Multiple sequence alignment - TraesCS6A01G384700

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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 TraesCS6A01G384700 chr6A 100.000 1982 0 0 1 1982 603044257 603046238 0.000000e+00 3661
1 TraesCS6A01G384700 chr6A 87.974 1979 207 9 6 1982 603093154 603095103 0.000000e+00 2307
2 TraesCS6A01G384700 chr6A 87.190 1975 216 11 8 1982 603102132 603104069 0.000000e+00 2211
3 TraesCS6A01G384700 chr6A 86.862 1979 221 8 6 1982 603083020 603084961 0.000000e+00 2178
4 TraesCS6A01G384700 chr6A 82.863 1809 267 26 52 1852 18462625 18464398 0.000000e+00 1583
5 TraesCS6A01G384700 chr6A 100.000 587 0 0 2284 2870 603046540 603047126 0.000000e+00 1085
6 TraesCS6A01G384700 chr6A 79.609 358 55 12 2456 2806 603085111 603085457 1.030000e-59 241
7 TraesCS6A01G384700 chr6B 89.737 1978 164 6 6 1982 693937077 693939016 0.000000e+00 2492
8 TraesCS6A01G384700 chr6B 89.282 1978 166 11 6 1979 693928506 693930441 0.000000e+00 2436
9 TraesCS6A01G384700 chr6D 87.867 1978 196 9 8 1982 456425904 456427840 0.000000e+00 2283
10 TraesCS6A01G384700 chr6D 86.196 1956 220 10 8 1959 456409951 456411860 0.000000e+00 2071
11 TraesCS6A01G384700 chr6D 82.721 1852 279 25 8 1852 17501714 17503531 0.000000e+00 1609
12 TraesCS6A01G384700 chr7D 79.894 1880 322 43 8 1861 629393332 629391483 0.000000e+00 1327
13 TraesCS6A01G384700 chr1A 77.630 1806 349 39 8 1793 530161855 530160085 0.000000e+00 1046
14 TraesCS6A01G384700 chr1D 78.033 783 135 27 1037 1812 431595445 431594693 2.610000e-125 459


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 TraesCS6A01G384700 chr6A 603044257 603047126 2869 False 2373.0 3661 100.0000 1 2870 2 chr6A.!!$F4 2869
1 TraesCS6A01G384700 chr6A 603093154 603095103 1949 False 2307.0 2307 87.9740 6 1982 1 chr6A.!!$F2 1976
2 TraesCS6A01G384700 chr6A 603102132 603104069 1937 False 2211.0 2211 87.1900 8 1982 1 chr6A.!!$F3 1974
3 TraesCS6A01G384700 chr6A 18462625 18464398 1773 False 1583.0 1583 82.8630 52 1852 1 chr6A.!!$F1 1800
4 TraesCS6A01G384700 chr6A 603083020 603085457 2437 False 1209.5 2178 83.2355 6 2806 2 chr6A.!!$F5 2800
5 TraesCS6A01G384700 chr6B 693937077 693939016 1939 False 2492.0 2492 89.7370 6 1982 1 chr6B.!!$F2 1976
6 TraesCS6A01G384700 chr6B 693928506 693930441 1935 False 2436.0 2436 89.2820 6 1979 1 chr6B.!!$F1 1973
7 TraesCS6A01G384700 chr6D 456425904 456427840 1936 False 2283.0 2283 87.8670 8 1982 1 chr6D.!!$F3 1974
8 TraesCS6A01G384700 chr6D 456409951 456411860 1909 False 2071.0 2071 86.1960 8 1959 1 chr6D.!!$F2 1951
9 TraesCS6A01G384700 chr6D 17501714 17503531 1817 False 1609.0 1609 82.7210 8 1852 1 chr6D.!!$F1 1844
10 TraesCS6A01G384700 chr7D 629391483 629393332 1849 True 1327.0 1327 79.8940 8 1861 1 chr7D.!!$R1 1853
11 TraesCS6A01G384700 chr1A 530160085 530161855 1770 True 1046.0 1046 77.6300 8 1793 1 chr1A.!!$R1 1785
12 TraesCS6A01G384700 chr1D 431594693 431595445 752 True 459.0 459 78.0330 1037 1812 1 chr1D.!!$R1 775

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
920 935 0.251916 CTTGGTAAGATCCGGCACCA 59.748 55.0 0.0 1.82 39.27 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2627 2692 0.110486 ATGGCGATGTAATGACCCCC 59.89 55.0 0.0 0.0 0.0 5.4 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
72 73 6.566753 CGAACAATTTCTTTCTTGGTCCTCTC 60.567 42.308 0.00 0.00 36.02 3.20
96 97 0.652592 CTGAAATAGGCGGCTTGACG 59.347 55.000 19.76 0.00 0.00 4.35
219 220 6.867662 AATTCCTTTGATAGTAGCATTCCG 57.132 37.500 0.00 0.00 0.00 4.30
304 305 5.714806 GGTGTGATTCCAAAAGATTTAGGGA 59.285 40.000 0.00 0.00 0.00 4.20
355 356 2.094752 GCACACAACAACTTGTCTGGTT 60.095 45.455 0.00 0.00 38.66 3.67
405 406 5.163343 GGCATCATTGTACCAGTTAGACCTA 60.163 44.000 0.00 0.00 0.00 3.08
408 409 6.387041 TCATTGTACCAGTTAGACCTATCG 57.613 41.667 0.00 0.00 0.00 2.92
454 455 3.870606 CACGGGGAGTGTTTAGCG 58.129 61.111 0.00 0.00 45.51 4.26
544 548 3.313249 CGCATGCCAGACAAAATCTATGA 59.687 43.478 13.15 0.00 35.15 2.15
643 650 3.096489 TGCTTGTTTCCTTGACAATGC 57.904 42.857 0.00 0.00 36.51 3.56
644 651 2.694628 TGCTTGTTTCCTTGACAATGCT 59.305 40.909 0.00 0.00 36.51 3.79
687 694 1.995542 ACAACCACAGGAGGATTCCAT 59.004 47.619 5.29 0.00 46.64 3.41
694 701 4.529897 CACAGGAGGATTCCATTTGATGA 58.470 43.478 5.29 0.00 46.64 2.92
759 766 3.146104 ACAAGTGGCTTTGCAGTAGAT 57.854 42.857 2.38 0.00 0.00 1.98
771 778 6.625740 GCTTTGCAGTAGATAATTTGCTTGGA 60.626 38.462 2.38 0.00 37.45 3.53
