Multiple sequence alignment - TraesCS5D01G137100

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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 TraesCS5D01G137100 chr5D 100.000 5636 0 0 1 5636 218050810 218056445 0.000000e+00 10408.0
1 TraesCS5D01G137100 chr5B 92.019 3007 132 47 104 3041 234294601 234297568 0.000000e+00 4124.0
2 TraesCS5D01G137100 chr5B 92.303 1624 86 14 3744 5354 234303459 234305056 0.000000e+00 2270.0
3 TraesCS5D01G137100 chr5B 96.888 707 21 1 3037 3742 234302635 234303341 0.000000e+00 1182.0
4 TraesCS5D01G137100 chr5B 89.212 241 14 7 5338 5578 234307401 234307629 1.990000e-74 291.0
5 TraesCS5D01G137100 chr5B 93.651 63 4 0 5574 5636 234307951 234308013 1.670000e-15 95.3
6 TraesCS5D01G137100 chr5B 95.238 42 1 1 1421 1462 649506414 649506454 1.310000e-06 65.8
7 TraesCS5D01G137100 chr5A 93.287 2711 156 7 2888 5578 290928122 290930826 0.000000e+00 3975.0
8 TraesCS5D01G137100 chr5A 91.210 2298 90 38 263 2503 290924273 290926515 0.000000e+00 3022.0
9 TraesCS5D01G137100 chr5A 93.291 477 26 5 5104 5578 290935491 290935963 0.000000e+00 699.0
10 TraesCS5D01G137100 chr5A 92.476 319 23 1 2514 2832 290927822 290928139 6.660000e-124 455.0
11 TraesCS5D01G137100 chr5A 90.291 103 10 0 2 104 53144089 53143987 9.850000e-28 135.0
12 TraesCS5D01G137100 chr5A 94.000 50 3 0 137 186 347410180 347410229 6.050000e-10 76.8
13 TraesCS5D01G137100 chr6B 87.996 1841 187 20 3150 4963 135114513 135116346 0.000000e+00 2145.0
14 TraesCS5D01G137100 chr6B 84.085 1508 163 37 3336 4810 130828474 130829937 0.000000e+00 1384.0
15 TraesCS5D01G137100 chr6B 83.560 1101 105 41 1463 2504 135112784 135113867 0.000000e+00 961.0
16 TraesCS5D01G137100 chr6B 83.204 387 41 13 992 1357 135112373 135112756 3.250000e-87 333.0
17 TraesCS5D01G137100 chr6B 81.786 280 22 20 998 1267 130822738 130822998 2.060000e-49 207.0
18 TraesCS5D01G137100 chr6B 84.000 150 18 3 1706 1855 130823321 130823464 7.610000e-29 139.0
19 TraesCS5D01G137100 chr6B 92.308 65 4 1 273 337 135109867 135109930 2.160000e-14 91.6
20 TraesCS5D01G137100 chr6B 95.000 40 0 2 1423 1462 581919441 581919404 1.700000e-05 62.1
21 TraesCS5D01G137100 chr6A 88.794 1749 178 13 3149 4888 77782350 77784089 0.000000e+00 2128.0
22 TraesCS5D01G137100 chr6A 82.557 1525 173 42 3336 4810 73555907 73557388 0.000000e+00 1256.0
23 TraesCS5D01G137100 chr6A 82.743 1101 115 40 1463 2504 77780714 77781798 0.000000e+00 911.0
24 TraesCS5D01G137100 chr6A 77.561 820 129 33 1706 2502 73542984 73543771 1.440000e-120 444.0
25 TraesCS5D01G137100 chr6A 83.256 430 44 17 998 1410 77780311 77780729 2.480000e-98 370.0
26 TraesCS5D01G137100 chr6A 85.222 203 22 6 1456 1650 73542765 73542967 9.570000e-48 202.0
27 TraesCS5D01G137100 chr6A 90.476 105 10 0 2 106 599682749 599682853 7.610000e-29 139.0
28 TraesCS5D01G137100 chr6A 91.667 60 5 0 2831 2890 430337273 430337332 3.620000e-12 84.2
29 TraesCS5D01G137100 chr6A 97.368 38 1 0 1425 1462 555770545 555770508 1.310000e-06 65.8
30 TraesCS5D01G137100 chr6D 83.729 1518 168 41 3336 4818 58239086 58240559 0.000000e+00 1362.0
31 TraesCS5D01G137100 chr6D 86.601 1112 101 20 3859 4950 61137517 61138600 0.000000e+00 1184.0
32 TraesCS5D01G137100 chr6D 85.261 1072 105 28 1471 2504 61135107 61136163 0.000000e+00 1055.0
33 TraesCS5D01G137100 chr6D 88.593 675 69 6 3150 3820 61136842 61137512 0.000000e+00 813.0
34 TraesCS5D01G137100 chr6D 81.400 457 72 7 2051 2500 58235129 58235579 1.490000e-95 361.0
35 TraesCS5D01G137100 chr6D 82.176 432 46 20 998 1410 61134695 61135114 5.410000e-90 342.0
36 TraesCS5D01G137100 chr6D 81.362 279 25 20 998 1267 58234188 58234448 9.570000e-48 202.0
37 TraesCS5D01G137100 chr6D 90.000 150 13 2 1706 1855 58234760 58234907 5.760000e-45 193.0
38 TraesCS5D01G137100 chr6D 95.122 41 1 1 1421 1460 460290234 460290194 4.710000e-06 63.9
39 TraesCS5D01G137100 chr1A 91.429 105 9 0 2 106 481919676 481919572 1.640000e-30 145.0
40 TraesCS5D01G137100 chr1A 89.720 107 11 0 2 108 53022093 53021987 2.740000e-28 137.0
41 TraesCS5D01G137100 chr1A 90.291 103 10 0 2 104 285433708 285433810 9.850000e-28 135.0
42 TraesCS5D01G137100 chr7A 90.566 106 10 0 2 107 8801684 8801579 2.120000e-29 141.0
