Multiple sequence alignment - TraesCS3B01G045800

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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 TraesCS3B01G045800 chr3B 100.000 2651 0 0 1 2651 23138522 23135872 0.000000e+00 4896.0
1 TraesCS3B01G045800 chr3B 85.714 196 22 3 430 623 280436683 280436874 4.470000e-48 202.0
2 TraesCS3B01G045800 chr3B 89.474 133 14 0 1129 1261 823095849 823095981 4.540000e-38 169.0
3 TraesCS3B01G045800 chr3B 80.405 148 22 6 2220 2364 20741355 20741212 3.610000e-19 106.0
4 TraesCS3B01G045800 chr3B 88.608 79 8 1 2285 2362 735120386 735120308 7.810000e-16 95.3
5 TraesCS3B01G045800 chr5B 95.321 1838 83 3 30 1864 399785583 399783746 0.000000e+00 2915.0
6 TraesCS3B01G045800 chr5B 95.968 496 19 1 1868 2362 399783133 399782638 0.000000e+00 804.0
7 TraesCS3B01G045800 chr5B 83.051 118 17 3 2248 2363 15660963 15661079 1.300000e-18 104.0
8 TraesCS3B01G045800 chr5B 88.889 81 8 1 2285 2364 333013788 333013868 6.040000e-17 99.0
9 TraesCS3B01G045800 chr4B 94.499 1836 95 4 32 1864 50402494 50404326 0.000000e+00 2826.0
10 TraesCS3B01G045800 chr4B 96.552 493 15 1 1868 2360 50404939 50405429 0.000000e+00 815.0
11 TraesCS3B01G045800 chr6B 95.748 1458 55 6 30 1481 37929625 37931081 0.000000e+00 2342.0
12 TraesCS3B01G045800 chr6B 97.374 495 13 0 1868 2362 37932234 37932728 0.000000e+00 843.0
13 TraesCS3B01G045800 chr6B 95.918 392 15 1 1474 1864 37931230 37931621 3.720000e-178 634.0
14 TraesCS3B01G045800 chr6B 80.741 405 42 20 27 428 663835510 663835139 1.550000e-72 283.0
15 TraesCS3B01G045800 chr6B 82.895 152 18 6 754 899 704144131 704143982 2.140000e-26 130.0
16 TraesCS3B01G045800 chr1B 94.354 1222 64 3 644 1864 532540657 532541874 0.000000e+00 1869.0
17 TraesCS3B01G045800 chr1B 96.128 439 16 1 1868 2306 532542487 532542924 0.000000e+00 715.0
18 TraesCS3B01G045800 chr1B 92.308 481 35 2 169 648 532531584 532532063 0.000000e+00 682.0
19 TraesCS3B01G045800 chr1B 84.865 370 39 14 30 396 73363929 73363574 9.020000e-95 357.0
20 TraesCS3B01G045800 chr1B 84.324 370 41 14 30 396 73316292 73315937 1.950000e-91 346.0
21 TraesCS3B01G045800 chr1B 85.211 142 10 8 1884 2016 635130023 635130162 4.600000e-28 135.0
22 TraesCS3B01G045800 chr2B 90.069 1309 88 18 430 1700 14601381 14600077 0.000000e+00 1659.0
23 TraesCS3B01G045800 chr2B 93.571 420 19 3 1944 2362 14598750 14598338 1.040000e-173 619.0
24 TraesCS3B01G045800 chr2B 85.484 372 37 6 1340 1700 119633739 119633374 3.220000e-99 372.0
25 TraesCS3B01G045800 chr2B 80.732 519 59 17 1212 1700 456700083 456699576 1.500000e-97 366.0
26 TraesCS3B01G045800 chr2B 80.539 519 60 16 1212 1700 693044264 693043757 6.980000e-96 361.0
27 TraesCS3B01G045800 chr2B 86.111 108 7 5 1918 2017 736109208 736109315 2.790000e-20 110.0
28 TraesCS3B01G045800 chr7B 93.372 513 16 8 1868 2364 84060522 84061032 0.000000e+00 743.0
29 TraesCS3B01G045800 chr7B 85.714 168 24 0 1129 1296 613871231 613871398 7.540000e-41 178.0
30 TraesCS3B01G045800 chr7B 86.614 127 17 0 1165 1291 404038166 404038292 9.890000e-30 141.0
31 TraesCS3B01G045800 chr1D 87.097 403 23 13 30 428 257318374 257317997 1.890000e-116 429.0
32 TraesCS3B01G045800 chr2D 85.791 373 34 8 1340 1700 77383234 77382869 6.930000e-101 377.0
33 TraesCS3B01G045800 chr4A 84.328 402 44 14 30 428 708396641 708396256 2.490000e-100 375.0
34 TraesCS3B01G045800 chr4D 83.541 401 45 16 30 428 78864656 78865037 3.250000e-94 355.0
35 TraesCS3B01G045800 chrUn 84.595 370 40 14 30 396 357027322 357026967 4.200000e-93 351.0
36 TraesCS3B01G045800 chrUn 86.441 177 24 0 1108 1284 32340396 32340220 7.490000e-46 195.0
37 TraesCS3B01G045800 chrUn 88.235 136 13 2 430 565 79335113 79335245 2.730000e-35 159.0
38 TraesCS3B01G045800 chrUn 83.916 143 12 8 1884 2017 462196416 462196556 2.770000e-25 126.0
39 TraesCS3B01G045800 chrUn 81.982 111 15 4 857 963 85467704 85467813 3.630000e-14 89.8
40 TraesCS3B01G045800 chr6D 87.629 194 19 4 430 623 110656277 110656465 1.240000e-53 220.0
41 TraesCS3B01G045800 chr1A 87.302 189 22 1 430 618 224081407 224081593 5.750000e-52 215.0


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 TraesCS3B01G045800 chr3B 23135872 23138522 2650 True 4896.0 4896 100.000000 1 2651 1 chr3B.!!$R2 2650
1 TraesCS3B01G045800 chr5B 399782638 399785583 2945 True 1859.5 2915 95.644500 30 2362 2 chr5B.!!$R1 2332
2 TraesCS3B01G045800 chr4B 50402494 50405429 2935 False 1820.5 2826 95.525500 32 2360 2 chr4B.!!$F1 2328
3 TraesCS3B01G045800 chr6B 37929625 37932728 3103 False 1273.0 2342 96.346667 30 2362 3 chr6B.!!$F1 2332
4 TraesCS3B01G045800 chr1B 532540657 532542924 2267 False 1292.0 1869 95.241000 644 2306 2 chr1B.!!$F3 1662
5 TraesCS3B01G045800 chr2B 14598338 14601381 3043 True 1139.0 1659 91.820000 430 2362 2 chr2B.!!$R4 1932
6 TraesCS3B01G045800 chr2B 456699576 456700083 507 True 366.0 366 80.732000 1212 1700 1 chr2B.!!$R2 488
7 TraesCS3B01G045800 chr2B 693043757 693044264 507 True 361.0 361 80.539000 1212 1700 1 chr2B.!!$R3 488
8 TraesCS3B01G045800 chr7B 84060522 84061032 510 False 743.0 743 93.372000 1868 2364 1 chr7B.!!$F1 496

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
967 992 0.319641 CTAGGCCCTCCGTTTATCGC 60.32 60.0 0.0 0.0 38.35 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2529 3907 0.03759 ACACGGGAGCCAAAATGCTA 59.962 50.0 0.0 0.0 42.95 3.49 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