799 806 5.337330 GGAAGGTATGGATCGGTGTATAAGG 60.337 48.000 0.00 0.00 0.00 2.69
809 816 2.814919 CGGTGTATAAGGGTTGTTTGCA 59.185 45.455 0.00 0.00 0.00 4.08
810 817 3.442273 CGGTGTATAAGGGTTGTTTGCAT 59.558 43.478 0.00 0.00 0.00 3.96
815 822 5.414454 TGTATAAGGGTTGTTTGCATCTCAC 59.586 40.000 0.00 0.00 0.00 3.51
818 825 2.624838 AGGGTTGTTTGCATCTCACAAG 59.375 45.455 0.00 0.00 31.10 3.16
859 866 7.955918 AGCTGTAAAGGTTTTTGATCTTCAAT 58.044 30.769 0.00 0.00 36.11 2.57
915 930 0.541863 AGGCACTTGGTAAGATCCGG 59.458 55.000 0.00 0.00 27.25 5.14
918 933 1.369625 CACTTGGTAAGATCCGGCAC 58.630 55.000 0.00 0.00 0.00 5.01
920 935 0.251916 CTTGGTAAGATCCGGCACCA 59.748 55.000 0.00 1.82 39.27 4.17
929 944 3.480470 AGATCCGGCACCATAATTTGAG 58.520 45.455 0.00 0.00 0.00 3.02
958 973 5.534407 TCATAACGTGTTGTTCAAGCTCTA 58.466 37.500 0.00 0.00 42.09 2.43
983 998 7.169158 ACTTGAACCAAAATGACTTCAAAGA 57.831 32.000 0.00 0.00 33.39 2.52
1075 1093 3.068024 TCAACTCCAAGGTTTGACATTGC 59.932 43.478 0.34 0.00 38.43 3.56
1128 1146 4.379186 GCTGATGCGCTAGATTATTTGCAT 60.379 41.667 9.73 0.00 44.95 3.96
1246 1266 3.265221 TGCAAAGATCCTCTCTGAACCAT 59.735 43.478 0.00 0.00 33.29 3.55
1249 1269 5.494724 CAAAGATCCTCTCTGAACCATCAA 58.505 41.667 0.00 0.00 34.49 2.57
1351 1378 7.520119 TTTCTCTAACATTACATACTGCACG 57.480 36.000 0.00 0.00 0.00 5.34
1437 1470 3.485463 TTAGAATATGGCGAAGGTGGG 57.515 47.619 0.00 0.00 0.00 4.61
1500 1533 5.655090 TGTCATCCTCGAGTTGTTTATAGGA 59.345 40.000 12.31 0.00 37.52 2.94
1599 1632 4.942761 AATGCAGATTGTTGAACCAGTT 57.057 36.364 0.00 0.00 0.00 3.16
1696 1738 5.619132 TGCCATATTCTCTGTCATGAAGA 57.381 39.130 0.00 2.26 0.00 2.87
1701 1743 6.485648 CCATATTCTCTGTCATGAAGATTGCA 59.514 38.462 0.00 0.00 0.00 4.08
1760 1802 2.681848 GCATGAAAGATGCTGCTACTGT 59.318 45.455 0.00 0.00 41.52 3.55
1824 1874 2.146342 GAAGAAGTTGCTACAGCTGCA 58.854 47.619 15.27 2.71 42.66 4.41
1854 1910 2.950433 AGGCATTTTGCTGAAACATCG 58.050 42.857 0.00 0.00 44.28 3.84
1870 1926 2.991167 ATCGAGGCCAGCCCCCTAAT 62.991 60.000 5.01 0.00 36.58 1.73
1895 1956 2.411547 GCATCACACACTCACGCTTAAC 60.412 50.000 0.00 0.00 0.00 2.01
1900 1961 5.294356 TCACACACTCACGCTTAACTAATT 58.706 37.500 0.00 0.00 0.00 1.40
1903 1964 4.451096 CACACTCACGCTTAACTAATTGGT 59.549 41.667 0.00 0.00 0.00 3.67
1930 1991 7.997107 TGTAGTAGTTATATTTTGCACTCGG 57.003 36.000 0.00 0.00 0.00 4.63
1959 2023 7.094377 GGTTTTGATATGTTAGTTTCTGGCTGA 60.094 37.037 0.00 0.00 0.00 4.26
2304 2368 4.487714 GGGGAGATGTCTACATTGTGAA 57.512 45.455 0.00 0.00 36.57 3.18
2305 2369 4.192317 GGGGAGATGTCTACATTGTGAAC 58.808 47.826 0.00 0.00 36.57 3.18
2306 2370 4.080863 GGGGAGATGTCTACATTGTGAACT 60.081 45.833 0.00 0.00 36.57 3.01
2307 2371 5.491982 GGGAGATGTCTACATTGTGAACTT 58.508 41.667 0.00 0.00 36.57 2.66
2308 2372 5.352569 GGGAGATGTCTACATTGTGAACTTG 59.647 44.000 0.00 0.00 36.57 3.16
2309 2373 5.934625 GGAGATGTCTACATTGTGAACTTGT 59.065 40.000 0.00 0.00 36.57 3.16
2310 2374 7.097192 GGAGATGTCTACATTGTGAACTTGTA 58.903 38.462 0.00 0.00 36.57 2.41
2311 2375 7.602644 GGAGATGTCTACATTGTGAACTTGTAA 59.397 37.037 0.00 0.00 36.57 2.41
2312 2376 9.155975 GAGATGTCTACATTGTGAACTTGTAAT 57.844 33.333 0.00 0.00 36.57 1.89
2313 2377 9.155975 AGATGTCTACATTGTGAACTTGTAATC 57.844 33.333 0.00 0.00 36.57 1.75
2314 2378 9.155975 GATGTCTACATTGTGAACTTGTAATCT 57.844 33.333 0.00 0.00 36.57 2.40
2315 2379 8.534333 TGTCTACATTGTGAACTTGTAATCTC 57.466 34.615 0.00 0.00 0.00 2.75
2316 2380 8.147704 TGTCTACATTGTGAACTTGTAATCTCA 58.852 33.333 0.00 0.00 0.00 3.27
2317 2381 9.155975 GTCTACATTGTGAACTTGTAATCTCAT 57.844 33.333 0.00 0.00 0.00 2.90
2318 2382 9.725019 TCTACATTGTGAACTTGTAATCTCATT 57.275 29.630 0.00 0.00 0.00 2.57
2321 2385 8.632679 ACATTGTGAACTTGTAATCTCATTTGT 58.367 29.630 0.00 0.00 0.00 2.83
2325 2389 9.500785 TGTGAACTTGTAATCTCATTTGTATCA 57.499 29.630 0.00 0.00 0.00 2.15
2326 2390 9.979270 GTGAACTTGTAATCTCATTTGTATCAG 57.021 33.333 0.00 0.00 0.00 2.90
2327 2391 8.668353 TGAACTTGTAATCTCATTTGTATCAGC 58.332 33.333 0.00 0.00 0.00 4.26
2328 2392 8.798859 AACTTGTAATCTCATTTGTATCAGCT 57.201 30.769 0.00 0.00 0.00 4.24
2329 2393 9.890629 AACTTGTAATCTCATTTGTATCAGCTA 57.109 29.630 0.00 0.00 0.00 3.32
2330 2394 9.319143 ACTTGTAATCTCATTTGTATCAGCTAC 57.681 33.333 0.00 0.00 0.00 3.58
2331 2395 8.662781 TTGTAATCTCATTTGTATCAGCTACC 57.337 34.615 0.00 0.00 0.00 3.18
2332 2396 6.923508 TGTAATCTCATTTGTATCAGCTACCG 59.076 38.462 0.00 0.00 0.00 4.02
