 45.455 0.00 0.00 0.00 3.56
2593 2756 3.127895 GCATTACGGGACAAAGTGCATTA 59.872 43.478 0.00 0.00 0.00 1.90
2594 2757 4.380023 GCATTACGGGACAAAGTGCATTAA 60.380 41.667 0.00 0.00 0.00 1.40
2595 2758 5.704888 CATTACGGGACAAAGTGCATTAAA 58.295 37.500 0.00 0.00 0.00 1.52
2596 2759 5.968528 TTACGGGACAAAGTGCATTAAAT 57.031 34.783 0.00 0.00 0.00 1.40
2597 2760 4.173036 ACGGGACAAAGTGCATTAAATG 57.827 40.909 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 50 4.209911 GCAAATCTGAAGGTTTTCAACAGC 59.790 41.667 0.00 0.00 42.48 4.40
116 119 7.873739 AAACTTTTCATGTAAGTTGCTATGC 57.126 32.000 21.10 0.00 43.14 3.14
137 142 5.159925 ACTGTTTTGCATTTTGCCAAAAAC 58.840 33.333 6.70 15.60 43.54 2.43
297 310 7.557719 CCATGATGAAATAACTTGTAAGGTCCT 59.442 37.037 0.00 0.00 0.00 3.85
398 417 2.024176 ATCCTTCCGATGAACAACCG 57.976 50.000 0.00 0.00 0.00 4.44
412 431 0.112995 TTGCAGCTCCAACCATCCTT 59.887 50.000 0.00 0.00 0.00 3.36
420 439 3.696051 GAGAATAATGGTTGCAGCTCCAA 59.304 43.478 12.56 0.00 37.27 3.53
447 466 3.449737 CCAGGATGCACATTCCATTTTCT 59.550 43.478 7.56 0.00 31.97 2.52
643 690 2.503356 AGGAGCAGCAGCACTACTTTAT 59.497 45.455 3.17 0.00 45.49 1.40
698 758 5.690409 CAGCAATTATCATGGAGAATGCAAC 59.310 40.000 13.46 0.00 42.43 4.17
769 862 1.843992 CAAACAGTGGAAGCACAAGC 58.156 50.000 0.00 0.00 42.56 4.01
838 936 9.424319 TGAAAGTTTTGTGCTACAACAATTTTA 57.576 25.926 11.78 7.63 36.57 1.52
872 970 7.961326 AACATTATTTGGAGCCATCTACTTT 57.039 32.000 0.00 0.00 0.00 2.66
873 971 7.961326 AAACATTATTTGGAGCCATCTACTT 57.039 32.000 0.00 0.00 0.00 2.24
874 972 7.961326 AAAACATTATTTGGAGCCATCTACT 57.039 32.000 0.00 0.00 0.00 2.57
928 1031 7.092716 AGAGGCAAGCAGTTAATACATTTTTG 58.907 34.615 0.00 0.00 0.00 2.44
956 1059 6.260493 ACACCATGAAAACACATCAAATTTGG 59.740 34.615 17.90 5.67 32.17 3.28
1268 1401 2.552315 CCTGCGGTGTTAGTGTCAAAAT 59.448 45.455 0.00 0.00 0.00 1.82
1323 1457 1.515521 CGTTCTCACCAACCAAGCCC 61.516 60.000 0.00 0.00 0.00 5.19
1489 1627 7.951591 ACAAATTTCTGCTTTACCAACATACT 58.048 30.769 0.00 0.00 0.00 2.12
1521 1659 3.995048 CCTCTGTAGGTTTCCGAAACTTC 59.005 47.826 20.63 12.76 41.14 3.01
1597 1737 9.546428 AATATCATCATCTTCGTCAACATGTTA 57.454 29.630 11.53 0.00 0.00 2.41
1728 1874 1.670083 GTACACCACCTCCCAACGC 60.670 63.158 0.00 0.00 0.00 4.84
1838 1984 6.294176 GCAGTTGTGAAGATGTGTTAGGAATT 60.294 38.462 0.00 0.00 0.00 2.17
1915 2065 4.152223 GCATTAAATTGGTGTTGAGCAACC 59.848 41.667 10.54 0.00 42.22 3.77
1941 2091 4.520492 CCACACTTAAAAAGATCAGCAGGT 59.480 41.667 0.00 0.00 0.00 4.00
