Multiple sequence alignment - TraesCS4A01G422100

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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 TraesCS4A01G422100 chr4A 100.000 5025 0 0 1 5025 692387045 692382021 0.000000e+00 9280.0
1 TraesCS4A01G422100 chr4A 95.536 112 2 2 3397 3505 597837505 597837394 5.170000e-40 176.0
2 TraesCS4A01G422100 chr4A 93.827 81 5 0 1980 2060 687562684 687562604 6.830000e-24 122.0
3 TraesCS4A01G422100 chr7D 94.967 4153 77 41 882 4990 32609923 32605859 0.000000e+00 6390.0
4 TraesCS4A01G422100 chr7D 98.276 58 0 1 812 868 32610921 32610864 3.200000e-17 100.0
5 TraesCS4A01G422100 chr7A 95.292 3823 90 40 812 4582 32633320 32629536 0.000000e+00 5980.0
6 TraesCS4A01G422100 chr7A 94.753 324 11 5 4668 4990 32629195 32628877 2.700000e-137 499.0
7 TraesCS4A01G422100 chr7A 98.462 65 1 0 4589 4653 32629250 32629186 1.140000e-21 115.0
8 TraesCS4A01G422100 chr4B 93.242 3374 118 48 812 4130 38028687 38025369 0.000000e+00 4867.0
9 TraesCS4A01G422100 chr4B 88.593 526 41 12 3517 4025 9948276 9948799 5.530000e-174 621.0
10 TraesCS4A01G422100 chr4B 90.196 459 23 10 4539 4990 9949510 9949953 3.370000e-161 579.0
11 TraesCS4A01G422100 chr4B 92.609 230 10 4 4232 4457 9949043 9949269 1.740000e-84 324.0
12 TraesCS4A01G422100 chr4B 95.146 103 5 0 2457 2559 9948089 9947987 4.030000e-36 163.0
13 TraesCS4A01G422100 chr4B 95.000 100 5 0 1 100 543809866 543809965 1.870000e-34 158.0
14 TraesCS4A01G422100 chr4B 92.632 95 6 1 4131 4225 9948875 9948968 8.780000e-28 135.0
15 TraesCS4A01G422100 chr4D 94.590 2865 88 21 1292 4130 25695632 25692809 0.000000e+00 4370.0
16 TraesCS4A01G422100 chr4D 86.170 1034 63 31 1841 2864 5684371 5685334 0.000000e+00 1044.0
17 TraesCS4A01G422100 chr4D 87.771 646 61 11 3497 4130 5685337 5685976 0.000000e+00 739.0
18 TraesCS4A01G422100 chr4D 89.213 445 11 12 812 1240 25696302 25695879 5.760000e-144 521.0
19 TraesCS4A01G422100 chr4D 83.041 513 49 24 1188 1676 5683735 5684233 9.990000e-117 431.0
20 TraesCS4A01G422100 chr4D 83.417 199 16 11 4737 4920 25692554 25692358 8.650000e-38 169.0
21 TraesCS4A01G422100 chr4D 100.000 29 0 0 4539 4567 5686079 5686107 3.000000e-03 54.7
22 TraesCS4A01G422100 chr6B 95.557 1598 59 9 1787 3380 626213761 626215350 0.000000e+00 2547.0
23 TraesCS4A01G422100 chr6B 88.076 1107 67 27 3381 4457 626216565 626217636 0.000000e+00 1253.0
24 TraesCS4A01G422100 chr6B 87.702 309 20 9 4456 4751 626217719 626218022 1.340000e-90 344.0
25 TraesCS4A01G422100 chr6B 82.372 312 35 17 1381 1676 626213386 626213693 2.320000e-63 254.0
26 TraesCS4A01G422100 chr6B 83.737 289 23 15 1080 1361 626212036 626212307 8.350000e-63 252.0
27 TraesCS4A01G422100 chr3B 93.353 677 29 2 150 811 815849995 815850670 0.000000e+00 987.0
28 TraesCS4A01G422100 chr3B 78.112 699 88 32 2748 3419 680750438 680751098 2.840000e-102 383.0
29 TraesCS4A01G422100 chr3B 82.159 454 52 17 2266 2711 680749907 680750339 3.700000e-96 363.0
30 TraesCS4A01G422100 chr3B 81.897 232 25 10 4244 4460 526735578 526735349 4.000000e-41 180.0
31 TraesCS4A01G422100 chr3B 97.000 100 3 0 1 100 104590927 104590828 8.650000e-38 169.0
32 TraesCS4A01G422100 chr3B 88.321 137 15 1 1125 1261 680748888 680749023 4.030000e-36 163.0
33 TraesCS4A01G422100 chr5B 93.225 679 30 2 150 813 697282218 697281541 0.000000e+00 985.0
34 TraesCS4A01G422100 chr1D 91.323 703 46 1 124 811 242022175 242021473 0.000000e+00 946.0
35 TraesCS4A01G422100 chr1D 91.724 145 11 1 670 813 2514572 2514716 3.070000e-47 200.0
36 TraesCS4A01G422100 chr1D 86.875 160 16 4 670 825 18805945 18805787 1.860000e-39 174.0
37 TraesCS4A01G422100 chr1D 82.439 205 16 8 1787 1971 145884812 145885016 1.450000e-35 161.0
38 TraesCS4A01G422100 chr1D 95.050 101 3 2 1 100 408159219 408159318 1.870000e-34 158.0
39 TraesCS4A01G422100 chr1D 94.000 100 6 0 1 100 63364124 63364025 8.710000e-33 152.0
40 TraesCS4A01G422100 chr1D 90.361 83 6 2 4456 4537 307448432 307448351 1.910000e-19 108.0