21 22 3.893720 GCAGAGTTTTCCAGACAACATG 58.106 45.455 0.00 0.00 0.00 3.21
22 23 3.565482 GCAGAGTTTTCCAGACAACATGA 59.435 43.478 0.00 0.00 0.00 3.07
23 24 4.036734 GCAGAGTTTTCCAGACAACATGAA 59.963 41.667 0.00 0.00 0.00 2.57
24 25 5.278660 GCAGAGTTTTCCAGACAACATGAAT 60.279 40.000 0.00 0.00 0.00 2.57
25 26 6.072508 GCAGAGTTTTCCAGACAACATGAATA 60.073 38.462 0.00 0.00 0.00 1.75
26 27 7.362401 GCAGAGTTTTCCAGACAACATGAATAT 60.362 37.037 0.00 0.00 0.00 1.28
27 28 9.166173 CAGAGTTTTCCAGACAACATGAATATA 57.834 33.333 0.00 0.00 0.00 0.86
28 29 9.911788 AGAGTTTTCCAGACAACATGAATATAT 57.088 29.630 0.00 0.00 0.00 0.86
126 128 1.512156 CGCGTGTTACTGGGGCTTTT 61.512 55.000 0.00 0.00 0.00 2.27
296 299 1.344114 GCTGGTTCCTTCATTTGCCAA 59.656 47.619 0.00 0.00 0.00 4.52
371 376 4.094739 GTCGGGACACTTACTTCTCTCTAC 59.905 50.000 0.00 0.00 0.00 2.59
465 470 3.608474 CGACACGTTATCTCTGTGTGTGA 60.608 47.826 1.50 0.00 46.13 3.58
634 657 4.555262 CCACGTTTGCCAATTTACTGATT 58.445 39.130 0.00 0.00 0.00 2.57
663 686 2.039879 TGCCTTCTAGGGTTTTCTGGTC 59.960 50.000 0.00 0.00 35.37 4.02
880 905 3.646715 CCTCCGTTTCCCCCAGCA 61.647 66.667 0.00 0.00 0.00 4.41
900 925 2.713770 GTCGAGATGGTAGCGCGA 59.286 61.111 12.10 0.00 35.30 5.87
967 992 0.319641 CTAGGCCCTCCGTTTATCGC 60.320 60.000 0.00 0.00 38.35 4.58
999 1024 1.002624 GTTGAAGGATGGGGCGACA 60.003 57.895 0.00 0.00 0.00 4.35
1003 1028 0.394352 GAAGGATGGGGCGACAATGT 60.394 55.000 0.00 0.00 0.00 2.71
1051 1077 4.443266 GAGGAAGAGCACGCGCCT 62.443 66.667 5.73 1.44 39.83 5.52
1190 1216 3.838271 CTCGCTTGCCGCCTCCTA 61.838 66.667 0.00 0.00 36.73 2.94
1259 1291 6.170506 CCAAACTAAGCCAAGTATGAGTACA 58.829 40.000 0.00 0.00 33.09 2.90
1452 1494 1.731433 CGGACGGGTGGATGTACGAT 61.731 60.000 0.00 0.00 45.15 3.73
1490 1710 2.895424 CGGGGCAAGTTCTCCTGGT 61.895 63.158 0.00 0.00 0.00 4.00
1632 1852 0.462759 GCAACGGCAGGAAGAGCTAT 60.463 55.000 0.00 0.00 40.72 2.97
1800 2527 1.211969 GAGGCATGCAGCTGTTGTG 59.788 57.895 21.36 12.53 44.79 3.33
1854 2581 1.066573 CCTTCACCATCGACAGCTTCT 60.067 52.381 0.00 0.00 0.00 2.85
1864 2591 3.778618 TCGACAGCTTCTGATTCATCTG 58.221 45.455 0.29 0.00 35.18 2.90
1865 2592 2.864946 CGACAGCTTCTGATTCATCTGG 59.135 50.000 0.29 0.00 35.18 3.86
2282 3660 4.021102 ACCACGAATTGAGTCTTGGAAT 57.979 40.909 10.38 0.00 38.85 3.01
2371 3749 8.040309 CGCACTATTCGCTAGTATGTTATATG 57.960 38.462 0.00 0.00 38.68 1.78
2372 3750 7.696872 CGCACTATTCGCTAGTATGTTATATGT 59.303 37.037 0.00 0.00 38.68 2.29
2373 3751 9.999009 GCACTATTCGCTAGTATGTTATATGTA 57.001 33.333 0.00 0.00 38.68 2.29
2395 3773 8.824756 TGTACATAGATAAGGAGTTCTTGAGT 57.175 34.615 0.00 0.00 36.93 3.41
2396 3774 8.687242 TGTACATAGATAAGGAGTTCTTGAGTG 58.313 37.037 0.00 0.00 36.93 3.51
2397 3775 7.726033 ACATAGATAAGGAGTTCTTGAGTGT 57.274 36.000 0.00 0.00 36.93 3.55
2398 3776 8.824756 ACATAGATAAGGAGTTCTTGAGTGTA 57.175 34.615 0.00 0.00 36.93 2.90
2399 3777 9.427821 ACATAGATAAGGAGTTCTTGAGTGTAT 57.572 33.333 0.00 0.00 36.93 2.29
2405 3783 7.674471 AAGGAGTTCTTGAGTGTATAAAAGC 57.326 36.000 0.00 0.00 33.76 3.51
2406 3784 6.769512 AGGAGTTCTTGAGTGTATAAAAGCA 58.230 36.000 0.00 0.00 0.00 3.91
2407 3785 7.398024 AGGAGTTCTTGAGTGTATAAAAGCAT 58.602 34.615 0.00 0.00 0.00 3.79
2408 3786 8.540388 AGGAGTTCTTGAGTGTATAAAAGCATA 58.460 33.333 0.00 0.00 0.00 3.14
2409 3787 8.604890 GGAGTTCTTGAGTGTATAAAAGCATAC 58.395 37.037 0.00 0.00 32.91 2.39
2410 3788 8.494016 AGTTCTTGAGTGTATAAAAGCATACC 57.506 34.615 0.00 0.00 31.52 2.73
2411 3789 8.322091 AGTTCTTGAGTGTATAAAAGCATACCT 58.678 33.333 0.00 0.00 31.52 3.08
2412 3790 9.595823 GTTCTTGAGTGTATAAAAGCATACCTA 57.404 33.333 0.00 0.00 31.52 3.08
2414 3792 9.982651 TCTTGAGTGTATAAAAGCATACCTATC 57.017 33.333 0.00 0.00 31.52 2.08
2415 3793 9.764363 CTTGAGTGTATAAAAGCATACCTATCA 57.236 33.333 0.00 0.00 31.52 2.15
2426 3804 9.866655 AAAAGCATACCTATCATATTTCCTGAA 57.133 29.630 0.00 0.00 0.00 3.02
2427 3805 9.866655 AAAGCATACCTATCATATTTCCTGAAA 57.133 29.630 0.00 0.00 34.46 2.69
2428 3806 8.854614 AGCATACCTATCATATTTCCTGAAAC 57.145 34.615 0.00 0.00 32.51 2.78
2429 3807 8.439971 AGCATACCTATCATATTTCCTGAAACA 58.560 33.333 0.00 0.00 32.51 2.83
2430 3808 8.507249 GCATACCTATCATATTTCCTGAAACAC 58.493 37.037 0.00 0.00 32.51 3.32
2431 3809 9.559732 CATACCTATCATATTTCCTGAAACACA 57.440 33.333 0.00 0.00 32.51 3.72
2433 3811 8.682936 ACCTATCATATTTCCTGAAACACATC 57.317 34.615 0.00 0.00 32.51 3.06
2434 3812 8.274322 ACCTATCATATTTCCTGAAACACATCA 58.726 33.333 0.00 0.00 32.51 3.07
2435 3813 8.781196 CCTATCATATTTCCTGAAACACATCAG 58.219 37.037 0.00 0.00 45.19 2.90
2436 3814 6.441093 TCATATTTCCTGAAACACATCAGC 57.559 37.500 0.00 0.00 44.43 4.26
2437 3815 5.945191 TCATATTTCCTGAAACACATCAGCA 59.055 36.000 0.00 0.00 44.43 4.41
2438 3816 6.604396 TCATATTTCCTGAAACACATCAGCAT 59.396 34.615 0.00 0.00 44.43 3.79
2439 3817 5.733620 ATTTCCTGAAACACATCAGCATT 57.266 34.783 0.00 0.00 44.43 3.56
2440 3818 4.771590 TTCCTGAAACACATCAGCATTC 57.228 40.909 0.00 0.00 44.43 2.67
2441 3819 4.025040 TCCTGAAACACATCAGCATTCT 57.975 40.909 0.00 0.00 44.43 2.40
2442 3820 5.164620 TCCTGAAACACATCAGCATTCTA 57.835 39.130 0.00 0.00 44.43 2.10
2443 3821 5.181009 TCCTGAAACACATCAGCATTCTAG 58.819 41.667 0.00 0.00 44.43 2.43
2444 3822 5.046376 TCCTGAAACACATCAGCATTCTAGA 60.046 40.000 0.00 0.00 44.43 2.43