2015 2169 5.324784 ACAAAGGAAACCTCAAGAACAAC 57.675 39.130 0.00 0.00 30.89 3.32
2042 2197 3.506398 ACAAAACTAATCAACCCCCAGG 58.494 45.455 0.00 0.00 40.04 4.45
2084 2244 1.388547 TTCGAGCAACTGCCAAACTT 58.611 45.000 0.00 0.00 43.38 2.66
2087 2247 1.474478 TGTTTTCGAGCAACTGCCAAA 59.526 42.857 10.06 0.00 43.38 3.28
2152 2313 5.297547 TCACTTTGAGCAAGTACTAACAGG 58.702 41.667 0.00 0.00 44.60 4.00
2231 2394 8.181487 ACAATACTAATTACTGCACACTAACG 57.819 34.615 0.00 0.00 0.00 3.18
2252 2415 3.003275 CACCGACAAACTAGCACAACAAT 59.997 43.478 0.00 0.00 0.00 2.71
2272 2435 1.822990 TCCCATAGGTGTCGTTCTCAC 59.177 52.381 0.00 0.00 35.36 3.51
2273 2436 2.225382 TCCCATAGGTGTCGTTCTCA 57.775 50.000 0.00 0.00 0.00 3.27
2274 2437 2.693591 TGATCCCATAGGTGTCGTTCTC 59.306 50.000 0.00 0.00 0.00 2.87
2275 2438 2.431057 GTGATCCCATAGGTGTCGTTCT 59.569 50.000 0.00 0.00 0.00 3.01
2276 2439 2.431057 AGTGATCCCATAGGTGTCGTTC 59.569 50.000 0.00 0.00 0.00 3.95
2277 2440 2.168521 CAGTGATCCCATAGGTGTCGTT 59.831 50.000 0.00 0.00 0.00 3.85
2278 2441 1.757118 CAGTGATCCCATAGGTGTCGT 59.243 52.381 0.00 0.00 0.00 4.34
2279 2442 1.069204 CCAGTGATCCCATAGGTGTCG 59.931 57.143 0.00 0.00 0.00 4.35
2280 2443 2.398588 TCCAGTGATCCCATAGGTGTC 58.601 52.381 0.00 0.00 0.00 3.67
2281 2444 2.568546 TCCAGTGATCCCATAGGTGT 57.431 50.000 0.00 0.00 0.00 4.16
2282 2445 3.244700 GGATTCCAGTGATCCCATAGGTG 60.245 52.174 0.00 0.00 0.00 4.00
2283 2446 2.982488 GGATTCCAGTGATCCCATAGGT 59.018 50.000 0.00 0.00 0.00 3.08
2284 2447 3.710209 GGATTCCAGTGATCCCATAGG 57.290 52.381 0.00 0.00 0.00 2.57
2290 2453 3.243907 CGTAGAAGGGATTCCAGTGATCC 60.244 52.174 4.80 2.78 34.83 3.36
2291 2454 3.243907 CCGTAGAAGGGATTCCAGTGATC 60.244 52.174 4.80 0.00 34.83 2.92
2292 2455 2.700897 CCGTAGAAGGGATTCCAGTGAT 59.299 50.000 4.80 0.00 34.83 3.06
2293 2456 2.108168 CCGTAGAAGGGATTCCAGTGA 58.892 52.381 4.80 0.00 34.83 3.41
2294 2457 1.831736 ACCGTAGAAGGGATTCCAGTG 59.168 52.381 4.80 0.00 35.02 3.66
2295 2458 2.108970 GACCGTAGAAGGGATTCCAGT 58.891 52.381 4.80 0.00 35.02 4.00
2296 2459 1.067212 CGACCGTAGAAGGGATTCCAG 59.933 57.143 4.80 0.00 35.02 3.86
2297 2460 1.108776 CGACCGTAGAAGGGATTCCA 58.891 55.000 4.80 0.00 35.02 3.53
2298 2461 0.388294 CCGACCGTAGAAGGGATTCC 59.612 60.000 0.00 0.00 35.02 3.01
2299 2462 0.249363 GCCGACCGTAGAAGGGATTC 60.249 60.000 0.00 0.00 35.02 2.52
2300 2463 1.821258 GCCGACCGTAGAAGGGATT 59.179 57.895 0.00 0.00 35.02 3.01
2301 2464 2.487532 CGCCGACCGTAGAAGGGAT 61.488 63.158 0.00 0.00 35.02 3.85
2302 2465 3.136123 CGCCGACCGTAGAAGGGA 61.136 66.667 0.00 0.00 35.02 4.20