41 TraesCS4A01G422100 chr1A 87.376 705 47 11 124 809 524281353 524282034 0.000000e+00 771.0
42 TraesCS4A01G422100 chr1A 83.111 225 19 13 4248 4454 511011779 511011556 2.390000e-43 187.0
43 TraesCS4A01G422100 chr3A 90.948 464 25 2 124 572 728315910 728316371 4.300000e-170 608.0
44 TraesCS4A01G422100 chr3A 79.569 788 115 31 3177 3939 651640693 651639927 5.760000e-144 521.0
45 TraesCS4A01G422100 chr3A 92.070 227 18 0 586 812 728318903 728319129 2.260000e-83 320.0
46 TraesCS4A01G422100 chr3A 87.209 86 10 1 4456 4541 644630008 644629924 4.140000e-16 97.1
47 TraesCS4A01G422100 chr3D 87.500 184 20 3 641 824 543682684 543682864 5.100000e-50 209.0
48 TraesCS4A01G422100 chr3D 81.858 226 19 13 4249 4454 318514058 318513835 2.410000e-38 171.0
49 TraesCS4A01G422100 chr3D 89.231 130 10 1 1846 1971 494379273 494379144 5.210000e-35 159.0
50 TraesCS4A01G422100 chr3D 92.453 106 8 0 1 106 354034366 354034261 8.710000e-33 152.0
51 TraesCS4A01G422100 chr2D 90.972 144 13 0 670 813 24913447 24913304 1.430000e-45 195.0
52 TraesCS4A01G422100 chr2D 97.000 100 3 0 1 100 619624139 619624238 8.650000e-38 169.0
53 TraesCS4A01G422100 chr2B 88.079 151 17 1 670 820 73802718 73802569 1.440000e-40 178.0
54 TraesCS4A01G422100 chr2B 82.273 220 21 15 4249 4454 525628777 525628562 1.860000e-39 174.0
55 TraesCS4A01G422100 chr2B 97.000 100 3 0 1 100 791390306 791390207 8.650000e-38 169.0
56 TraesCS4A01G422100 chr2B 85.714 91 11 2 4456 4545 27542093 27542004 1.490000e-15 95.3
57 TraesCS4A01G422100 chr2A 81.614 223 23 11 4250 4454 751491999 751491777 8.650000e-38 169.0
58 TraesCS4A01G422100 chr2A 91.566 83 5 2 4456 4537 429161401 429161482 4.110000e-21 113.0
59 TraesCS4A01G422100 chr1B 81.778 225 18 15 4249 4453 263981673 263981452 3.110000e-37 167.0
60 TraesCS4A01G422100 chr1B 94.872 78 4 0 1980 2057 35096862 35096939 6.830000e-24 122.0
61 TraesCS4A01G422100 chr5D 89.231 130 10 1 1846 1971 485215540 485215411 5.210000e-35 159.0
62 TraesCS4A01G422100 chr7B 95.050 101 3 2 1 100 727384392 727384293 1.870000e-34 158.0
63 TraesCS4A01G422100 chr7B 93.827 81 5 0 1980 2060 747303738 747303658 6.830000e-24 122.0
64 TraesCS4A01G422100 chr6D 94.059 101 5 1 1 100 350511034 350510934 8.710000e-33 152.0
65 TraesCS4A01G422100 chr6D 87.059 85 11 0 4457 4541 11918788 11918872 4.140000e-16 97.1
66 TraesCS4A01G422100 chrUn 90.805 87 7 1 4456 4542 309799503 309799588 1.140000e-21 115.0
67 TraesCS4A01G422100 chrUn 90.805 87 7 1 4456 4542 315208250 315208335 1.140000e-21 115.0
68 TraesCS4A01G422100 chr6A 93.878 49 2 1 4250 4297 140545071 140545023 6.980000e-09 73.1


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 TraesCS4A01G422100 chr4A 692382021 692387045 5024 True 9280.000000 9280 100.000000 1 5025 1 chr4A.!!$R3 5024
1 TraesCS4A01G422100 chr7D 32605859 32610921 5062 True 3245.000000 6390 96.621500 812 4990 2 chr7D.!!$R1 4178
2 TraesCS4A01G422100 chr7A 32628877 32633320 4443 True 2198.000000 5980 96.169000 812 4990 3 chr7A.!!$R1 4178
3 TraesCS4A01G422100 chr4B 38025369 38028687 3318 True 4867.000000 4867 93.242000 812 4130 1 chr4B.!!$R2 3318
4 TraesCS4A01G422100 chr4B 9948276 9949953 1677 False 414.750000 621 91.007500 3517 4990 4 chr4B.!!$F2 1473
5 TraesCS4A01G422100 chr4D 25692358 25696302 3944 True 1686.666667 4370 89.073333 812 4920 3 chr4D.!!$R1 4108
6 TraesCS4A01G422100 chr4D 5683735 5686107 2372 False 567.175000 1044 89.245500 1188 4567 4 chr4D.!!$F1 3379
7 TraesCS4A01G422100 chr6B 626212036 626218022 5986 False 930.000000 2547 87.488800 1080 4751 5 chr6B.!!$F1 3671
8 TraesCS4A01G422100 chr3B 815849995 815850670 675 False 987.000000 987 93.353000 150 811 1 chr3B.!!$F1 661
9 TraesCS4A01G422100 chr3B 680748888 680751098 2210 False 303.000000 383 82.864000 1125 3419 3 chr3B.!!$F2 2294
10 TraesCS4A01G422100 chr5B 697281541 697282218 677 True 985.000000 985 93.225000 150 813 1 chr5B.!!$R1 663
11 TraesCS4A01G422100 chr1D 242021473 242022175 702 True 946.000000 946 91.323000 124 811 1 chr1D.!!$R3 687