2333 2397 5.537300 ATCTCATTTGTATCAGCTACCGT 57.463 39.130 0.00 0.00 0.00 4.83
2334 2398 5.339008 TCTCATTTGTATCAGCTACCGTT 57.661 39.130 0.00 0.00 0.00 4.44
2335 2399 5.730550 TCTCATTTGTATCAGCTACCGTTT 58.269 37.500 0.00 0.00 0.00 3.60
2336 2400 6.869695 TCTCATTTGTATCAGCTACCGTTTA 58.130 36.000 0.00 0.00 0.00 2.01
2337 2401 7.497595 TCTCATTTGTATCAGCTACCGTTTAT 58.502 34.615 0.00 0.00 0.00 1.40
2338 2402 7.652105 TCTCATTTGTATCAGCTACCGTTTATC 59.348 37.037 0.00 0.00 0.00 1.75
2339 2403 6.704493 TCATTTGTATCAGCTACCGTTTATCC 59.296 38.462 0.00 0.00 0.00 2.59
2340 2404 5.864418 TTGTATCAGCTACCGTTTATCCT 57.136 39.130 0.00 0.00 0.00 3.24
2341 2405 5.196341 TGTATCAGCTACCGTTTATCCTG 57.804 43.478 0.00 0.00 0.00 3.86
2342 2406 4.647853 TGTATCAGCTACCGTTTATCCTGT 59.352 41.667 0.00 0.00 0.00 4.00
2343 2407 3.795623 TCAGCTACCGTTTATCCTGTC 57.204 47.619 0.00 0.00 0.00 3.51
2344 2408 3.362706 TCAGCTACCGTTTATCCTGTCT 58.637 45.455 0.00 0.00 0.00 3.41
2345 2409 3.767673 TCAGCTACCGTTTATCCTGTCTT 59.232 43.478 0.00 0.00 0.00 3.01
2346 2410 4.222145 TCAGCTACCGTTTATCCTGTCTTT 59.778 41.667 0.00 0.00 0.00 2.52
2380 2444 9.566432 ACAGATATTAGTGAATTCCCTTTCATC 57.434 33.333 2.27 0.98 37.88 2.92
2388 2452 8.940397 AGTGAATTCCCTTTCATCTAAAAGAA 57.060 30.769 2.27 0.00 38.30 2.52
2405 2469 9.601217 TCTAAAAGAAAGGTATAGCTTCATGAC 57.399 33.333 17.11 7.42 0.00 3.06
2417 2481 7.902387 ATAGCTTCATGACATATGCACTAAG 57.098 36.000 1.58 9.76 0.00 2.18
2418 2482 5.678583 AGCTTCATGACATATGCACTAAGT 58.321 37.500 1.58 0.00 0.00 2.24
2419 2483 6.118170 AGCTTCATGACATATGCACTAAGTT 58.882 36.000 1.58 5.15 0.00 2.66
2420 2484 7.275183 AGCTTCATGACATATGCACTAAGTTA 58.725 34.615 1.58 0.00 0.00 2.24
2421 2485 7.440556 AGCTTCATGACATATGCACTAAGTTAG 59.559 37.037 8.41 8.41 0.00 2.34
2422 2486 7.482654 TTCATGACATATGCACTAAGTTAGC 57.517 36.000 9.92 0.00 0.00 3.09
2423 2487 5.991606 TCATGACATATGCACTAAGTTAGCC 59.008 40.000 9.92 2.36 0.00 3.93
2424 2488 5.351948 TGACATATGCACTAAGTTAGCCA 57.648 39.130 9.92 7.90 0.00 4.75
2425 2489 5.739959 TGACATATGCACTAAGTTAGCCAA 58.260 37.500 9.92 0.00 0.00 4.52
2426 2490 6.356556 TGACATATGCACTAAGTTAGCCAAT 58.643 36.000 9.92 3.86 0.00 3.16
2427 2491 7.505258 TGACATATGCACTAAGTTAGCCAATA 58.495 34.615 9.92 5.81 0.00 1.90
2428 2492 7.657354 TGACATATGCACTAAGTTAGCCAATAG 59.343 37.037 9.92 4.79 0.00 1.73
2429 2493 7.509546 ACATATGCACTAAGTTAGCCAATAGT 58.490 34.615 9.92 5.30 0.00 2.12
2430 2494 8.647796 ACATATGCACTAAGTTAGCCAATAGTA 58.352 33.333 9.92 0.00 0.00 1.82
2431 2495 9.658799 CATATGCACTAAGTTAGCCAATAGTAT 57.341 33.333 9.92 0.98 0.00 2.12
2432 2496 7.969536 ATGCACTAAGTTAGCCAATAGTATG 57.030 36.000 9.92 0.00 0.00 2.39
2433 2497 5.758296 TGCACTAAGTTAGCCAATAGTATGC 59.242 40.000 9.92 9.13 0.00 3.14
2434 2498 5.179555 GCACTAAGTTAGCCAATAGTATGCC 59.820 44.000 9.92 0.00 0.00 4.40
2435 2499 5.701290 CACTAAGTTAGCCAATAGTATGCCC 59.299 44.000 9.92 0.00 0.00 5.36
2436 2500 4.788925 AAGTTAGCCAATAGTATGCCCA 57.211 40.909 0.00 0.00 0.00 5.36
2437 2501 4.788925 AGTTAGCCAATAGTATGCCCAA 57.211 40.909 0.00 0.00 0.00 4.12
2438 2502 5.324832 AGTTAGCCAATAGTATGCCCAAT 57.675 39.130 0.00 0.00 0.00 3.16
2439 2503 6.448369 AGTTAGCCAATAGTATGCCCAATA 57.552 37.500 0.00 0.00 0.00 1.90
2440 2504 6.848069 AGTTAGCCAATAGTATGCCCAATAA 58.152 36.000 0.00 0.00 0.00 1.40
2450 2514 5.061179 AGTATGCCCAATAATAACACGACC 58.939 41.667 0.00 0.00 0.00 4.79
2451 2515 3.351794 TGCCCAATAATAACACGACCA 57.648 42.857 0.00 0.00 0.00 4.02
2452 2516 3.687125 TGCCCAATAATAACACGACCAA 58.313 40.909 0.00 0.00 0.00 3.67
2453 2517 3.692101 TGCCCAATAATAACACGACCAAG 59.308 43.478 0.00 0.00 0.00 3.61
2454 2518 3.066203 GCCCAATAATAACACGACCAAGG 59.934 47.826 0.00 0.00 0.00 3.61
2459 2523 7.363443 CCCAATAATAACACGACCAAGGAAATT 60.363 37.037 0.00 0.00 0.00 1.82
2464 2528 4.823790 ACACGACCAAGGAAATTTGTAC 57.176 40.909 0.00 0.00 0.00 2.90
2483 2548 7.562454 TTGTACTTTGTTCCCAGAGTTTAAG 57.438 36.000 0.00 0.00 37.27 1.85
2484 2549 6.059484 TGTACTTTGTTCCCAGAGTTTAAGG 58.941 40.000 0.00 0.00 37.27 2.69
2500 2565 9.225682 AGAGTTTAAGGGGTCATTATATGAAGA 57.774 33.333 0.00 0.00 41.69 2.87
2532 2597 7.116075 TGTATAAACAAAGGGCAGATACATGT 58.884 34.615 2.69 2.69 30.91 3.21
2534 2599 4.789012 AACAAAGGGCAGATACATGTTG 57.211 40.909 2.30 0.00 0.00 3.33
2536 2601 4.012374 ACAAAGGGCAGATACATGTTGAG 58.988 43.478 2.30 0.00 0.00 3.02
2541 2606 4.410228 AGGGCAGATACATGTTGAGTATGT 59.590 41.667 2.30 0.00 41.36 2.29