2303 2466 4.203076 CCGCCGACCGTAGAAGGG 62.203 72.222 0.00 0.00 35.02 3.95
2304 2467 4.203076 CCCGCCGACCGTAGAAGG 62.203 72.222 0.00 0.00 34.38 3.46
2305 2468 4.867599 GCCCGCCGACCGTAGAAG 62.868 72.222 0.00 0.00 34.38 2.85
2322 2485 3.649277 CTCTCCTCACAACCCCGCG 62.649 68.421 0.00 0.00 0.00 6.46
2323 2486 2.266055 CTCTCCTCACAACCCCGC 59.734 66.667 0.00 0.00 0.00 6.13
2324 2487 2.266055 GCTCTCCTCACAACCCCG 59.734 66.667 0.00 0.00 0.00 5.73
2325 2488 1.298014 CTGCTCTCCTCACAACCCC 59.702 63.158 0.00 0.00 0.00 4.95
2326 2489 1.298014 CCTGCTCTCCTCACAACCC 59.702 63.158 0.00 0.00 0.00 4.11
2327 2490 0.036858 GACCTGCTCTCCTCACAACC 60.037 60.000 0.00 0.00 0.00 3.77
2328 2491 0.036858 GGACCTGCTCTCCTCACAAC 60.037 60.000 0.00 0.00 0.00 3.32
2329 2492 0.471780 TGGACCTGCTCTCCTCACAA 60.472 55.000 0.00 0.00 0.00 3.33
2330 2493 0.902048 CTGGACCTGCTCTCCTCACA 60.902 60.000 0.00 0.00 0.00 3.58
2331 2494 1.612395 CCTGGACCTGCTCTCCTCAC 61.612 65.000 0.00 0.00 0.00 3.51
2332 2495 1.305633 CCTGGACCTGCTCTCCTCA 60.306 63.158 0.00 0.00 0.00 3.86
2333 2496 1.000993 TCCTGGACCTGCTCTCCTC 59.999 63.158 0.00 0.00 0.00 3.71
2334 2497 1.001503 CTCCTGGACCTGCTCTCCT 59.998 63.158 0.00 0.00 0.00 3.69
2335 2498 2.730524 GCTCCTGGACCTGCTCTCC 61.731 68.421 0.00 0.00 0.00 3.71
2336 2499 2.730524 GGCTCCTGGACCTGCTCTC 61.731 68.421 6.40 0.00 0.00 3.20
2337 2500 2.686835 GGCTCCTGGACCTGCTCT 60.687 66.667 6.40 0.00 0.00 4.09
2338 2501 3.005539 TGGCTCCTGGACCTGCTC 61.006 66.667 13.91 3.53 0.00 4.26
2339 2502 3.007920 CTGGCTCCTGGACCTGCT 61.008 66.667 13.91 0.00 0.00 4.24
2340 2503 4.792804 GCTGGCTCCTGGACCTGC 62.793 72.222 21.68 21.68 42.56 4.85
2341 2504 3.324930 TGCTGGCTCCTGGACCTG 61.325 66.667 13.91 13.87 0.00 4.00
2342 2505 3.325753 GTGCTGGCTCCTGGACCT 61.326 66.667 13.91 0.00 32.00 3.85
2343 2506 3.196207 TTGTGCTGGCTCCTGGACC 62.196 63.158 13.18 0.01 35.91 4.46
2344 2507 1.673665 CTTGTGCTGGCTCCTGGAC 60.674 63.158 9.82 9.82 36.92 4.02
2345 2508 2.752358 CTTGTGCTGGCTCCTGGA 59.248 61.111 0.00 0.00 0.00 3.86
2346 2509 2.207501 ATCCTTGTGCTGGCTCCTGG 62.208 60.000 0.00 0.00 0.00 4.45
2347 2510 0.747283 GATCCTTGTGCTGGCTCCTG 60.747 60.000 0.00 0.00 0.00 3.86
2348 2511 1.606531 GATCCTTGTGCTGGCTCCT 59.393 57.895 0.00 0.00 0.00 3.69
2349 2512 1.817099 CGATCCTTGTGCTGGCTCC 60.817 63.158 0.00 0.00 0.00 4.70
2350 2513 0.674895 AACGATCCTTGTGCTGGCTC 60.675 55.000 0.00 0.00 0.00 4.70
2351 2514 0.250901 AAACGATCCTTGTGCTGGCT 60.251 50.000 0.00 0.00 0.00 4.75
2352 2515 1.130561 GTAAACGATCCTTGTGCTGGC 59.869 52.381 0.00 0.00 0.00 4.85