12 TraesCS4A01G422100 chr1A 524281353 524282034 681 False 771.000000 771 87.376000 124 809 1 chr1A.!!$F1 685
13 TraesCS4A01G422100 chr3A 651639927 651640693 766 True 521.000000 521 79.569000 3177 3939 1 chr3A.!!$R2 762
14 TraesCS4A01G422100 chr3A 728315910 728319129 3219 False 464.000000 608 91.509000 124 812 2 chr3A.!!$F1 688

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
103 104 0.037605 ACTTTCTAGGTCCGCCGTTG 60.038 55.000 0.0 0.00 40.50 4.10 F
105 106 0.037975 TTTCTAGGTCCGCCGTTGAC 60.038 55.000 0.0 0.00 40.50 3.18 F
808 3342 0.233848 CGTGTGGGCGTTAGTGTTTC 59.766 55.000 0.0 0.00 0.00 2.78 F
1017 4503 0.617249 ACTTGGAGCCTGGAGGAGAG 60.617 60.000 0.0 0.00 37.39 3.20 F
1851 6716 0.664466 TCAGCGCTGTCGAACTGAAG 60.664 55.000 34.7 6.97 33.84 3.02 F
3406 9649 2.159268 GGTTAGGTAAGTCGGTCTCTGC 60.159 54.545 0.0 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1017 4503 1.753078 GAGGGGATTTGGGTTCGCC 60.753 63.158 0.0 0.0 44.34 5.54 R
1322 5042 1.815421 CCGCCGATCCAACCAGAAG 60.815 63.158 0.0 0.0 0.00 2.85 R
2760 7768 2.749076 GGCACAACATAACTCATGCAGA 59.251 45.455 0.0 0.0 38.29 4.26 R
3175 8205 2.828520 CTGGACTAACAGCCTCAGAAGA 59.171 50.000 0.0 0.0 0.00 2.87 R
3766 10035 0.779997 AGCCAAGGGTCTGGTTGATT 59.220 50.000 0.0 0.0 38.86 2.57 R
4958 11846 1.126846 GAGAAAATGCAGTCGTGGACG 59.873 52.381 0.0 0.0 37.67 4.79 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
25 26 8.484641 TTGTGTTTTGTGAAAAATATGCTCAA 57.515 26.923 0.00 0.00 31.13 3.02
26 27 8.484641 TGTGTTTTGTGAAAAATATGCTCAAA 57.515 26.923 0.00 0.00 31.13 2.69
27 28 9.107177 TGTGTTTTGTGAAAAATATGCTCAAAT 57.893 25.926 0.00 0.00 31.13 2.32
28 29 9.934190 GTGTTTTGTGAAAAATATGCTCAAATT 57.066 25.926 0.00 0.00 31.13 1.82
34 35 9.761504 TGTGAAAAATATGCTCAAATTCTTTGA 57.238 25.926 2.63 2.63 46.68 2.69
36 37 9.985730 TGAAAAATATGCTCAAATTCTTTGACT 57.014 25.926 0.00 0.00 44.21 3.41
45 46 9.725019 TGCTCAAATTCTTTGACTTTCTATAGA 57.275 29.630 0.00 0.00 44.21 1.98
53 54 9.561069 TTCTTTGACTTTCTATAGAATATGCCC 57.439 33.333 15.82 4.07 33.54 5.36
54 55 8.157476 TCTTTGACTTTCTATAGAATATGCCCC 58.843 37.037 15.82 3.16 33.54 5.80
55 56 6.374417 TGACTTTCTATAGAATATGCCCCC 57.626 41.667 15.82 1.83 33.54 5.40
56 57 5.849475 TGACTTTCTATAGAATATGCCCCCA 59.151 40.000 15.82 4.05 33.54 4.96
57 58 6.128138 ACTTTCTATAGAATATGCCCCCAC 57.872 41.667 15.82 0.00 33.54 4.61
58 59 5.852250 ACTTTCTATAGAATATGCCCCCACT 59.148 40.000 15.82 0.00 33.54 4.00
59 60 6.013293 ACTTTCTATAGAATATGCCCCCACTC 60.013 42.308 15.82 0.00 33.54 3.51
60 61 5.023514 TCTATAGAATATGCCCCCACTCA 57.976 43.478 0.00 0.00 0.00 3.41
61 62 5.411493 TCTATAGAATATGCCCCCACTCAA 58.589 41.667 0.00 0.00 0.00 3.02
62 63 6.032039 TCTATAGAATATGCCCCCACTCAAT 58.968 40.000 0.00 0.00 0.00 2.57
63 64 3.979501 AGAATATGCCCCCACTCAATT 57.020 42.857 0.00 0.00 0.00 2.32
64 65 6.718593 ATAGAATATGCCCCCACTCAATTA 57.281 37.500 0.00 0.00 0.00 1.40
65 66 4.990526 AGAATATGCCCCCACTCAATTAG 58.009 43.478 0.00 0.00 0.00 1.73
66 67 4.416848 AGAATATGCCCCCACTCAATTAGT 59.583 41.667 0.00 0.00 39.81 2.24
67 68 4.814224 ATATGCCCCCACTCAATTAGTT 57.186 40.909 0.00 0.00 35.76 2.24
68 69 2.990740 TGCCCCCACTCAATTAGTTT 57.009 45.000 0.00 0.00 35.76 2.66
69 70 2.524306 TGCCCCCACTCAATTAGTTTG 58.476 47.619 0.00 0.00 35.76 2.93
70 71 1.204704 GCCCCCACTCAATTAGTTTGC 59.795 52.381 0.00 0.00 35.76 3.68
71 72 1.824852 CCCCCACTCAATTAGTTTGCC 59.175 52.381 0.00 0.00 35.76 4.52
72 73 1.824852 CCCCACTCAATTAGTTTGCCC 59.175 52.381 0.00 0.00 35.76 5.36
73 74 1.824852 CCCACTCAATTAGTTTGCCCC 59.175 52.381 0.00 0.00 35.76 5.80
74 75 1.824852 CCACTCAATTAGTTTGCCCCC 59.175 52.381 0.00 0.00 35.76 5.40
75 76 2.524306 CACTCAATTAGTTTGCCCCCA 58.476 47.619 0.00 0.00 35.76 4.96
76 77 2.231235 CACTCAATTAGTTTGCCCCCAC 59.769 50.000 0.00 0.00 35.76 4.61
77 78 2.110011 ACTCAATTAGTTTGCCCCCACT 59.890 45.455 0.00 0.00 33.35 4.00
78 79 2.755103 CTCAATTAGTTTGCCCCCACTC 59.245 50.000 0.00 0.00 35.16 3.51
