Multiple sequence alignment - TraesCS5A01G366100

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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 TraesCS5A01G366100 chr5A 100.000 7512 0 0 1 7512 565759474 565751963 0.000000e+00 13873.0
1 TraesCS5A01G366100 chr5B 94.460 5217 194 42 1533 6706 546831460 546826296 0.000000e+00 7945.0
2 TraesCS5A01G366100 chr5B 87.953 1461 124 30 89 1533 546832936 546831512 0.000000e+00 1676.0
3 TraesCS5A01G366100 chr5B 87.561 820 78 14 6699 7510 546820064 546819261 0.000000e+00 928.0
4 TraesCS5A01G366100 chr5D 94.156 2584 130 12 4174 6743 447882980 447880404 0.000000e+00 3916.0
5 TraesCS5A01G366100 chr5D 90.877 1721 117 23 108 1808 447886989 447885289 0.000000e+00 2272.0
6 TraesCS5A01G366100 chr5D 91.092 797 45 10 2862 3643 447884364 447883579 0.000000e+00 1055.0
7 TraesCS5A01G366100 chr5D 88.582 832 64 13 1935 2763 447885165 447884362 0.000000e+00 981.0
8 TraesCS5A01G366100 chr5D 86.334 461 32 7 3722 4176 447883446 447883011 2.450000e-129 473.0
9 TraesCS5A01G366100 chr5D 97.297 37 1 0 3683 3719 447883583 447883547 6.290000e-06 63.9
10 TraesCS5A01G366100 chr7A 91.954 261 20 1 1549 1809 96203778 96204037 1.540000e-96 364.0
11 TraesCS5A01G366100 chr7A 92.520 254 17 1 1935 2188 96204158 96204409 5.540000e-96 363.0
12 TraesCS5A01G366100 chr7A 96.104 77 3 0 1457 1533 96203646 96203722 7.910000e-25 126.0
13 TraesCS5A01G366100 chr2A 91.188 261 22 1 1549 1809 622753335 622753594 3.330000e-93 353.0
14 TraesCS5A01G366100 chr2A 91.732 254 19 1 1935 2188 622753715 622753966 1.200000e-92 351.0
15 TraesCS5A01G366100 chr2A 91.085 258 22 1 1552 1809 108513246 108512990 1.550000e-91 348.0
16 TraesCS5A01G366100 chr2A 89.370 254 24 2 1935 2188 108512869 108512619 4.370000e-82 316.0
17 TraesCS5A01G366100 chr2A 96.104 77 3 0 1457 1533 108513381 108513305 7.910000e-25 126.0
18 TraesCS5A01G366100 chr2A 100.000 31 0 0 5899 5929 497652988 497652958 2.930000e-04 58.4
19 TraesCS5A01G366100 chr2B 80.769 208 36 2 7305 7512 66484344 66484547 7.800000e-35 159.0
20 TraesCS5A01G366100 chr2B 79.412 136 19 7 7301 7432 375170404 375170534 3.730000e-13 87.9
21 TraesCS5A01G366100 chr2D 94.595 37 2 0 5899 5935 367503058 367503022 2.930000e-04 58.4


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 TraesCS5A01G366100 chr5A 565751963 565759474 7511 True 13873.000000 13873 100.000000 1 7512 1 chr5A.!!$R1 7511
1 TraesCS5A01G366100 chr5B 546826296 546832936 6640 True 4810.500000 7945 91.206500 89 6706 2 chr5B.!!$R2 6617
2 TraesCS5A01G366100 chr5B 546819261 546820064 803 True 928.000000 928 87.561000 6699 7510 1 chr5B.!!$R1 811
3 TraesCS5A01G366100 chr5D 447880404 447886989 6585 True 1460.150000 3916 91.389667 108 6743 6 chr5D.!!$R1 6635
4 TraesCS5A01G366100 chr7A 96203646 96204409 763 False 284.333333 364 93.526000 1457 2188 3 chr7A.!!$F1 731
5 TraesCS5A01G366100 chr2A 622753335 622753966 631 False 352.000000 353 91.460000 1549 2188 2 chr2A.!!$F1 639
6 TraesCS5A01G366100 chr2A 108512619 108513381 762 True 263.333333 348 92.186333 1457 2188 3 chr2A.!!$R2 731

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
660 671 0.249398 GAGGTAAGCCGTCACCATGT 59.751 55.000 0.00 0.0 40.50 3.21 F
1342 1373 0.531532 CGGCCTTGCTCTCCTGTATG 60.532 60.000 0.00 0.0 0.00 2.39 F
2685 2812 0.250338 GGACCCGTGTTCTTCTGCTT 60.250 55.000 0.00 0.0 0.00 3.91 F
2799 2927 0.308684 CATTGCGTTGCACAGACACT 59.691 50.000 0.00 0.0 38.71 3.55 F
3403 3548 0.902984 ATCCAGTACACGACCTGGCA 60.903 55.000 0.00 0.0 36.94 4.92 F
4449 4744 1.480954 GATAGGTCGGTTCTCAAGGCA 59.519 52.381 0.00 0.0 0.00 4.75 F
4907 5203 2.945008 GCAATATACTGGTCAAGCTGCA 59.055 45.455 1.02 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2159 0.327924 TCTGCACATACAACAGGGGG 59.672 55.000 0.0 0.0 32.19 5.40 R
2843 2971 0.550914 TGCAGAGAAACACAAGGGGT 59.449 50.000 0.0 0.0 0.00 4.95 R
4187 4474 0.538057 ACTGTTCCCATGCACACCAG 60.538 55.000 0.0 0.0 0.00 4.00 R
4189 4476 1.904287 TAACTGTTCCCATGCACACC 58.096 50.000 0.0 0.0 0.00 4.16 R
5333 5637 1.444119 AAACACACATCGCAACCGCT 61.444 50.000 0.0 0.0 35.30 5.52 R
5585 5889 1.300465 CATGACGAGGAGGATGGCG 60.300 63.158 0.0 0.0 0.00 5.69 R
6856 7160 0.255033 TGTCCTAGCAGTAGAGGCGA 59.745 55.000 0.0 0.0 36.08 5.54 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
32 33 8.959676 AAAATATACCAAAGTTTAAGACCCCA 57.040 30.769 0.00 0.00 0.00 4.96
33 34 9.555411 AAAATATACCAAAGTTTAAGACCCCAT 57.445 29.630 0.00 0.00 0.00 4.00
34 35 9.555411 AAATATACCAAAGTTTAAGACCCCATT 57.445 29.630 0.00 0.00 0.00 3.16
35 36 9.555411 AATATACCAAAGTTTAAGACCCCATTT 57.445 29.630 0.00 0.00 0.00 2.32
40 41 9.555411 ACCAAAGTTTAAGACCCCATTTATATT 57.445 29.630 0.00 0.00 0.00 1.28
61 62 3.715628 AATATTGAATCGCAACTGCCC 57.284 42.857 0.00 0.00 39.78 5.36
62 63 2.121291 TATTGAATCGCAACTGCCCA 57.879 45.000 0.00 0.00 39.78 5.36
63 64 1.255882 ATTGAATCGCAACTGCCCAA 58.744 45.000 0.00 0.00 39.78 4.12
64 65 1.035923 TTGAATCGCAACTGCCCAAA 58.964 45.000 0.00 0.00 37.91 3.28
65 66 1.035923 TGAATCGCAACTGCCCAAAA 58.964 45.000 0.00 0.00 37.91 2.44
66 67 1.000385 TGAATCGCAACTGCCCAAAAG 60.000 47.619 0.00 0.00 37.91 2.27
67 68 0.319813 AATCGCAACTGCCCAAAAGC 60.320 50.000 0.00 0.00 37.91 3.51
68 69 1.462731 ATCGCAACTGCCCAAAAGCA 61.463 50.000 0.00 0.00 41.46 3.91
69 70 1.227205 CGCAACTGCCCAAAAGCAA 60.227 52.632 0.00 0.00 43.52 3.91