43 TraesCS5D01G137100 chr7A 90.291 103 10 0 2 104 521964082 521963980 9.850000e-28 135.0
44 TraesCS5D01G137100 chr7A 100.000 36 0 0 215 250 365207768 365207733 3.640000e-07 67.6
45 TraesCS5D01G137100 chr4A 91.262 103 9 0 2 104 445072920 445073022 2.120000e-29 141.0
46 TraesCS5D01G137100 chr4A 79.699 133 13 8 137 256 465488919 465488788 3.620000e-12 84.2
47 TraesCS5D01G137100 chr3A 91.089 101 9 0 4 104 259836422 259836322 2.740000e-28 137.0
48 TraesCS5D01G137100 chr3A 79.699 133 14 7 137 256 405573593 405573725 3.620000e-12 84.2
49 TraesCS5D01G137100 chr3A 97.143 35 1 0 1428 1462 21009405 21009439 6.100000e-05 60.2
50 TraesCS5D01G137100 chr3B 89.691 97 10 0 1904 2000 802770689 802770593 2.130000e-24 124.0
51 TraesCS5D01G137100 chr3B 81.679 131 11 4 137 255 1382937 1382808 4.650000e-16 97.1
52 TraesCS5D01G137100 chr7B 83.206 131 10 5 137 255 684000239 684000109 5.970000e-20 110.0
53 TraesCS5D01G137100 chr7B 98.246 57 1 0 2382 2438 711054719 711054663 3.590000e-17 100.0
54 TraesCS5D01G137100 chr7D 96.491 57 2 0 2382 2438 619556239 619556295 1.670000e-15 95.3
55 TraesCS5D01G137100 chr7D 93.478 46 2 1 1416 1461 54793211 54793255 3.640000e-07 67.6
56 TraesCS5D01G137100 chr4D 96.491 57 2 0 2382 2438 34592255 34592199 1.670000e-15 95.3
57 TraesCS5D01G137100 chr2D 93.617 47 1 2 1416 1462 598247538 598247494 1.010000e-07 69.4


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 TraesCS5D01G137100 chr5D 218050810 218056445 5635 False 10408.000000 10408 100.000000 1 5636 1 chr5D.!!$F1 5635
1 TraesCS5D01G137100 chr5B 234294601 234297568 2967 False 4124.000000 4124 92.019000 104 3041 1 chr5B.!!$F1 2937
2 TraesCS5D01G137100 chr5B 234302635 234308013 5378 False 959.575000 2270 93.013500 3037 5636 4 chr5B.!!$F3 2599
3 TraesCS5D01G137100 chr5A 290924273 290930826 6553 False 2484.000000 3975 92.324333 263 5578 3 chr5A.!!$F3 5315
4 TraesCS5D01G137100 chr6B 130828474 130829937 1463 False 1384.000000 1384 84.085000 3336 4810 1 chr6B.!!$F1 1474
5 TraesCS5D01G137100 chr6B 135109867 135116346 6479 False 882.650000 2145 86.767000 273 4963 4 chr6B.!!$F3 4690
6 TraesCS5D01G137100 chr6A 73555907 73557388 1481 False 1256.000000 1256 82.557000 3336 4810 1 chr6A.!!$F1 1474
7 TraesCS5D01G137100 chr6A 77780311 77784089 3778 False 1136.333333 2128 84.931000 998 4888 3 chr6A.!!$F5 3890
8 TraesCS5D01G137100 chr6A 73542765 73543771 1006 False 323.000000 444 81.391500 1456 2502 2 chr6A.!!$F4 1046
9 TraesCS5D01G137100 chr6D 61134695 61138600 3905 False 848.500000 1184 85.657750 998 4950 4 chr6D.!!$F2 3952
10 TraesCS5D01G137100 chr6D 58234188 58240559 6371 False 529.500000 1362 84.122750 998 4818 4 chr6D.!!$F1 3820

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
218 219 0.449388 CGATCCAAAAGCAGCCTGAC 59.551 55.000 0.0 0.0 0.0 3.51 F
1494 3571 0.034863 ATGGTTACGGGTGCGGAAAT 60.035 50.000 0.0 0.0 0.0 2.17 F
1496 3573 1.002888 TGGTTACGGGTGCGGAAATTA 59.997 47.619 0.0 0.0 0.0 1.40 F
2960 9125 0.247655 GCACACACACACACACTTCG 60.248 55.000 0.0 0.0 0.0 3.79 F
3265 9469 0.951558 CTTAACCACAGCACACCCAC 59.048 55.000 0.0 0.0 0.0 4.61 F
3934 10317 1.014564 GTGGACACTACAAGCCGAGC 61.015 60.000 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 3598 1.068541 GCCACCTTCGTTCAATCCAAC 60.069 52.381 0.0 0.0 0.00 3.77 R
2744 8895 0.678395 CTCGCCCTCATGTAGATGCT 59.322 55.000 0.0 0.0 0.00 3.79 R
3244 9448 1.235724 GGGTGTGCTGTGGTTAAGAC 58.764 55.000 0.0 0.0 0.00 3.01 R
3934 10317 0.037605 AGTTGGTAAGGTTCTCCGCG 60.038 55.000 0.0 0.0 39.05 6.46 R
4230 10621 0.106819 GTGAAGATGGCCCAGATGCT 60.107 55.000 0.0 0.0 0.00 3.79 R
4819 11234 1.343142 GACATTTGGCGGGAAAAAGGT 59.657 47.619 0.0 0.0 33.38 3.50 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
26 27 8.779354 TCTTAAATAAGAGAAGACAAGCCTTC 57.221 34.615 0.00 0.00 37.40 3.46
35 36 3.305398 AGACAAGCCTTCTCTTACACG 57.695 47.619 0.00 0.00 0.00 4.49
36 37 2.628657 AGACAAGCCTTCTCTTACACGT 59.371 45.455 0.00 0.00 0.00 4.49
37 38 3.069729 AGACAAGCCTTCTCTTACACGTT 59.930 43.478 0.00 0.00 0.00 3.99
38 39 4.280174 AGACAAGCCTTCTCTTACACGTTA 59.720 41.667 0.00 0.00 0.00 3.18
39 40 5.047235 AGACAAGCCTTCTCTTACACGTTAT 60.047 40.000 0.00 0.00 0.00 1.89
40 41 5.169295 ACAAGCCTTCTCTTACACGTTATC 58.831 41.667 0.00 0.00 0.00 1.75