2445 3823 5.645067 CCTGAAACACATCAGCATTCTAGAA 59.355 40.000 7.82 7.82 44.43 2.10
2446 3824 6.149973 CCTGAAACACATCAGCATTCTAGAAA 59.850 38.462 9.71 0.00 44.43 2.52
2447 3825 7.308770 CCTGAAACACATCAGCATTCTAGAAAA 60.309 37.037 9.71 0.00 44.43 2.29
2448 3826 7.939782 TGAAACACATCAGCATTCTAGAAAAA 58.060 30.769 9.71 0.00 0.00 1.94
2449 3827 7.862372 TGAAACACATCAGCATTCTAGAAAAAC 59.138 33.333 9.71 2.03 0.00 2.43
2450 3828 7.516198 AACACATCAGCATTCTAGAAAAACT 57.484 32.000 9.71 4.43 0.00 2.66
2451 3829 6.906659 ACACATCAGCATTCTAGAAAAACTG 58.093 36.000 19.27 19.27 0.00 3.16
2452 3830 5.798934 CACATCAGCATTCTAGAAAAACTGC 59.201 40.000 17.33 17.33 0.00 4.40
2453 3831 5.709164 ACATCAGCATTCTAGAAAAACTGCT 59.291 36.000 20.56 20.56 40.38 4.24
2454 3832 6.881065 ACATCAGCATTCTAGAAAAACTGCTA 59.119 34.615 23.98 15.65 37.84 3.49
2455 3833 7.555554 ACATCAGCATTCTAGAAAAACTGCTAT 59.444 33.333 23.98 16.73 37.84 2.97
2456 3834 7.928307 TCAGCATTCTAGAAAAACTGCTATT 57.072 32.000 23.98 6.98 37.84 1.73
2457 3835 7.755591 TCAGCATTCTAGAAAAACTGCTATTG 58.244 34.615 23.98 16.07 37.84 1.90
2458 3836 7.391554 TCAGCATTCTAGAAAAACTGCTATTGT 59.608 33.333 23.98 6.39 37.84 2.71
2459 3837 8.668353 CAGCATTCTAGAAAAACTGCTATTGTA 58.332 33.333 23.98 0.00 37.84 2.41
2460 3838 8.887717 AGCATTCTAGAAAAACTGCTATTGTAG 58.112 33.333 23.45 0.00 38.13 2.74
2461 3839 8.883731 GCATTCTAGAAAAACTGCTATTGTAGA 58.116 33.333 17.62 0.00 30.01 2.59
2467 3845 8.677148 AGAAAAACTGCTATTGTAGAAGAACA 57.323 30.769 0.00 0.00 34.88 3.18
2468 3846 9.289782 AGAAAAACTGCTATTGTAGAAGAACAT 57.710 29.630 0.00 0.00 34.88 2.71
2471 3849 9.944376 AAAACTGCTATTGTAGAAGAACATAGA 57.056 29.630 0.00 0.00 34.88 1.98
2472 3850 9.593134 AAACTGCTATTGTAGAAGAACATAGAG 57.407 33.333 0.00 0.00 34.88 2.43
2473 3851 8.526667 ACTGCTATTGTAGAAGAACATAGAGA 57.473 34.615 0.00 0.00 34.88 3.10
2474 3852 8.410141 ACTGCTATTGTAGAAGAACATAGAGAC 58.590 37.037 0.00 0.00 34.88 3.36
2475 3853 8.293699 TGCTATTGTAGAAGAACATAGAGACA 57.706 34.615 0.00 0.00 0.00 3.41
2476 3854 8.749354 TGCTATTGTAGAAGAACATAGAGACAA 58.251 33.333 0.00 0.00 0.00 3.18
2477 3855 9.757227 GCTATTGTAGAAGAACATAGAGACAAT 57.243 33.333 0.00 0.00 39.11 2.71
2482 3860 9.996554 TGTAGAAGAACATAGAGACAATTTTCA 57.003 29.630 0.00 0.00 0.00 2.69
2485 3863 8.997323 AGAAGAACATAGAGACAATTTTCACTG 58.003 33.333 2.25 0.00 0.00 3.66
2486 3864 8.682936 AAGAACATAGAGACAATTTTCACTGT 57.317 30.769 2.25 0.00 0.00 3.55
2487 3865 9.778741 AAGAACATAGAGACAATTTTCACTGTA 57.221 29.630 2.25 0.00 0.00 2.74
2488 3866 9.429359 AGAACATAGAGACAATTTTCACTGTAG 57.571 33.333 2.25 0.00 0.00 2.74
2489 3867 7.602517 ACATAGAGACAATTTTCACTGTAGC 57.397 36.000 2.25 0.00 0.00 3.58
2490 3868 7.161404 ACATAGAGACAATTTTCACTGTAGCA 58.839 34.615 2.25 0.00 0.00 3.49
2491 3869 7.826252 ACATAGAGACAATTTTCACTGTAGCAT 59.174 33.333 2.25 0.00 0.00 3.79
2492 3870 9.317936 CATAGAGACAATTTTCACTGTAGCATA 57.682 33.333 2.25 0.00 0.00 3.14
2494 3872 8.798859 AGAGACAATTTTCACTGTAGCATATT 57.201 30.769 0.00 0.00 0.00 1.28
2495 3873 8.671921 AGAGACAATTTTCACTGTAGCATATTG 58.328 33.333 0.00 0.00 0.00 1.90
2496 3874 7.253422 AGACAATTTTCACTGTAGCATATTGC 58.747 34.615 0.00 0.00 45.46 3.56
2509 3887 4.007282 GCATATTGCGTATACTGGCATG 57.993 45.455 6.32 4.09 39.21 4.06
2510 3888 3.436704 GCATATTGCGTATACTGGCATGT 59.563 43.478 6.32 2.60 39.21 3.21
2511 3889 4.669965 GCATATTGCGTATACTGGCATGTG 60.670 45.833 6.32 7.04 39.21 3.21
2512 3890 2.394930 TTGCGTATACTGGCATGTGT 57.605 45.000 6.32 0.00 39.21 3.72
2513 3891 1.934589 TGCGTATACTGGCATGTGTC 58.065 50.000 0.56 0.00 33.52 3.67
2514 3892 1.217882 GCGTATACTGGCATGTGTCC 58.782 55.000 0.56 0.00 0.00 4.02
2515 3893 1.202533 GCGTATACTGGCATGTGTCCT 60.203 52.381 0.56 0.00 0.00 3.85
2516 3894 2.741878 GCGTATACTGGCATGTGTCCTT 60.742 50.000 0.56 0.00 0.00 3.36
2517 3895 3.491964 GCGTATACTGGCATGTGTCCTTA 60.492 47.826 0.56 0.00 0.00 2.69
2518 3896 4.049186 CGTATACTGGCATGTGTCCTTAC 58.951 47.826 0.56 0.00 0.00 2.34
2519 3897 2.665649 TACTGGCATGTGTCCTTACG 57.334 50.000 0.00 0.00 0.00 3.18
2520 3898 0.673644 ACTGGCATGTGTCCTTACGC 60.674 55.000 0.00 0.00 36.62 4.42
2521 3899 0.391661 CTGGCATGTGTCCTTACGCT 60.392 55.000 0.00 0.00 37.03 5.07
2522 3900 0.899019 TGGCATGTGTCCTTACGCTA 59.101 50.000 0.00 0.00 37.03 4.26
2523 3901 1.276705 TGGCATGTGTCCTTACGCTAA 59.723 47.619 0.00 0.00 37.03 3.09
2524 3902 1.933853 GGCATGTGTCCTTACGCTAAG 59.066 52.381 0.00 0.00 37.03 2.18
2525 3903 2.618053 GCATGTGTCCTTACGCTAAGT 58.382 47.619 0.00 0.00 37.03 2.24
2526 3904 2.348666 GCATGTGTCCTTACGCTAAGTG 59.651 50.000 0.00 0.00 37.03 3.16
2527 3905 3.845178 CATGTGTCCTTACGCTAAGTGA 58.155 45.455 0.00 0.76 37.03 3.41
2528 3906 3.293311 TGTGTCCTTACGCTAAGTGAC 57.707 47.619 13.18 13.18 37.03 3.67
2529 3907 2.889045 TGTGTCCTTACGCTAAGTGACT 59.111 45.455 16.87 0.00 37.13 3.41
2530 3908 4.074259 TGTGTCCTTACGCTAAGTGACTA 58.926 43.478 16.87 10.08 37.13 2.59
2531 3909 4.155462 TGTGTCCTTACGCTAAGTGACTAG 59.845 45.833 16.87 0.00 37.13 2.57
2532 3910 3.128242 TGTCCTTACGCTAAGTGACTAGC 59.872 47.826 16.87 0.00 40.83 3.42
2533 3911 3.128242 GTCCTTACGCTAAGTGACTAGCA 59.872 47.826 12.26 0.00 43.84 3.49
2534 3912 3.952323 TCCTTACGCTAAGTGACTAGCAT 59.048 43.478 12.26 2.64 43.84 3.79
2535 3913 4.401519 TCCTTACGCTAAGTGACTAGCATT 59.598 41.667 12.26 3.92 43.84 3.56