70 71 1.489881 CGCAACTGCCCAAAAGCAAC 61.490 55.000 0.00 0.00 43.52 4.17
71 72 0.461693 GCAACTGCCCAAAAGCAACA 60.462 50.000 0.00 0.00 43.52 3.33
72 73 1.289276 CAACTGCCCAAAAGCAACAC 58.711 50.000 0.00 0.00 43.52 3.32
73 74 0.901124 AACTGCCCAAAAGCAACACA 59.099 45.000 0.00 0.00 43.52 3.72
74 75 1.122227 ACTGCCCAAAAGCAACACAT 58.878 45.000 0.00 0.00 43.52 3.21
75 76 1.485895 ACTGCCCAAAAGCAACACATT 59.514 42.857 0.00 0.00 43.52 2.71
76 77 2.093021 ACTGCCCAAAAGCAACACATTT 60.093 40.909 0.00 0.00 43.52 2.32
77 78 2.944349 CTGCCCAAAAGCAACACATTTT 59.056 40.909 0.00 0.00 43.52 1.82
78 79 3.350833 TGCCCAAAAGCAACACATTTTT 58.649 36.364 0.00 0.00 40.56 1.94
147 148 2.364186 GGTGGGCCTTTCATGGGG 60.364 66.667 4.53 0.00 0.00 4.96
193 194 3.455543 CCAAATGTTGGCATAAATCCCCT 59.544 43.478 0.00 0.00 45.17 4.79
204 205 6.671779 TGGCATAAATCCCCTTGTTTAATCTT 59.328 34.615 0.00 0.00 0.00 2.40
220 221 4.961438 AATCTTGTGGGCATGTCTTTTT 57.039 36.364 0.00 0.00 0.00 1.94
222 223 3.295093 TCTTGTGGGCATGTCTTTTTCA 58.705 40.909 0.00 0.00 0.00 2.69
242 244 5.745312 TCAAGGAAAGAAGAGACATGCTA 57.255 39.130 0.00 0.00 0.00 3.49
245 247 3.118956 AGGAAAGAAGAGACATGCTACCG 60.119 47.826 0.00 0.00 0.00 4.02
312 314 7.041107 GCCCACTTAGATTATTTCAAATGCAA 58.959 34.615 0.00 0.00 0.00 4.08
314 316 8.872845 CCCACTTAGATTATTTCAAATGCAAAC 58.127 33.333 0.00 0.00 0.00 2.93
352 355 6.708949 GTCATTAGGTTCCTGTTGTTGTCTTA 59.291 38.462 1.12 0.00 0.00 2.10
361 364 2.811431 TGTTGTTGTCTTATTGCCTCCG 59.189 45.455 0.00 0.00 0.00 4.63
363 366 3.627395 TGTTGTCTTATTGCCTCCGAT 57.373 42.857 0.00 0.00 0.00 4.18
366 369 5.116180 TGTTGTCTTATTGCCTCCGATAAG 58.884 41.667 4.90 4.90 42.85 1.73
409 419 3.058708 CGTATGTGGTGGCATGATTCATC 60.059 47.826 0.00 0.00 0.00 2.92
428 438 0.934496 CTCGTGCCAAGTCGTTTTCA 59.066 50.000 0.00 0.00 0.00 2.69
432 442 2.223157 CGTGCCAAGTCGTTTTCAAAGA 60.223 45.455 0.00 0.00 0.00 2.52
433 443 3.105937 GTGCCAAGTCGTTTTCAAAGAC 58.894 45.455 0.00 0.00 35.30 3.01
456 466 7.559897 AGACGGTGGTTTAATTATTTGGATCAT 59.440 33.333 0.00 0.00 0.00 2.45
462 472 7.866898 TGGTTTAATTATTTGGATCATGATGCG 59.133 33.333 20.61 0.00 31.21 4.73
467 477 2.416680 TTGGATCATGATGCGGACAA 57.583 45.000 20.61 7.98 31.21 3.18
497 507 2.497675 GCTAGCATCGGGATCCTATTCA 59.502 50.000 12.58 0.00 0.00 2.57
505 515 1.416401 GGGATCCTATTCAGAACGCCA 59.584 52.381 12.58 0.00 0.00 5.69
553 563 1.869132 CGAATGACGCACCATCATCAT 59.131 47.619 0.00 0.00 35.72 2.45
627 637 8.507524 AGTAGCCATAGACAAGTTAAAATTCC 57.492 34.615 0.00 0.00 0.00 3.01
648 659 6.525578 TCCATTATAGTATGCCGAGGTAAG 57.474 41.667 0.00 0.00 0.00 2.34
660 671 0.249398 GAGGTAAGCCGTCACCATGT 59.751 55.000 0.00 0.00 40.50 3.21
661 672 1.479323 GAGGTAAGCCGTCACCATGTA 59.521 52.381 0.00 0.00 40.50 2.29
688 699 2.067013 GACTAACTTGCCGAGACAACC 58.933 52.381 0.00 0.00 0.00 3.77
709 720 5.238583 ACCTCTCAAGGATAACAAAACTCG 58.761 41.667 0.00 0.00 46.67 4.18
724 735 5.065988 ACAAAACTCGCAAACTCACTAACAT 59.934 36.000 0.00 0.00 0.00 2.71
725 736 4.732285 AACTCGCAAACTCACTAACATG 57.268 40.909 0.00 0.00 0.00 3.21
727 738 2.416547 CTCGCAAACTCACTAACATGGG 59.583 50.000 0.00 0.00 0.00 4.00
740 751 2.028420 ACATGGGTGACATCGACATG 57.972 50.000 8.01 8.01 43.29 3.21
811 822 1.004277 ACAAACACCCCATACGCTGAT 59.996 47.619 0.00 0.00 0.00 2.90
861 873 0.676782 CCTGCCGGTTCCTCGAAAAT 60.677 55.000 1.90 0.00 0.00 1.82
863 875 2.352388 CTGCCGGTTCCTCGAAAATAA 58.648 47.619 1.90 0.00 0.00 1.40
865 877 3.349022 TGCCGGTTCCTCGAAAATAAAT 58.651 40.909 1.90 0.00 0.00 1.40
936 950 4.392940 CTCCCATTTATGCTCCTCGAATT 58.607 43.478 0.00 0.00 0.00 2.17
947 961 3.804873 GCTCCTCGAATTATTGGAGACAC 59.195 47.826 17.71 3.71 46.53 3.67
1004 1018 1.066858 TCTCTGCTCCACATCCGAAAC 60.067 52.381 0.00 0.00 0.00 2.78
1044 1061 2.648318 GCGCCGCAAGAAGCAAAAC 61.648 57.895 3.15 0.00 46.13 2.43
1294 1324 1.678101 GTTGCTTTTGACTGCCTCTGT 59.322 47.619 0.00 0.00 0.00 3.41
1312 1343 0.961753 GTGCCTTTTGGAACCCTCTG 59.038 55.000 0.00 0.00 42.60 3.35
1342 1373 0.531532 CGGCCTTGCTCTCCTGTATG 60.532 60.000 0.00 0.00 0.00 2.39
1510 1544 5.801350 AATGAGATATGTTGTCGTTGGTG 57.199 39.130 0.00 0.00 0.00 4.17
1558 1645 8.189119 AGACTGAGATAGTTCTTGACTTCTTT 57.811 34.615 0.00 0.00 40.53 2.52
1607 1694 1.202915 TGCTGATTGACTGGCCTGAAA 60.203 47.619 17.64 10.46 0.00 2.69
1641 1728 2.322161 GAGACCGTTTCGACGAATGAA 58.678 47.619 11.71 0.00 34.64 2.57
1648 1735 2.798283 GTTTCGACGAATGAAGACACCA 59.202 45.455 11.71 0.00 0.00 4.17
1680 1767 1.140312 TGTGGGAGCTGGAAAAGAGT 58.860 50.000 0.00 0.00 0.00 3.24
1698 1785 2.106166 GAGTCTTGATCAGCCCATGGAT 59.894 50.000 15.22 0.00 0.00 3.41
1824 1916 5.982516 TGCAGTATTTTGTTTGACACAATCC 59.017 36.000 0.00 0.00 45.17 3.01
1888 1980 4.082625 TGGCTTTAGCATTGAACATCACAG 60.083 41.667 3.88 0.00 44.36 3.66
1920 2029 6.560003 TTTGTAGAGCATTCTCCCTGATAA 57.440 37.500 0.00 0.00 40.22 1.75
1967 2090 5.316167 TGCAGAGTCATTTGGTGTCTTTAT 58.684 37.500 0.00 0.00 0.00 1.40
1982 2107 8.744652 TGGTGTCTTTATTTTGAACTTCTGAAA 58.255 29.630 0.00 0.00 0.00 2.69
2034 2159 2.700722 TTGTTTTTGCCCTGTTTCCC 57.299 45.000 0.00 0.00 0.00 3.97
2035 2160 0.833949 TGTTTTTGCCCTGTTTCCCC 59.166 50.000 0.00 0.00 0.00 4.81
2058 2183 3.118261 CCCTGTTGTATGTGCAGACCTAT 60.118 47.826 0.00 0.00 32.39 2.57
2112 2237 2.026945 GCCTTGGTGTGGTGTTTGGG 62.027 60.000 0.00 0.00 0.00 4.12
2175 2300 5.923733 TTCCTGAGAAGATAGAAGACACC 57.076 43.478 0.00 0.00 0.00 4.16