79 80 1.824852 CAATTAGTTTGCCCCCACTCC 59.175 52.381 0.00 0.00 0.00 3.85
80 81 1.080638 ATTAGTTTGCCCCCACTCCA 58.919 50.000 0.00 0.00 0.00 3.86
81 82 0.854218 TTAGTTTGCCCCCACTCCAA 59.146 50.000 0.00 0.00 0.00 3.53
82 83 0.854218 TAGTTTGCCCCCACTCCAAA 59.146 50.000 0.00 0.00 0.00 3.28
83 84 0.190815 AGTTTGCCCCCACTCCAAAT 59.809 50.000 0.00 0.00 31.93 2.32
84 85 1.431243 AGTTTGCCCCCACTCCAAATA 59.569 47.619 0.00 0.00 31.93 1.40
85 86 1.548719 GTTTGCCCCCACTCCAAATAC 59.451 52.381 0.00 0.00 31.93 1.89
86 87 1.080638 TTGCCCCCACTCCAAATACT 58.919 50.000 0.00 0.00 0.00 2.12
87 88 1.080638 TGCCCCCACTCCAAATACTT 58.919 50.000 0.00 0.00 0.00 2.24
88 89 1.431243 TGCCCCCACTCCAAATACTTT 59.569 47.619 0.00 0.00 0.00 2.66
89 90 2.100197 GCCCCCACTCCAAATACTTTC 58.900 52.381 0.00 0.00 0.00 2.62
90 91 2.291605 GCCCCCACTCCAAATACTTTCT 60.292 50.000 0.00 0.00 0.00 2.52
91 92 3.053917 GCCCCCACTCCAAATACTTTCTA 60.054 47.826 0.00 0.00 0.00 2.10
92 93 4.781934 CCCCCACTCCAAATACTTTCTAG 58.218 47.826 0.00 0.00 0.00 2.43
93 94 4.385310 CCCCCACTCCAAATACTTTCTAGG 60.385 50.000 0.00 0.00 0.00 3.02
94 95 4.227527 CCCCACTCCAAATACTTTCTAGGT 59.772 45.833 0.00 0.00 0.00 3.08
95 96 5.429130 CCCACTCCAAATACTTTCTAGGTC 58.571 45.833 0.00 0.00 0.00 3.85
96 97 5.429130 CCACTCCAAATACTTTCTAGGTCC 58.571 45.833 0.00 0.00 0.00 4.46
97 98 5.109903 CACTCCAAATACTTTCTAGGTCCG 58.890 45.833 0.00 0.00 0.00 4.79
98 99 4.120589 CTCCAAATACTTTCTAGGTCCGC 58.879 47.826 0.00 0.00 0.00 5.54
99 100 3.118519 TCCAAATACTTTCTAGGTCCGCC 60.119 47.826 0.00 0.00 0.00 6.13
100 101 2.864343 CAAATACTTTCTAGGTCCGCCG 59.136 50.000 0.00 0.00 40.50 6.46
101 102 1.772836 ATACTTTCTAGGTCCGCCGT 58.227 50.000 0.00 0.00 40.50 5.68
102 103 1.549203 TACTTTCTAGGTCCGCCGTT 58.451 50.000 0.00 0.00 40.50 4.44
103 104 0.037605 ACTTTCTAGGTCCGCCGTTG 60.038 55.000 0.00 0.00 40.50 4.10
104 105 0.245539 CTTTCTAGGTCCGCCGTTGA 59.754 55.000 0.00 0.00 40.50 3.18
105 106 0.037975 TTTCTAGGTCCGCCGTTGAC 60.038 55.000 0.00 0.00 40.50 3.18
106 107 1.180456 TTCTAGGTCCGCCGTTGACA 61.180 55.000 0.00 0.00 40.50 3.58
107 108 1.180456 TCTAGGTCCGCCGTTGACAA 61.180 55.000 0.00 0.00 40.50 3.18
108 109 1.005867 TAGGTCCGCCGTTGACAAC 60.006 57.895 8.34 8.34 40.50 3.32
109 110 1.746322 TAGGTCCGCCGTTGACAACA 61.746 55.000 18.09 0.00 40.50 3.33
110 111 1.964373 GGTCCGCCGTTGACAACAT 60.964 57.895 18.09 0.00 34.36 2.71
111 112 1.495951 GTCCGCCGTTGACAACATC 59.504 57.895 18.09 7.76 32.91 3.06
112 113 1.669760 TCCGCCGTTGACAACATCC 60.670 57.895 18.09 4.75 0.00 3.51
113 114 2.686816 CCGCCGTTGACAACATCCC 61.687 63.158 18.09 2.46 0.00 3.85
114 115 2.686816 CGCCGTTGACAACATCCCC 61.687 63.158 18.09 0.84 0.00 4.81
115 116 2.340328 GCCGTTGACAACATCCCCC 61.340 63.158 18.09 0.00 0.00 5.40
142 143 1.597854 CCCGACAACAAGCAGCTCA 60.598 57.895 0.00 0.00 0.00 4.26
287 303 4.680237 CGTCGCAGGCAGGGAACA 62.680 66.667 0.00 0.00 41.26 3.18
313 329 0.972983 AGCACCGAGGACAGTAGCAT 60.973 55.000 0.00 0.00 0.00 3.79
527 543 1.741401 CTGAAGATTCCGCCGCACA 60.741 57.895 0.00 0.00 0.00 4.57
539 555 2.259818 CGCACAAGCTCGAGAGGT 59.740 61.111 18.75 7.45 41.53 3.85
599 3133 5.010282 GGAGTGGATAAGATTTGTGTGGTT 58.990 41.667 0.00 0.00 0.00 3.67
653 3187 0.666274 CAGTGCGAGAAACCAGCGTA 60.666 55.000 0.00 0.00 0.00 4.42
676 3210 2.680913 CGAGCTGCCAAAACTCCCG 61.681 63.158 0.00 0.00 0.00 5.14
747 3281 7.011576 TGTTAAGATTCGTGCAAACTTAACTGA 59.988 33.333 24.77 14.21 45.79 3.41
760 3294 3.070446 ACTTAACTGAACGGTGATCCACA 59.930 43.478 0.00 0.00 35.86 4.17
775 3309 2.587753 ACACGTGTGGGCGAGTTG 60.588 61.111 22.71 0.00 32.21 3.16
808 3342 0.233848 CGTGTGGGCGTTAGTGTTTC 59.766 55.000 0.00 0.00 0.00 2.78
947 4424 1.221909 TAGGACAGCCCCAGAGGAGA 61.222 60.000 0.00 0.00 38.24 3.71
948 4425 2.063378 GGACAGCCCCAGAGGAGAG 61.063 68.421 0.00 0.00 38.24 3.20
949 4426 2.040278 ACAGCCCCAGAGGAGAGG 59.960 66.667 0.00 0.00 38.24 3.69
950 4427 2.366167 CAGCCCCAGAGGAGAGGA 59.634 66.667 0.00 0.00 38.24 3.71