2353 2516 1.737793 GGTAAACGATCCTTGTGCTGG 59.262 52.381 0.00 0.00 0.00 4.85
2354 2517 1.737793 GGGTAAACGATCCTTGTGCTG 59.262 52.381 0.00 0.00 0.00 4.41
2355 2518 1.349688 TGGGTAAACGATCCTTGTGCT 59.650 47.619 0.00 0.00 0.00 4.40
2356 2519 1.737793 CTGGGTAAACGATCCTTGTGC 59.262 52.381 0.00 0.00 0.00 4.57
2357 2520 2.290071 ACCTGGGTAAACGATCCTTGTG 60.290 50.000 0.00 0.00 0.00 3.33
2358 2521 1.982958 ACCTGGGTAAACGATCCTTGT 59.017 47.619 0.00 0.00 0.00 3.16
2359 2522 2.781681 ACCTGGGTAAACGATCCTTG 57.218 50.000 0.00 0.00 0.00 3.61
2360 2523 2.354403 CGAACCTGGGTAAACGATCCTT 60.354 50.000 0.00 0.00 0.00 3.36
2361 2524 1.206371 CGAACCTGGGTAAACGATCCT 59.794 52.381 0.00 0.00 0.00 3.24
2362 2525 1.648504 CGAACCTGGGTAAACGATCC 58.351 55.000 0.00 0.00 0.00 3.36
2363 2526 1.648504 CCGAACCTGGGTAAACGATC 58.351 55.000 0.00 0.00 0.00 3.69
2364 2527 0.251073 CCCGAACCTGGGTAAACGAT 59.749 55.000 0.00 0.00 44.76 3.73
2365 2528 1.672898 CCCGAACCTGGGTAAACGA 59.327 57.895 0.00 0.00 44.76 3.85
2366 2529 4.289312 CCCGAACCTGGGTAAACG 57.711 61.111 0.00 0.00 44.76 3.60
2386 2549 0.743345 AGGGTTTTACGCATCCTCGC 60.743 55.000 0.00 0.00 32.95 5.03
2387 2550 2.159142 ACTAGGGTTTTACGCATCCTCG 60.159 50.000 0.00 0.00 32.95 4.63
2388 2551 3.455327 GACTAGGGTTTTACGCATCCTC 58.545 50.000 0.00 0.00 32.95 3.71
2389 2552 2.169978 GGACTAGGGTTTTACGCATCCT 59.830 50.000 0.00 0.00 32.95 3.24
2390 2553 2.169978 AGGACTAGGGTTTTACGCATCC 59.830 50.000 0.00 0.00 33.23 3.51
2391 2554 3.195661 CAGGACTAGGGTTTTACGCATC 58.804 50.000 0.00 0.00 32.95 3.91
2392 2555 2.679930 GCAGGACTAGGGTTTTACGCAT 60.680 50.000 0.00 0.00 32.95 4.73
2393 2556 1.338389 GCAGGACTAGGGTTTTACGCA 60.338 52.381 0.00 0.00 32.95 5.24
2394 2557 1.066358 AGCAGGACTAGGGTTTTACGC 60.066 52.381 0.00 0.00 0.00 4.42
2395 2558 3.329929 AAGCAGGACTAGGGTTTTACG 57.670 47.619 0.00 0.00 0.00 3.18
2396 2559 3.756963 CCAAAGCAGGACTAGGGTTTTAC 59.243 47.826 0.00 0.00 32.89 2.01
2397 2560 3.396611 ACCAAAGCAGGACTAGGGTTTTA 59.603 43.478 0.00 0.00 32.49 1.52
2398 2561 2.177016 ACCAAAGCAGGACTAGGGTTTT 59.823 45.455 0.00 0.00 32.49 2.43
2399 2562 1.780919 ACCAAAGCAGGACTAGGGTTT 59.219 47.619 0.00 0.00 32.49 3.27
2400 2563 1.073923 CACCAAAGCAGGACTAGGGTT 59.926 52.381 0.00 0.00 33.77 4.11
2401 2564 0.693049 CACCAAAGCAGGACTAGGGT 59.307 55.000 0.00 0.00 35.81 4.34
2402 2565 0.035056 CCACCAAAGCAGGACTAGGG 60.035 60.000 0.00 0.00 0.00 3.53
2403 2566 0.984230 TCCACCAAAGCAGGACTAGG 59.016 55.000 0.00 0.00 0.00 3.02