2536 3914 5.105473 TCCTTACGCTAAGTGACTAGCATTT 60.105 40.000 12.26 0.00 43.84 2.32
2537 3915 5.581085 CCTTACGCTAAGTGACTAGCATTTT 59.419 40.000 12.26 0.00 43.84 1.82
2538 3916 4.928661 ACGCTAAGTGACTAGCATTTTG 57.071 40.909 12.26 0.00 43.84 2.44
2539 3917 3.684788 ACGCTAAGTGACTAGCATTTTGG 59.315 43.478 12.26 1.31 43.84 3.28
2540 3918 3.485877 CGCTAAGTGACTAGCATTTTGGC 60.486 47.826 12.26 2.10 43.84 4.52
2541 3919 5.683751 CGCTAAGTGACTAGCATTTTGGCT 61.684 45.833 12.26 0.00 43.84 4.75
2542 3920 4.201861 GCTAAGTGACTAGCATTTTGGCTC 60.202 45.833 8.50 0.00 44.54 4.70
2543 3921 2.716217 AGTGACTAGCATTTTGGCTCC 58.284 47.619 0.00 0.00 44.54 4.70
2544 3922 1.745653 GTGACTAGCATTTTGGCTCCC 59.254 52.381 0.00 0.00 44.54 4.30
2545 3923 1.017387 GACTAGCATTTTGGCTCCCG 58.983 55.000 0.00 0.00 44.54 5.14
2546 3924 0.328258 ACTAGCATTTTGGCTCCCGT 59.672 50.000 0.00 0.00 44.54 5.28
2547 3925 0.734889 CTAGCATTTTGGCTCCCGTG 59.265 55.000 0.00 0.00 44.54 4.94
2548 3926 0.037590 TAGCATTTTGGCTCCCGTGT 59.962 50.000 0.00 0.00 44.54 4.49
2549 3927 1.212751 GCATTTTGGCTCCCGTGTC 59.787 57.895 0.00 0.00 0.00 3.67
2550 3928 1.883021 CATTTTGGCTCCCGTGTCC 59.117 57.895 0.00 0.00 0.00 4.02
2551 3929 0.893270 CATTTTGGCTCCCGTGTCCA 60.893 55.000 0.00 0.00 0.00 4.02
2552 3930 0.039618 ATTTTGGCTCCCGTGTCCAT 59.960 50.000 0.00 0.00 0.00 3.41
2553 3931 0.608035 TTTTGGCTCCCGTGTCCATC 60.608 55.000 0.00 0.00 0.00 3.51
2554 3932 1.488705 TTTGGCTCCCGTGTCCATCT 61.489 55.000 0.00 0.00 0.00 2.90
2555 3933 0.616395 TTGGCTCCCGTGTCCATCTA 60.616 55.000 0.00 0.00 0.00 1.98
2556 3934 1.327690 TGGCTCCCGTGTCCATCTAC 61.328 60.000 0.00 0.00 0.00 2.59
2557 3935 1.043673 GGCTCCCGTGTCCATCTACT 61.044 60.000 0.00 0.00 0.00 2.57
2558 3936 0.386113 GCTCCCGTGTCCATCTACTC 59.614 60.000 0.00 0.00 0.00 2.59
2559 3937 2.024825 GCTCCCGTGTCCATCTACTCT 61.025 57.143 0.00 0.00 0.00 3.24
2560 3938 1.950909 CTCCCGTGTCCATCTACTCTC 59.049 57.143 0.00 0.00 0.00 3.20
2561 3939 0.663688 CCCGTGTCCATCTACTCTCG 59.336 60.000 0.00 0.00 0.00 4.04
2562 3940 1.664873 CCGTGTCCATCTACTCTCGA 58.335 55.000 0.00 0.00 0.00 4.04
2563 3941 2.222886 CCGTGTCCATCTACTCTCGAT 58.777 52.381 0.00 0.00 0.00 3.59
2564 3942 3.400255 CCGTGTCCATCTACTCTCGATA 58.600 50.000 0.00 0.00 0.00 2.92
2565 3943 4.004314 CCGTGTCCATCTACTCTCGATAT 58.996 47.826 0.00 0.00 0.00 1.63
2566 3944 4.093703 CCGTGTCCATCTACTCTCGATATC 59.906 50.000 0.00 0.00 0.00 1.63
2567 3945 4.932799 CGTGTCCATCTACTCTCGATATCT 59.067 45.833 0.34 0.00 0.00 1.98
2568 3946 5.163903 CGTGTCCATCTACTCTCGATATCTG 60.164 48.000 0.34 0.00 0.00 2.90
2569 3947 5.123186 GTGTCCATCTACTCTCGATATCTGG 59.877 48.000 0.34 0.00 0.00 3.86
2570 3948 5.013183 TGTCCATCTACTCTCGATATCTGGA 59.987 44.000 0.34 1.03 0.00 3.86
2571 3949 5.353123 GTCCATCTACTCTCGATATCTGGAC 59.647 48.000 15.24 15.24 34.97 4.02
2572 3950 4.638421 CCATCTACTCTCGATATCTGGACC 59.362 50.000 0.34 0.00 0.00 4.46
2573 3951 4.976540 TCTACTCTCGATATCTGGACCA 57.023 45.455 0.34 0.00 0.00 4.02
2574 3952 5.506730 TCTACTCTCGATATCTGGACCAT 57.493 43.478 0.00 0.00 0.00 3.55
2575 3953 5.492895 TCTACTCTCGATATCTGGACCATC 58.507 45.833 0.00 0.00 0.00 3.51
2576 3954 3.426615 ACTCTCGATATCTGGACCATCC 58.573 50.000 0.00 0.00 36.96 3.51
2577 3955 3.181428 ACTCTCGATATCTGGACCATCCA 60.181 47.826 0.00 0.00 45.98 3.41
2588 3966 3.750371 TGGACCATCCAAGTTGTAGTTG 58.250 45.455 1.45 0.00 45.00 3.16
2589 3967 3.392947 TGGACCATCCAAGTTGTAGTTGA 59.607 43.478 1.45 0.00 45.00 3.18
2590 3968 4.003648 GGACCATCCAAGTTGTAGTTGAG 58.996 47.826 1.45 0.00 36.28 3.02
2591 3969 4.262894 GGACCATCCAAGTTGTAGTTGAGA 60.263 45.833 1.45 0.00 36.28 3.27
2592 3970 5.491982 GACCATCCAAGTTGTAGTTGAGAT 58.508 41.667 1.45 0.00 30.18 2.75
2593 3971 5.880901 ACCATCCAAGTTGTAGTTGAGATT 58.119 37.500 1.45 0.00 30.18 2.40
2594 3972 6.306987 ACCATCCAAGTTGTAGTTGAGATTT 58.693 36.000 1.45 0.00 30.18 2.17
2595 3973 6.207417 ACCATCCAAGTTGTAGTTGAGATTTG 59.793 38.462 1.45 0.00 30.18 2.32
2596 3974 6.207417 CCATCCAAGTTGTAGTTGAGATTTGT 59.793 38.462 1.45 0.00 30.18 2.83
2597 3975 6.618287 TCCAAGTTGTAGTTGAGATTTGTG 57.382 37.500 1.45 0.00 30.18 3.33
2598 3976 5.008613 TCCAAGTTGTAGTTGAGATTTGTGC 59.991 40.000 1.45 0.00 30.18 4.57
2599 3977 5.215160 CAAGTTGTAGTTGAGATTTGTGCC 58.785 41.667 0.00 0.00 30.18 5.01
2600 3978 4.460263 AGTTGTAGTTGAGATTTGTGCCA 58.540 39.130 0.00 0.00 0.00 4.92
2601 3979 4.887071 AGTTGTAGTTGAGATTTGTGCCAA 59.113 37.500 0.00 0.00 0.00 4.52
2602 3980 5.359576 AGTTGTAGTTGAGATTTGTGCCAAA 59.640 36.000 3.33 3.33 0.00 3.28
2603 3981 5.843673 TGTAGTTGAGATTTGTGCCAAAA 57.156 34.783 4.76 0.00 0.00 2.44
2604 3982 6.403866 TGTAGTTGAGATTTGTGCCAAAAT 57.596 33.333 4.76 0.00 32.43 1.82
2605 3983 6.446318 TGTAGTTGAGATTTGTGCCAAAATC 58.554 36.000 11.41 11.41 43.79 2.17
2606 3984 5.534207 AGTTGAGATTTGTGCCAAAATCA 57.466 34.783 18.27 14.63 45.20 2.57
2607 3985 5.916318 AGTTGAGATTTGTGCCAAAATCAA 58.084 33.333 18.27 17.93 45.20 2.57
2608 3986 6.527423 AGTTGAGATTTGTGCCAAAATCAAT 58.473 32.000 20.95 13.78 45.20 2.57
2609 3987 6.993902 AGTTGAGATTTGTGCCAAAATCAATT 59.006 30.769 20.95 17.49 45.20 2.32
2610 3988 8.149647 AGTTGAGATTTGTGCCAAAATCAATTA 58.850 29.630 20.95 8.45 45.20 1.40
2611 3989 7.887996 TGAGATTTGTGCCAAAATCAATTAC 57.112 32.000 18.27 8.47 45.20 1.89
2612 3990 7.669427 TGAGATTTGTGCCAAAATCAATTACT 58.331 30.769 18.27 2.55 45.20 2.24