2289 2414 6.438763 CGATAATGGCCAAGGTAAGAATTTC 58.561 40.000 10.96 0.00 0.00 2.17
2308 2433 5.902613 TTTCTGCCTCAGTTATGGAAATG 57.097 39.130 0.00 0.00 32.61 2.32
2328 2453 7.309194 GGAAATGTTAAACTGTTCATAGCTGGT 60.309 37.037 0.00 0.00 0.00 4.00
2329 2454 6.743575 ATGTTAAACTGTTCATAGCTGGTC 57.256 37.500 0.00 0.00 0.00 4.02
2330 2455 5.001232 TGTTAAACTGTTCATAGCTGGTCC 58.999 41.667 0.00 0.00 0.00 4.46
2331 2456 5.221843 TGTTAAACTGTTCATAGCTGGTCCT 60.222 40.000 0.00 0.00 0.00 3.85
2332 2457 3.340814 AACTGTTCATAGCTGGTCCTG 57.659 47.619 0.00 0.00 0.00 3.86
2333 2458 1.556911 ACTGTTCATAGCTGGTCCTGG 59.443 52.381 0.00 0.00 0.00 4.45
2397 2522 6.538021 AGCATGTTCTATGAACATCTGAAGAC 59.462 38.462 19.23 7.83 38.69 3.01
2414 2539 6.379703 TCTGAAGACCACCTGAAAATGAAAAA 59.620 34.615 0.00 0.00 0.00 1.94
2426 2553 9.927668 CCTGAAAATGAAAAACTAATGTATGGT 57.072 29.630 0.00 0.00 0.00 3.55
2462 2589 4.974645 TCTGGTCAAGAGCTTCCTAAAA 57.025 40.909 0.69 0.00 0.00 1.52
2474 2601 4.713321 AGCTTCCTAAAATCCATGCAACAT 59.287 37.500 0.00 0.00 0.00 2.71
2489 2616 5.811399 TGCAACATTACAGTTATGTAGGC 57.189 39.130 16.55 16.55 42.72 3.93
2493 2620 6.458342 GCAACATTACAGTTATGTAGGCCTTC 60.458 42.308 12.58 6.47 42.72 3.46
2507 2634 1.300481 GCCTTCTATTGGTTCGGCTC 58.700 55.000 0.00 0.00 34.80 4.70
2516 2643 5.873164 TCTATTGGTTCGGCTCTAAACTTTC 59.127 40.000 0.00 0.00 0.00 2.62
2521 2648 4.626172 GGTTCGGCTCTAAACTTTCTACTG 59.374 45.833 0.00 0.00 0.00 2.74
2525 2652 4.505808 GGCTCTAAACTTTCTACTGTCCC 58.494 47.826 0.00 0.00 0.00 4.46
2527 2654 4.930405 GCTCTAAACTTTCTACTGTCCCAC 59.070 45.833 0.00 0.00 0.00 4.61
2542 2669 7.454260 ACTGTCCCACATAAAGAGATTTTTC 57.546 36.000 0.00 0.00 0.00 2.29
2544 2671 7.725844 ACTGTCCCACATAAAGAGATTTTTCTT 59.274 33.333 0.00 0.00 39.03 2.52
2546 2673 9.581289 TGTCCCACATAAAGAGATTTTTCTTAA 57.419 29.630 0.00 0.00 36.42 1.85
2547 2674 9.841880 GTCCCACATAAAGAGATTTTTCTTAAC 57.158 33.333 0.00 0.00 36.42 2.01
2548 2675 9.581289 TCCCACATAAAGAGATTTTTCTTAACA 57.419 29.630 0.00 0.00 36.42 2.41
2549 2676 9.626045 CCCACATAAAGAGATTTTTCTTAACAC 57.374 33.333 0.00 0.00 36.42 3.32
2556 2683 9.717892 AAAGAGATTTTTCTTAACACTTCGAAC 57.282 29.630 0.00 0.00 36.42 3.95
2591 2718 9.990868 AACTAGTTATCCTTCCCATGTAAAAAT 57.009 29.630 6.26 0.00 0.00 1.82
2598 2725 7.475137 TCCTTCCCATGTAAAAATAAGTTGG 57.525 36.000 0.00 0.00 0.00 3.77
2657 2784 8.954350 GCTGATAATAGACAATAAAGCCATCAT 58.046 33.333 0.00 0.00 0.00 2.45
2675 2802 3.104512 TCATTCTAAGATGGACCCGTGT 58.895 45.455 0.00 0.00 0.00 4.49
2676 2803 3.517901 TCATTCTAAGATGGACCCGTGTT 59.482 43.478 0.00 0.00 0.00 3.32
2685 2812 0.250338 GGACCCGTGTTCTTCTGCTT 60.250 55.000 0.00 0.00 0.00 3.91
2710 2837 1.826327 CCACAAGTTTTGTCTGTGCG 58.174 50.000 0.00 0.00 43.23 5.34
2757 2885 7.620880 AGTTTAGTGTGCCATAGACAATAAGA 58.379 34.615 0.00 0.00 35.84 2.10
2799 2927 0.308684 CATTGCGTTGCACAGACACT 59.691 50.000 0.00 0.00 38.71 3.55
2838 2966 7.229506 GGGATGCTTATGAGTTTACTGCTATTT 59.770 37.037 0.00 0.00 0.00 1.40
3155 3283 1.542915 AGGTGAGTGCATGCATGTTTC 59.457 47.619 25.64 20.36 0.00 2.78
3158 3286 2.921121 GTGAGTGCATGCATGTTTCATG 59.079 45.455 25.64 2.44 43.02 3.07
3159 3287 2.094442 TGAGTGCATGCATGTTTCATGG 60.094 45.455 25.64 0.03 41.08 3.66
3160 3288 2.164827 GAGTGCATGCATGTTTCATGGA 59.835 45.455 25.64 8.78 41.08 3.41
3161 3289 2.165641 AGTGCATGCATGTTTCATGGAG 59.834 45.455 25.64 0.00 41.71 3.86
3198 3335 9.708222 CTCAAAAATGATATTGTTAGGAGAACG 57.292 33.333 0.00 0.00 0.00 3.95
3226 3363 4.521146 CTTTCAGCCTGACATGAACCTAT 58.479 43.478 0.00 0.00 35.25 2.57
3403 3548 0.902984 ATCCAGTACACGACCTGGCA 60.903 55.000 0.00 0.00 36.94 4.92
3494 3640 3.367395 GCGGAAAGGAGAAAGATTTTGGG 60.367 47.826 0.00 0.00 0.00 4.12
3676 3822 5.992217 GCTAGGGAATGATAAACCTGTACAG 59.008 44.000 16.34 16.34 34.59 2.74
3677 3823 6.183360 GCTAGGGAATGATAAACCTGTACAGA 60.183 42.308 24.68 4.30 34.59 3.41
3678 3824 6.831664 AGGGAATGATAAACCTGTACAGAT 57.168 37.500 24.68 3.45 30.71 2.90
3679 3825 7.931015 AGGGAATGATAAACCTGTACAGATA 57.069 36.000 24.68 13.77 30.71 1.98
3680 3826 8.331931 AGGGAATGATAAACCTGTACAGATAA 57.668 34.615 24.68 3.10 30.71 1.75
3681 3827 8.211629 AGGGAATGATAAACCTGTACAGATAAC 58.788 37.037 24.68 12.51 30.71 1.89
3719 3865 2.437085 TAGCTGCCTGTAGAGTGCTA 57.563 50.000 0.00 0.00 32.72 3.49
3742 3986 4.567971 GATGGAGCATCTGAGATTACCAG 58.432 47.826 14.21 0.00 37.82 4.00
3754 3998 4.760715 TGAGATTACCAGCTACTCCGTATC 59.239 45.833 0.00 0.00 0.00 2.24
3774 4023 5.850557 ATCATTTTTGTCCACAACAGACA 57.149 34.783 0.00 0.00 42.36 3.41
3796 4045 7.067494 AGACAAGTGTTGCTTTACTGATTTCTT 59.933 33.333 0.00 0.00 34.69 2.52
3812 4061 9.822185 ACTGATTTCTTTCAATTTTAGCTGTTT 57.178 25.926 0.00 0.00 0.00 2.83
4120 4374 8.641498 AATTCACCATATTCTTTTCTCTGTGT 57.359 30.769 0.00 0.00 0.00 3.72
4138 4392 9.890629 TCTCTGTGTAATGATAAGCTTAACATT 57.109 29.630 31.94 31.94 38.88 2.71
4169 4423 6.935771 TGTGATTTGAAGCATTGCCTTTTATT 59.064 30.769 4.70 0.00 0.00 1.40
4187 4474 8.021396 CCTTTTATTGTAGGAACTTTGTAGTGC 58.979 37.037 0.00 0.00 41.75 4.40
4189 4476 7.667043 TTATTGTAGGAACTTTGTAGTGCTG 57.333 36.000 0.00 0.00 41.75 4.41
4449 4744 1.480954 GATAGGTCGGTTCTCAAGGCA 59.519 52.381 0.00 0.00 0.00 4.75
4714 5009 6.928492 TGTGATTGTTCTTCGCTATGCATATA 59.072 34.615 6.92 0.00 0.00 0.86
4764 5059 8.135529 GCACTCAGTTTTATTTTGTTAGAGGTT 58.864 33.333 0.00 0.00 0.00 3.50
4907 5203 2.945008 GCAATATACTGGTCAAGCTGCA 59.055 45.455 1.02 0.00 0.00 4.41