2542 2607 5.602561 AGGGCAGATACATGTTGAGTATGTA 59.397 40.000 2.30 0.00 43.05 2.29
2577 2642 9.765795 TTCTGTTCTACTAGAAGAAGAAAAAGG 57.234 33.333 15.50 0.00 36.22 3.11
2578 2643 8.925338 TCTGTTCTACTAGAAGAAGAAAAAGGT 58.075 33.333 0.00 0.00 36.19 3.50
2580 2645 9.978044 TGTTCTACTAGAAGAAGAAAAAGGTAC 57.022 33.333 0.00 0.00 36.19 3.34
2583 2648 9.364653 TCTACTAGAAGAAGAAAAAGGTACTGT 57.635 33.333 0.00 0.00 40.86 3.55
2595 2660 9.557061 AGAAAAAGGTACTGTAACTCTTTTAGG 57.443 33.333 17.59 0.00 40.86 2.69
2612 2677 6.676632 TCTTTTAGGTGGAGAAAGGATATCCA 59.323 38.462 23.81 0.00 40.80 3.41
2615 2680 3.713764 AGGTGGAGAAAGGATATCCAGTG 59.286 47.826 23.81 0.00 43.61 3.66
2622 2687 2.485966 AGGATATCCAGTGCTCACCT 57.514 50.000 23.81 0.00 38.89 4.00
2623 2688 2.324541 AGGATATCCAGTGCTCACCTC 58.675 52.381 23.81 0.00 38.89 3.85
2624 2689 1.346068 GGATATCCAGTGCTCACCTCC 59.654 57.143 17.34 0.00 35.64 4.30
2625 2690 2.042464 GATATCCAGTGCTCACCTCCA 58.958 52.381 0.00 0.00 0.00 3.86
2626 2691 1.489481 TATCCAGTGCTCACCTCCAG 58.511 55.000 0.00 0.00 0.00 3.86
2627 2692 1.270414 ATCCAGTGCTCACCTCCAGG 61.270 60.000 0.00 0.00 42.17 4.45
2628 2693 2.667418 CAGTGCTCACCTCCAGGG 59.333 66.667 0.00 0.00 40.27 4.45
2629 2694 2.608988 AGTGCTCACCTCCAGGGG 60.609 66.667 0.00 0.00 40.94 4.79
2644 2712 4.475527 GGGGGTCATTACATCGCC 57.524 61.111 0.00 0.00 0.00 5.54
2654 2722 1.368641 TTACATCGCCATGTCACAGC 58.631 50.000 0.00 0.00 42.66 4.40
2672 2740 5.011635 TCACAGCCAATACTTGTCTTCAGTA 59.988 40.000 0.00 0.00 0.00 2.74
2673 2741 5.120830 CACAGCCAATACTTGTCTTCAGTAC 59.879 44.000 0.00 0.00 0.00 2.73
2680 2748 7.760340 CCAATACTTGTCTTCAGTACCTTCTAC 59.240 40.741 0.00 0.00 0.00 2.59
2681 2749 8.304596 CAATACTTGTCTTCAGTACCTTCTACA 58.695 37.037 0.00 0.00 0.00 2.74
2686 2757 5.185249 TGTCTTCAGTACCTTCTACATGTCC 59.815 44.000 0.00 0.00 0.00 4.02
2689 2760 7.122353 GTCTTCAGTACCTTCTACATGTCCTTA 59.878 40.741 0.00 0.00 0.00 2.69
2690 2761 6.770746 TCAGTACCTTCTACATGTCCTTAC 57.229 41.667 0.00 0.00 0.00 2.34
2701 2772 5.528043 ACATGTCCTTACAAAATGCAACA 57.472 34.783 0.00 0.00 39.58 3.33
2702 2773 5.288804 ACATGTCCTTACAAAATGCAACAC 58.711 37.500 0.00 0.00 39.58 3.32
2704 2775 4.930963 TGTCCTTACAAAATGCAACACTG 58.069 39.130 0.00 0.00 30.91 3.66
2705 2776 4.400884 TGTCCTTACAAAATGCAACACTGT 59.599 37.500 0.00 0.00 30.91 3.55
2706 2777 5.105554 TGTCCTTACAAAATGCAACACTGTT 60.106 36.000 0.00 0.00 30.91 3.16
2707 2778 5.810074 GTCCTTACAAAATGCAACACTGTTT 59.190 36.000 0.00 0.00 0.00 2.83
2708 2779 6.312672 GTCCTTACAAAATGCAACACTGTTTT 59.687 34.615 0.00 0.00 0.00 2.43
2709 2780 6.533367 TCCTTACAAAATGCAACACTGTTTTC 59.467 34.615 0.00 0.00 0.00 2.29
2710 2781 6.534793 CCTTACAAAATGCAACACTGTTTTCT 59.465 34.615 0.00 0.00 0.00 2.52
2721 2792 4.747810 ACACTGTTTTCTCCTGCTTTTTG 58.252 39.130 0.00 0.00 0.00 2.44
2723 2794 4.023291 ACTGTTTTCTCCTGCTTTTTGGA 58.977 39.130 0.00 0.00 0.00 3.53
2726 2797 5.175127 TGTTTTCTCCTGCTTTTTGGAAAC 58.825 37.500 0.00 0.00 31.23 2.78
2727 2798 5.175127 GTTTTCTCCTGCTTTTTGGAAACA 58.825 37.500 0.00 0.00 39.83 2.83
2731 2802 4.097892 TCTCCTGCTTTTTGGAAACAGAAC 59.902 41.667 0.00 0.00 44.54 3.01
2733 2804 4.405358 TCCTGCTTTTTGGAAACAGAACAT 59.595 37.500 0.00 0.00 44.54 2.71
2737 2808 6.738114 TGCTTTTTGGAAACAGAACATAGAG 58.262 36.000 0.00 0.00 44.54 2.43
2739 2810 5.705609 TTTTGGAAACAGAACATAGAGGC 57.294 39.130 0.00 0.00 44.54 4.70
2749 2820 3.514309 AGAACATAGAGGCGGTGTTAAGT 59.486 43.478 0.00 0.00 36.30 2.24
2750 2821 3.247006 ACATAGAGGCGGTGTTAAGTG 57.753 47.619 0.00 0.00 0.00 3.16
2752 2823 1.927487 TAGAGGCGGTGTTAAGTGGA 58.073 50.000 0.00 0.00 0.00 4.02
2755 2826 0.690762 AGGCGGTGTTAAGTGGACAT 59.309 50.000 0.00 0.00 0.00 3.06
2756 2827 1.084289 GGCGGTGTTAAGTGGACATC 58.916 55.000 0.00 0.00 0.00 3.06
2760 2831 3.587797 GGTGTTAAGTGGACATCGAGA 57.412 47.619 0.00 0.00 0.00 4.04
2772 2843 4.992319 TGGACATCGAGAAAATAACAACGT 59.008 37.500 0.00 0.00 0.00 3.99
2774 2845 5.277601 ACATCGAGAAAATAACAACGTGG 57.722 39.130 0.00 0.00 0.00 4.94
2777 2848 5.333046 TCGAGAAAATAACAACGTGGTTC 57.667 39.130 12.63 0.00 32.29 3.62
2785 2856 8.710835 AAAATAACAACGTGGTTCAGAAAAAT 57.289 26.923 12.63 0.00 32.29 1.82
2786 2857 8.710835 AAATAACAACGTGGTTCAGAAAAATT 57.289 26.923 12.63 1.68 32.29 1.82
2797 2868 8.968242 GTGGTTCAGAAAAATTAAGTGAACATC 58.032 33.333 17.66 10.26 45.77 3.06
2827 2898 9.944376 AAATAAAAATACTGCTACTGAGAGACA 57.056 29.630 0.00 0.00 0.00 3.41