2613 3991 7.599621 TGAGATTTGTGCCAAAATCAATTACTG 59.400 33.333 18.27 0.00 45.20 2.74
2614 3992 7.669427 AGATTTGTGCCAAAATCAATTACTGA 58.331 30.769 18.27 0.00 45.20 3.41
2615 3993 7.599998 AGATTTGTGCCAAAATCAATTACTGAC 59.400 33.333 18.27 0.00 45.20 3.51
2616 3994 5.781210 TGTGCCAAAATCAATTACTGACA 57.219 34.783 0.00 0.00 36.69 3.58
2617 3995 6.154203 TGTGCCAAAATCAATTACTGACAA 57.846 33.333 0.00 0.00 36.69 3.18
2618 3996 5.982516 TGTGCCAAAATCAATTACTGACAAC 59.017 36.000 0.00 0.00 36.69 3.32
2619 3997 5.982516 GTGCCAAAATCAATTACTGACAACA 59.017 36.000 0.00 0.00 36.69 3.33
2620 3998 6.646240 GTGCCAAAATCAATTACTGACAACAT 59.354 34.615 0.00 0.00 36.69 2.71
2621 3999 7.812191 GTGCCAAAATCAATTACTGACAACATA 59.188 33.333 0.00 0.00 36.69 2.29
2622 4000 8.530311 TGCCAAAATCAATTACTGACAACATAT 58.470 29.630 0.00 0.00 36.69 1.78
2623 4001 8.810427 GCCAAAATCAATTACTGACAACATATG 58.190 33.333 0.00 0.00 36.69 1.78
2626 4004 8.915871 AAATCAATTACTGACAACATATGTGC 57.084 30.769 9.63 3.00 44.12 4.57
2627 4005 7.628769 ATCAATTACTGACAACATATGTGCA 57.371 32.000 9.63 7.54 44.12 4.57
2628 4006 7.628769 TCAATTACTGACAACATATGTGCAT 57.371 32.000 9.63 0.00 44.12 3.96
2629 4007 7.474190 TCAATTACTGACAACATATGTGCATG 58.526 34.615 9.63 6.80 44.12 4.06
2630 4008 3.770263 ACTGACAACATATGTGCATGC 57.230 42.857 11.82 11.82 44.12 4.06
2631 4009 3.083293 ACTGACAACATATGTGCATGCA 58.917 40.909 18.46 18.46 44.12 3.96
2632 4010 3.697542 ACTGACAACATATGTGCATGCAT 59.302 39.130 25.64 11.73 44.12 3.96
2633 4011 4.883006 ACTGACAACATATGTGCATGCATA 59.117 37.500 25.64 22.69 44.12 3.14
2634 4012 5.357596 ACTGACAACATATGTGCATGCATAA 59.642 36.000 25.64 16.04 44.12 1.90
2635 4013 6.127675 ACTGACAACATATGTGCATGCATAAA 60.128 34.615 25.64 13.31 44.12 1.40
2636 4014 6.035217 TGACAACATATGTGCATGCATAAAC 58.965 36.000 25.64 11.56 44.12 2.01
2637 4015 6.127675 TGACAACATATGTGCATGCATAAACT 60.128 34.615 25.64 9.03 44.12 2.66
2638 4016 6.267817 ACAACATATGTGCATGCATAAACTC 58.732 36.000 25.64 10.35 41.93 3.01
2639 4017 5.099484 ACATATGTGCATGCATAAACTCG 57.901 39.130 25.64 11.76 35.30 4.18
2640 4018 4.576053 ACATATGTGCATGCATAAACTCGT 59.424 37.500 25.64 13.33 35.30 4.18
2641 4019 2.898181 TGTGCATGCATAAACTCGTG 57.102 45.000 25.64 0.00 0.00 4.35
2642 4020 2.150390 TGTGCATGCATAAACTCGTGT 58.850 42.857 25.64 0.00 0.00 4.49
2643 4021 3.330267 TGTGCATGCATAAACTCGTGTA 58.670 40.909 25.64 0.00 0.00 2.90
2644 4022 3.938334 TGTGCATGCATAAACTCGTGTAT 59.062 39.130 25.64 0.00 0.00 2.29
2645 4023 4.394610 TGTGCATGCATAAACTCGTGTATT 59.605 37.500 25.64 0.00 0.00 1.89
2646 4024 4.963953 GTGCATGCATAAACTCGTGTATTC 59.036 41.667 25.64 0.38 0.00 1.75
2647 4025 4.633565 TGCATGCATAAACTCGTGTATTCA 59.366 37.500 18.46 0.00 0.00 2.57
2648 4026 5.296531 TGCATGCATAAACTCGTGTATTCAT 59.703 36.000 18.46 0.00 0.00 2.57
2649 4027 6.183360 TGCATGCATAAACTCGTGTATTCATT 60.183 34.615 18.46 0.00 0.00 2.57
2650 4028 6.358030 GCATGCATAAACTCGTGTATTCATTC 59.642 38.462 14.21 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.565482 TCATGTTGTCTGGAAAACTCTGC 59.435 43.478 5.41 0.00 0.00 4.26
1 2 5.756195 TTCATGTTGTCTGGAAAACTCTG 57.244 39.130 5.41 3.81 0.00 3.35
2 3 9.911788 ATATATTCATGTTGTCTGGAAAACTCT 57.088 29.630 5.41 0.00 0.00 3.24
27 28 9.406113 CTTACGGGCCTAGTATTCTTAGTATAT 57.594 37.037 0.84 0.00 0.00 0.86
28 29 7.831193 CCTTACGGGCCTAGTATTCTTAGTATA 59.169 40.741 0.84 0.00 0.00 1.47
59 60 9.567776 AAATAATCCGGAAAAACCAGAAAATTT 57.432 25.926 9.01 0.00 38.90 1.82
80 81 7.730784 TCATTTTCTCAGGGGTGGTAAAAATAA 59.269 33.333 0.00 0.00 0.00 1.40
126 128 3.368116 GCTAAGAAGTAGGAACGGCAAGA 60.368 47.826 0.00 0.00 0.00 3.02
177 180 6.349363 GGGCATTCAATAGAAAGAAAGACGTT 60.349 38.462 0.00 0.00 37.29 3.99
358 363 7.598759 ACTGGAGTTTTGTAGAGAGAAGTAA 57.401 36.000 0.00 0.00 0.00 2.24
371 376 6.323203 ACATGAGATTGAACTGGAGTTTTG 57.677 37.500 0.00 0.00 38.56 2.44
465 470 4.341520 GGAAGGTCGATGTAGGATGTACTT 59.658 45.833 0.00 0.00 0.00 2.24
634 657 0.320374 CCCTAGAAGGCAACGTGTCA 59.680 55.000 0.00 0.00 46.39 3.58
663 686 5.556947 GCAAAGAAAAACAAAGATGAAGCCG 60.557 40.000 0.00 0.00 0.00 5.52
817 841 1.619669 GGTTGGGGGAGGATGAGGT 60.620 63.158 0.00 0.00 0.00 3.85
880 905 1.437986 GCGCTACCATCTCGACCTT 59.562 57.895 0.00 0.00 0.00 3.50
967 992 4.326766 CAACGCCAACACCGCCAG 62.327 66.667 0.00 0.00 0.00 4.85
999 1024 1.254026 TCCAAGAGTCCGACGACATT 58.746 50.000 0.00 0.00 41.87 2.71
1003 1028 1.604693 GCTTTTCCAAGAGTCCGACGA 60.605 52.381 0.00 0.00 30.57 4.20
1259 1291 3.769844 AGGAAAGTACATGACCATCGTCT 59.230 43.478 0.00 0.00 39.94 4.18
1632 1852 0.319211 CTTACTGGTCGCCGTTGACA 60.319 55.000 6.61 0.00 40.72 3.58
1696 1923 1.601759 GCAGGGCTGAGCACAAGAA 60.602 57.895 10.32 0.00 32.33 2.52
1731 2458 6.931838 ACCGAACTGAATACACAAGAGAATA 58.068 36.000 0.00 0.00 0.00 1.75
1800 2527 1.075659 AGAAGAACAAGGCCTGCCC 59.924 57.895 5.69 0.00 36.58 5.36
2173 3539 8.974292 ATAGTGATAGTGGGTAATGGAAGTAT 57.026 34.615 0.00 0.00 0.00 2.12
2369 3747 9.427821 ACTCAAGAACTCCTTATCTATGTACAT 57.572 33.333 13.93 13.93 32.86 2.29
2370 3748 8.687242 CACTCAAGAACTCCTTATCTATGTACA 58.313 37.037 0.00 0.00 32.86 2.90
2371 3749 8.688151 ACACTCAAGAACTCCTTATCTATGTAC 58.312 37.037 0.00 0.00 32.86 2.90
2372 3750 8.824756 ACACTCAAGAACTCCTTATCTATGTA 57.175 34.615 0.00 0.00 32.86 2.29