4918 5214 4.019051 TGGTCAAGCTGCATATATAGCCAT 60.019 41.667 1.02 0.00 40.76 4.40
5004 5300 3.644966 TTCCCCGATTAAGTGATTGCT 57.355 42.857 0.00 0.00 0.00 3.91
5585 5889 3.423154 CCTCTCGTGTTTGCCGCC 61.423 66.667 0.00 0.00 0.00 6.13
5606 5910 1.620819 GCCATCCTCCTCGTCATGTAT 59.379 52.381 0.00 0.00 0.00 2.29
5618 5922 3.868661 TCGTCATGTATGTGTGGCATTAC 59.131 43.478 0.00 0.00 38.94 1.89
6073 6377 1.077357 AGGAGCTGATCGACGAGGT 60.077 57.895 3.01 0.00 0.00 3.85
6194 6498 4.382320 GCTACAACGGCGACCCCA 62.382 66.667 16.62 0.00 0.00 4.96
6284 6588 1.001974 CTTGGGAACACCGTCATCAGA 59.998 52.381 0.00 0.00 44.64 3.27
6399 6703 0.842030 TGTTCCCCATGAGAGCCTGT 60.842 55.000 0.00 0.00 0.00 4.00
6602 6906 4.609783 GCAATTTTCAGTGCAGTGCAAATC 60.610 41.667 25.63 14.57 43.75 2.17
6763 7067 4.823442 TGAGGATCAGCGAAATATTTGCAT 59.177 37.500 18.49 8.97 42.56 3.96
6793 7097 2.959507 AACAACTGGTGCCTTTGAAC 57.040 45.000 0.00 0.00 0.00 3.18
6795 7099 2.456577 ACAACTGGTGCCTTTGAACTT 58.543 42.857 0.00 0.00 0.00 2.66
6801 7105 3.295093 TGGTGCCTTTGAACTTGAATGA 58.705 40.909 0.00 0.00 0.00 2.57
6814 7118 6.315144 TGAACTTGAATGATATGTAACCCACG 59.685 38.462 0.00 0.00 0.00 4.94
6835 7139 6.175087 CACGCAAAATAAATAAATTGGCGAC 58.825 36.000 12.83 0.00 41.86 5.19
6856 7160 8.068380 GGCGACTTTTCTAATAATTTATTCGCT 58.932 33.333 19.17 0.00 38.99 4.93
6858 7162 9.291155 CGACTTTTCTAATAATTTATTCGCTCG 57.709 33.333 4.94 1.63 0.00 5.03
6865 7169 6.707599 AATAATTTATTCGCTCGCCTCTAC 57.292 37.500 0.00 0.00 0.00 2.59
6866 7170 4.323553 AATTTATTCGCTCGCCTCTACT 57.676 40.909 0.00 0.00 0.00 2.57
6879 7183 3.318275 CGCCTCTACTGCTAGGACAAATA 59.682 47.826 0.00 0.00 34.58 1.40
6888 7192 5.604650 ACTGCTAGGACAAATATAGCCTTCT 59.395 40.000 0.00 0.00 40.97 2.85
6895 7199 7.830739 AGGACAAATATAGCCTTCTGTTTTTG 58.169 34.615 0.00 0.00 37.89 2.44
6904 7208 2.293122 CCTTCTGTTTTTGGCATCGACA 59.707 45.455 0.00 0.00 0.00 4.35
6905 7209 3.558505 CTTCTGTTTTTGGCATCGACAG 58.441 45.455 14.70 14.70 39.16 3.51
6906 7210 2.571212 TCTGTTTTTGGCATCGACAGT 58.429 42.857 18.13 0.00 38.95 3.55
6907 7211 2.290367 TCTGTTTTTGGCATCGACAGTG 59.710 45.455 18.13 0.00 38.95 3.66
6908 7212 1.336440 TGTTTTTGGCATCGACAGTGG 59.664 47.619 0.00 0.00 0.00 4.00
6909 7213 0.313672 TTTTTGGCATCGACAGTGGC 59.686 50.000 4.23 4.23 41.99 5.01
6910 7214 1.851021 TTTTGGCATCGACAGTGGCG 61.851 55.000 13.62 13.62 44.31 5.69
6911 7215 2.723586 TTTGGCATCGACAGTGGCGA 62.724 55.000 25.81 25.81 44.31 5.54
6931 7235 3.931468 CGATGACTCAAATCTGCAGAAGT 59.069 43.478 22.50 19.22 0.00 3.01
6933 7237 4.341366 TGACTCAAATCTGCAGAAGTGA 57.659 40.909 22.50 23.31 0.00 3.41
6940 7244 1.376424 CTGCAGAAGTGATGGCGGT 60.376 57.895 8.42 0.00 0.00 5.68
6960 7264 3.695060 GGTGACGACTTCAATCTCTAGGA 59.305 47.826 0.00 0.00 35.39 2.94
6964 7268 2.287308 CGACTTCAATCTCTAGGAGCGG 60.287 54.545 0.00 0.00 0.00 5.52
6965 7269 2.952978 GACTTCAATCTCTAGGAGCGGA 59.047 50.000 0.00 0.00 0.00 5.54
6969 7273 3.366396 TCAATCTCTAGGAGCGGAAAGT 58.634 45.455 0.00 0.00 0.00 2.66
6978 7282 0.603975 GAGCGGAAAGTGCTTGTCCT 60.604 55.000 9.64 0.00 44.18 3.85
7000 7304 1.134901 CGTCTTGGAGTCCGTCTCG 59.865 63.158 4.30 3.60 43.60 4.04
7008 7312 1.406614 GGAGTCCGTCTCGTCTTCCTA 60.407 57.143 0.00 0.00 43.60 2.94
7017 7321 2.018515 CTCGTCTTCCTAGGTGTCCTC 58.981 57.143 9.08 0.00 34.61 3.71
7055 7359 0.543410 TCGTCAGCTCCAAAGGGGTA 60.543 55.000 0.00 0.00 38.11 3.69
7056 7360 0.108138 CGTCAGCTCCAAAGGGGTAG 60.108 60.000 0.00 0.00 38.11 3.18
7057 7361 0.253327 GTCAGCTCCAAAGGGGTAGG 59.747 60.000 0.00 0.00 38.11 3.18
7058 7362 0.178873 TCAGCTCCAAAGGGGTAGGT 60.179 55.000 0.00 0.00 38.11 3.08
7059 7363 1.079825 TCAGCTCCAAAGGGGTAGGTA 59.920 52.381 0.00 0.00 38.11 3.08
7060 7364 1.209747 CAGCTCCAAAGGGGTAGGTAC 59.790 57.143 0.00 0.00 38.11 3.34
7104 7408 0.175073 GGTCGTTAGGTAGGGTGCAG 59.825 60.000 0.00 0.00 0.00 4.41
7115 7419 0.609131 AGGGTGCAGGGTCAATTTCG 60.609 55.000 0.00 0.00 0.00 3.46
7118 7422 1.228398 TGCAGGGTCAATTTCGCCA 60.228 52.632 0.00 0.00 0.00 5.69
7123 7427 1.349688 AGGGTCAATTTCGCCAGTACA 59.650 47.619 0.00 0.00 0.00 2.90
7137 7441 3.266636 CCAGTACATACCGCAACATCAA 58.733 45.455 0.00 0.00 0.00 2.57
7141 7445 6.321717 CAGTACATACCGCAACATCAATTTT 58.678 36.000 0.00 0.00 0.00 1.82
7142 7446 6.251163 CAGTACATACCGCAACATCAATTTTG 59.749 38.462 0.00 0.00 0.00 2.44
7143 7447 3.925913 ACATACCGCAACATCAATTTTGC 59.074 39.130 4.20 4.20 43.90 3.68
7146 7450 1.727880 CCGCAACATCAATTTTGCCAG 59.272 47.619 7.96 0.00 44.39 4.85
7162 7466 2.190981 GCCAGTAAGTCGGTAATGACG 58.809 52.381 0.00 0.00 43.70 4.35
7167 7471 4.557690 CAGTAAGTCGGTAATGACGAACAG 59.442 45.833 0.00 0.00 43.70 3.16
7193 7497 4.550076 AGCTAGTTGTTCAGAGAGCAAT 57.450 40.909 0.00 0.00 35.46 3.56
7221 7525 3.844640 AGTTGTTATTTCAGGCTTGGGT 58.155 40.909 0.00 0.00 0.00 4.51
7231 7535 0.251341 AGGCTTGGGTCATGTTGGTC 60.251 55.000 0.00 0.00 0.00 4.02
7242 7546 4.051237 GTCATGTTGGTCCAAAAGAAAGC 58.949 43.478 5.69 0.00 0.00 3.51
7248 7552 1.334689 GGTCCAAAAGAAAGCGGTTCG 60.335 52.381 0.00 0.00 41.52 3.95
7269 7573 3.609644 CGTCCGAGTGATAAGCCTATGAC 60.610 52.174 0.00 0.00 0.00 3.06
7272 7576 2.028930 CGAGTGATAAGCCTATGACCCC 60.029 54.545 0.00 0.00 0.00 4.95
7296 7600 1.496857 TGGTCCAATGTCAACCCAAGA 59.503 47.619 0.00 0.00 31.78 3.02
7310 7623 1.694150 CCCAAGATAGGGCGAATCTGA 59.306 52.381 1.49 0.00 43.10 3.27