41 42 5.047235 ACAAGCCTTCTCTTACACGTTATCT 60.047 40.000 0.00 0.00 0.00 1.98
42 43 5.251601 AGCCTTCTCTTACACGTTATCTC 57.748 43.478 0.00 0.00 0.00 2.75
43 44 4.951094 AGCCTTCTCTTACACGTTATCTCT 59.049 41.667 0.00 0.00 0.00 3.10
44 45 5.038033 GCCTTCTCTTACACGTTATCTCTG 58.962 45.833 0.00 0.00 0.00 3.35
45 46 5.038033 CCTTCTCTTACACGTTATCTCTGC 58.962 45.833 0.00 0.00 0.00 4.26
46 47 5.163602 CCTTCTCTTACACGTTATCTCTGCT 60.164 44.000 0.00 0.00 0.00 4.24
47 48 5.899120 TCTCTTACACGTTATCTCTGCTT 57.101 39.130 0.00 0.00 0.00 3.91
48 49 5.881447 TCTCTTACACGTTATCTCTGCTTC 58.119 41.667 0.00 0.00 0.00 3.86
49 50 5.414765 TCTCTTACACGTTATCTCTGCTTCA 59.585 40.000 0.00 0.00 0.00 3.02
50 51 5.399858 TCTTACACGTTATCTCTGCTTCAC 58.600 41.667 0.00 0.00 0.00 3.18
51 52 2.960819 ACACGTTATCTCTGCTTCACC 58.039 47.619 0.00 0.00 0.00 4.02
52 53 2.563179 ACACGTTATCTCTGCTTCACCT 59.437 45.455 0.00 0.00 0.00 4.00
53 54 3.006967 ACACGTTATCTCTGCTTCACCTT 59.993 43.478 0.00 0.00 0.00 3.50
54 55 4.219944 ACACGTTATCTCTGCTTCACCTTA 59.780 41.667 0.00 0.00 0.00 2.69
55 56 5.105310 ACACGTTATCTCTGCTTCACCTTAT 60.105 40.000 0.00 0.00 0.00 1.73
56 57 5.460419 CACGTTATCTCTGCTTCACCTTATC 59.540 44.000 0.00 0.00 0.00 1.75
57 58 5.127194 ACGTTATCTCTGCTTCACCTTATCA 59.873 40.000 0.00 0.00 0.00 2.15
58 59 6.183360 ACGTTATCTCTGCTTCACCTTATCAT 60.183 38.462 0.00 0.00 0.00 2.45
59 60 6.703607 CGTTATCTCTGCTTCACCTTATCATT 59.296 38.462 0.00 0.00 0.00 2.57
60 61 7.225538 CGTTATCTCTGCTTCACCTTATCATTT 59.774 37.037 0.00 0.00 0.00 2.32
61 62 9.547753 GTTATCTCTGCTTCACCTTATCATTTA 57.452 33.333 0.00 0.00 0.00 1.40
63 64 8.845413 ATCTCTGCTTCACCTTATCATTTATC 57.155 34.615 0.00 0.00 0.00 1.75
64 65 7.220030 TCTCTGCTTCACCTTATCATTTATCC 58.780 38.462 0.00 0.00 0.00 2.59
65 66 7.071698 TCTCTGCTTCACCTTATCATTTATCCT 59.928 37.037 0.00 0.00 0.00 3.24
66 67 8.262601 TCTGCTTCACCTTATCATTTATCCTA 57.737 34.615 0.00 0.00 0.00 2.94
67 68 8.150945 TCTGCTTCACCTTATCATTTATCCTAC 58.849 37.037 0.00 0.00 0.00 3.18
68 69 6.929049 TGCTTCACCTTATCATTTATCCTACG 59.071 38.462 0.00 0.00 0.00 3.51
69 70 6.929606 GCTTCACCTTATCATTTATCCTACGT 59.070 38.462 0.00 0.00 0.00 3.57
70 71 8.086522 GCTTCACCTTATCATTTATCCTACGTA 58.913 37.037 0.00 0.00 0.00 3.57
71 72 9.976511 CTTCACCTTATCATTTATCCTACGTAA 57.023 33.333 0.00 0.00 0.00 3.18
72 73 9.754382 TTCACCTTATCATTTATCCTACGTAAC 57.246 33.333 0.00 0.00 0.00 2.50
73 74 8.916062 TCACCTTATCATTTATCCTACGTAACA 58.084 33.333 0.00 0.00 0.00 2.41
74 75 8.975439 CACCTTATCATTTATCCTACGTAACAC 58.025 37.037 0.00 0.00 0.00 3.32
75 76 8.921205 ACCTTATCATTTATCCTACGTAACACT 58.079 33.333 0.00 0.00 0.00 3.55
76 77 9.760077 CCTTATCATTTATCCTACGTAACACTT 57.240 33.333 0.00 0.00 0.00 3.16
86 87 7.256756 TCCTACGTAACACTTCTAAGATAGC 57.743 40.000 0.00 0.00 0.00 2.97
87 88 6.825213 TCCTACGTAACACTTCTAAGATAGCA 59.175 38.462 0.00 0.00 0.00 3.49
88 89 6.911511 CCTACGTAACACTTCTAAGATAGCAC 59.088 42.308 0.00 0.00 0.00 4.40
89 90 5.648572 ACGTAACACTTCTAAGATAGCACC 58.351 41.667 0.00 0.00 0.00 5.01
90 91 5.184479 ACGTAACACTTCTAAGATAGCACCA 59.816 40.000 0.00 0.00 0.00 4.17
91 92 6.127423 ACGTAACACTTCTAAGATAGCACCAT 60.127 38.462 0.00 0.00 0.00 3.55
92 93 6.757010 CGTAACACTTCTAAGATAGCACCATT 59.243 38.462 0.00 0.00 0.00 3.16
93 94 6.992063 AACACTTCTAAGATAGCACCATTG 57.008 37.500 0.00 0.00 0.00 2.82
94 95 6.054860 ACACTTCTAAGATAGCACCATTGT 57.945 37.500 0.00 0.00 0.00 2.71
95 96 7.182817 ACACTTCTAAGATAGCACCATTGTA 57.817 36.000 0.00 0.00 0.00 2.41
96 97 7.042335 ACACTTCTAAGATAGCACCATTGTAC 58.958 38.462 0.00 0.00 0.00 2.90
97 98 7.041721 CACTTCTAAGATAGCACCATTGTACA 58.958 38.462 0.00 0.00 0.00 2.90
98 99 7.549134 CACTTCTAAGATAGCACCATTGTACAA 59.451 37.037 11.41 11.41 0.00 2.41
99 100 7.766278 ACTTCTAAGATAGCACCATTGTACAAG 59.234 37.037 14.65 3.88 0.00 3.16
100 101 6.049149 TCTAAGATAGCACCATTGTACAAGC 58.951 40.000 14.65 11.54 0.00 4.01
101 102 3.545703 AGATAGCACCATTGTACAAGCC 58.454 45.455 14.65 0.14 0.00 4.35
102 103 2.122783 TAGCACCATTGTACAAGCCC 57.877 50.000 14.65 1.01 0.00 5.19
113 114 4.561500 TGTACAAGCCCTTACAAGCATA 57.438 40.909 0.00 0.00 0.00 3.14
119 120 5.105756 ACAAGCCCTTACAAGCATATTTGAC 60.106 40.000 0.00 0.00 0.00 3.18
120 121 3.627577 AGCCCTTACAAGCATATTTGACG 59.372 43.478 0.00 0.00 0.00 4.35