2373 3751 7.726033 ACACTCAAGAACTCCTTATCTATGT 57.274 36.000 0.00 0.00 32.86 2.29
2379 3757 9.384764 GCTTTTATACACTCAAGAACTCCTTAT 57.615 33.333 0.00 0.00 32.86 1.73
2380 3758 8.372459 TGCTTTTATACACTCAAGAACTCCTTA 58.628 33.333 0.00 0.00 32.86 2.69
2381 3759 7.224297 TGCTTTTATACACTCAAGAACTCCTT 58.776 34.615 0.00 0.00 34.91 3.36
2382 3760 6.769512 TGCTTTTATACACTCAAGAACTCCT 58.230 36.000 0.00 0.00 0.00 3.69
2383 3761 7.617041 ATGCTTTTATACACTCAAGAACTCC 57.383 36.000 0.00 0.00 0.00 3.85
2384 3762 8.604890 GGTATGCTTTTATACACTCAAGAACTC 58.395 37.037 0.00 0.00 35.67 3.01
2385 3763 8.322091 AGGTATGCTTTTATACACTCAAGAACT 58.678 33.333 0.00 0.00 35.67 3.01
2386 3764 8.494016 AGGTATGCTTTTATACACTCAAGAAC 57.506 34.615 0.00 0.00 35.67 3.01
2388 3766 9.982651 GATAGGTATGCTTTTATACACTCAAGA 57.017 33.333 0.00 0.00 35.67 3.02
2389 3767 9.764363 TGATAGGTATGCTTTTATACACTCAAG 57.236 33.333 0.00 0.00 35.67 3.02
2400 3778 9.866655 TTCAGGAAATATGATAGGTATGCTTTT 57.133 29.630 0.00 0.00 0.00 2.27
2401 3779 9.866655 TTTCAGGAAATATGATAGGTATGCTTT 57.133 29.630 0.00 0.00 0.00 3.51
2402 3780 9.289782 GTTTCAGGAAATATGATAGGTATGCTT 57.710 33.333 0.00 0.00 32.36 3.91
2403 3781 8.439971 TGTTTCAGGAAATATGATAGGTATGCT 58.560 33.333 0.00 0.00 32.36 3.79
2404 3782 8.507249 GTGTTTCAGGAAATATGATAGGTATGC 58.493 37.037 0.00 0.00 32.36 3.14
2405 3783 9.559732 TGTGTTTCAGGAAATATGATAGGTATG 57.440 33.333 0.00 0.00 32.36 2.39
2407 3785 9.778741 GATGTGTTTCAGGAAATATGATAGGTA 57.221 33.333 0.00 0.00 32.36 3.08
2408 3786 8.274322 TGATGTGTTTCAGGAAATATGATAGGT 58.726 33.333 0.00 0.00 32.36 3.08
2409 3787 8.681486 TGATGTGTTTCAGGAAATATGATAGG 57.319 34.615 0.00 0.00 32.36 2.57
2410 3788 8.288208 GCTGATGTGTTTCAGGAAATATGATAG 58.712 37.037 3.85 0.00 42.78 2.08
2411 3789 7.774625 TGCTGATGTGTTTCAGGAAATATGATA 59.225 33.333 3.85 0.00 40.57 2.15
2412 3790 6.604396 TGCTGATGTGTTTCAGGAAATATGAT 59.396 34.615 3.85 0.00 40.57 2.45
2413 3791 5.945191 TGCTGATGTGTTTCAGGAAATATGA 59.055 36.000 3.85 0.00 40.57 2.15
2414 3792 6.198650 TGCTGATGTGTTTCAGGAAATATG 57.801 37.500 3.85 0.00 40.57 1.78
2415 3793 7.341256 AGAATGCTGATGTGTTTCAGGAAATAT 59.659 33.333 0.00 0.00 45.50 1.28
2416 3794 6.660521 AGAATGCTGATGTGTTTCAGGAAATA 59.339 34.615 0.00 0.00 45.50 1.40
2417 3795 5.479375 AGAATGCTGATGTGTTTCAGGAAAT 59.521 36.000 0.00 0.00 45.50 2.17
2418 3796 4.828939 AGAATGCTGATGTGTTTCAGGAAA 59.171 37.500 0.00 0.00 45.50 3.13
2419 3797 4.401022 AGAATGCTGATGTGTTTCAGGAA 58.599 39.130 0.00 0.00 45.50 3.36
2420 3798 4.025040 AGAATGCTGATGTGTTTCAGGA 57.975 40.909 3.85 1.11 46.25 3.86
2421 3799 5.181009 TCTAGAATGCTGATGTGTTTCAGG 58.819 41.667 3.85 0.00 42.78 3.86
2422 3800 6.732531 TTCTAGAATGCTGATGTGTTTCAG 57.267 37.500 0.00 0.00 44.87 3.02
2423 3801 7.509141 TTTTCTAGAATGCTGATGTGTTTCA 57.491 32.000 5.89 0.00 0.00 2.69
2424 3802 8.078596 AGTTTTTCTAGAATGCTGATGTGTTTC 58.921 33.333 5.89 0.00 0.00 2.78
2425 3803 7.864379 CAGTTTTTCTAGAATGCTGATGTGTTT 59.136 33.333 18.71 0.00 0.00 2.83
2426 3804 7.365741 CAGTTTTTCTAGAATGCTGATGTGTT 58.634 34.615 18.71 0.00 0.00 3.32
2427 3805 6.569226 GCAGTTTTTCTAGAATGCTGATGTGT 60.569 38.462 23.79 0.00 0.00 3.72
2428 3806 5.798934 GCAGTTTTTCTAGAATGCTGATGTG 59.201 40.000 23.79 10.23 0.00 3.21
2429 3807 5.709164 AGCAGTTTTTCTAGAATGCTGATGT 59.291 36.000 23.88 6.20 42.11 3.06
2430 3808 6.192234 AGCAGTTTTTCTAGAATGCTGATG 57.808 37.500 23.88 12.26 42.11 3.07
2431 3809 8.404000 CAATAGCAGTTTTTCTAGAATGCTGAT 58.596 33.333 29.11 23.85 43.41 2.90
2432 3810 7.391554 ACAATAGCAGTTTTTCTAGAATGCTGA 59.608 33.333 29.11 18.48 43.41 4.26
2433 3811 7.533426 ACAATAGCAGTTTTTCTAGAATGCTG 58.467 34.615 29.11 23.88 43.41 4.41
2434 3812 7.693969 ACAATAGCAGTTTTTCTAGAATGCT 57.306 32.000 26.27 26.27 45.35 3.79
2435 3813 8.883731 TCTACAATAGCAGTTTTTCTAGAATGC 58.116 33.333 17.33 17.33 0.00 3.56
2441 3819 9.772973 TGTTCTTCTACAATAGCAGTTTTTCTA 57.227 29.630 0.00 0.00 0.00 2.10
2442 3820 8.677148 TGTTCTTCTACAATAGCAGTTTTTCT 57.323 30.769 0.00 0.00 0.00 2.52
2445 3823 9.944376 TCTATGTTCTTCTACAATAGCAGTTTT 57.056 29.630 0.00 0.00 0.00 2.43
2446 3824 9.593134 CTCTATGTTCTTCTACAATAGCAGTTT 57.407 33.333 0.00 0.00 0.00 2.66
2447 3825 8.972127 TCTCTATGTTCTTCTACAATAGCAGTT 58.028 33.333 0.00 0.00 0.00 3.16
2448 3826 8.410141 GTCTCTATGTTCTTCTACAATAGCAGT 58.590 37.037 0.00 0.00 0.00 4.40
2449 3827 8.409371 TGTCTCTATGTTCTTCTACAATAGCAG 58.591 37.037 0.00 0.00 0.00 4.24
2450 3828 8.293699 TGTCTCTATGTTCTTCTACAATAGCA 57.706 34.615 0.00 0.00 0.00 3.49
2451 3829 9.757227 ATTGTCTCTATGTTCTTCTACAATAGC 57.243 33.333 0.00 0.00 35.25 2.97
2456 3834 9.996554 TGAAAATTGTCTCTATGTTCTTCTACA 57.003 29.630 0.00 0.00 0.00 2.74
2459 3837 8.997323 CAGTGAAAATTGTCTCTATGTTCTTCT 58.003 33.333 0.00 0.00 0.00 2.85
2460 3838 8.778358 ACAGTGAAAATTGTCTCTATGTTCTTC 58.222 33.333 0.00 0.00 0.00 2.87
2461 3839 8.682936 ACAGTGAAAATTGTCTCTATGTTCTT 57.317 30.769 0.00 0.00 0.00 2.52
2462 3840 9.429359 CTACAGTGAAAATTGTCTCTATGTTCT 57.571 33.333 0.00 0.00 0.00 3.01
2463 3841 8.171840 GCTACAGTGAAAATTGTCTCTATGTTC 58.828 37.037 0.00 0.00 0.00 3.18
2464 3842 7.661437 TGCTACAGTGAAAATTGTCTCTATGTT 59.339 33.333 0.00 0.00 0.00 2.71
2465 3843 7.161404 TGCTACAGTGAAAATTGTCTCTATGT 58.839 34.615 0.00 0.04 0.00 2.29
2466 3844 7.601073 TGCTACAGTGAAAATTGTCTCTATG 57.399 36.000 0.00 0.00 0.00 2.23
2468 3846 9.890629 AATATGCTACAGTGAAAATTGTCTCTA 57.109 29.630 0.00 0.00 0.00 2.43