7318 7631 3.460857 AGGGCGAATCTGAACTACATC 57.539 47.619 0.00 0.00 0.00 3.06
7330 7643 7.709269 TCTGAACTACATCTACAACAACAAC 57.291 36.000 0.00 0.00 0.00 3.32
7331 7644 7.269316 TCTGAACTACATCTACAACAACAACA 58.731 34.615 0.00 0.00 0.00 3.33
7332 7645 7.766738 TCTGAACTACATCTACAACAACAACAA 59.233 33.333 0.00 0.00 0.00 2.83
7343 7656 8.635328 TCTACAACAACAACAATGTAGAGACTA 58.365 33.333 9.69 0.00 45.52 2.59
7345 7658 8.087982 ACAACAACAACAATGTAGAGACTATG 57.912 34.615 0.00 0.00 39.40 2.23
7362 7675 3.940852 ACTATGAACATGCTTCGAATGCA 59.059 39.130 19.64 19.64 44.95 3.96
7387 7700 5.772521 AGATCATCGTTTCCCAAGTTTTTG 58.227 37.500 0.00 0.00 0.00 2.44
7400 7713 5.744666 CAAGTTTTTGGAGACGTTTAGGA 57.255 39.130 0.00 0.00 0.00 2.94
7401 7714 5.507974 CAAGTTTTTGGAGACGTTTAGGAC 58.492 41.667 0.00 0.00 0.00 3.85
7408 7721 1.897802 GAGACGTTTAGGACCAAGGGA 59.102 52.381 0.00 0.00 0.00 4.20
7409 7722 1.622312 AGACGTTTAGGACCAAGGGAC 59.378 52.381 0.00 0.00 0.00 4.46
7423 7736 6.079712 ACCAAGGGACTGCTAAAAGATAAT 57.920 37.500 0.00 0.00 40.86 1.28
7478 7791 2.616376 TGTTCCTTCATGTTGTTGGTCG 59.384 45.455 0.00 0.00 0.00 4.79
7488 7801 4.594123 TGTTGTTGGTCGTAATCAGAGA 57.406 40.909 0.00 0.00 0.00 3.10
7489 7802 5.147330 TGTTGTTGGTCGTAATCAGAGAT 57.853 39.130 0.00 0.00 0.00 2.75
7497 7810 9.692749 GTTGGTCGTAATCAGAGATATTCATTA 57.307 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.382307 TGGGGTCTTAAACTTTGGTATATTTTT 57.618 29.630 0.00 0.00 0.00 1.94
7 8 8.959676 TGGGGTCTTAAACTTTGGTATATTTT 57.040 30.769 0.00 0.00 0.00 1.82
8 9 9.555411 AATGGGGTCTTAAACTTTGGTATATTT 57.445 29.630 0.00 0.00 0.00 1.40
9 10 9.555411 AAATGGGGTCTTAAACTTTGGTATATT 57.445 29.630 0.00 0.00 0.00 1.28
14 15 9.555411 AATATAAATGGGGTCTTAAACTTTGGT 57.445 29.630 0.00 0.00 0.00 3.67
35 36 8.673711 GGGCAGTTGCGATTCAATATTAATATA 58.326 33.333 8.39 0.00 43.26 0.86
36 37 7.176515 TGGGCAGTTGCGATTCAATATTAATAT 59.823 33.333 1.91 1.91 43.26 1.28
37 38 6.488344 TGGGCAGTTGCGATTCAATATTAATA 59.512 34.615 0.00 0.00 43.26 0.98
38 39 5.301551 TGGGCAGTTGCGATTCAATATTAAT 59.698 36.000 0.00 0.00 43.26 1.40
39 40 4.642437 TGGGCAGTTGCGATTCAATATTAA 59.358 37.500 0.00 0.00 43.26 1.40
40 41 4.203226 TGGGCAGTTGCGATTCAATATTA 58.797 39.130 0.00 0.00 43.26 0.98
41 42 3.023119 TGGGCAGTTGCGATTCAATATT 58.977 40.909 0.00 0.00 43.26 1.28
42 43 2.653726 TGGGCAGTTGCGATTCAATAT 58.346 42.857 0.00 0.00 43.26 1.28
43 44 2.121291 TGGGCAGTTGCGATTCAATA 57.879 45.000 0.00 0.00 43.26 1.90
44 45 1.255882 TTGGGCAGTTGCGATTCAAT 58.744 45.000 0.00 0.00 43.26 2.57
45 46 1.035923 TTTGGGCAGTTGCGATTCAA 58.964 45.000 0.00 0.00 43.26 2.69
46 47 1.000385 CTTTTGGGCAGTTGCGATTCA 60.000 47.619 0.00 0.00 43.26 2.57
47 48 1.701704 CTTTTGGGCAGTTGCGATTC 58.298 50.000 0.00 0.00 43.26 2.52
48 49 0.319813 GCTTTTGGGCAGTTGCGATT 60.320 50.000 0.00 0.00 43.26 3.34
49 50 1.290009 GCTTTTGGGCAGTTGCGAT 59.710 52.632 0.00 0.00 43.26 4.58
50 51 1.670949 TTGCTTTTGGGCAGTTGCGA 61.671 50.000 0.00 0.00 43.39 5.10
51 52 1.227205 TTGCTTTTGGGCAGTTGCG 60.227 52.632 0.00 0.00 43.39 4.85
52 53 0.461693 TGTTGCTTTTGGGCAGTTGC 60.462 50.000 0.00 0.00 43.39 4.17
53 54 1.289276 GTGTTGCTTTTGGGCAGTTG 58.711 50.000 0.00 0.00 43.39 3.16
54 55 0.901124 TGTGTTGCTTTTGGGCAGTT 59.099 45.000 0.00 0.00 43.39 3.16
55 56 1.122227 ATGTGTTGCTTTTGGGCAGT 58.878 45.000 0.00 0.00 43.39 4.40
56 57 2.243602 AATGTGTTGCTTTTGGGCAG 57.756 45.000 0.00 0.00 43.39 4.85
57 58 2.706339 AAATGTGTTGCTTTTGGGCA 57.294 40.000 0.00 0.00 40.74 5.36
76 77 3.352648 CCGCTTTAGGATCCCTCAAAAA 58.647 45.455 8.55 1.21 34.61 1.94
77 78 2.944094 GCCGCTTTAGGATCCCTCAAAA 60.944 50.000 8.55 3.71 34.61 2.44
78 79 1.408266 GCCGCTTTAGGATCCCTCAAA 60.408 52.381 8.55 5.89 34.61 2.69
79 80 0.180406 GCCGCTTTAGGATCCCTCAA 59.820 55.000 8.55 0.00 34.61 3.02
80 81 0.980754 TGCCGCTTTAGGATCCCTCA 60.981 55.000 8.55 0.00 34.61 3.86
81 82 0.533085 GTGCCGCTTTAGGATCCCTC 60.533 60.000 8.55 0.00 34.61 4.30
82 83 1.271840 TGTGCCGCTTTAGGATCCCT 61.272 55.000 8.55 0.00 37.71 4.20
83 84 0.179018 ATGTGCCGCTTTAGGATCCC 60.179 55.000 8.55 0.00 0.00 3.85
84 85 2.543777 TATGTGCCGCTTTAGGATCC 57.456 50.000 2.48 2.48 0.00 3.36
85 86 3.728845 TCTTATGTGCCGCTTTAGGATC 58.271 45.455 0.00 0.00 0.00 3.36
86 87 3.733337 CTCTTATGTGCCGCTTTAGGAT 58.267 45.455 0.00 0.00 0.00 3.24
87 88 2.741878 GCTCTTATGTGCCGCTTTAGGA 60.742 50.000 0.00 0.00 0.00 2.94
147 148 2.062971 ACCATGAACCATCCATCTGC 57.937 50.000 0.00 0.00 0.00 4.26
176 177 3.182887 ACAAGGGGATTTATGCCAACA 57.817 42.857 2.60 0.00 40.49 3.33
187 188 4.352893 CCCACAAGATTAAACAAGGGGAT 58.647 43.478 0.00 0.00 34.97 3.85
193 194 4.832266 AGACATGCCCACAAGATTAAACAA 59.168 37.500 0.00 0.00 0.00 2.83
204 205 2.364970 CCTTGAAAAAGACATGCCCACA 59.635 45.455 0.00 0.00 0.00 4.17
220 221 4.630644 AGCATGTCTCTTCTTTCCTTGA 57.369 40.909 0.00 0.00 0.00 3.02
222 223 4.621747 CGGTAGCATGTCTCTTCTTTCCTT 60.622 45.833 0.00 0.00 0.00 3.36
245 247 5.046950 AGAAGTTCTCTAAGTGGATCCACAC 60.047 44.000 39.38 27.92 40.04 3.82
287 289 6.572519 TGCATTTGAAATAATCTAAGTGGGC 58.427 36.000 0.00 0.00 0.00 5.36
314 316 9.014297 AGGAACCTAATGACAACTTATTTTCTG 57.986 33.333 0.00 0.00 0.00 3.02
321 324 6.597562 ACAACAGGAACCTAATGACAACTTA 58.402 36.000 10.58 0.00 0.00 2.24
352 355 5.296151 TCAAGATTCTTATCGGAGGCAAT 57.704 39.130 0.00 0.00 35.85 3.56
363 366 8.750298 ACGAGAGAAACCTAATCAAGATTCTTA 58.250 33.333 0.00 0.00 33.75 2.10