951 4428 1.761667 CAGCCCCAGAGGAGAGGAG 60.762 68.421 0.00 0.00 38.24 3.69
999 4482 4.642542 GGCGCCCGATCTCCGTAC 62.643 72.222 18.11 0.00 36.31 3.67
1000 4483 3.593794 GCGCCCGATCTCCGTACT 61.594 66.667 0.00 0.00 36.31 2.73
1001 4484 3.117372 CGCCCGATCTCCGTACTT 58.883 61.111 0.00 0.00 36.31 2.24
1002 4485 1.299165 CGCCCGATCTCCGTACTTG 60.299 63.158 0.00 0.00 36.31 3.16
1003 4486 1.067582 GCCCGATCTCCGTACTTGG 59.932 63.158 0.00 0.00 36.31 3.61
1004 4487 1.389609 GCCCGATCTCCGTACTTGGA 61.390 60.000 0.00 0.00 36.31 3.53
1017 4503 0.617249 ACTTGGAGCCTGGAGGAGAG 60.617 60.000 0.00 0.00 37.39 3.20
1018 4504 1.306482 TTGGAGCCTGGAGGAGAGG 60.306 63.158 0.00 0.00 37.39 3.69
1026 4512 2.683933 GGAGGAGAGGCGAACCCA 60.684 66.667 0.00 0.00 36.11 4.51
1041 4554 3.420482 CCAAATCCCCTCCCGCCT 61.420 66.667 0.00 0.00 0.00 5.52
1042 4555 2.193248 CAAATCCCCTCCCGCCTC 59.807 66.667 0.00 0.00 0.00 4.70
1043 4556 3.480133 AAATCCCCTCCCGCCTCG 61.480 66.667 0.00 0.00 0.00 4.63
1044 4557 3.995809 AAATCCCCTCCCGCCTCGA 62.996 63.158 0.00 0.00 0.00 4.04
1045 4558 3.776016 AATCCCCTCCCGCCTCGAT 62.776 63.158 0.00 0.00 0.00 3.59
1046 4559 4.916314 TCCCCTCCCGCCTCGATC 62.916 72.222 0.00 0.00 0.00 3.69
1047 4560 4.924187 CCCCTCCCGCCTCGATCT 62.924 72.222 0.00 0.00 0.00 2.75
1048 4561 3.299190 CCCTCCCGCCTCGATCTC 61.299 72.222 0.00 0.00 0.00 2.75
1049 4562 2.203422 CCTCCCGCCTCGATCTCT 60.203 66.667 0.00 0.00 0.00 3.10
1050 4563 2.265182 CCTCCCGCCTCGATCTCTC 61.265 68.421 0.00 0.00 0.00 3.20
1051 4564 2.203365 TCCCGCCTCGATCTCTCC 60.203 66.667 0.00 0.00 0.00 3.71
1052 4565 3.299190 CCCGCCTCGATCTCTCCC 61.299 72.222 0.00 0.00 0.00 4.30
1053 4566 3.665226 CCGCCTCGATCTCTCCCG 61.665 72.222 0.00 0.00 0.00 5.14
1054 4567 4.335584 CGCCTCGATCTCTCCCGC 62.336 72.222 0.00 0.00 0.00 6.13
1055 4568 3.984749 GCCTCGATCTCTCCCGCC 61.985 72.222 0.00 0.00 0.00 6.13
1056 4569 3.665226 CCTCGATCTCTCCCGCCG 61.665 72.222 0.00 0.00 0.00 6.46
1057 4570 4.335584 CTCGATCTCTCCCGCCGC 62.336 72.222 0.00 0.00 0.00 6.53
1103 4616 1.062047 CTCGAATCCGCGACTCGAA 59.938 57.895 21.49 10.47 39.68 3.71
1104 4617 0.926174 CTCGAATCCGCGACTCGAAG 60.926 60.000 21.49 14.42 39.68 3.79
1106 4619 1.226717 GAATCCGCGACTCGAAGCT 60.227 57.895 8.23 0.00 41.67 3.74
1107 4620 1.203600 GAATCCGCGACTCGAAGCTC 61.204 60.000 8.23 0.00 41.67 4.09
1283 4834 3.075005 CTTCTCCCCCGCTTCCGA 61.075 66.667 0.00 0.00 36.29 4.55
1322 5042 5.351740 AGCTCGCATCTTTTCTAGGTTTTAC 59.648 40.000 0.00 0.00 0.00 2.01
1508 6300 2.404215 TCAAGCTTGCGAGTAAGACAC 58.596 47.619 21.99 0.00 0.00 3.67
1661 6486 5.545063 TGTGAAGATTGTGTTAGTGAGGA 57.455 39.130 0.00 0.00 0.00 3.71
1842 6707 0.734253 ATGACTCGTTCAGCGCTGTC 60.734 55.000 34.70 26.02 37.77 3.51
1851 6716 0.664466 TCAGCGCTGTCGAACTGAAG 60.664 55.000 34.70 6.97 33.84 3.02
2036 6920 5.292589 GGTTGCAGCCATATCTGAATTTTTG 59.707 40.000 15.64 0.00 36.19 2.44
2469 7376 4.811555 TTGAGTGTGAAAATGGAAGACG 57.188 40.909 0.00 0.00 0.00 4.18
2501 7408 3.913107 AGGGACTTCTGCCAGCTT 58.087 55.556 0.00 0.00 27.25 3.74
2760 7768 6.705825 GTCTTGCATGAGTTTTTGGGTTAATT 59.294 34.615 1.91 0.00 0.00 1.40
3406 9649 2.159268 GGTTAGGTAAGTCGGTCTCTGC 60.159 54.545 0.00 0.00 0.00 4.26
3600 9853 5.751680 CATCGCAGAGGTAAATTAACATGG 58.248 41.667 0.00 0.00 43.63 3.66
3883 10161 3.464833 AGAGGTGGATTATTGGATTGCCT 59.535 43.478 0.00 0.00 34.31 4.75
3884 10162 3.569491 AGGTGGATTATTGGATTGCCTG 58.431 45.455 0.00 0.00 34.31 4.85
3947 10228 2.218603 ACGGTTTCCAAAGCTACACAG 58.781 47.619 0.00 0.00 34.41 3.66
4117 10419 2.479566 ACATCTTCGGCAGTTGATGT 57.520 45.000 16.29 16.29 42.93 3.06
4141 10461 0.609957 TGAGCAGAAATGGTGGCCTG 60.610 55.000 3.32 0.00 0.00 4.85
4159 10479 1.332889 TGCCGGCAGATGATGAGACT 61.333 55.000 29.03 0.00 0.00 3.24
4227 10548 9.667107 CAAGGGAGTTGAACAAAAGATATAGTA 57.333 33.333 0.00 0.00 38.60 1.82
4382 10781 7.328249 CACAATGCACGTGTAAAATTTTAGGAT 59.672 33.333 18.38 3.55 0.00 3.24
4409 10808 3.228188 AGTTGAAATGAGGGCTGTGAA 57.772 42.857 0.00 0.00 0.00 3.18