2404 2567 2.026822 ACATCCACCAAAGCAGGACTAG 60.027 50.000 0.00 0.00 33.57 2.57
2405 2568 1.985159 ACATCCACCAAAGCAGGACTA 59.015 47.619 0.00 0.00 33.57 2.59
2406 2569 0.773644 ACATCCACCAAAGCAGGACT 59.226 50.000 0.00 0.00 33.57 3.85
2407 2570 2.489938 TACATCCACCAAAGCAGGAC 57.510 50.000 0.00 0.00 33.57 3.85
2408 2571 3.010027 TCAATACATCCACCAAAGCAGGA 59.990 43.478 0.00 0.00 35.59 3.86
2409 2572 3.355378 TCAATACATCCACCAAAGCAGG 58.645 45.455 0.00 0.00 0.00 4.85
2410 2573 4.012374 ACTCAATACATCCACCAAAGCAG 58.988 43.478 0.00 0.00 0.00 4.24
2411 2574 3.758023 CACTCAATACATCCACCAAAGCA 59.242 43.478 0.00 0.00 0.00 3.91
2412 2575 3.758554 ACACTCAATACATCCACCAAAGC 59.241 43.478 0.00 0.00 0.00 3.51
2413 2576 5.707298 AGAACACTCAATACATCCACCAAAG 59.293 40.000 0.00 0.00 0.00 2.77
2414 2577 5.630121 AGAACACTCAATACATCCACCAAA 58.370 37.500 0.00 0.00 0.00 3.28
2415 2578 5.241403 AGAACACTCAATACATCCACCAA 57.759 39.130 0.00 0.00 0.00 3.67
2416 2579 4.908601 AGAACACTCAATACATCCACCA 57.091 40.909 0.00 0.00 0.00 4.17
2417 2580 5.245531 TCAAGAACACTCAATACATCCACC 58.754 41.667 0.00 0.00 0.00 4.61
2418 2581 5.163814 GCTCAAGAACACTCAATACATCCAC 60.164 44.000 0.00 0.00 0.00 4.02
2419 2582 4.937620 GCTCAAGAACACTCAATACATCCA 59.062 41.667 0.00 0.00 0.00 3.41
2420 2583 5.181748 AGCTCAAGAACACTCAATACATCC 58.818 41.667 0.00 0.00 0.00 3.51
2421 2584 6.734104 AAGCTCAAGAACACTCAATACATC 57.266 37.500 0.00 0.00 0.00 3.06
2422 2585 6.128445 CGAAAGCTCAAGAACACTCAATACAT 60.128 38.462 0.00 0.00 0.00 2.29
2423 2586 5.177511 CGAAAGCTCAAGAACACTCAATACA 59.822 40.000 0.00 0.00 0.00 2.29
2424 2587 5.405571 TCGAAAGCTCAAGAACACTCAATAC 59.594 40.000 0.00 0.00 0.00 1.89
2425 2588 5.538118 TCGAAAGCTCAAGAACACTCAATA 58.462 37.500 0.00 0.00 0.00 1.90
2426 2589 4.380531 TCGAAAGCTCAAGAACACTCAAT 58.619 39.130 0.00 0.00 0.00 2.57
2427 2590 3.792401 TCGAAAGCTCAAGAACACTCAA 58.208 40.909 0.00 0.00 0.00 3.02
2428 2591 3.452755 TCGAAAGCTCAAGAACACTCA 57.547 42.857 0.00 0.00 0.00 3.41
2429 2592 3.804873 AGTTCGAAAGCTCAAGAACACTC 59.195 43.478 21.89 4.16 43.71 3.51
2430 2593 3.798202 AGTTCGAAAGCTCAAGAACACT 58.202 40.909 21.89 7.13 43.71 3.55
2431 2594 4.376514 GCTAGTTCGAAAGCTCAAGAACAC 60.377 45.833 21.89 12.12 43.71 3.32
2432 2595 3.741344 GCTAGTTCGAAAGCTCAAGAACA 59.259 43.478 21.89 11.98 43.71 3.18
2433 2596 3.991121 AGCTAGTTCGAAAGCTCAAGAAC 59.009 43.478 16.78 15.86 45.92 3.01
2434 2597 4.258702 AGCTAGTTCGAAAGCTCAAGAA 57.741 40.909 16.78 0.00 45.92 2.52
2435 2598 3.944055 AGCTAGTTCGAAAGCTCAAGA 57.056 42.857 16.78 0.00 45.92 3.02