127 128 4.913376 ACAAGCATATTTGACGAGATTGC 58.087 39.130 0.00 0.00 0.00 3.56
159 160 6.530019 AGTCCAACAATAATTAAAGCCCAG 57.470 37.500 0.00 0.00 0.00 4.45
167 168 6.496911 ACAATAATTAAAGCCCAGACCAAACT 59.503 34.615 0.00 0.00 0.00 2.66
173 174 2.863809 AGCCCAGACCAAACTAAACTG 58.136 47.619 0.00 0.00 0.00 3.16
174 175 2.441750 AGCCCAGACCAAACTAAACTGA 59.558 45.455 0.00 0.00 0.00 3.41
196 197 5.124776 TGATTTAGGCACTTAACCCATTTCG 59.875 40.000 0.00 0.00 41.75 3.46
199 200 1.471287 GGCACTTAACCCATTTCGTCC 59.529 52.381 0.00 0.00 0.00 4.79
200 201 1.129811 GCACTTAACCCATTTCGTCCG 59.870 52.381 0.00 0.00 0.00 4.79
211 212 1.885560 TTTCGTCCGATCCAAAAGCA 58.114 45.000 0.00 0.00 0.00 3.91
215 216 0.678048 GTCCGATCCAAAAGCAGCCT 60.678 55.000 0.00 0.00 0.00 4.58
216 217 0.677731 TCCGATCCAAAAGCAGCCTG 60.678 55.000 0.00 0.00 0.00 4.85
218 219 0.449388 CGATCCAAAAGCAGCCTGAC 59.551 55.000 0.00 0.00 0.00 3.51
219 220 1.831580 GATCCAAAAGCAGCCTGACT 58.168 50.000 0.00 0.00 0.00 3.41
250 251 1.904287 TTCAGTCCAAACCATTCCCG 58.096 50.000 0.00 0.00 0.00 5.14
271 272 4.525912 GGGTTACCGGGTGTATATACTG 57.474 50.000 10.66 2.07 0.00 2.74
457 993 1.424403 TGCGTTTGGACATAGACGTG 58.576 50.000 0.00 0.00 37.78 4.49
471 1015 3.264897 CGTGCTATGTGCCGCTCC 61.265 66.667 0.00 0.00 42.00 4.70
495 1039 6.705825 CCAGAATCATCACATACATAAACCGA 59.294 38.462 0.00 0.00 0.00 4.69
497 1041 6.931281 AGAATCATCACATACATAAACCGAGG 59.069 38.462 0.00 0.00 0.00 4.63
570 1145 3.313526 ACAGCAATTCTGAGTCAACACAC 59.686 43.478 10.61 0.00 45.72 3.82
571 1146 3.313249 CAGCAATTCTGAGTCAACACACA 59.687 43.478 0.00 0.00 45.72 3.72
572 1147 4.023450 CAGCAATTCTGAGTCAACACACAT 60.023 41.667 0.00 0.00 45.72 3.21
574 1149 4.705492 CAATTCTGAGTCAACACACATCG 58.295 43.478 0.00 0.00 0.00 3.84
575 1150 3.452755 TTCTGAGTCAACACACATCGT 57.547 42.857 0.00 0.00 0.00 3.73
576 1151 3.452755 TCTGAGTCAACACACATCGTT 57.547 42.857 0.00 0.00 0.00 3.85
625 2576 3.936203 GGCACGGTGGACAGGACA 61.936 66.667 10.60 0.00 0.00 4.02
628 2579 2.520020 ACGGTGGACAGGACACGA 60.520 61.111 0.00 0.00 39.69 4.35
629 2580 2.049433 CGGTGGACAGGACACGAC 60.049 66.667 0.00 0.00 39.69 4.34
630 2581 2.342648 GGTGGACAGGACACGACC 59.657 66.667 0.00 0.00 39.69 4.79
631 2582 2.342648 GTGGACAGGACACGACCC 59.657 66.667 0.00 0.00 0.00 4.46
664 2615 4.498520 ATCTGCGACCGCGTCCAG 62.499 66.667 4.92 11.78 45.51 3.86
777 2750 4.814234 TGCGCTCTCTTTTTCTTTCTGTTA 59.186 37.500 9.73 0.00 0.00 2.41
823 2796 2.509336 CGTAGTTCCCGCCAGCAG 60.509 66.667 0.00 0.00 0.00 4.24
824 2797 2.125106 GTAGTTCCCGCCAGCAGG 60.125 66.667 0.00 0.00 38.23 4.85
845 2824 7.885399 AGCAGGACAGAAAACTAACTCAATAAT 59.115 33.333 0.00 0.00 0.00 1.28
846 2825 9.162764 GCAGGACAGAAAACTAACTCAATAATA 57.837 33.333 0.00 0.00 0.00 0.98
941 2948 1.613630 TGCTGACTCCTCCTTCCCC 60.614 63.158 0.00 0.00 0.00 4.81
943 2950 1.394151 CTGACTCCTCCTTCCCCCT 59.606 63.158 0.00 0.00 0.00 4.79
954 2961 1.001760 TTCCCCCTTCCTCCTCGAG 59.998 63.158 5.13 5.13 0.00 4.04
985 2992 6.548321 ACAACCATTAGTCCATTACCTTGAA 58.452 36.000 0.00 0.00 0.00 2.69
988 2995 6.365520 ACCATTAGTCCATTACCTTGAATCC 58.634 40.000 0.00 0.00 0.00 3.01
989 2996 6.160459 ACCATTAGTCCATTACCTTGAATCCT 59.840 38.462 0.00 0.00 0.00 3.24
990 2997 7.062957 CCATTAGTCCATTACCTTGAATCCTT 58.937 38.462 0.00 0.00 0.00 3.36
991 2998 7.013655 CCATTAGTCCATTACCTTGAATCCTTG 59.986 40.741 0.00 0.00 0.00 3.61
1014 3046 1.062810 AGGTAGATGGAGGTGGAGACC 60.063 57.143 0.00 0.00 43.52 3.85
1239 3292 5.815581 AGCAAAAGGATAACATGACTACCA 58.184 37.500 0.00 0.00 0.00 3.25
1240 3293 6.426587 AGCAAAAGGATAACATGACTACCAT 58.573 36.000 0.00 0.00 35.44 3.55
1318 3375 0.114364 ACCCGCCTTTCTTGGGATTT 59.886 50.000 3.03 0.00 46.41 2.17
1489 3559 0.390603 TCTTGATGGTTACGGGTGCG 60.391 55.000 0.00 0.00 0.00 5.34
1494 3571 0.034863 ATGGTTACGGGTGCGGAAAT 60.035 50.000 0.00 0.00 0.00 2.17
1496 3573 1.002888 TGGTTACGGGTGCGGAAATTA 59.997 47.619 0.00 0.00 0.00 1.40
1500 3577 1.900245 ACGGGTGCGGAAATTAAACT 58.100 45.000 0.00 0.00 0.00 2.66
1502 3579 1.538075 CGGGTGCGGAAATTAAACTGT 59.462 47.619 0.00 0.00 0.00 3.55
1672 3768 1.109323 CCCTTTCCCCGCATCAATCC 61.109 60.000 0.00 0.00 0.00 3.01
2029 4220 2.854963 TCTGAAGCTTGCACTGTTGAT 58.145 42.857 2.10 0.00 0.00 2.57