2469 3847 8.671921 CAATATGCTACAGTGAAAATTGTCTCT 58.328 33.333 0.00 0.00 0.00 3.10
2470 3848 7.430502 GCAATATGCTACAGTGAAAATTGTCTC 59.569 37.037 0.00 0.00 40.96 3.36
2471 3849 7.253422 GCAATATGCTACAGTGAAAATTGTCT 58.747 34.615 0.00 0.00 40.96 3.41
2472 3850 6.195244 CGCAATATGCTACAGTGAAAATTGTC 59.805 38.462 0.00 0.00 42.25 3.18
2473 3851 6.029607 CGCAATATGCTACAGTGAAAATTGT 58.970 36.000 0.00 0.00 42.25 2.71
2474 3852 6.029607 ACGCAATATGCTACAGTGAAAATTG 58.970 36.000 0.00 0.00 42.25 2.32
2475 3853 6.194796 ACGCAATATGCTACAGTGAAAATT 57.805 33.333 0.00 0.00 42.25 1.82
2476 3854 5.818136 ACGCAATATGCTACAGTGAAAAT 57.182 34.783 0.00 0.00 42.25 1.82
2477 3855 6.918892 ATACGCAATATGCTACAGTGAAAA 57.081 33.333 0.00 0.00 42.25 2.29
2478 3856 7.169140 CAGTATACGCAATATGCTACAGTGAAA 59.831 37.037 0.00 0.00 42.25 2.69
2479 3857 6.640907 CAGTATACGCAATATGCTACAGTGAA 59.359 38.462 0.00 0.00 42.25 3.18
2480 3858 6.149633 CAGTATACGCAATATGCTACAGTGA 58.850 40.000 0.00 0.00 42.25 3.41
2481 3859 5.346011 CCAGTATACGCAATATGCTACAGTG 59.654 44.000 0.00 0.00 42.25 3.66
2482 3860 5.470368 CCAGTATACGCAATATGCTACAGT 58.530 41.667 0.00 0.00 42.25 3.55
2483 3861 4.327357 GCCAGTATACGCAATATGCTACAG 59.673 45.833 0.00 0.00 42.25 2.74
2484 3862 4.242475 GCCAGTATACGCAATATGCTACA 58.758 43.478 0.00 0.00 42.25 2.74
2485 3863 4.242475 TGCCAGTATACGCAATATGCTAC 58.758 43.478 3.29 0.00 42.25 3.58
2486 3864 4.529109 TGCCAGTATACGCAATATGCTA 57.471 40.909 3.29 0.00 42.25 3.49
2487 3865 3.401033 TGCCAGTATACGCAATATGCT 57.599 42.857 3.29 0.00 42.25 3.79
2488 3866 3.436704 ACATGCCAGTATACGCAATATGC 59.563 43.478 9.13 0.00 38.75 3.14
2489 3867 4.452114 ACACATGCCAGTATACGCAATATG 59.548 41.667 9.13 9.76 38.75 1.78
2490 3868 4.641396 ACACATGCCAGTATACGCAATAT 58.359 39.130 9.13 0.00 38.75 1.28
2491 3869 4.055360 GACACATGCCAGTATACGCAATA 58.945 43.478 9.13 0.00 38.75 1.90
2492 3870 2.872245 GACACATGCCAGTATACGCAAT 59.128 45.455 9.13 0.00 38.75 3.56
2493 3871 2.276201 GACACATGCCAGTATACGCAA 58.724 47.619 9.13 0.00 38.75 4.85
2494 3872 1.472552 GGACACATGCCAGTATACGCA 60.473 52.381 7.74 7.74 39.79 5.24
2495 3873 1.202533 AGGACACATGCCAGTATACGC 60.203 52.381 0.00 0.00 0.00 4.42
2496 3874 2.890808 AGGACACATGCCAGTATACG 57.109 50.000 0.00 0.00 0.00 3.06
2497 3875 4.049186 CGTAAGGACACATGCCAGTATAC 58.951 47.826 0.00 0.00 0.00 1.47
2498 3876 3.491964 GCGTAAGGACACATGCCAGTATA 60.492 47.826 0.00 0.00 38.28 1.47
2499 3877 2.741878 GCGTAAGGACACATGCCAGTAT 60.742 50.000 0.00 0.00 38.28 2.12
2500 3878 1.404986 GCGTAAGGACACATGCCAGTA 60.405 52.381 0.00 0.00 38.28 2.74
2501 3879 0.673644 GCGTAAGGACACATGCCAGT 60.674 55.000 0.00 0.00 38.28 4.00
2502 3880 0.391661 AGCGTAAGGACACATGCCAG 60.392 55.000 0.00 0.00 38.28 4.85
2503 3881 0.899019 TAGCGTAAGGACACATGCCA 59.101 50.000 0.00 0.00 38.28 4.92
2504 3882 1.933853 CTTAGCGTAAGGACACATGCC 59.066 52.381 0.00 0.00 38.28 4.40
2505 3883 2.348666 CACTTAGCGTAAGGACACATGC 59.651 50.000 0.00 0.00 40.08 4.06
2506 3884 3.612860 GTCACTTAGCGTAAGGACACATG 59.387 47.826 0.00 0.00 40.08 3.21
2507 3885 3.510360 AGTCACTTAGCGTAAGGACACAT 59.490 43.478 17.55 5.77 40.08 3.21
2508 3886 2.889045 AGTCACTTAGCGTAAGGACACA 59.111 45.455 17.55 0.00 40.08 3.72
2509 3887 3.572604 AGTCACTTAGCGTAAGGACAC 57.427 47.619 17.55 9.51 40.08 3.67
2510 3888 3.128242 GCTAGTCACTTAGCGTAAGGACA 59.872 47.826 17.55 9.97 40.08 4.02
2511 3889 3.693654 GCTAGTCACTTAGCGTAAGGAC 58.306 50.000 8.83 11.06 40.08 3.85
2519 3897 3.691609 AGCCAAAATGCTAGTCACTTAGC 59.308 43.478 0.00 0.00 44.97 3.09
2520 3898 4.333926 GGAGCCAAAATGCTAGTCACTTAG 59.666 45.833 0.00 0.00 42.95 2.18
2521 3899 4.261801 GGAGCCAAAATGCTAGTCACTTA 58.738 43.478 0.00 0.00 42.95 2.24
2522 3900 3.084786 GGAGCCAAAATGCTAGTCACTT 58.915 45.455 0.00 0.00 42.95 3.16
2523 3901 2.619074 GGGAGCCAAAATGCTAGTCACT 60.619 50.000 0.00 0.00 42.95 3.41
2524 3902 1.745653 GGGAGCCAAAATGCTAGTCAC 59.254 52.381 0.00 0.00 42.95 3.67
2525 3903 1.678728 CGGGAGCCAAAATGCTAGTCA 60.679 52.381 0.00 0.00 42.95 3.41
2526 3904 1.017387 CGGGAGCCAAAATGCTAGTC 58.983 55.000 0.00 0.00 42.95 2.59
2527 3905 0.328258 ACGGGAGCCAAAATGCTAGT 59.672 50.000 0.00 0.00 42.95 2.57
2528 3906 0.734889 CACGGGAGCCAAAATGCTAG 59.265 55.000 0.00 0.00 42.95 3.42
2529 3907 0.037590 ACACGGGAGCCAAAATGCTA 59.962 50.000 0.00 0.00 42.95 3.49
2530 3908 1.228552 ACACGGGAGCCAAAATGCT 60.229 52.632 0.00 0.00 46.37 3.79
2531 3909 1.212751 GACACGGGAGCCAAAATGC 59.787 57.895 0.00 0.00 0.00 3.56
2532 3910 0.893270 TGGACACGGGAGCCAAAATG 60.893 55.000 0.00 0.00 0.00 2.32
2533 3911 0.039618 ATGGACACGGGAGCCAAAAT 59.960 50.000 8.02 0.00 34.95 1.82
2534 3912 0.608035 GATGGACACGGGAGCCAAAA 60.608 55.000 8.02 0.00 34.95 2.44
2535 3913 1.002624 GATGGACACGGGAGCCAAA 60.003 57.895 8.02 0.00 34.95 3.28
2536 3914 0.616395 TAGATGGACACGGGAGCCAA 60.616 55.000 8.02 0.00 34.95 4.52
2537 3915 1.001120 TAGATGGACACGGGAGCCA 59.999 57.895 6.49 6.49 35.91 4.75
2538 3916 1.043673 AGTAGATGGACACGGGAGCC 61.044 60.000 0.00 0.00 0.00 4.70
2539 3917 0.386113 GAGTAGATGGACACGGGAGC 59.614 60.000 0.00 0.00 0.00 4.70
2540 3918 1.950909 GAGAGTAGATGGACACGGGAG 59.049 57.143 0.00 0.00 0.00 4.30
2541 3919 1.746171 CGAGAGTAGATGGACACGGGA 60.746 57.143 0.00 0.00 0.00 5.14
2542 3920 0.663688 CGAGAGTAGATGGACACGGG 59.336 60.000 0.00 0.00 0.00 5.28