2436 2599 4.564769 CCTTAGCTAGTTCGAAAGCTCAAG 59.435 45.833 23.90 21.65 45.92 3.02
2437 2600 4.021368 ACCTTAGCTAGTTCGAAAGCTCAA 60.021 41.667 23.90 15.98 45.92 3.02
2438 2601 3.510360 ACCTTAGCTAGTTCGAAAGCTCA 59.490 43.478 23.90 14.62 45.92 4.26
2439 2602 3.860536 CACCTTAGCTAGTTCGAAAGCTC 59.139 47.826 23.90 1.55 45.92 4.09
2441 2604 2.930682 CCACCTTAGCTAGTTCGAAAGC 59.069 50.000 12.90 12.90 39.08 3.51
2442 2605 2.930682 GCCACCTTAGCTAGTTCGAAAG 59.069 50.000 0.00 0.00 0.00 2.62
2443 2606 2.565834 AGCCACCTTAGCTAGTTCGAAA 59.434 45.455 0.00 0.00 39.29 3.46
2444 2607 2.094182 CAGCCACCTTAGCTAGTTCGAA 60.094 50.000 0.00 0.00 38.95 3.71
2445 2608 1.476891 CAGCCACCTTAGCTAGTTCGA 59.523 52.381 0.00 0.00 38.95 3.71
2446 2609 1.471676 CCAGCCACCTTAGCTAGTTCG 60.472 57.143 0.00 0.00 38.95 3.95
2447 2610 1.831736 TCCAGCCACCTTAGCTAGTTC 59.168 52.381 0.00 0.00 38.95 3.01
2448 2611 1.952621 TCCAGCCACCTTAGCTAGTT 58.047 50.000 0.00 0.00 38.95 2.24
2449 2612 1.952621 TTCCAGCCACCTTAGCTAGT 58.047 50.000 0.00 0.00 38.95 2.57
2450 2613 2.224402 GGATTCCAGCCACCTTAGCTAG 60.224 54.545 0.00 0.00 38.95 3.42
2451 2614 1.768870 GGATTCCAGCCACCTTAGCTA 59.231 52.381 0.00 0.00 38.95 3.32
2452 2615 0.548510 GGATTCCAGCCACCTTAGCT 59.451 55.000 0.00 0.00 42.70 3.32
2453 2616 0.466372 GGGATTCCAGCCACCTTAGC 60.466 60.000 4.80 0.00 0.00 3.09
2454 2617 1.141858 GAGGGATTCCAGCCACCTTAG 59.858 57.143 4.80 0.00 34.83 2.18
2455 2618 1.213296 GAGGGATTCCAGCCACCTTA 58.787 55.000 4.80 0.00 34.83 2.69
2456 2619 0.551131 AGAGGGATTCCAGCCACCTT 60.551 55.000 4.80 0.00 34.83 3.50
2457 2620 0.985490 GAGAGGGATTCCAGCCACCT 60.985 60.000 4.80 0.00 34.83 4.00
2458 2621 1.529309 GAGAGGGATTCCAGCCACC 59.471 63.158 4.80 0.00 34.83 4.61
2459 2622 0.985490 AGGAGAGGGATTCCAGCCAC 60.985 60.000 4.80 0.00 37.18 5.01
2460 2623 0.984961 CAGGAGAGGGATTCCAGCCA 60.985 60.000 4.80 0.00 37.18 4.75
2461 2624 1.704007 CCAGGAGAGGGATTCCAGCC 61.704 65.000 4.80 0.00 37.18 4.85
2462 2625 0.985490 ACCAGGAGAGGGATTCCAGC 60.985 60.000 4.80 0.00 37.18 4.85
2463 2626 1.127343 GACCAGGAGAGGGATTCCAG 58.873 60.000 4.80 0.00 37.18 3.86
2464 2627 0.687757 CGACCAGGAGAGGGATTCCA 60.688 60.000 4.80 0.00 37.18 3.53
2465 2628 2.034048 GCGACCAGGAGAGGGATTCC 62.034 65.000 0.00 0.00 34.83 3.01
2466 2629 1.443828 GCGACCAGGAGAGGGATTC 59.556 63.158 0.00 0.00 0.00 2.52
2467 2630 2.066999 GGCGACCAGGAGAGGGATT 61.067 63.158 0.00 0.00 0.00 3.01
2468 2631 2.444895 GGCGACCAGGAGAGGGAT 60.445 66.667 0.00 0.00 0.00 3.85
2469 2632 3.663815 GAGGCGACCAGGAGAGGGA 62.664 68.421 0.00 0.00 0.00 4.20