2060 4257 7.281549 ACTTCTGCTTGCAAAATTTTGAAATCT 59.718 29.630 30.40 6.71 40.55 2.40
2191 4394 4.655963 AGAAAATGACTGCCACTGTGTAT 58.344 39.130 7.08 0.00 0.00 2.29
2206 4409 7.412891 GCCACTGTGTATTATCAAAATTTTGCC 60.413 37.037 23.36 9.00 38.05 4.52
2299 4516 6.308041 GCACGGAAATTGATAAGTCTTTTTCC 59.692 38.462 12.79 12.79 39.75 3.13
2707 8858 5.975344 GGTGTAAAGACAAAACTAAGCCAAC 59.025 40.000 0.00 0.00 37.31 3.77
2880 9041 2.125512 CGCTTTCAGAGGGTCCGG 60.126 66.667 0.00 0.00 33.85 5.14
2887 9048 2.060980 CAGAGGGTCCGGAGAAGGG 61.061 68.421 3.06 0.00 0.00 3.95
2960 9125 0.247655 GCACACACACACACACTTCG 60.248 55.000 0.00 0.00 0.00 3.79
3230 9434 5.133221 CCTAGCCTGTGCCATTTATACTTT 58.867 41.667 0.00 0.00 38.69 2.66
3244 9448 9.210426 CCATTTATACTTTTCTTCGATTGTTCG 57.790 33.333 0.00 0.00 46.87 3.95
3265 9469 0.951558 CTTAACCACAGCACACCCAC 59.048 55.000 0.00 0.00 0.00 4.61
3303 9508 8.532977 AGTCATAACAAATTGCCACATTAAAC 57.467 30.769 0.00 0.00 0.00 2.01
3439 9677 6.611613 TCTGGAGAATCACTTGATACAAGT 57.388 37.500 10.73 10.73 36.25 3.16
3542 9780 7.052873 ACTCACAGAATTTTATAGCTGCTGAT 58.947 34.615 13.43 4.77 31.74 2.90
3715 9955 8.960591 AGAAAATGGAGTTATCAAGGTATTGTG 58.039 33.333 0.00 0.00 37.68 3.33
3742 9983 4.040755 ACCACCATCCTATCTTAGTGCTT 58.959 43.478 0.00 0.00 0.00 3.91
3839 10222 7.275888 AGCATACTCACAATTTTGTTCTTGA 57.724 32.000 0.00 0.00 39.91 3.02
3874 10257 5.184287 TGGATGCATTGTGCTAATATGATGG 59.816 40.000 0.00 0.00 45.31 3.51
3910 10293 1.634973 TCATTTCAGTCCATCTGGGCA 59.365 47.619 3.27 0.00 43.78 5.36
3922 10305 3.557898 CCATCTGGGCATATAGTGGACAC 60.558 52.174 0.00 0.00 0.00 3.67
3934 10317 1.014564 GTGGACACTACAAGCCGAGC 61.015 60.000 0.00 0.00 0.00 5.03
4020 10403 7.827729 AGTTGAGGTATACTATTTTTGGTCCAC 59.172 37.037 2.25 0.00 0.00 4.02
4128 10516 4.956700 TCCACCAAGGAAGACTACTATGAG 59.043 45.833 0.00 0.00 45.65 2.90
4230 10621 5.935945 TCCAACATGGTAGAAGAAGACAAA 58.064 37.500 0.00 0.00 39.03 2.83
4344 10738 1.406205 GGCCTGCAAAGTCCTAGAGAC 60.406 57.143 0.00 0.00 46.71 3.36
4933 11368 3.356529 AACATGAGGGACAAAGCCTAG 57.643 47.619 0.00 0.00 0.00 3.02
4995 11430 6.293407 CGACTAAAGAGAGGTGCATTTGAAAA 60.293 38.462 0.00 0.00 0.00 2.29
4996 11431 6.739112 ACTAAAGAGAGGTGCATTTGAAAAC 58.261 36.000 0.00 0.00 0.00 2.43
5003 11438 5.009410 AGAGGTGCATTTGAAAACTTCTCAG 59.991 40.000 0.00 0.00 0.00 3.35
5012 11447 9.007901 CATTTGAAAACTTCTCAGAGTATCCTT 57.992 33.333 0.00 0.00 33.66 3.36
5018 11453 8.602472 AAACTTCTCAGAGTATCCTTACTGAT 57.398 34.615 0.00 0.00 38.81 2.90
5102 11537 2.014554 CGGCGATATCACCGGTTCG 61.015 63.158 21.91 19.58 45.74 3.95
5141 11576 0.108585 TCCACCTTCAGTTCACCTGC 59.891 55.000 0.00 0.00 41.25 4.85
5170 11605 8.429493 AATGTGTGAATATACTGTCATCACTG 57.571 34.615 12.93 0.00 40.70 3.66
5187 11622 2.299013 CACTGCTACTTAGTCACCACCA 59.701 50.000 0.00 0.00 0.00 4.17
5380 14176 8.910351 ATAATAATCTAAGAACAGGCAAGACC 57.090 34.615 0.00 0.00 39.61 3.85
5420 14216 1.208052 TCAGAAAGGAGGAATGAGGCG 59.792 52.381 0.00 0.00 0.00 5.52
5520 14316 3.975168 AAGTCGGGCTGTAACTTACAT 57.025 42.857 2.02 0.00 38.15 2.29
5530 14326 6.373216 GGGCTGTAACTTACATCAACACAATA 59.627 38.462 2.02 0.00 38.15 1.90
5555 14351 5.185828 AGCAAATTCTCCCACTTTACAATCC 59.814 40.000 0.00 0.00 0.00 3.01
5586 14708 5.010516 AGAGAGAGATAATCCATGACAACCG 59.989 44.000 0.00 0.00 0.00 4.44
5619 14741 5.645067 ACCATTGACATCTCAACAGTACATG 59.355 40.000 0.00 0.00 39.28 3.21
5625 14747 4.774726 ACATCTCAACAGTACATGGACTCT 59.225 41.667 7.91 0.00 0.00 3.24
5626 14748 4.790765 TCTCAACAGTACATGGACTCTG 57.209 45.455 7.91 8.96 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.779354 GAAGGCTTGTCTTCTCTTATTTAAGA 57.221 34.615 3.46 0.44 39.84 2.10
13 14 3.675698 CGTGTAAGAGAAGGCTTGTCTTC 59.324 47.826 34.48 26.12 41.71 2.87
14 15 3.069729 ACGTGTAAGAGAAGGCTTGTCTT 59.930 43.478 33.39 33.39 44.39 3.01
15 16 2.628657 ACGTGTAAGAGAAGGCTTGTCT 59.371 45.455 20.19 20.19 34.32 3.41
16 17 3.027974 ACGTGTAAGAGAAGGCTTGTC 57.972 47.619 16.04 16.04 0.00 3.18
17 18 3.470645 AACGTGTAAGAGAAGGCTTGT 57.529 42.857 3.46 0.00 0.00 3.16
18 19 5.411781 AGATAACGTGTAAGAGAAGGCTTG 58.588 41.667 3.46 0.00 0.00 4.01
19 20 5.419471 AGAGATAACGTGTAAGAGAAGGCTT 59.581 40.000 0.00 0.00 0.00 4.35