2829 2900 9.757227 ATAAAAATACTGCTACTGAGAGACATC 57.243 33.333 0.00 0.00 0.00 3.06
2830 2901 6.782082 AAATACTGCTACTGAGAGACATCA 57.218 37.500 0.00 0.00 0.00 3.07
2831 2902 6.782082 AATACTGCTACTGAGAGACATCAA 57.218 37.500 0.00 0.00 0.00 2.57
2832 2903 4.717233 ACTGCTACTGAGAGACATCAAG 57.283 45.455 0.00 0.00 0.00 3.02
2833 2904 4.085733 ACTGCTACTGAGAGACATCAAGT 58.914 43.478 0.00 0.00 0.00 3.16
2834 2905 5.257262 ACTGCTACTGAGAGACATCAAGTA 58.743 41.667 0.00 0.00 0.00 2.24
2835 2906 5.712446 ACTGCTACTGAGAGACATCAAGTAA 59.288 40.000 0.00 0.00 30.74 2.24
2836 2907 6.379703 ACTGCTACTGAGAGACATCAAGTAAT 59.620 38.462 0.00 0.00 30.74 1.89
2837 2908 7.558081 ACTGCTACTGAGAGACATCAAGTAATA 59.442 37.037 0.00 0.00 30.74 0.98
2838 2909 8.470657 TGCTACTGAGAGACATCAAGTAATAT 57.529 34.615 0.00 0.00 30.74 1.28
2839 2910 8.355913 TGCTACTGAGAGACATCAAGTAATATG 58.644 37.037 0.00 0.00 30.74 1.78
2840 2911 8.572185 GCTACTGAGAGACATCAAGTAATATGA 58.428 37.037 0.00 0.00 30.74 2.15
2867 2938 8.818141 ATGTACACATCCTAAAATGTAGATCG 57.182 34.615 0.00 0.00 37.78 3.69
2868 2939 6.700081 TGTACACATCCTAAAATGTAGATCGC 59.300 38.462 0.00 0.00 37.78 4.58
2869 2940 5.057149 ACACATCCTAAAATGTAGATCGCC 58.943 41.667 0.00 0.00 37.78 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.236006 GCCAAGGATGATATGTTAAAGATGTAT 57.764 33.333 0.00 0.00 0.00 2.29
4 5 8.217111 TGCCAAGGATGATATGTTAAAGATGTA 58.783 33.333 0.00 0.00 0.00 2.29
39 40 7.434897 CCAAGAAAGAAATTGTTCGACAAATGA 59.565 33.333 4.87 0.00 41.96 2.57
40 41 7.222611 ACCAAGAAAGAAATTGTTCGACAAATG 59.777 33.333 4.87 0.00 41.96 2.32
96 97 7.439356 TGTGATAAGTATAGACATGCAAGCTTC 59.561 37.037 0.00 0.00 0.00 3.86
167 168 4.380531 CAACCTGAGTTCTGTCAAGCTTA 58.619 43.478 0.00 0.00 32.45 3.09
219 220 4.492570 CCTCGCATTTTGTTGATAGACGAC 60.493 45.833 0.00 0.00 0.00 4.34
304 305 2.042979 ACTGTTCAAGGCCACCCATTAT 59.957 45.455 5.01 0.00 0.00 1.28
355 356 6.489603 TGTTTTCCAAGCTTTCTGGGATATA 58.510 36.000 0.00 0.00 41.99 0.86
454 455 5.522460 CACCAAATGAAAATCCAGATGCATC 59.478 40.000 19.37 19.37 0.00 3.91
544 548 1.200020 GCGTTTGCTAAAGCCATGTCT 59.800 47.619 7.51 0.00 41.18 3.41
694 701 4.532126 TGTAACTCTGGGATGACTGTCATT 59.468 41.667 23.03 9.11 37.20 2.57
759 766 4.998051 ACCTTCCTCTTCCAAGCAAATTA 58.002 39.130 0.00 0.00 0.00 1.40
771 778 2.700897 CACCGATCCATACCTTCCTCTT 59.299 50.000 0.00 0.00 0.00 2.85
799 806 3.715628 ACTTGTGAGATGCAAACAACC 57.284 42.857 0.00 0.00 30.93 3.77
809 816 5.188555 ACTGTGGTCATCATACTTGTGAGAT 59.811 40.000 0.00 0.00 0.00 2.75
810 817 4.528206 ACTGTGGTCATCATACTTGTGAGA 59.472 41.667 0.00 0.00 0.00 3.27
815 822 4.807834 CAGCTACTGTGGTCATCATACTTG 59.192 45.833 0.00 0.00 0.00 3.16
818 825 4.392921 ACAGCTACTGTGGTCATCATAC 57.607 45.455 0.00 0.00 43.63 2.39
859 866 7.736893 AGAAAACTTTTGGAAGAGCTAGACTA 58.263 34.615 0.00 0.00 36.69 2.59
865 872 5.240403 CAGCTAGAAAACTTTTGGAAGAGCT 59.760 40.000 0.00 0.00 36.55 4.09
929 944 6.615839 GCTTGAACAACACGTTATGAGACTAC 60.616 42.308 4.45 0.00 38.19 2.73
958 973 7.545615 GTCTTTGAAGTCATTTTGGTTCAAGTT 59.454 33.333 0.00 0.00 39.43 2.66
983 998 2.226437 GGCATGAACTCGAACACAATGT 59.774 45.455 0.00 0.00 0.00 2.71
1128 1146 7.285629 TGAATTATTGGTGGTTCACAGTTGTTA 59.714 33.333 0.38 0.00 35.86 2.41
1179 1197 5.884792 AGCAACTAAATCCTCATTGAGAAGG 59.115 40.000 15.36 0.00 0.00 3.46
1233 1253 3.859443 CTCAGTTGATGGTTCAGAGAGG 58.141 50.000 0.00 0.00 32.27 3.69
1246 1266 5.065235 TGAATTGATCAGTTGCTCAGTTGA 58.935 37.500 8.35 0.00 33.04 3.18
1249 1269 5.766670 TCTTTGAATTGATCAGTTGCTCAGT 59.233 36.000 8.35 0.00 39.77 3.41
1406 1439 9.862371 CTTCGCCATATTCTAAAGTACATAGAT 57.138 33.333 8.66 3.89 29.93 1.98
1407 1440 8.304596 CCTTCGCCATATTCTAAAGTACATAGA 58.695 37.037 0.00 0.00 0.00 1.98
1408 1441 8.088981 ACCTTCGCCATATTCTAAAGTACATAG 58.911 37.037 0.00 0.00 0.00 2.23
1409 1442 7.870954 CACCTTCGCCATATTCTAAAGTACATA 59.129 37.037 0.00 0.00 0.00 2.29
1410 1443 6.706270 CACCTTCGCCATATTCTAAAGTACAT 59.294 38.462 0.00 0.00 0.00 2.29
1411 1444 6.046593 CACCTTCGCCATATTCTAAAGTACA 58.953 40.000 0.00 0.00 0.00 2.90
1412 1445 5.465724 CCACCTTCGCCATATTCTAAAGTAC 59.534 44.000 0.00 0.00 0.00 2.73
1413 1446 5.454187 CCCACCTTCGCCATATTCTAAAGTA 60.454 44.000 0.00 0.00 0.00 2.24
1414 1447 4.451900 CCACCTTCGCCATATTCTAAAGT 58.548 43.478 0.00 0.00 0.00 2.66
1415 1448 3.815401 CCCACCTTCGCCATATTCTAAAG 59.185 47.826 0.00 0.00 0.00 1.85
1416 1449 3.815809 CCCACCTTCGCCATATTCTAAA 58.184 45.455 0.00 0.00 0.00 1.85