2543 3921 1.664873 TCGAGAGTAGATGGACACGG 58.335 55.000 0.00 0.00 0.00 4.94
2544 3922 4.932799 AGATATCGAGAGTAGATGGACACG 59.067 45.833 0.00 0.00 0.00 4.49
2545 3923 5.123186 CCAGATATCGAGAGTAGATGGACAC 59.877 48.000 0.00 0.00 0.00 3.67
2546 3924 5.013183 TCCAGATATCGAGAGTAGATGGACA 59.987 44.000 0.00 0.00 0.00 4.02
2547 3925 5.353123 GTCCAGATATCGAGAGTAGATGGAC 59.647 48.000 15.24 15.24 33.40 4.02
2548 3926 5.492895 GTCCAGATATCGAGAGTAGATGGA 58.507 45.833 0.00 0.00 0.00 3.41
2549 3927 4.638421 GGTCCAGATATCGAGAGTAGATGG 59.362 50.000 0.00 0.00 0.00 3.51
2550 3928 5.249420 TGGTCCAGATATCGAGAGTAGATG 58.751 45.833 0.00 0.00 0.00 2.90
2551 3929 5.506730 TGGTCCAGATATCGAGAGTAGAT 57.493 43.478 0.00 0.00 0.00 1.98
2552 3930 4.976540 TGGTCCAGATATCGAGAGTAGA 57.023 45.455 0.00 0.00 0.00 2.59
2553 3931 4.638421 GGATGGTCCAGATATCGAGAGTAG 59.362 50.000 0.00 0.00 36.28 2.57
2554 3932 4.042934 TGGATGGTCCAGATATCGAGAGTA 59.957 45.833 0.00 0.00 42.67 2.59
2555 3933 3.181428 TGGATGGTCCAGATATCGAGAGT 60.181 47.826 0.00 0.00 42.67 3.24
2556 3934 3.425659 TGGATGGTCCAGATATCGAGAG 58.574 50.000 0.00 0.00 42.67 3.20
2557 3935 3.525800 TGGATGGTCCAGATATCGAGA 57.474 47.619 0.00 0.00 42.67 4.04
2567 3945 3.392947 TCAACTACAACTTGGATGGTCCA 59.607 43.478 0.00 0.00 46.61 4.02
2568 3946 4.003648 CTCAACTACAACTTGGATGGTCC 58.996 47.826 0.00 0.00 36.96 4.46
2569 3947 4.894784 TCTCAACTACAACTTGGATGGTC 58.105 43.478 0.00 0.00 0.00 4.02
2570 3948 4.974645 TCTCAACTACAACTTGGATGGT 57.025 40.909 0.00 0.00 0.00 3.55
2571 3949 6.207417 ACAAATCTCAACTACAACTTGGATGG 59.793 38.462 0.00 0.00 0.00 3.51
2572 3950 7.080099 CACAAATCTCAACTACAACTTGGATG 58.920 38.462 0.00 0.00 0.00 3.51
2573 3951 6.294176 GCACAAATCTCAACTACAACTTGGAT 60.294 38.462 0.00 0.00 0.00 3.41
2574 3952 5.008613 GCACAAATCTCAACTACAACTTGGA 59.991 40.000 0.00 0.00 0.00 3.53
2575 3953 5.215160 GCACAAATCTCAACTACAACTTGG 58.785 41.667 0.00 0.00 0.00 3.61
2576 3954 5.215160 GGCACAAATCTCAACTACAACTTG 58.785 41.667 0.00 0.00 0.00 3.16
2577 3955 4.887071 TGGCACAAATCTCAACTACAACTT 59.113 37.500 0.00 0.00 31.92 2.66
2578 3956 4.460263 TGGCACAAATCTCAACTACAACT 58.540 39.130 0.00 0.00 31.92 3.16
2579 3957 4.829064 TGGCACAAATCTCAACTACAAC 57.171 40.909 0.00 0.00 31.92 3.32
2589 3967 7.599998 GTCAGTAATTGATTTTGGCACAAATCT 59.400 33.333 23.15 13.42 40.54 2.40
2590 3968 7.384660 TGTCAGTAATTGATTTTGGCACAAATC 59.615 33.333 19.37 19.37 40.54 2.17
2591 3969 7.215789 TGTCAGTAATTGATTTTGGCACAAAT 58.784 30.769 7.16 7.16 40.54 2.32
2592 3970 6.577103 TGTCAGTAATTGATTTTGGCACAAA 58.423 32.000 0.00 0.00 40.54 2.83
2593 3971 6.154203 TGTCAGTAATTGATTTTGGCACAA 57.846 33.333 0.00 0.00 40.54 3.33
2594 3972 5.781210 TGTCAGTAATTGATTTTGGCACA 57.219 34.783 0.00 0.00 38.29 4.57
2595 3973 5.982516 TGTTGTCAGTAATTGATTTTGGCAC 59.017 36.000 0.00 0.00 38.29 5.01
2596 3974 6.154203 TGTTGTCAGTAATTGATTTTGGCA 57.846 33.333 0.00 0.00 38.29 4.92
2597 3975 8.810427 CATATGTTGTCAGTAATTGATTTTGGC 58.190 33.333 0.00 0.00 38.29 4.52
2598 3976 9.859427 ACATATGTTGTCAGTAATTGATTTTGG 57.141 29.630 1.41 0.00 38.29 3.28
2600 3978 9.357652 GCACATATGTTGTCAGTAATTGATTTT 57.642 29.630 5.37 0.00 38.29 1.82
2601 3979 8.522003 TGCACATATGTTGTCAGTAATTGATTT 58.478 29.630 5.37 0.00 38.29 2.17
2602 3980 8.054152 TGCACATATGTTGTCAGTAATTGATT 57.946 30.769 5.37 0.00 38.29 2.57
2603 3981 7.628769 TGCACATATGTTGTCAGTAATTGAT 57.371 32.000 5.37 0.00 38.29 2.57
2604 3982 7.474190 CATGCACATATGTTGTCAGTAATTGA 58.526 34.615 5.37 0.00 36.00 2.57
2605 3983 6.197655 GCATGCACATATGTTGTCAGTAATTG 59.802 38.462 14.21 1.60 36.00 2.32
2606 3984 6.127675 TGCATGCACATATGTTGTCAGTAATT 60.128 34.615 18.46 0.00 36.00 1.40
2607 3985 5.357596 TGCATGCACATATGTTGTCAGTAAT 59.642 36.000 18.46 0.00 36.00 1.89
2608 3986 4.699257 TGCATGCACATATGTTGTCAGTAA 59.301 37.500 18.46 0.00 36.00 2.24
2609 3987 4.260170 TGCATGCACATATGTTGTCAGTA 58.740 39.130 18.46 0.00 36.00 2.74
2610 3988 3.083293 TGCATGCACATATGTTGTCAGT 58.917 40.909 18.46 0.00 36.00 3.41
2611 3989 3.768468 TGCATGCACATATGTTGTCAG 57.232 42.857 18.46 0.00 36.00 3.51
2612 3990 5.831702 TTATGCATGCACATATGTTGTCA 57.168 34.783 25.37 5.21 36.00 3.58
2613 3991 6.267817 AGTTTATGCATGCACATATGTTGTC 58.732 36.000 25.37 5.54 36.00 3.18
2614 3992 6.211587 AGTTTATGCATGCACATATGTTGT 57.788 33.333 25.37 6.17 39.91 3.32
2615 3993 5.397240 CGAGTTTATGCATGCACATATGTTG 59.603 40.000 25.37 6.58 32.71 3.33
2616 3994 5.066375 ACGAGTTTATGCATGCACATATGTT 59.934 36.000 25.37 7.84 32.71 2.71
2617 3995 4.576053 ACGAGTTTATGCATGCACATATGT 59.424 37.500 25.37 12.85 32.71 2.29
2618 3996 4.907582 CACGAGTTTATGCATGCACATATG 59.092 41.667 25.37 12.19 32.71 1.78
2619 3997 4.576053 ACACGAGTTTATGCATGCACATAT 59.424 37.500 25.37 9.96 32.71 1.78
2620 3998 3.938334 ACACGAGTTTATGCATGCACATA 59.062 39.130 25.37 10.03 0.00 2.29
2621 3999 2.749076 ACACGAGTTTATGCATGCACAT 59.251 40.909 25.37 11.24 0.00 3.21
2622 4000 2.150390 ACACGAGTTTATGCATGCACA 58.850 42.857 25.37 9.23 0.00 4.57
2623 4001 2.900122 ACACGAGTTTATGCATGCAC 57.100 45.000 25.37 10.53 0.00 4.57
2624 4002 4.633565 TGAATACACGAGTTTATGCATGCA 59.366 37.500 25.04 25.04 0.00 3.96
2625 4003 5.155509 TGAATACACGAGTTTATGCATGC 57.844 39.130 11.82 11.82 0.00 4.06
2626 4004 7.827156 GAATGAATACACGAGTTTATGCATG 57.173 36.000 10.16 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.