20 21 4.951094 AGAGATAACGTGTAAGAGAAGGCT 59.049 41.667 0.00 0.00 0.00 4.58
21 22 5.038033 CAGAGATAACGTGTAAGAGAAGGC 58.962 45.833 0.00 0.00 0.00 4.35
22 23 5.038033 GCAGAGATAACGTGTAAGAGAAGG 58.962 45.833 0.00 0.00 0.00 3.46
23 24 5.885881 AGCAGAGATAACGTGTAAGAGAAG 58.114 41.667 0.00 0.00 0.00 2.85
24 25 5.899120 AGCAGAGATAACGTGTAAGAGAA 57.101 39.130 0.00 0.00 0.00 2.87
25 26 5.414765 TGAAGCAGAGATAACGTGTAAGAGA 59.585 40.000 0.00 0.00 0.00 3.10
26 27 5.513495 GTGAAGCAGAGATAACGTGTAAGAG 59.487 44.000 0.00 0.00 0.00 2.85
27 28 5.399858 GTGAAGCAGAGATAACGTGTAAGA 58.600 41.667 0.00 0.00 0.00 2.10
28 29 4.563184 GGTGAAGCAGAGATAACGTGTAAG 59.437 45.833 0.00 0.00 0.00 2.34
29 30 4.219944 AGGTGAAGCAGAGATAACGTGTAA 59.780 41.667 0.00 0.00 0.00 2.41
30 31 3.762288 AGGTGAAGCAGAGATAACGTGTA 59.238 43.478 0.00 0.00 0.00 2.90
31 32 2.563179 AGGTGAAGCAGAGATAACGTGT 59.437 45.455 0.00 0.00 0.00 4.49
32 33 3.238108 AGGTGAAGCAGAGATAACGTG 57.762 47.619 0.00 0.00 0.00 4.49
33 34 3.963428 AAGGTGAAGCAGAGATAACGT 57.037 42.857 0.00 0.00 0.00 3.99
34 35 5.592054 TGATAAGGTGAAGCAGAGATAACG 58.408 41.667 0.00 0.00 0.00 3.18
35 36 8.443953 AAATGATAAGGTGAAGCAGAGATAAC 57.556 34.615 0.00 0.00 0.00 1.89
37 38 9.935241 GATAAATGATAAGGTGAAGCAGAGATA 57.065 33.333 0.00 0.00 0.00 1.98
38 39 7.882271 GGATAAATGATAAGGTGAAGCAGAGAT 59.118 37.037 0.00 0.00 0.00 2.75
39 40 7.071698 AGGATAAATGATAAGGTGAAGCAGAGA 59.928 37.037 0.00 0.00 0.00 3.10
40 41 7.222872 AGGATAAATGATAAGGTGAAGCAGAG 58.777 38.462 0.00 0.00 0.00 3.35
41 42 7.141758 AGGATAAATGATAAGGTGAAGCAGA 57.858 36.000 0.00 0.00 0.00 4.26
42 43 7.116948 CGTAGGATAAATGATAAGGTGAAGCAG 59.883 40.741 0.00 0.00 0.00 4.24
43 44 6.929049 CGTAGGATAAATGATAAGGTGAAGCA 59.071 38.462 0.00 0.00 0.00 3.91
44 45 6.929606 ACGTAGGATAAATGATAAGGTGAAGC 59.070 38.462 0.00 0.00 0.00 3.86
45 46 9.976511 TTACGTAGGATAAATGATAAGGTGAAG 57.023 33.333 0.00 0.00 0.00 3.02
46 47 9.754382 GTTACGTAGGATAAATGATAAGGTGAA 57.246 33.333 0.00 0.00 0.00 3.18
47 48 8.916062 TGTTACGTAGGATAAATGATAAGGTGA 58.084 33.333 0.00 0.00 0.00 4.02
48 49 8.975439 GTGTTACGTAGGATAAATGATAAGGTG 58.025 37.037 0.00 0.00 0.00 4.00
49 50 8.921205 AGTGTTACGTAGGATAAATGATAAGGT 58.079 33.333 0.00 0.00 0.00 3.50
50 51 9.760077 AAGTGTTACGTAGGATAAATGATAAGG 57.240 33.333 0.00 0.00 0.00 2.69
60 61 8.997323 GCTATCTTAGAAGTGTTACGTAGGATA 58.003 37.037 0.00 0.00 0.00 2.59
61 62 7.501559 TGCTATCTTAGAAGTGTTACGTAGGAT 59.498 37.037 0.00 0.00 0.00 3.24
62 63 6.825213 TGCTATCTTAGAAGTGTTACGTAGGA 59.175 38.462 0.00 0.00 0.00 2.94
63 64 6.911511 GTGCTATCTTAGAAGTGTTACGTAGG 59.088 42.308 0.00 0.00 0.00 3.18
64 65 6.911511 GGTGCTATCTTAGAAGTGTTACGTAG 59.088 42.308 0.00 0.00 0.00 3.51
65 66 6.375174 TGGTGCTATCTTAGAAGTGTTACGTA 59.625 38.462 0.00 0.00 0.00 3.57
66 67 5.184479 TGGTGCTATCTTAGAAGTGTTACGT 59.816 40.000 0.00 0.00 0.00 3.57
67 68 5.647589 TGGTGCTATCTTAGAAGTGTTACG 58.352 41.667 0.00 0.00 0.00 3.18
68 69 7.549488 ACAATGGTGCTATCTTAGAAGTGTTAC 59.451 37.037 0.00 0.00 0.00 2.50
69 70 7.620880 ACAATGGTGCTATCTTAGAAGTGTTA 58.379 34.615 0.00 0.00 0.00 2.41
70 71 6.476378 ACAATGGTGCTATCTTAGAAGTGTT 58.524 36.000 0.00 0.00 0.00 3.32
71 72 6.054860 ACAATGGTGCTATCTTAGAAGTGT 57.945 37.500 0.00 0.00 0.00 3.55
72 73 7.041721 TGTACAATGGTGCTATCTTAGAAGTG 58.958 38.462 0.00 0.00 0.00 3.16
73 74 7.182817 TGTACAATGGTGCTATCTTAGAAGT 57.817 36.000 0.00 0.00 0.00 3.01
74 75 7.254590 GCTTGTACAATGGTGCTATCTTAGAAG 60.255 40.741 9.13 0.00 0.00 2.85
75 76 6.538742 GCTTGTACAATGGTGCTATCTTAGAA 59.461 38.462 9.13 0.00 0.00 2.10
76 77 6.049149 GCTTGTACAATGGTGCTATCTTAGA 58.951 40.000 9.13 0.00 0.00 2.10
77 78 5.237344 GGCTTGTACAATGGTGCTATCTTAG 59.763 44.000 9.13 0.00 0.00 2.18
78 79 5.123227 GGCTTGTACAATGGTGCTATCTTA 58.877 41.667 9.13 0.00 0.00 2.10
79 80 3.947834 GGCTTGTACAATGGTGCTATCTT 59.052 43.478 9.13 0.00 0.00 2.40
80 81 3.545703 GGCTTGTACAATGGTGCTATCT 58.454 45.455 9.13 0.00 0.00 1.98
81 82 2.618709 GGGCTTGTACAATGGTGCTATC 59.381 50.000 9.13 0.00 0.00 2.08
82 83 2.242196 AGGGCTTGTACAATGGTGCTAT 59.758 45.455 9.13 0.00 0.00 2.97
83 84 1.633432 AGGGCTTGTACAATGGTGCTA 59.367 47.619 9.13 0.00 0.00 3.49
84 85 0.405585 AGGGCTTGTACAATGGTGCT 59.594 50.000 9.13 0.00 0.00 4.40