1417 1450 2.486548 GCCCACCTTCGCCATATTCTAA 60.487 50.000 0.00 0.00 0.00 2.10
1437 1470 4.217118 ACATCTCCACATGAAGAAACTTGC 59.783 41.667 0.00 0.00 0.00 4.01
1500 1533 3.054139 ACATGTCATGAGTAGGTGCCATT 60.054 43.478 19.77 0.00 0.00 3.16
1599 1632 2.563179 GGCTTCTTCAGTGGACAGTAGA 59.437 50.000 0.00 0.00 0.00 2.59
1647 1680 4.276642 TGCTGCCATGTTCCATTATGTTA 58.723 39.130 0.00 0.00 0.00 2.41
1652 1685 5.739647 GCATTATTGCTGCCATGTTCCATTA 60.740 40.000 0.00 0.00 45.77 1.90
1667 1700 7.027760 CATGACAGAGAATATGGCATTATTGC 58.972 38.462 4.78 0.83 44.09 3.56
1668 1701 8.331730 TCATGACAGAGAATATGGCATTATTG 57.668 34.615 4.78 0.00 44.09 1.90
1669 1702 8.929260 TTCATGACAGAGAATATGGCATTATT 57.071 30.769 4.78 3.63 44.09 1.40
1670 1703 8.380867 TCTTCATGACAGAGAATATGGCATTAT 58.619 33.333 4.78 0.00 44.09 1.28
1671 1704 7.738847 TCTTCATGACAGAGAATATGGCATTA 58.261 34.615 4.78 0.00 44.09 1.90
1672 1705 6.598503 TCTTCATGACAGAGAATATGGCATT 58.401 36.000 4.78 0.00 44.09 3.56
1760 1802 3.181440 GCCATCCCTTATCCTGTGAATCA 60.181 47.826 0.00 0.00 0.00 2.57
1854 1910 2.386935 ACATTAGGGGGCTGGCCTC 61.387 63.158 20.47 17.10 36.10 4.70
1930 1991 7.312899 CCAGAAACTAACATATCAAAACCACC 58.687 38.462 0.00 0.00 0.00 4.61
1959 2023 4.973168 TCAACAAGCTAAGAGAACATGGT 58.027 39.130 0.00 0.00 0.00 3.55
2283 2347 4.080863 AGTTCACAATGTAGACATCTCCCC 60.081 45.833 0.00 0.00 35.10 4.81
2284 2348 5.091261 AGTTCACAATGTAGACATCTCCC 57.909 43.478 0.00 0.00 35.10 4.30
2285 2349 5.934625 ACAAGTTCACAATGTAGACATCTCC 59.065 40.000 0.00 0.00 35.10 3.71
2286 2350 8.534333 TTACAAGTTCACAATGTAGACATCTC 57.466 34.615 0.00 0.00 35.10 2.75
2287 2351 9.155975 GATTACAAGTTCACAATGTAGACATCT 57.844 33.333 0.00 0.00 35.10 2.90
2288 2352 9.155975 AGATTACAAGTTCACAATGTAGACATC 57.844 33.333 0.00 0.00 35.10 3.06
2289 2353 9.155975 GAGATTACAAGTTCACAATGTAGACAT 57.844 33.333 0.00 0.00 38.41 3.06
2290 2354 8.147704 TGAGATTACAAGTTCACAATGTAGACA 58.852 33.333 0.00 0.00 31.72 3.41
2291 2355 8.534333 TGAGATTACAAGTTCACAATGTAGAC 57.466 34.615 0.00 0.00 31.72 2.59
2292 2356 9.725019 AATGAGATTACAAGTTCACAATGTAGA 57.275 29.630 0.00 0.00 31.72 2.59
2295 2359 8.632679 ACAAATGAGATTACAAGTTCACAATGT 58.367 29.630 0.00 0.00 0.00 2.71
2299 2363 9.500785 TGATACAAATGAGATTACAAGTTCACA 57.499 29.630 0.00 0.00 0.00 3.58
2300 2364 9.979270 CTGATACAAATGAGATTACAAGTTCAC 57.021 33.333 0.00 0.00 0.00 3.18
2301 2365 8.668353 GCTGATACAAATGAGATTACAAGTTCA 58.332 33.333 0.00 0.00 0.00 3.18
2302 2366 8.887717 AGCTGATACAAATGAGATTACAAGTTC 58.112 33.333 0.00 0.00 0.00 3.01
2303 2367 8.798859 AGCTGATACAAATGAGATTACAAGTT 57.201 30.769 0.00 0.00 0.00 2.66
2304 2368 9.319143 GTAGCTGATACAAATGAGATTACAAGT 57.681 33.333 0.00 0.00 34.26 3.16
2305 2369 8.768955 GGTAGCTGATACAAATGAGATTACAAG 58.231 37.037 5.36 0.00 35.96 3.16
2306 2370 7.438160 CGGTAGCTGATACAAATGAGATTACAA 59.562 37.037 5.36 0.00 35.96 2.41
2307 2371 6.923508 CGGTAGCTGATACAAATGAGATTACA 59.076 38.462 5.36 0.00 35.96 2.41
2308 2372 6.924060 ACGGTAGCTGATACAAATGAGATTAC 59.076 38.462 5.36 0.00 35.96 1.89
2309 2373 7.050970 ACGGTAGCTGATACAAATGAGATTA 57.949 36.000 5.36 0.00 35.96 1.75
2310 2374 5.918608 ACGGTAGCTGATACAAATGAGATT 58.081 37.500 5.36 0.00 35.96 2.40
2311 2375 5.537300 ACGGTAGCTGATACAAATGAGAT 57.463 39.130 5.36 0.00 35.96 2.75
2312 2376 5.339008 AACGGTAGCTGATACAAATGAGA 57.661 39.130 5.36 0.00 35.96 3.27
2313 2377 7.095607 GGATAAACGGTAGCTGATACAAATGAG 60.096 40.741 5.36 0.00 35.96 2.90
2314 2378 6.704493 GGATAAACGGTAGCTGATACAAATGA 59.296 38.462 5.36 0.00 35.96 2.57
2315 2379 6.706270 AGGATAAACGGTAGCTGATACAAATG 59.294 38.462 5.36 0.00 35.96 2.32
2316 2380 6.706270 CAGGATAAACGGTAGCTGATACAAAT 59.294 38.462 5.36 0.00 35.96 2.32
2317 2381 6.046593 CAGGATAAACGGTAGCTGATACAAA 58.953 40.000 5.36 0.00 35.96 2.83
2318 2382 5.128171 ACAGGATAAACGGTAGCTGATACAA 59.872 40.000 5.36 0.00 35.96 2.41
2319 2383 4.647853 ACAGGATAAACGGTAGCTGATACA 59.352 41.667 5.36 0.00 35.96 2.29
2320 2384 5.009811 AGACAGGATAAACGGTAGCTGATAC 59.990 44.000 0.00 0.00 0.00 2.24
2321 2385 5.138276 AGACAGGATAAACGGTAGCTGATA 58.862 41.667 0.00 0.00 0.00 2.15
2322 2386 3.961408 AGACAGGATAAACGGTAGCTGAT 59.039 43.478 0.00 0.00 0.00 2.90
2323 2387 3.362706 AGACAGGATAAACGGTAGCTGA 58.637 45.455 0.00 0.00 0.00 4.26
2324 2388 3.802948 AGACAGGATAAACGGTAGCTG 57.197 47.619 0.00 0.00 0.00 4.24
2325 2389 4.382793 GGAAAGACAGGATAAACGGTAGCT 60.383 45.833 0.00 0.00 0.00 3.32