2470 2633 3.151022 GAGGCGACCAGGAGAGGG 61.151 72.222 0.00 0.00 0.00 4.30
2471 2634 3.522731 CGAGGCGACCAGGAGAGG 61.523 72.222 0.00 0.00 0.00 3.69
2472 2635 3.522731 CCGAGGCGACCAGGAGAG 61.523 72.222 0.00 0.00 0.00 3.20
2484 2647 2.047830 ACTATAAAAGGAGGCCCGAGG 58.952 52.381 0.00 0.00 37.58 4.63
2485 2648 2.698797 TCACTATAAAAGGAGGCCCGAG 59.301 50.000 0.00 0.00 37.58 4.63
2486 2649 2.754465 TCACTATAAAAGGAGGCCCGA 58.246 47.619 0.00 0.00 37.58 5.14
2487 2650 3.553828 TTCACTATAAAAGGAGGCCCG 57.446 47.619 0.00 0.00 37.58 6.13
2488 2651 5.836821 CTTTTCACTATAAAAGGAGGCCC 57.163 43.478 0.00 0.00 40.97 5.80
2495 2658 4.142160 GGCAGCCCCTTTTCACTATAAAAG 60.142 45.833 0.00 0.00 43.19 2.27
2496 2659 3.767131 GGCAGCCCCTTTTCACTATAAAA 59.233 43.478 0.00 0.00 0.00 1.52
2497 2660 3.245443 TGGCAGCCCCTTTTCACTATAAA 60.245 43.478 9.64 0.00 0.00 1.40
2498 2661 2.310349 TGGCAGCCCCTTTTCACTATAA 59.690 45.455 9.64 0.00 0.00 0.98
2499 2662 1.919654 TGGCAGCCCCTTTTCACTATA 59.080 47.619 9.64 0.00 0.00 1.31
2500 2663 0.704076 TGGCAGCCCCTTTTCACTAT 59.296 50.000 9.64 0.00 0.00 2.12
2501 2664 0.251165 GTGGCAGCCCCTTTTCACTA 60.251 55.000 9.64 0.00 0.00 2.74
2502 2665 1.531602 GTGGCAGCCCCTTTTCACT 60.532 57.895 9.64 0.00 0.00 3.41
2503 2666 1.809567 CTGTGGCAGCCCCTTTTCAC 61.810 60.000 9.64 0.00 0.00 3.18
2504 2667 1.531365 CTGTGGCAGCCCCTTTTCA 60.531 57.895 9.64 0.00 0.00 2.69
2505 2668 1.531602 ACTGTGGCAGCCCCTTTTC 60.532 57.895 9.64 0.00 34.37 2.29
2506 2669 1.833934 CACTGTGGCAGCCCCTTTT 60.834 57.895 9.64 0.00 34.37 2.27
2507 2670 2.203538 CACTGTGGCAGCCCCTTT 60.204 61.111 9.64 0.00 34.37 3.11
2508 2671 4.290622 CCACTGTGGCAGCCCCTT 62.291 66.667 14.87 0.00 34.37 3.95
2517 2680 1.598962 CTCCTGTGTGCCACTGTGG 60.599 63.158 22.46 22.46 41.55 4.17
2518 2681 1.598962 CCTCCTGTGTGCCACTGTG 60.599 63.158 0.00 0.00 35.11 3.66
2519 2682 2.072487 ACCTCCTGTGTGCCACTGT 61.072 57.895 0.00 0.00 35.11 3.55
2520 2683 1.598962 CACCTCCTGTGTGCCACTG 60.599 63.158 0.00 6.17 40.26 3.66
2521 2684 2.822637 CCACCTCCTGTGTGCCACT 61.823 63.158 0.00 0.00 43.85 4.00
2522 2685 2.281761 CCACCTCCTGTGTGCCAC 60.282 66.667 0.00 0.00 43.85 5.01
2523 2686 1.640593 TTTCCACCTCCTGTGTGCCA 61.641 55.000 0.00 0.00 43.85 4.92
2524 2687 0.890996 CTTTCCACCTCCTGTGTGCC 60.891 60.000 0.00 0.00 43.85 5.01
2525 2688 0.890996 CCTTTCCACCTCCTGTGTGC 60.891 60.000 0.00 0.00 43.85 4.57
2526 2689 0.474184 ACCTTTCCACCTCCTGTGTG 59.526 55.000 0.00 0.00 43.85 3.82
2527 2690 0.474184 CACCTTTCCACCTCCTGTGT 59.526 55.000 0.00 0.00 43.85 3.72