366 369 8.973378 CATACGAGAGAAACCTAATCAAGATTC 58.027 37.037 0.00 0.00 32.50 2.52
370 373 6.477033 CCACATACGAGAGAAACCTAATCAAG 59.523 42.308 0.00 0.00 0.00 3.02
409 419 0.934496 TGAAAACGACTTGGCACGAG 59.066 50.000 2.83 0.00 0.00 4.18
428 438 7.527568 TCCAAATAATTAAACCACCGTCTTT 57.472 32.000 0.00 0.00 0.00 2.52
432 442 7.340743 TCATGATCCAAATAATTAAACCACCGT 59.659 33.333 0.00 0.00 0.00 4.83
433 443 7.711846 TCATGATCCAAATAATTAAACCACCG 58.288 34.615 0.00 0.00 0.00 4.94
497 507 1.139058 AGACAAGACAACTGGCGTTCT 59.861 47.619 0.00 0.00 0.00 3.01
505 515 6.992123 TGTTCATCATGTAAGACAAGACAACT 59.008 34.615 0.00 0.00 29.94 3.16
563 573 2.552599 TGATGGTGGTACTTTGCGAA 57.447 45.000 0.00 0.00 0.00 4.70
564 574 2.027653 TGATGATGGTGGTACTTTGCGA 60.028 45.455 0.00 0.00 0.00 5.10
565 575 2.095853 GTGATGATGGTGGTACTTTGCG 59.904 50.000 0.00 0.00 0.00 4.85
567 577 6.655003 AGTTAAGTGATGATGGTGGTACTTTG 59.345 38.462 0.00 0.00 31.55 2.77
626 636 5.109903 GCTTACCTCGGCATACTATAATGG 58.890 45.833 0.00 0.00 0.00 3.16
627 637 5.109903 GGCTTACCTCGGCATACTATAATG 58.890 45.833 0.00 0.00 0.00 1.90
648 659 3.247648 GTCATTGTATACATGGTGACGGC 59.752 47.826 20.94 7.96 0.00 5.68
660 671 6.127563 TGTCTCGGCAAGTTAGTCATTGTATA 60.128 38.462 0.00 0.00 0.00 1.47
661 672 5.109903 GTCTCGGCAAGTTAGTCATTGTAT 58.890 41.667 0.00 0.00 0.00 2.29
688 699 4.690748 TGCGAGTTTTGTTATCCTTGAGAG 59.309 41.667 0.00 0.00 0.00 3.20
709 720 3.058224 GTCACCCATGTTAGTGAGTTTGC 60.058 47.826 9.89 0.00 43.36 3.68
724 735 1.078497 GCCATGTCGATGTCACCCA 60.078 57.895 0.00 0.00 0.00 4.51
725 736 1.078497 TGCCATGTCGATGTCACCC 60.078 57.895 0.00 0.00 0.00 4.61
727 738 1.155889 TTGTGCCATGTCGATGTCAC 58.844 50.000 0.00 0.00 38.65 3.67
740 751 4.568760 TCAAAACCGAATTCTTTTTGTGCC 59.431 37.500 25.84 0.00 39.92 5.01
799 810 2.022764 TGTCAACATCAGCGTATGGG 57.977 50.000 6.33 0.00 0.00 4.00
800 811 3.374988 ACAATGTCAACATCAGCGTATGG 59.625 43.478 6.33 0.00 35.10 2.74
811 822 5.462729 GTCAAAATCATGCACAATGTCAACA 59.537 36.000 0.00 0.00 37.56 3.33
865 877 7.167635 TGCGCTGTCAAATTCGTTTTATTTTTA 59.832 29.630 9.73 0.00 0.00 1.52
876 888 3.487536 TGTTATTGCGCTGTCAAATTCG 58.512 40.909 9.73 0.00 0.00 3.34
877 889 7.504922 TTATTGTTATTGCGCTGTCAAATTC 57.495 32.000 9.73 0.00 0.00 2.17
880 892 4.856487 GCTTATTGTTATTGCGCTGTCAAA 59.144 37.500 9.73 0.00 0.00 2.69
913 927 1.070758 TCGAGGAGCATAAATGGGAGC 59.929 52.381 0.00 0.00 0.00 4.70
936 950 2.030540 GCTATACGGCGTGTCTCCAATA 60.031 50.000 24.86 9.47 0.00 1.90
963 977 4.080638 AGAGGAGTGGAGATGATTTGGAAC 60.081 45.833 0.00 0.00 0.00 3.62
1004 1018 5.557893 CGCAGTCTTTCTTTTTCTGTCAGAG 60.558 44.000 2.12 0.00 0.00 3.35
1044 1061 0.960861 GCCGGGGAGAAAAGTTGGAG 60.961 60.000 2.18 0.00 0.00 3.86
1149 1179 3.682292 AATGAGCTCGGCCGGTTCC 62.682 63.158 27.83 13.17 0.00 3.62
1150 1180 2.125106 AATGAGCTCGGCCGGTTC 60.125 61.111 27.83 22.29 0.00 3.62
1151 1181 2.436646 CAATGAGCTCGGCCGGTT 60.437 61.111 27.83 14.32 0.00 4.44
1155 1185 3.512516 GTGGCAATGAGCTCGGCC 61.513 66.667 27.63 27.63 46.58 6.13
1156 1186 3.869272 CGTGGCAATGAGCTCGGC 61.869 66.667 9.64 12.44 44.79 5.54
1157 1187 3.869272 GCGTGGCAATGAGCTCGG 61.869 66.667 9.64 2.19 44.79 4.63
1158 1188 2.466982 ATGCGTGGCAATGAGCTCG 61.467 57.895 9.64 0.00 43.62 5.03
1159 1189 1.063649 CATGCGTGGCAATGAGCTC 59.936 57.895 6.82 6.82 43.62 4.09
1294 1324 0.178964 CCAGAGGGTTCCAAAAGGCA 60.179 55.000 0.00 0.00 0.00 4.75
1327 1358 5.016051 ACATACACATACAGGAGAGCAAG 57.984 43.478 0.00 0.00 0.00 4.01
1342 1373 3.126831 GACTCCAGCTGCATACATACAC 58.873 50.000 8.66 0.00 0.00 2.90
1510 1544 1.338105 TGCTGCACAGAGTACATGACC 60.338 52.381 0.00 0.00 0.00 4.02
1558 1645 2.268762 TGTCACAAACTGCAGGCATA 57.731 45.000 19.93 0.00 0.00 3.14
1607 1694 1.759445 CGGTCTCCATGAGGTTCAGAT 59.241 52.381 0.00 0.00 35.89 2.90
1641 1728 3.971702 GCCCCCTTGCTGGTGTCT 61.972 66.667 0.00 0.00 0.00 3.41
1648 1735 4.431131 CCACATCGCCCCCTTGCT 62.431 66.667 0.00 0.00 0.00 3.91
1680 1767 1.478105 GCATCCATGGGCTGATCAAGA 60.478 52.381 13.02 0.00 0.00 3.02
1698 1785 4.704103 AGTCTCCCGGCCTCTGCA 62.704 66.667 0.00 0.00 40.13 4.41
1824 1916 6.603201 ACATTAGGTGTTCCATGACCTTTATG 59.397 38.462 8.96 13.67 39.75 1.90
1842 1934 6.808212 CCATGTTGTTAAGAAAGCACATTAGG 59.192 38.462 0.00 0.00 0.00 2.69
1853 1945 6.588719 ATGCTAAAGCCATGTTGTTAAGAA 57.411 33.333 0.00 0.00 41.18 2.52
1855 1947 6.389091 TCAATGCTAAAGCCATGTTGTTAAG 58.611 36.000 0.00 0.00 41.18 1.85
1888 1980 6.417930 GGAGAATGCTCTACAAAACACAAAAC 59.582 38.462 0.00 0.00 41.06 2.43
1920 2029 9.118300 GCATCTTAGGCAAAGCATATAGATAAT 57.882 33.333 0.00 0.00 34.97 1.28
1933 2042 3.701205 TGACTCTGCATCTTAGGCAAA 57.299 42.857 0.00 0.00 41.39 3.68
2034 2159 0.327924 TCTGCACATACAACAGGGGG 59.672 55.000 0.00 0.00 32.19 5.40
2035 2160 1.453155 GTCTGCACATACAACAGGGG 58.547 55.000 0.00 0.00 32.19 4.79
2040 2165 4.137116 TGGATAGGTCTGCACATACAAC 57.863 45.455 0.00 0.00 0.00 3.32
2058 2183 4.887071 AGTTGTAGCATCAAAACTGTTGGA 59.113 37.500 0.00 0.00 31.82 3.53
2175 2300 1.750778 AGTGCCCCAATAATTTGCTCG 59.249 47.619 0.00 0.00 0.00 5.03
2271 2396 2.825532 GCAGAAATTCTTACCTTGGCCA 59.174 45.455 0.00 0.00 0.00 5.36
2289 2414 6.757897 TTAACATTTCCATAACTGAGGCAG 57.242 37.500 0.00 0.00 37.52 4.85
2308 2433 5.122396 CAGGACCAGCTATGAACAGTTTAAC 59.878 44.000 0.00 0.00 0.00 2.01
2328 2453 5.935945 TCAAACAAATAAGACAGACCAGGA 58.064 37.500 0.00 0.00 0.00 3.86