2326 2390 3.869832 GGAAAGACAGGATAAACGGTAGC 59.130 47.826 0.00 0.00 0.00 3.58
2327 2391 5.340439 AGGAAAGACAGGATAAACGGTAG 57.660 43.478 0.00 0.00 0.00 3.18
2328 2392 6.855763 TTAGGAAAGACAGGATAAACGGTA 57.144 37.500 0.00 0.00 0.00 4.02
2329 2393 5.750352 TTAGGAAAGACAGGATAAACGGT 57.250 39.130 0.00 0.00 0.00 4.83
2330 2394 7.767198 TGTATTTAGGAAAGACAGGATAAACGG 59.233 37.037 0.00 0.00 37.65 4.44
2331 2395 8.712285 TGTATTTAGGAAAGACAGGATAAACG 57.288 34.615 0.00 0.00 37.65 3.60
2380 2444 9.383519 TGTCATGAAGCTATACCTTTCTTTTAG 57.616 33.333 0.00 0.00 0.00 1.85
2388 2452 6.652481 GTGCATATGTCATGAAGCTATACCTT 59.348 38.462 4.29 0.00 0.00 3.50
2396 2460 5.998454 ACTTAGTGCATATGTCATGAAGC 57.002 39.130 4.29 0.00 0.00 3.86
2399 2463 5.991606 GGCTAACTTAGTGCATATGTCATGA 59.008 40.000 4.29 0.00 0.00 3.07
2405 2469 7.969536 ACTATTGGCTAACTTAGTGCATATG 57.030 36.000 0.00 0.00 0.00 1.78
2417 2481 7.703058 ATTATTGGGCATACTATTGGCTAAC 57.297 36.000 0.00 0.00 43.53 2.34
2418 2482 9.238368 GTTATTATTGGGCATACTATTGGCTAA 57.762 33.333 0.00 0.00 44.52 3.09
2419 2483 8.387039 TGTTATTATTGGGCATACTATTGGCTA 58.613 33.333 0.00 0.00 41.61 3.93
2420 2484 7.176690 GTGTTATTATTGGGCATACTATTGGCT 59.823 37.037 0.00 0.00 41.61 4.75
2421 2485 7.312899 GTGTTATTATTGGGCATACTATTGGC 58.687 38.462 0.00 0.00 41.20 4.52
2422 2486 7.389330 TCGTGTTATTATTGGGCATACTATTGG 59.611 37.037 0.00 0.00 0.00 3.16
2423 2487 8.227791 GTCGTGTTATTATTGGGCATACTATTG 58.772 37.037 0.00 0.00 0.00 1.90
2424 2488 7.389607 GGTCGTGTTATTATTGGGCATACTATT 59.610 37.037 0.00 0.00 0.00 1.73
2425 2489 6.877322 GGTCGTGTTATTATTGGGCATACTAT 59.123 38.462 0.00 0.00 0.00 2.12
2426 2490 6.183360 TGGTCGTGTTATTATTGGGCATACTA 60.183 38.462 0.00 0.00 0.00 1.82
2427 2491 5.061179 GGTCGTGTTATTATTGGGCATACT 58.939 41.667 0.00 0.00 0.00 2.12
2428 2492 4.817464 TGGTCGTGTTATTATTGGGCATAC 59.183 41.667 0.00 0.00 0.00 2.39
2429 2493 5.037383 TGGTCGTGTTATTATTGGGCATA 57.963 39.130 0.00 0.00 0.00 3.14
2430 2494 3.892284 TGGTCGTGTTATTATTGGGCAT 58.108 40.909 0.00 0.00 0.00 4.40
2431 2495 3.351794 TGGTCGTGTTATTATTGGGCA 57.648 42.857 0.00 0.00 0.00 5.36
2432 2496 3.066203 CCTTGGTCGTGTTATTATTGGGC 59.934 47.826 0.00 0.00 0.00 5.36
2433 2497 4.519213 TCCTTGGTCGTGTTATTATTGGG 58.481 43.478 0.00 0.00 0.00 4.12
2434 2498 6.503589 TTTCCTTGGTCGTGTTATTATTGG 57.496 37.500 0.00 0.00 0.00 3.16
2435 2499 8.859156 CAAATTTCCTTGGTCGTGTTATTATTG 58.141 33.333 0.00 0.00 0.00 1.90
2436 2500 8.581578 ACAAATTTCCTTGGTCGTGTTATTATT 58.418 29.630 0.00 0.00 0.00 1.40
2437 2501 8.117813 ACAAATTTCCTTGGTCGTGTTATTAT 57.882 30.769 0.00 0.00 0.00 1.28
2438 2502 7.513371 ACAAATTTCCTTGGTCGTGTTATTA 57.487 32.000 0.00 0.00 0.00 0.98
2439 2503 6.399639 ACAAATTTCCTTGGTCGTGTTATT 57.600 33.333 0.00 0.00 0.00 1.40
2440 2504 6.713450 AGTACAAATTTCCTTGGTCGTGTTAT 59.287 34.615 0.00 0.00 0.00 1.89
2450 2514 6.578023 TGGGAACAAAGTACAAATTTCCTTG 58.422 36.000 13.11 0.00 37.44 3.61
2451 2515 6.609616 TCTGGGAACAAAGTACAAATTTCCTT 59.390 34.615 13.11 0.00 42.06 3.36
2452 2516 6.133356 TCTGGGAACAAAGTACAAATTTCCT 58.867 36.000 13.11 0.00 42.06 3.36
2453 2517 6.040504 ACTCTGGGAACAAAGTACAAATTTCC 59.959 38.462 0.00 1.84 40.68 3.13
2454 2518 7.039313 ACTCTGGGAACAAAGTACAAATTTC 57.961 36.000 0.00 0.00 40.68 2.17
2459 2523 6.544564 CCTTAAACTCTGGGAACAAAGTACAA 59.455 38.462 0.00 0.00 41.95 2.41
2464 2528 3.826729 CCCCTTAAACTCTGGGAACAAAG 59.173 47.826 0.00 0.00 43.47 2.77
2483 2548 9.965902 ACAAATCTATCTTCATATAATGACCCC 57.034 33.333 0.00 0.00 39.39 4.95
2515 2580 4.012374 ACTCAACATGTATCTGCCCTTTG 58.988 43.478 0.00 0.00 0.00 2.77
2561 2626 9.984190 AGTTACAGTACCTTTTTCTTCTTCTAG 57.016 33.333 0.00 0.00 0.00 2.43
2569 2634 9.557061 CCTAAAAGAGTTACAGTACCTTTTTCT 57.443 33.333 14.70 2.70 37.90 2.52
2570 2635 9.334947 ACCTAAAAGAGTTACAGTACCTTTTTC 57.665 33.333 14.70 0.00 37.90 2.29
2576 2641 6.210185 TCTCCACCTAAAAGAGTTACAGTACC 59.790 42.308 0.00 0.00 0.00 3.34
2577 2642 7.224522 TCTCCACCTAAAAGAGTTACAGTAC 57.775 40.000 0.00 0.00 0.00 2.73
2578 2643 7.844493 TTCTCCACCTAAAAGAGTTACAGTA 57.156 36.000 0.00 0.00 0.00 2.74
2579 2644 6.742559 TTCTCCACCTAAAAGAGTTACAGT 57.257 37.500 0.00 0.00 0.00 3.55
2580 2645 6.651225 CCTTTCTCCACCTAAAAGAGTTACAG 59.349 42.308 0.00 0.00 32.89 2.74
2581 2646 6.328148 TCCTTTCTCCACCTAAAAGAGTTACA 59.672 38.462 0.00 0.00 32.89 2.41
2582 2647 6.766429 TCCTTTCTCCACCTAAAAGAGTTAC 58.234 40.000 0.00 0.00 32.89 2.50
2583 2648 7.569599 ATCCTTTCTCCACCTAAAAGAGTTA 57.430 36.000 0.00 0.00 32.89 2.24