4775 11647 7.083858 TGTTTGCATGTTTCTTCTAGCATAAC 58.916 34.615 0.00 0.00 0.00 1.89
4914 11802 2.405892 ACTGCAAAAGCGCAAACTAG 57.594 45.000 11.47 2.92 42.45 2.57
4923 11811 1.003108 GCGCAAACTAGAAGAGAGGC 58.997 55.000 0.30 0.00 0.00 4.70
4976 11864 0.165944 CCGTCCACGACTGCATTTTC 59.834 55.000 0.00 0.00 43.02 2.29
4978 11866 1.126846 CGTCCACGACTGCATTTTCTC 59.873 52.381 0.00 0.00 43.02 2.87
4982 11870 2.095567 CCACGACTGCATTTTCTCCAAG 60.096 50.000 0.00 0.00 0.00 3.61
4983 11871 1.537202 ACGACTGCATTTTCTCCAAGC 59.463 47.619 0.00 0.00 0.00 4.01
4984 11872 1.536766 CGACTGCATTTTCTCCAAGCA 59.463 47.619 0.00 0.00 0.00 3.91
4985 11873 2.163010 CGACTGCATTTTCTCCAAGCAT 59.837 45.455 0.00 0.00 34.35 3.79
4986 11874 3.508762 GACTGCATTTTCTCCAAGCATG 58.491 45.455 0.00 0.00 34.35 4.06
4988 11876 3.575256 ACTGCATTTTCTCCAAGCATGAA 59.425 39.130 0.00 0.00 34.35 2.57
4989 11877 4.039488 ACTGCATTTTCTCCAAGCATGAAA 59.961 37.500 0.00 0.00 34.35 2.69
4990 11878 4.958509 TGCATTTTCTCCAAGCATGAAAA 58.041 34.783 0.00 0.00 41.75 2.29
4991 11879 5.366460 TGCATTTTCTCCAAGCATGAAAAA 58.634 33.333 0.00 0.00 41.16 1.94
5007 11895 2.888834 AAAAACAACCGCTGATGCTT 57.111 40.000 0.00 0.00 36.97 3.91
5008 11896 2.422276 AAAACAACCGCTGATGCTTC 57.578 45.000 0.00 0.00 36.97 3.86
5009 11897 1.317613 AAACAACCGCTGATGCTTCA 58.682 45.000 1.92 1.92 36.97 3.02
5010 11898 1.317613 AACAACCGCTGATGCTTCAA 58.682 45.000 3.65 0.00 36.97 2.69
5011 11899 0.877071 ACAACCGCTGATGCTTCAAG 59.123 50.000 3.65 1.40 36.97 3.02
5012 11900 1.159285 CAACCGCTGATGCTTCAAGA 58.841 50.000 3.65 0.00 36.97 3.02
5013 11901 1.135859 CAACCGCTGATGCTTCAAGAC 60.136 52.381 3.65 0.00 36.97 3.01
5014 11902 0.322975 ACCGCTGATGCTTCAAGACT 59.677 50.000 3.65 0.00 36.97 3.24
5015 11903 1.550524 ACCGCTGATGCTTCAAGACTA 59.449 47.619 3.65 0.00 36.97 2.59
5016 11904 1.929836 CCGCTGATGCTTCAAGACTAC 59.070 52.381 3.65 0.00 36.97 2.73
5017 11905 2.417924 CCGCTGATGCTTCAAGACTACT 60.418 50.000 3.65 0.00 36.97 2.57
5018 11906 2.857152 CGCTGATGCTTCAAGACTACTC 59.143 50.000 3.65 0.00 36.97 2.59
5019 11907 3.674410 CGCTGATGCTTCAAGACTACTCA 60.674 47.826 3.65 0.00 36.97 3.41
5020 11908 3.616379 GCTGATGCTTCAAGACTACTCAC 59.384 47.826 3.65 0.00 36.03 3.51
5021 11909 4.814147 CTGATGCTTCAAGACTACTCACA 58.186 43.478 3.65 0.00 0.00 3.58
5022 11910 4.814147 TGATGCTTCAAGACTACTCACAG 58.186 43.478 0.00 0.00 0.00 3.66
5023 11911 3.032017 TGCTTCAAGACTACTCACAGC 57.968 47.619 0.00 0.00 0.00 4.40
5024 11912 2.630098 TGCTTCAAGACTACTCACAGCT 59.370 45.455 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.484641 TTGAGCATATTTTTCACAAAACACAA 57.515 26.923 0.00 0.00 34.63 3.33
1 2 8.484641 TTTGAGCATATTTTTCACAAAACACA 57.515 26.923 0.00 0.00 34.63 3.72
2 3 9.934190 AATTTGAGCATATTTTTCACAAAACAC 57.066 25.926 0.00 0.00 34.63 3.32
27 28 9.561069 GGGCATATTCTATAGAAAGTCAAAGAA 57.439 33.333 18.79 0.00 37.61 2.52
28 29 8.157476 GGGGCATATTCTATAGAAAGTCAAAGA 58.843 37.037 18.79 0.00 37.61 2.52
29 30 7.391833 GGGGGCATATTCTATAGAAAGTCAAAG 59.608 40.741 18.79 6.65 37.61 2.77
30 31 7.147213 TGGGGGCATATTCTATAGAAAGTCAAA 60.147 37.037 18.79 0.00 37.61 2.69
31 32 6.331572 TGGGGGCATATTCTATAGAAAGTCAA 59.668 38.462 18.79 3.78 37.61 3.18
32 33 5.849475 TGGGGGCATATTCTATAGAAAGTCA 59.151 40.000 18.79 5.73 37.61 3.41
33 34 6.013293 AGTGGGGGCATATTCTATAGAAAGTC 60.013 42.308 18.79 12.74 37.61 3.01
34 35 5.852250 AGTGGGGGCATATTCTATAGAAAGT 59.148 40.000 18.79 6.55 37.61 2.66
35 36 6.013379 TGAGTGGGGGCATATTCTATAGAAAG 60.013 42.308 18.79 12.56 37.61 2.62
36 37 5.849475 TGAGTGGGGGCATATTCTATAGAAA 59.151 40.000 18.79 9.08 37.61 2.52
37 38 5.411493 TGAGTGGGGGCATATTCTATAGAA 58.589 41.667 17.32 17.32 38.56 2.10
38 39 5.023514 TGAGTGGGGGCATATTCTATAGA 57.976 43.478 0.00 0.00 0.00 1.98
39 40 5.762179 TTGAGTGGGGGCATATTCTATAG 57.238 43.478 0.00 0.00 0.00 1.31
40 41 6.718593 AATTGAGTGGGGGCATATTCTATA 57.281 37.500 0.00 0.00 0.00 1.31
41 42 5.605540 AATTGAGTGGGGGCATATTCTAT 57.394 39.130 0.00 0.00 0.00 1.98