85 86 1.256812 AAGGGCTTGTACAATGGTGC 58.743 50.000 9.13 8.83 0.00 5.01
86 87 3.417101 TGTAAGGGCTTGTACAATGGTG 58.583 45.455 9.13 0.00 0.00 4.17
87 88 3.799432 TGTAAGGGCTTGTACAATGGT 57.201 42.857 9.13 0.00 0.00 3.55
88 89 3.119495 GCTTGTAAGGGCTTGTACAATGG 60.119 47.826 9.13 0.00 39.00 3.16
89 90 3.505680 TGCTTGTAAGGGCTTGTACAATG 59.494 43.478 9.13 4.83 39.00 2.82
90 91 3.761897 TGCTTGTAAGGGCTTGTACAAT 58.238 40.909 9.13 0.00 39.00 2.71
91 92 3.216187 TGCTTGTAAGGGCTTGTACAA 57.784 42.857 8.28 8.28 37.77 2.41
92 93 2.940994 TGCTTGTAAGGGCTTGTACA 57.059 45.000 0.00 0.00 0.00 2.90
93 94 6.094881 TCAAATATGCTTGTAAGGGCTTGTAC 59.905 38.462 0.00 0.00 0.00 2.90
94 95 6.094881 GTCAAATATGCTTGTAAGGGCTTGTA 59.905 38.462 0.00 0.00 0.00 2.41
95 96 5.016173 TCAAATATGCTTGTAAGGGCTTGT 58.984 37.500 0.00 0.00 0.00 3.16
96 97 5.343249 GTCAAATATGCTTGTAAGGGCTTG 58.657 41.667 0.00 0.00 0.00 4.01
97 98 4.096382 CGTCAAATATGCTTGTAAGGGCTT 59.904 41.667 0.00 0.00 0.00 4.35
98 99 3.627577 CGTCAAATATGCTTGTAAGGGCT 59.372 43.478 0.00 0.00 0.00 5.19
99 100 3.625764 TCGTCAAATATGCTTGTAAGGGC 59.374 43.478 0.00 0.00 0.00 5.19
100 101 5.116180 TCTCGTCAAATATGCTTGTAAGGG 58.884 41.667 0.00 0.00 0.00 3.95
101 102 6.851222 ATCTCGTCAAATATGCTTGTAAGG 57.149 37.500 0.00 0.00 0.00 2.69
102 103 6.630443 GCAATCTCGTCAAATATGCTTGTAAG 59.370 38.462 0.00 0.00 0.00 2.34
113 114 2.015736 AGCTCGCAATCTCGTCAAAT 57.984 45.000 0.00 0.00 0.00 2.32
119 120 1.322936 GACTTGAAGCTCGCAATCTCG 59.677 52.381 2.84 0.00 0.00 4.04
120 121 1.663135 GGACTTGAAGCTCGCAATCTC 59.337 52.381 2.84 2.02 0.00 2.75
127 128 5.551760 ATTATTGTTGGACTTGAAGCTCG 57.448 39.130 0.00 0.00 0.00 5.03
159 160 6.206829 AGTGCCTAAATCAGTTTAGTTTGGTC 59.793 38.462 7.05 0.00 43.37 4.02
167 168 6.544650 TGGGTTAAGTGCCTAAATCAGTTTA 58.455 36.000 0.00 0.00 0.00 2.01
173 174 5.124936 ACGAAATGGGTTAAGTGCCTAAATC 59.875 40.000 0.00 0.00 0.00 2.17
174 175 5.014202 ACGAAATGGGTTAAGTGCCTAAAT 58.986 37.500 0.00 0.00 0.00 1.40
180 181 1.129811 CGGACGAAATGGGTTAAGTGC 59.870 52.381 0.00 0.00 0.00 4.40
196 197 0.678048 AGGCTGCTTTTGGATCGGAC 60.678 55.000 0.00 0.00 0.00 4.79
199 200 0.449388 GTCAGGCTGCTTTTGGATCG 59.551 55.000 10.34 0.00 0.00 3.69
200 201 1.471684 CAGTCAGGCTGCTTTTGGATC 59.528 52.381 10.34 0.00 38.52 3.36
211 212 4.373156 AAACCATAGTTTCAGTCAGGCT 57.627 40.909 0.00 0.00 42.67 4.58
233 234 0.965363 CCCGGGAATGGTTTGGACTG 60.965 60.000 18.48 0.00 0.00 3.51
250 251 3.897505 ACAGTATATACACCCGGTAACCC 59.102 47.826 15.18 0.00 35.14 4.11
255 256 5.068198 CACAGTAACAGTATATACACCCGGT 59.932 44.000 15.18 2.14 0.00 5.28
256 257 5.300034 TCACAGTAACAGTATATACACCCGG 59.700 44.000 15.18 0.00 0.00 5.73
258 259 6.204359 CGTCACAGTAACAGTATATACACCC 58.796 44.000 15.18 0.00 0.00 4.61
261 262 6.459161 CCAGCGTCACAGTAACAGTATATACA 60.459 42.308 15.18 0.00 0.00 2.29
268 269 0.033504 CCCAGCGTCACAGTAACAGT 59.966 55.000 0.00 0.00 0.00 3.55
271 272 2.033194 GGCCCAGCGTCACAGTAAC 61.033 63.158 0.00 0.00 0.00 2.50
306 307 1.533219 CATGGCAGGTGGCTCCATA 59.467 57.895 8.51 0.00 44.01 2.74
403 404 5.248477 TCAAGTACTGTTAGCTTTCCTGGAT 59.752 40.000 0.00 0.00 0.00 3.41
457 993 0.533755 ATTCTGGAGCGGCACATAGC 60.534 55.000 1.45 0.00 44.65 2.97
466 1010 3.721035 TGTATGTGATGATTCTGGAGCG 58.279 45.455 0.00 0.00 0.00 5.03
471 1015 7.095481 CCTCGGTTTATGTATGTGATGATTCTG 60.095 40.741 0.00 0.00 0.00 3.02
495 1039 0.631753 TGCTCCTGCTACCTACTCCT 59.368 55.000 0.00 0.00 40.48 3.69
497 1041 3.462021 CAAATGCTCCTGCTACCTACTC 58.538 50.000 0.00 0.00 40.48 2.59
558 1133 3.792401 AGAAACGATGTGTGTTGACTCA 58.208 40.909 0.00 0.00 0.00 3.41
570 1145 0.304705 GCGGGCACATAGAAACGATG 59.695 55.000 0.00 0.00 0.00 3.84
571 1146 0.178068 AGCGGGCACATAGAAACGAT 59.822 50.000 0.00 0.00 0.00 3.73
572 1147 0.459585 GAGCGGGCACATAGAAACGA 60.460 55.000 0.00 0.00 0.00 3.85
574 1149 0.107654 AGGAGCGGGCACATAGAAAC 60.108 55.000 0.00 0.00 0.00 2.78
575 1150 0.107703 CAGGAGCGGGCACATAGAAA 60.108 55.000 0.00 0.00 0.00 2.52
576 1151 1.522092 CAGGAGCGGGCACATAGAA 59.478 57.895 0.00 0.00 0.00 2.10
777 2750 2.807676 ACAGAAAGATTTCCCGGCAAT 58.192 42.857 0.00 0.00 37.92 3.56
823 2796 9.989869 GCTTATTATTGAGTTAGTTTTCTGTCC 57.010 33.333 0.00 0.00 0.00 4.02