2595 2660 3.135530 AGCACTGGATATCCTTTCTCCAC 59.864 47.826 22.35 4.55 35.29 4.02
2612 2677 2.608988 CCCCTGGAGGTGAGCACT 60.609 66.667 0.00 0.00 0.00 4.40
2627 2692 0.110486 ATGGCGATGTAATGACCCCC 59.890 55.000 0.00 0.00 0.00 5.40
2628 2693 1.238439 CATGGCGATGTAATGACCCC 58.762 55.000 0.00 0.00 0.00 4.95
2629 2694 1.873591 GACATGGCGATGTAATGACCC 59.126 52.381 14.81 0.00 43.22 4.46
2641 2709 0.378257 GTATTGGCTGTGACATGGCG 59.622 55.000 0.00 0.00 0.00 5.69
2672 2740 6.151144 GCATTTTGTAAGGACATGTAGAAGGT 59.849 38.462 0.00 0.00 34.86 3.50
2673 2741 6.150976 TGCATTTTGTAAGGACATGTAGAAGG 59.849 38.462 0.00 0.00 34.86 3.46
2680 2748 5.403166 CAGTGTTGCATTTTGTAAGGACATG 59.597 40.000 0.00 0.00 34.86 3.21
2681 2749 5.068987 ACAGTGTTGCATTTTGTAAGGACAT 59.931 36.000 0.00 0.00 34.86 3.06
2686 2757 7.254084 GGAGAAAACAGTGTTGCATTTTGTAAG 60.254 37.037 9.79 0.00 0.00 2.34
2689 2760 4.869861 GGAGAAAACAGTGTTGCATTTTGT 59.130 37.500 9.79 0.00 0.00 2.83
2690 2761 5.005971 CAGGAGAAAACAGTGTTGCATTTTG 59.994 40.000 9.79 1.71 0.00 2.44
2701 2772 4.023291 TCCAAAAAGCAGGAGAAAACAGT 58.977 39.130 0.00 0.00 0.00 3.55
2702 2773 4.654091 TCCAAAAAGCAGGAGAAAACAG 57.346 40.909 0.00 0.00 0.00 3.16
2704 2775 5.175127 TGTTTCCAAAAAGCAGGAGAAAAC 58.825 37.500 0.00 0.00 34.91 2.43
2705 2776 5.186797 TCTGTTTCCAAAAAGCAGGAGAAAA 59.813 36.000 2.49 0.00 34.91 2.29
2706 2777 4.709397 TCTGTTTCCAAAAAGCAGGAGAAA 59.291 37.500 2.49 0.00 34.91 2.52
2707 2778 4.277476 TCTGTTTCCAAAAAGCAGGAGAA 58.723 39.130 2.49 0.00 34.91 2.87
2708 2779 3.897239 TCTGTTTCCAAAAAGCAGGAGA 58.103 40.909 2.49 0.00 34.91 3.71
2709 2780 4.142182 TGTTCTGTTTCCAAAAAGCAGGAG 60.142 41.667 2.49 0.00 34.91 3.69
2710 2781 3.766591 TGTTCTGTTTCCAAAAAGCAGGA 59.233 39.130 2.49 0.00 0.00 3.86
2721 2792 2.280628 CCGCCTCTATGTTCTGTTTCC 58.719 52.381 0.00 0.00 0.00 3.13
2723 2794 2.038557 ACACCGCCTCTATGTTCTGTTT 59.961 45.455 0.00 0.00 0.00 2.83
2726 2797 2.386661 AACACCGCCTCTATGTTCTG 57.613 50.000 0.00 0.00 30.82 3.02
2727 2798 3.514309 ACTTAACACCGCCTCTATGTTCT 59.486 43.478 0.00 0.00 37.68 3.01
2731 2802 2.167693 TCCACTTAACACCGCCTCTATG 59.832 50.000 0.00 0.00 0.00 2.23
2733 2804 1.547372 GTCCACTTAACACCGCCTCTA 59.453 52.381 0.00 0.00 0.00 2.43
2737 2808 1.084289 GATGTCCACTTAACACCGCC 58.916 55.000 0.00 0.00 0.00 6.13
2739 2810 2.094906 TCTCGATGTCCACTTAACACCG 60.095 50.000 0.00 0.00 34.89 4.94
2749 2820 4.992319 ACGTTGTTATTTTCTCGATGTCCA 59.008 37.500 0.00 0.00 0.00 4.02
2750 2821 5.313623 CACGTTGTTATTTTCTCGATGTCC 58.686 41.667 0.00 0.00 0.00 4.02
2752 2823 4.753107 ACCACGTTGTTATTTTCTCGATGT 59.247 37.500 0.00 0.00 0.00 3.06
2755 2826 4.809958 TGAACCACGTTGTTATTTTCTCGA 59.190 37.500 4.82 0.00 0.00 4.04
2756 2827 5.050634 TCTGAACCACGTTGTTATTTTCTCG 60.051 40.000 4.82 0.00 0.00 4.04
2760 2831 8.710835 ATTTTTCTGAACCACGTTGTTATTTT 57.289 26.923 4.82 0.00 0.00 1.82
2772 2843 8.690884 TGATGTTCACTTAATTTTTCTGAACCA 58.309 29.630 12.04 5.14 39.91 3.67
2801 2872 9.944376 TGTCTCTCAGTAGCAGTATTTTTATTT 57.056 29.630 0.00 0.00 0.00 1.40
2806 2877 7.175347 TGATGTCTCTCAGTAGCAGTATTTT 57.825 36.000 0.00 0.00 0.00 1.82
2807 2878 6.782082 TGATGTCTCTCAGTAGCAGTATTT 57.218 37.500 0.00 0.00 0.00 1.40
2808 2879 6.379703 ACTTGATGTCTCTCAGTAGCAGTATT 59.620 38.462 0.00 0.00 0.00 1.89
2809 2880 5.890985 ACTTGATGTCTCTCAGTAGCAGTAT 59.109 40.000 0.00 0.00 0.00 2.12
2810 2881 5.257262 ACTTGATGTCTCTCAGTAGCAGTA 58.743 41.667 0.00 0.00 0.00 2.74
2811 2882 4.085733 ACTTGATGTCTCTCAGTAGCAGT 58.914 43.478 0.00 0.00 0.00 4.40
2812 2883 4.717233 ACTTGATGTCTCTCAGTAGCAG 57.283 45.455 0.00 0.00 0.00 4.24
2813 2884 6.782082 ATTACTTGATGTCTCTCAGTAGCA 57.218 37.500 0.00 0.00 0.00 3.49
2814 2885 8.572185 TCATATTACTTGATGTCTCTCAGTAGC 58.428 37.037 0.00 0.00 0.00 3.58
2841 2912 9.908152 CGATCTACATTTTAGGATGTGTACATA 57.092 33.333 0.00 0.00 40.33 2.29
2842 2913 7.385205 GCGATCTACATTTTAGGATGTGTACAT 59.615 37.037 0.00 0.00 40.33 2.29
2843 2914 6.700081 GCGATCTACATTTTAGGATGTGTACA 59.300 38.462 0.00 0.00 40.33 2.90
2844 2915 6.145696 GGCGATCTACATTTTAGGATGTGTAC 59.854 42.308 1.03 0.00 40.33 2.90
2845 2916 6.220930 GGCGATCTACATTTTAGGATGTGTA 58.779 40.000 1.03 0.00 40.33 2.90
2846 2917 5.057149 GGCGATCTACATTTTAGGATGTGT 58.943 41.667 1.03 0.00 40.33 3.72
2847 2918 5.597813 GGCGATCTACATTTTAGGATGTG 57.402 43.478 1.03 0.00 40.33 3.21


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

AutoCloner maintained by Alex Coulton.