42 43 5.610982 ACTAATTGAGTGGGGGCATATTCTA 59.389 40.000 0.00 0.00 36.87 2.10
43 44 3.979501 AATTGAGTGGGGGCATATTCT 57.020 42.857 0.00 0.00 0.00 2.40
44 45 4.729868 ACTAATTGAGTGGGGGCATATTC 58.270 43.478 0.00 0.00 36.87 1.75
45 46 4.814224 ACTAATTGAGTGGGGGCATATT 57.186 40.909 0.00 0.00 36.87 1.28
46 47 4.814224 AACTAATTGAGTGGGGGCATAT 57.186 40.909 0.00 0.00 38.87 1.78
47 48 4.277476 CAAACTAATTGAGTGGGGGCATA 58.723 43.478 0.00 0.00 41.85 3.14
48 49 3.099141 CAAACTAATTGAGTGGGGGCAT 58.901 45.455 0.00 0.00 41.85 4.40
49 50 2.524306 CAAACTAATTGAGTGGGGGCA 58.476 47.619 0.00 0.00 41.85 5.36
50 51 1.204704 GCAAACTAATTGAGTGGGGGC 59.795 52.381 0.00 0.00 41.85 5.80
51 52 1.824852 GGCAAACTAATTGAGTGGGGG 59.175 52.381 0.00 0.00 41.85 5.40
52 53 1.824852 GGGCAAACTAATTGAGTGGGG 59.175 52.381 0.00 0.00 41.85 4.96
53 54 1.824852 GGGGCAAACTAATTGAGTGGG 59.175 52.381 0.00 0.00 41.85 4.61
54 55 1.824852 GGGGGCAAACTAATTGAGTGG 59.175 52.381 0.00 0.00 41.85 4.00
55 56 2.231235 GTGGGGGCAAACTAATTGAGTG 59.769 50.000 0.00 0.00 41.85 3.51
56 57 2.110011 AGTGGGGGCAAACTAATTGAGT 59.890 45.455 0.00 0.00 41.85 3.41
57 58 2.755103 GAGTGGGGGCAAACTAATTGAG 59.245 50.000 0.00 0.00 41.85 3.02
58 59 2.556559 GGAGTGGGGGCAAACTAATTGA 60.557 50.000 0.00 0.00 41.85 2.57
59 60 1.824852 GGAGTGGGGGCAAACTAATTG 59.175 52.381 0.00 0.00 42.21 2.32
60 61 1.431243 TGGAGTGGGGGCAAACTAATT 59.569 47.619 0.00 0.00 0.00 1.40
61 62 1.080638 TGGAGTGGGGGCAAACTAAT 58.919 50.000 0.00 0.00 0.00 1.73
62 63 0.854218 TTGGAGTGGGGGCAAACTAA 59.146 50.000 0.00 0.00 0.00 2.24
63 64 0.854218 TTTGGAGTGGGGGCAAACTA 59.146 50.000 0.00 0.00 0.00 2.24
64 65 0.190815 ATTTGGAGTGGGGGCAAACT 59.809 50.000 0.00 0.00 0.00 2.66
65 66 1.548719 GTATTTGGAGTGGGGGCAAAC 59.451 52.381 0.00 0.00 0.00 2.93
66 67 1.431243 AGTATTTGGAGTGGGGGCAAA 59.569 47.619 0.00 0.00 0.00 3.68
67 68 1.080638 AGTATTTGGAGTGGGGGCAA 58.919 50.000 0.00 0.00 0.00 4.52
68 69 1.080638 AAGTATTTGGAGTGGGGGCA 58.919 50.000 0.00 0.00 0.00 5.36
69 70 2.100197 GAAAGTATTTGGAGTGGGGGC 58.900 52.381 0.00 0.00 39.27 5.80
70 71 3.739401 AGAAAGTATTTGGAGTGGGGG 57.261 47.619 0.00 0.00 39.27 5.40
71 72 4.227527 ACCTAGAAAGTATTTGGAGTGGGG 59.772 45.833 0.00 0.00 39.27 4.96
72 73 5.429130 GACCTAGAAAGTATTTGGAGTGGG 58.571 45.833 0.00 0.00 39.27 4.61
73 74 5.429130 GGACCTAGAAAGTATTTGGAGTGG 58.571 45.833 0.00 0.00 39.27 4.00
74 75 5.109903 CGGACCTAGAAAGTATTTGGAGTG 58.890 45.833 0.00 0.00 39.27 3.51
75 76 4.382793 GCGGACCTAGAAAGTATTTGGAGT 60.383 45.833 0.00 0.00 39.27 3.85
76 77 4.120589 GCGGACCTAGAAAGTATTTGGAG 58.879 47.826 0.00 0.00 39.27 3.86
77 78 3.118519 GGCGGACCTAGAAAGTATTTGGA 60.119 47.826 0.00 0.00 39.27 3.53
78 79 3.203716 GGCGGACCTAGAAAGTATTTGG 58.796 50.000 0.00 0.00 39.27 3.28
79 80 2.864343 CGGCGGACCTAGAAAGTATTTG 59.136 50.000 0.00 0.00 39.27 2.32
80 81 2.498885 ACGGCGGACCTAGAAAGTATTT 59.501 45.455 13.24 0.00 43.98 1.40
81 82 2.105766 ACGGCGGACCTAGAAAGTATT 58.894 47.619 13.24 0.00 0.00 1.89
82 83 1.772836 ACGGCGGACCTAGAAAGTAT 58.227 50.000 13.24 0.00 0.00 2.12
83 84 1.203052 CAACGGCGGACCTAGAAAGTA 59.797 52.381 13.24 0.00 0.00 2.24
84 85 0.037605 CAACGGCGGACCTAGAAAGT 60.038 55.000 13.24 0.00 0.00 2.66
85 86 0.245539 TCAACGGCGGACCTAGAAAG 59.754 55.000 13.24 0.00 0.00 2.62
86 87 0.037975 GTCAACGGCGGACCTAGAAA 60.038 55.000 13.24 0.00 0.00 2.52
87 88 1.180456 TGTCAACGGCGGACCTAGAA 61.180 55.000 13.24 0.00 34.36 2.10
88 89 1.180456 TTGTCAACGGCGGACCTAGA 61.180 55.000 13.24 0.00 34.36 2.43
89 90 1.012486 GTTGTCAACGGCGGACCTAG 61.012 60.000 13.24 0.00 34.36 3.02
90 91 1.005867 GTTGTCAACGGCGGACCTA 60.006 57.895 13.24 0.00 34.36 3.08
91 92 2.280592 GTTGTCAACGGCGGACCT 60.281 61.111 13.24 0.00 34.36 3.85
92 93 1.908066 GATGTTGTCAACGGCGGACC 61.908 60.000 13.24 0.00 34.36 4.46
93 94 1.495951 GATGTTGTCAACGGCGGAC 59.504 57.895 13.24 10.74 35.83 4.79
94 95 1.669760 GGATGTTGTCAACGGCGGA 60.670 57.895 13.24 0.00 0.00 5.54
95 96 2.686816 GGGATGTTGTCAACGGCGG 61.687 63.158 13.24 0.00 0.00 6.13