2329 2454 5.997746 TCTCAAACAAATAAGACAGACCAGG 59.002 40.000 0.00 0.00 0.00 4.45
2330 2455 7.678947 ATCTCAAACAAATAAGACAGACCAG 57.321 36.000 0.00 0.00 0.00 4.00
2331 2456 9.739276 ATTATCTCAAACAAATAAGACAGACCA 57.261 29.630 0.00 0.00 0.00 4.02
2332 2457 9.994432 CATTATCTCAAACAAATAAGACAGACC 57.006 33.333 0.00 0.00 0.00 3.85
2333 2458 9.495754 GCATTATCTCAAACAAATAAGACAGAC 57.504 33.333 0.00 0.00 0.00 3.51
2397 2522 9.927668 ATACATTAGTTTTTCATTTTCAGGTGG 57.072 29.630 0.00 0.00 0.00 4.61
2426 2553 6.213397 TCTTGACCAGAATTTCCTCTGTATGA 59.787 38.462 0.35 0.00 41.15 2.15
2462 2589 7.229306 CCTACATAACTGTAATGTTGCATGGAT 59.771 37.037 0.00 0.00 37.41 3.41
2474 2601 7.126726 ACCAATAGAAGGCCTACATAACTGTAA 59.873 37.037 5.16 0.00 37.41 2.41
2489 2616 2.990066 AGAGCCGAACCAATAGAAGG 57.010 50.000 0.00 0.00 0.00 3.46
2493 2620 5.875359 AGAAAGTTTAGAGCCGAACCAATAG 59.125 40.000 0.00 0.00 0.00 1.73
2507 2634 8.842358 TTTATGTGGGACAGTAGAAAGTTTAG 57.158 34.615 0.00 0.00 41.80 1.85
2516 2643 8.567285 AAAAATCTCTTTATGTGGGACAGTAG 57.433 34.615 0.00 0.00 41.80 2.57
2521 2648 9.841880 GTTAAGAAAAATCTCTTTATGTGGGAC 57.158 33.333 0.00 0.00 36.95 4.46
2578 2705 8.024145 ACAAACCAACTTATTTTTACATGGGA 57.976 30.769 0.00 0.00 0.00 4.37
2657 2784 3.170717 AGAACACGGGTCCATCTTAGAA 58.829 45.455 0.00 0.00 0.00 2.10
2672 2799 2.878406 TGGCAACTAAGCAGAAGAACAC 59.122 45.455 0.00 0.00 35.83 3.32
2675 2802 3.207265 TGTGGCAACTAAGCAGAAGAA 57.793 42.857 0.00 0.00 35.83 2.52
2676 2803 2.928801 TGTGGCAACTAAGCAGAAGA 57.071 45.000 0.00 0.00 35.83 2.87
2685 2812 4.013728 ACAGACAAAACTTGTGGCAACTA 58.986 39.130 0.00 0.00 45.52 2.24
2717 2844 4.023193 CACTAAACTTTGTGCCCTACTTGG 60.023 45.833 0.00 0.00 0.00 3.61
2799 2927 4.796110 AAGCATCCCTATTTTAGGCAGA 57.204 40.909 0.00 0.00 44.86 4.26
2843 2971 0.550914 TGCAGAGAAACACAAGGGGT 59.449 50.000 0.00 0.00 0.00 4.95
3155 3283 9.731819 CATTTTTGAGAAATCTGATACTCCATG 57.268 33.333 16.50 11.64 0.00 3.66
3253 3390 8.885346 TCCCAAATATTTCTGGTTTTTGGTAAT 58.115 29.630 10.76 0.00 42.99 1.89
3403 3548 2.444766 AGCAAGCCCTAGAGCCATTATT 59.555 45.455 0.00 0.00 0.00 1.40
3638 3784 9.866655 ATCATTCCCTAGCTTGTGATTTTTATA 57.133 29.630 0.00 0.00 0.00 0.98
3647 3793 5.297776 CAGGTTTATCATTCCCTAGCTTGTG 59.702 44.000 0.00 0.00 0.00 3.33
3676 3822 9.275231 CTATGTACAAGGATCGTTATCGTTATC 57.725 37.037 0.00 0.00 37.96 1.75
3677 3823 7.754027 GCTATGTACAAGGATCGTTATCGTTAT 59.246 37.037 0.00 0.00 37.96 1.89
3678 3824 7.040892 AGCTATGTACAAGGATCGTTATCGTTA 60.041 37.037 0.00 0.00 37.96 3.18
3679 3825 5.919141 GCTATGTACAAGGATCGTTATCGTT 59.081 40.000 0.00 0.00 40.05 3.85
3680 3826 5.241064 AGCTATGTACAAGGATCGTTATCGT 59.759 40.000 0.00 0.00 38.33 3.73
3681 3827 5.569441 CAGCTATGTACAAGGATCGTTATCG 59.431 44.000 0.00 0.00 38.55 2.92
3742 3986 8.956100 TTGTGGACAAAAATGATACGGAGTAGC 61.956 40.741 0.00 0.00 40.48 3.58
3774 4023 7.771183 TGAAAGAAATCAGTAAAGCAACACTT 58.229 30.769 0.00 0.00 41.70 3.16
3812 4061 8.565896 ACAAGCATCACAAAGAAGATATGTAA 57.434 30.769 0.00 0.00 0.00 2.41
4138 4392 5.335897 GGCAATGCTTCAAATCACAGTTAGA 60.336 40.000 4.82 0.00 0.00 2.10
4169 4423 3.389983 ACCAGCACTACAAAGTTCCTACA 59.610 43.478 0.00 0.00 31.97 2.74
4187 4474 0.538057 ACTGTTCCCATGCACACCAG 60.538 55.000 0.00 0.00 0.00 4.00
4189 4476 1.904287 TAACTGTTCCCATGCACACC 58.096 50.000 0.00 0.00 0.00 4.16
4246 4541 9.252962 CATGGGAAAATAATAAAATGAGTCAGC 57.747 33.333 0.00 0.00 0.00 4.26
4907 5203 7.503566 ACTTTGTCTTTGTGCATGGCTATATAT 59.496 33.333 0.00 0.00 0.00 0.86
4918 5214 2.297701 GGGAGACTTTGTCTTTGTGCA 58.702 47.619 1.58 0.00 43.53 4.57
5320 5619 2.869192 GCAACCGCTGAAATTTTGGAAA 59.131 40.909 0.00 0.00 34.30 3.13
5321 5620 2.478831 GCAACCGCTGAAATTTTGGAA 58.521 42.857 0.00 0.00 34.30 3.53
5324 5628 1.764851 TCGCAACCGCTGAAATTTTG 58.235 45.000 0.00 0.00 35.30 2.44
5333 5637 1.444119 AAACACACATCGCAACCGCT 61.444 50.000 0.00 0.00 35.30 5.52
5585 5889 1.300465 CATGACGAGGAGGATGGCG 60.300 63.158 0.00 0.00 0.00 5.69
5606 5910 2.321333 CGTGCCGTAATGCCACACA 61.321 57.895 0.00 0.00 0.00 3.72
5711 6015 1.382695 CACCAGACCTATCCCGGGT 60.383 63.158 22.86 10.79 40.13 5.28
6073 6377 3.226429 GACCTGGCGTCACTGCTCA 62.226 63.158 0.00 0.00 41.54 4.26
6194 6498 3.157680 CCCACGGTCTCAAACCCT 58.842 61.111 0.00 0.00 46.27 4.34
6399 6703 1.686052 GAACACCTGCCCAACATTCAA 59.314 47.619 0.00 0.00 0.00 2.69
6572 6876 4.883006 ACTGCACTGAAAATTGCCATTTTT 59.117 33.333 9.63 0.00 41.79 1.94
6583 6887 2.429971 TGGATTTGCACTGCACTGAAAA 59.570 40.909 2.26 2.40 38.71 2.29
6679 6983 6.487299 TTTAAACCTAAACCTTGGTGCAAT 57.513 33.333 0.00 0.00 36.57 3.56
6763 7067 5.299782 AGGCACCAGTTGTTTTATAACGAAA 59.700 36.000 0.00 0.00 37.06 3.46
6771 7075 4.464597 AGTTCAAAGGCACCAGTTGTTTTA 59.535 37.500 0.00 0.00 0.00 1.52
6776 7080 2.426738 TCAAGTTCAAAGGCACCAGTTG 59.573 45.455 0.00 0.00 0.00 3.16
6778 7082 2.435372 TCAAGTTCAAAGGCACCAGT 57.565 45.000 0.00 0.00 0.00 4.00
6779 7083 3.318839 TCATTCAAGTTCAAAGGCACCAG 59.681 43.478 0.00 0.00 0.00 4.00
6793 7097 4.574421 TGCGTGGGTTACATATCATTCAAG 59.426 41.667 0.00 0.00 0.00 3.02
6795 7099 4.143986 TGCGTGGGTTACATATCATTCA 57.856 40.909 0.00 0.00 0.00 2.57
6814 7118 9.261318 GAAAAGTCGCCAATTTATTTATTTTGC 57.739 29.630 0.00 0.00 0.00 3.68
6835 7139 8.283291 AGGCGAGCGAATAAATTATTAGAAAAG 58.717 33.333 9.51 0.48 0.00 2.27
6843 7147 5.864474 CAGTAGAGGCGAGCGAATAAATTAT 59.136 40.000 0.00 0.00 0.00 1.28