2528 2691 0.474184 ACACCTTTCCACCTCCTGTG 59.526 55.000 0.00 0.00 45.01 3.66
2529 2692 1.697982 GTACACCTTTCCACCTCCTGT 59.302 52.381 0.00 0.00 0.00 4.00
2530 2693 1.697432 TGTACACCTTTCCACCTCCTG 59.303 52.381 0.00 0.00 0.00 3.86
2531 2694 1.978580 CTGTACACCTTTCCACCTCCT 59.021 52.381 0.00 0.00 0.00 3.69
2532 2695 1.697982 ACTGTACACCTTTCCACCTCC 59.302 52.381 0.00 0.00 0.00 4.30
2533 2696 2.767505 CACTGTACACCTTTCCACCTC 58.232 52.381 0.00 0.00 0.00 3.85
2534 2697 1.202770 GCACTGTACACCTTTCCACCT 60.203 52.381 0.00 0.00 0.00 4.00
2535 2698 1.235724 GCACTGTACACCTTTCCACC 58.764 55.000 0.00 0.00 0.00 4.61
2536 2699 0.865769 CGCACTGTACACCTTTCCAC 59.134 55.000 0.00 0.00 0.00 4.02
2537 2700 0.882927 GCGCACTGTACACCTTTCCA 60.883 55.000 0.30 0.00 0.00 3.53
2538 2701 1.866925 GCGCACTGTACACCTTTCC 59.133 57.895 0.30 0.00 0.00 3.13
2539 2702 0.942410 TCGCGCACTGTACACCTTTC 60.942 55.000 8.75 0.00 0.00 2.62
2540 2703 0.944311 CTCGCGCACTGTACACCTTT 60.944 55.000 8.75 0.00 0.00 3.11
2541 2704 1.372997 CTCGCGCACTGTACACCTT 60.373 57.895 8.75 0.00 0.00 3.50
2542 2705 2.258591 CTCGCGCACTGTACACCT 59.741 61.111 8.75 0.00 0.00 4.00
2543 2706 3.479269 GCTCGCGCACTGTACACC 61.479 66.667 8.75 0.00 35.78 4.16
2544 2707 0.731514 TAAGCTCGCGCACTGTACAC 60.732 55.000 8.75 0.00 39.10 2.90
2545 2708 0.172578 ATAAGCTCGCGCACTGTACA 59.827 50.000 8.75 0.00 39.10 2.90
2546 2709 0.847035 GATAAGCTCGCGCACTGTAC 59.153 55.000 8.75 0.00 39.10 2.90
2547 2710 0.591488 CGATAAGCTCGCGCACTGTA 60.591 55.000 8.75 0.00 41.14 2.74
2548 2711 1.874019 CGATAAGCTCGCGCACTGT 60.874 57.895 8.75 0.00 41.14 3.55
2549 2712 2.916423 CGATAAGCTCGCGCACTG 59.084 61.111 8.75 0.00 41.14 3.66
2560 2723 1.289109 CCGTAATGCCGGGCGATAAG 61.289 60.000 15.40 11.51 44.32 1.73
2561 2724 1.301087 CCGTAATGCCGGGCGATAA 60.301 57.895 15.40 0.00 44.32 1.75
2562 2725 2.340809 CCGTAATGCCGGGCGATA 59.659 61.111 15.40 7.01 44.32 2.92
2569 2732 0.446222 CACTTTGTCCCGTAATGCCG 59.554 55.000 0.00 0.00 0.00 5.69
2570 2733 0.170339 GCACTTTGTCCCGTAATGCC 59.830 55.000 0.00 0.00 0.00 4.40
2571 2734 0.878416 TGCACTTTGTCCCGTAATGC 59.122 50.000 0.00 0.00 0.00 3.56
2572 2735 3.848272 AATGCACTTTGTCCCGTAATG 57.152 42.857 0.00 0.00 0.00 1.90
2573 2736 5.968528 TTTAATGCACTTTGTCCCGTAAT 57.031 34.783 0.00 0.00 0.00 1.89
2574 2737 5.704888 CATTTAATGCACTTTGTCCCGTAA 58.295 37.500 0.00 0.00 0.00 3.18
2575 2738 5.303747 CATTTAATGCACTTTGTCCCGTA 57.696 39.130 0.00 0.00 0.00 4.02
2576 2739 4.173036 CATTTAATGCACTTTGTCCCGT 57.827 40.909 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.