824 2797 9.690434 CGCTTATTATTGAGTTAGTTTTCTGTC 57.310 33.333 0.00 0.00 0.00 3.51
846 2825 9.593134 TGGACAATAATTTAATTTAATGCGCTT 57.407 25.926 9.73 0.00 0.00 4.68
954 2961 4.216411 TGGACTAATGGTTGTAGCCTTC 57.784 45.455 0.00 0.00 0.00 3.46
958 2965 5.681639 AGGTAATGGACTAATGGTTGTAGC 58.318 41.667 0.00 0.00 0.00 3.58
988 2995 4.483950 TCCACCTCCATCTACCTATCAAG 58.516 47.826 0.00 0.00 0.00 3.02
989 2996 4.170053 TCTCCACCTCCATCTACCTATCAA 59.830 45.833 0.00 0.00 0.00 2.57
990 2997 3.727391 TCTCCACCTCCATCTACCTATCA 59.273 47.826 0.00 0.00 0.00 2.15
991 2998 4.083565 GTCTCCACCTCCATCTACCTATC 58.916 52.174 0.00 0.00 0.00 2.08
1042 3083 4.379243 CTCCCGCACGGCAGAGTT 62.379 66.667 2.83 0.00 0.00 3.01
1217 3261 6.498304 CATGGTAGTCATGTTATCCTTTTGC 58.502 40.000 0.00 0.00 46.11 3.68
1232 3285 7.039313 AGGAAAAGAAACAAACATGGTAGTC 57.961 36.000 0.00 0.00 0.00 2.59
1239 3292 6.767423 CCAAATGGAGGAAAAGAAACAAACAT 59.233 34.615 0.00 0.00 37.39 2.71
1240 3293 6.112058 CCAAATGGAGGAAAAGAAACAAACA 58.888 36.000 0.00 0.00 37.39 2.83
1241 3294 6.112734 ACCAAATGGAGGAAAAGAAACAAAC 58.887 36.000 6.42 0.00 38.94 2.93
1454 3524 5.748630 CCATCAAGACAAATCAATGATGCAG 59.251 40.000 0.00 0.00 43.38 4.41
1509 3598 1.068541 GCCACCTTCGTTCAATCCAAC 60.069 52.381 0.00 0.00 0.00 3.77
1520 3609 4.093952 CAGCGCTTGCCACCTTCG 62.094 66.667 7.50 0.00 40.41 3.79
1688 3787 1.989508 GGGGAAAAGGCCATGGTGG 60.990 63.158 14.67 0.00 41.55 4.61
1910 4044 1.225373 TGGGGAGCATAGAAAGGCAT 58.775 50.000 0.00 0.00 33.96 4.40
2029 4220 2.346766 TTTGCAAGCAGAAGTCCAGA 57.653 45.000 0.00 0.00 0.00 3.86
2206 4409 4.616381 TGATTGCATCATTTCGTTTGAACG 59.384 37.500 9.84 9.84 43.13 3.95
2299 4516 4.825546 ATCGAGCCTGAATATGCAAAAG 57.174 40.909 0.00 0.00 0.00 2.27
2387 4604 6.332735 TGATCTTACTGGACCAAGATATCG 57.667 41.667 7.08 0.00 40.68 2.92
2619 8767 7.961326 AACTAAATATCATTCCCAGCAAACT 57.039 32.000 0.00 0.00 0.00 2.66
2707 8858 0.802607 GTCGAAGTTAGGCAGGCTCG 60.803 60.000 0.00 0.00 0.00 5.03
2744 8895 0.678395 CTCGCCCTCATGTAGATGCT 59.322 55.000 0.00 0.00 0.00 3.79
2880 9041 4.273318 ACAATGGCATTAAGACCCTTCTC 58.727 43.478 13.23 0.00 0.00 2.87
2960 9125 7.319646 TCCACATTATTGACCAATAAGTTTGC 58.680 34.615 17.03 0.00 43.85 3.68
3244 9448 1.235724 GGGTGTGCTGTGGTTAAGAC 58.764 55.000 0.00 0.00 0.00 3.01
3303 9508 5.443185 TGCTCAACAATCTTCTTCCAAAG 57.557 39.130 0.00 0.00 0.00 2.77
3542 9780 9.621629 ATCTTCCAAAACATTATATAACGGTGA 57.378 29.630 0.00 0.00 0.00 4.02
3715 9955 4.902448 ACTAAGATAGGATGGTGGTTCTCC 59.098 45.833 0.00 0.00 0.00 3.71
3839 10222 3.767673 ACAATGCATCCAATGAGAAAGCT 59.232 39.130 0.00 0.00 0.00 3.74
3874 10257 6.429385 ACTGAAATGAGAAGAGATCACCAAAC 59.571 38.462 0.00 0.00 0.00 2.93
3910 10293 4.212716 TCGGCTTGTAGTGTCCACTATAT 58.787 43.478 10.15 0.00 44.73 0.86
3934 10317 0.037605 AGTTGGTAAGGTTCTCCGCG 60.038 55.000 0.00 0.00 39.05 6.46
4020 10403 7.060383 ACATAGGAGTGTGATTAGATTCAGG 57.940 40.000 0.00 0.00 0.00 3.86
4128 10516 5.869579 TCTTTGATATTAGGCACTGGATCC 58.130 41.667 4.20 4.20 41.52 3.36
4230 10621 0.106819 GTGAAGATGGCCCAGATGCT 60.107 55.000 0.00 0.00 0.00 3.79
4293 10687 3.072622 AGGTTCTTTGGTAGGTTGGTCTC 59.927 47.826 0.00 0.00 0.00 3.36
4819 11234 1.343142 GACATTTGGCGGGAAAAAGGT 59.657 47.619 0.00 0.00 33.38 3.50
4861 11276 8.853077 ATGACATATGAAACAGAAAACTCTGA 57.147 30.769 10.38 0.00 39.99 3.27
5102 11537 6.313658 GGTGGATGAATTTAAAAAGATGTGCC 59.686 38.462 0.00 0.00 0.00 5.01
5108 11543 8.477419 ACTGAAGGTGGATGAATTTAAAAAGA 57.523 30.769 0.00 0.00 0.00 2.52
5168 11603 2.675317 GCTGGTGGTGACTAAGTAGCAG 60.675 54.545 0.00 0.00 39.23 4.24
5170 11605 1.736032 CGCTGGTGGTGACTAAGTAGC 60.736 57.143 0.00 0.00 0.00 3.58
5407 14203 4.160439 TGATATATGTCGCCTCATTCCTCC 59.840 45.833 0.00 0.00 0.00 4.30
5507 14303 7.481798 GCTTATTGTGTTGATGTAAGTTACAGC 59.518 37.037 21.57 21.57 44.83 4.40
5520 14316 5.538053 TGGGAGAATTTGCTTATTGTGTTGA 59.462 36.000 0.00 0.00 0.00 3.18
5530 14326 6.295292 GGATTGTAAAGTGGGAGAATTTGCTT 60.295 38.462 0.00 0.00 0.00 3.91
5555 14351 7.599621 GTCATGGATTATCTCTCTCTGAACATG 59.400 40.741 0.00 0.00 33.93 3.21
5586 14708 8.190122 TGTTGAGATGTCAATGGTAAATAATGC 58.810 33.333 8.72 0.00 44.58 3.56


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

AutoCloner maintained by Alex Coulton.