6851 7155 0.746923 TAGCAGTAGAGGCGAGCGAA 60.747 55.000 0.00 0.00 36.08 4.70
6856 7160 0.255033 TGTCCTAGCAGTAGAGGCGA 59.745 55.000 0.00 0.00 36.08 5.54
6858 7162 3.828875 ATTTGTCCTAGCAGTAGAGGC 57.171 47.619 0.00 0.00 32.40 4.70
6865 7169 5.931146 CAGAAGGCTATATTTGTCCTAGCAG 59.069 44.000 0.00 0.00 39.67 4.24
6866 7170 5.366768 ACAGAAGGCTATATTTGTCCTAGCA 59.633 40.000 0.00 0.00 39.67 3.49
6888 7192 1.336440 CCACTGTCGATGCCAAAAACA 59.664 47.619 0.00 0.00 0.00 2.83
6895 7199 2.202932 ATCGCCACTGTCGATGCC 60.203 61.111 3.91 0.00 44.00 4.40
6899 7203 1.241315 TGAGTCATCGCCACTGTCGA 61.241 55.000 0.00 0.00 40.45 4.20
6904 7208 2.625737 CAGATTTGAGTCATCGCCACT 58.374 47.619 0.00 0.00 0.00 4.00
6905 7209 1.063174 GCAGATTTGAGTCATCGCCAC 59.937 52.381 0.00 0.00 0.00 5.01
6906 7210 1.338960 TGCAGATTTGAGTCATCGCCA 60.339 47.619 0.00 0.00 0.00 5.69
6907 7211 1.329906 CTGCAGATTTGAGTCATCGCC 59.670 52.381 8.42 0.00 0.00 5.54
6908 7212 2.274437 TCTGCAGATTTGAGTCATCGC 58.726 47.619 13.74 0.00 0.00 4.58
6909 7213 3.931468 ACTTCTGCAGATTTGAGTCATCG 59.069 43.478 19.04 0.00 0.00 3.84
6910 7214 4.934001 TCACTTCTGCAGATTTGAGTCATC 59.066 41.667 19.04 0.00 0.00 2.92
6911 7215 4.903054 TCACTTCTGCAGATTTGAGTCAT 58.097 39.130 19.04 0.00 0.00 3.06
6912 7216 4.341366 TCACTTCTGCAGATTTGAGTCA 57.659 40.909 19.04 0.74 0.00 3.41
6913 7217 4.094590 CCATCACTTCTGCAGATTTGAGTC 59.905 45.833 24.34 0.00 0.00 3.36
6914 7218 4.008330 CCATCACTTCTGCAGATTTGAGT 58.992 43.478 24.34 19.10 0.00 3.41
6931 7235 1.080093 GAAGTCGTCACCGCCATCA 60.080 57.895 0.00 0.00 0.00 3.07
6933 7237 0.036388 ATTGAAGTCGTCACCGCCAT 60.036 50.000 0.00 0.00 35.39 4.40
6940 7244 3.378742 GCTCCTAGAGATTGAAGTCGTCA 59.621 47.826 0.00 0.00 0.00 4.35
6946 7250 4.142049 ACTTTCCGCTCCTAGAGATTGAAG 60.142 45.833 0.00 0.00 0.00 3.02
6956 7260 0.685097 ACAAGCACTTTCCGCTCCTA 59.315 50.000 0.00 0.00 39.29 2.94
6960 7264 0.603975 GAGGACAAGCACTTTCCGCT 60.604 55.000 0.00 0.00 42.98 5.52
6964 7268 2.476997 GACGAAGAGGACAAGCACTTTC 59.523 50.000 0.00 0.00 0.00 2.62
6965 7269 2.103263 AGACGAAGAGGACAAGCACTTT 59.897 45.455 0.00 0.00 0.00 2.66
6969 7273 1.270305 CCAAGACGAAGAGGACAAGCA 60.270 52.381 0.00 0.00 0.00 3.91
6978 7282 0.879765 GACGGACTCCAAGACGAAGA 59.120 55.000 0.00 0.00 0.00 2.87
7000 7304 1.744522 GACGAGGACACCTAGGAAGAC 59.255 57.143 17.98 7.80 31.76 3.01
7008 7312 1.979693 GCCAGAGACGAGGACACCT 60.980 63.158 0.00 0.00 36.03 4.00
7040 7344 1.209747 GTACCTACCCCTTTGGAGCTG 59.790 57.143 0.00 0.00 38.00 4.24
7044 7348 2.672703 ATGGTACCTACCCCTTTGGA 57.327 50.000 14.36 0.00 45.87 3.53
7104 7408 1.816074 TGTACTGGCGAAATTGACCC 58.184 50.000 0.00 0.00 0.00 4.46
7115 7419 1.597663 GATGTTGCGGTATGTACTGGC 59.402 52.381 0.00 1.57 33.20 4.85
7118 7422 6.321717 CAAAATTGATGTTGCGGTATGTACT 58.678 36.000 0.00 0.00 0.00 2.73
7137 7441 5.123344 GTCATTACCGACTTACTGGCAAAAT 59.877 40.000 0.00 0.00 32.92 1.82
7141 7445 2.416296 CGTCATTACCGACTTACTGGCA 60.416 50.000 0.00 0.00 33.54 4.92
7142 7446 2.159338 TCGTCATTACCGACTTACTGGC 60.159 50.000 0.00 0.00 33.54 4.85
7143 7447 3.770263 TCGTCATTACCGACTTACTGG 57.230 47.619 0.00 0.00 33.54 4.00
7146 7450 4.726416 TCTGTTCGTCATTACCGACTTAC 58.274 43.478 0.00 0.00 33.41 2.34
7162 7466 5.928839 TCTGAACAACTAGCTTCATCTGTTC 59.071 40.000 14.78 14.78 41.80 3.18
7167 7471 4.566360 GCTCTCTGAACAACTAGCTTCATC 59.434 45.833 0.00 0.00 0.00 2.92
7193 7497 7.552687 CCAAGCCTGAAATAACAACTATGAGTA 59.447 37.037 0.00 0.00 0.00 2.59
7208 7512 1.962807 CAACATGACCCAAGCCTGAAA 59.037 47.619 0.00 0.00 0.00 2.69
7221 7525 3.243367 CGCTTTCTTTTGGACCAACATGA 60.243 43.478 6.36 2.71 0.00 3.07
7231 7535 1.334689 GGACGAACCGCTTTCTTTTGG 60.335 52.381 0.00 0.00 31.20 3.28
7248 7552 3.305471 GGTCATAGGCTTATCACTCGGAC 60.305 52.174 0.00 0.00 0.00 4.79
7269 7573 3.023832 GTTGACATTGGACCATAAGGGG 58.976 50.000 0.00 0.00 42.91 4.79
7272 7576 3.696045 TGGGTTGACATTGGACCATAAG 58.304 45.455 0.00 0.00 35.11 1.73
7296 7600 4.835615 AGATGTAGTTCAGATTCGCCCTAT 59.164 41.667 0.00 0.00 0.00 2.57
7310 7623 8.220755 ACATTGTTGTTGTTGTAGATGTAGTT 57.779 30.769 0.00 0.00 29.55 2.24
7318 7631 7.715265 AGTCTCTACATTGTTGTTGTTGTAG 57.285 36.000 0.00 0.00 41.75 2.74
7330 7643 7.306457 CGAAGCATGTTCATAGTCTCTACATTG 60.306 40.741 0.00 0.00 0.00 2.82
7331 7644 6.699204 CGAAGCATGTTCATAGTCTCTACATT 59.301 38.462 0.00 0.00 0.00 2.71
7332 7645 6.039829 TCGAAGCATGTTCATAGTCTCTACAT 59.960 38.462 0.00 0.00 0.00 2.29
7343 7656 3.853831 TTGCATTCGAAGCATGTTCAT 57.146 38.095 18.55 0.00 42.33 2.57
7345 7658 3.825308 TCTTTGCATTCGAAGCATGTTC 58.175 40.909 18.55 0.00 42.33 3.18
7362 7675 6.405278 AAAACTTGGGAAACGATGATCTTT 57.595 33.333 0.00 0.00 0.00 2.52
7387 7700 1.066358 CCCTTGGTCCTAAACGTCTCC 60.066 57.143 0.00 0.00 0.00 3.71
7390 7703 1.622312 AGTCCCTTGGTCCTAAACGTC 59.378 52.381 0.00 0.00 0.00 4.34
7393 7706 1.351350 AGCAGTCCCTTGGTCCTAAAC 59.649 52.381 0.00 0.00 0.00 2.01
7400 7713 5.514500 TTATCTTTTAGCAGTCCCTTGGT 57.486 39.130 0.00 0.00 0.00 3.67
7401 7714 7.391833 GGATATTATCTTTTAGCAGTCCCTTGG 59.608 40.741 3.77 0.00 0.00 3.61
7408 7721 7.499232 GGTGTGTGGATATTATCTTTTAGCAGT 59.501 37.037 3.77 0.00 0.00 4.40
7409 7722 7.716998 AGGTGTGTGGATATTATCTTTTAGCAG 59.283 37.037 3.77 0.00 0.00 4.24
7447 7760 6.037391 ACAACATGAAGGAACAAGCAAATTTG 59.963 34.615 14.03 14.03 0.00 2.32
7458 7771 2.616842 ACGACCAACAACATGAAGGAAC 59.383 45.455 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.