96 97 2.686816 GGGGATGTTGTCAACGGCG 61.687 63.158 4.80 4.80 0.00 6.46
97 98 2.340328 GGGGGATGTTGTCAACGGC 61.340 63.158 11.03 5.31 0.00 5.68
98 99 3.996614 GGGGGATGTTGTCAACGG 58.003 61.111 11.03 0.00 0.00 4.44
121 122 3.726517 CTGCTTGTTGTCGGGGCG 61.727 66.667 0.00 0.00 0.00 6.13
122 123 4.043200 GCTGCTTGTTGTCGGGGC 62.043 66.667 0.00 0.00 0.00 5.80
339 355 2.696125 GGGAAGGAGATGGGGGCA 60.696 66.667 0.00 0.00 0.00 5.36
500 516 1.646189 GGAATCTTCAGAGACCACGC 58.354 55.000 0.00 0.00 33.99 5.34
527 543 0.106419 CTCCCCTACCTCTCGAGCTT 60.106 60.000 7.81 0.00 0.00 3.74
539 555 0.033405 CGGGTTCACTCTCTCCCCTA 60.033 60.000 0.00 0.00 36.84 3.53
563 579 1.207488 CCACTCCCCCATCCACTTCA 61.207 60.000 0.00 0.00 0.00 3.02
565 581 0.253820 ATCCACTCCCCCATCCACTT 60.254 55.000 0.00 0.00 0.00 3.16
676 3210 0.955919 GTAGGACAAGGCTGGTGTGC 60.956 60.000 0.00 0.00 37.58 4.57
710 3244 3.123621 CGAATCTTAACACACTGAGGCAC 59.876 47.826 0.00 0.00 0.00 5.01
747 3281 0.878523 CACACGTGTGGATCACCGTT 60.879 55.000 35.65 0.55 43.51 4.44
760 3294 4.539083 TGCAACTCGCCCACACGT 62.539 61.111 0.00 0.00 41.33 4.49
762 3296 1.291877 CTACTGCAACTCGCCCACAC 61.292 60.000 0.00 0.00 41.33 3.82
775 3309 1.594293 ACACGTGTGGCACTACTGC 60.594 57.895 22.71 3.25 43.41 4.40
789 3323 0.233848 GAAACACTAACGCCCACACG 59.766 55.000 0.00 0.00 39.50 4.49
796 3330 8.831000 AATTTTTATATCGGAAACACTAACGC 57.169 30.769 0.00 0.00 0.00 4.84
947 4424 1.693627 CGGCTGTGTATACTCCTCCT 58.306 55.000 4.17 0.00 0.00 3.69
948 4425 0.032267 GCGGCTGTGTATACTCCTCC 59.968 60.000 4.17 3.89 0.00 4.30
949 4426 1.033574 AGCGGCTGTGTATACTCCTC 58.966 55.000 0.00 0.00 0.00 3.71
950 4427 2.231529 CTAGCGGCTGTGTATACTCCT 58.768 52.381 13.86 0.00 0.00 3.69
951 4428 1.336056 GCTAGCGGCTGTGTATACTCC 60.336 57.143 13.86 0.00 38.06 3.85
995 4478 0.970937 TCCTCCAGGCTCCAAGTACG 60.971 60.000 0.00 0.00 34.44 3.67
996 4479 0.827368 CTCCTCCAGGCTCCAAGTAC 59.173 60.000 0.00 0.00 34.44 2.73
997 4480 0.710588 TCTCCTCCAGGCTCCAAGTA 59.289 55.000 0.00 0.00 34.44 2.24
998 4481 0.617249 CTCTCCTCCAGGCTCCAAGT 60.617 60.000 0.00 0.00 34.44 3.16
999 4482 1.336632 CCTCTCCTCCAGGCTCCAAG 61.337 65.000 0.00 0.00 34.44 3.61
1000 4483 1.306482 CCTCTCCTCCAGGCTCCAA 60.306 63.158 0.00 0.00 34.44 3.53
1001 4484 2.366167 CCTCTCCTCCAGGCTCCA 59.634 66.667 0.00 0.00 34.44 3.86
1007 4493 2.726351 GGGTTCGCCTCTCCTCCAG 61.726 68.421 0.00 0.00 37.45 3.86
1017 4503 1.753078 GAGGGGATTTGGGTTCGCC 60.753 63.158 0.00 0.00 44.34 5.54
1018 4504 1.753078 GGAGGGGATTTGGGTTCGC 60.753 63.158 0.00 0.00 0.00 4.70
1026 4512 3.480133 CGAGGCGGGAGGGGATTT 61.480 66.667 0.00 0.00 0.00 2.17
1053 4566 4.959596 GATCTCTCCTGCGGCGGC 62.960 72.222 9.78 9.68 40.52 6.53
1054 4567 4.292178 GGATCTCTCCTGCGGCGG 62.292 72.222 9.78 0.65 38.65 6.13
1055 4568 4.292178 GGGATCTCTCCTGCGGCG 62.292 72.222 0.51 0.51 41.74 6.46
1056 4569 4.292178 CGGGATCTCTCCTGCGGC 62.292 72.222 0.00 0.00 41.05 6.53
1263 4780 3.798511 GAAGCGGGGGAGAAGGGG 61.799 72.222 0.00 0.00 0.00 4.79
1322 5042 1.815421 CCGCCGATCCAACCAGAAG 60.815 63.158 0.00 0.00 0.00 2.85
1654 6479 5.704515 CACACAGAATCAAAATCTCCTCACT 59.295 40.000 0.00 0.00 0.00 3.41
1842 6707 6.134061 GGTAACTAAACAAAGCTTCAGTTCG 58.866 40.000 15.13 12.26 0.00 3.95
1851 6716 3.629438 TTGCCGGTAACTAAACAAAGC 57.371 42.857 0.00 0.00 0.00 3.51
2469 7376 5.184671 AGAAGTCCCTTTCAAATGCATCTTC 59.815 40.000 0.00 4.54 0.00 2.87
2501 7408 4.739587 TGTGTCCATGTAATACGGCTTA 57.260 40.909 0.00 0.00 0.00 3.09
2760 7768 2.749076 GGCACAACATAACTCATGCAGA 59.251 45.455 0.00 0.00 38.29 4.26
3175 8205 2.828520 CTGGACTAACAGCCTCAGAAGA 59.171 50.000 0.00 0.00 0.00 2.87
3406 9649 0.912486 CTAACTGGAAGGGGTGGAGG 59.088 60.000 0.00 0.00 39.30 4.30
3600 9853 0.819259 TTCACACCAGGAGCACAAGC 60.819 55.000 0.00 0.00 42.56 4.01
3766 10035 0.779997 AGCCAAGGGTCTGGTTGATT 59.220 50.000 0.00 0.00 38.86 2.57
3883 10161 2.139323 ATAGTACAGCCGAGTCACCA 57.861 50.000 0.00 0.00 0.00 4.17
3884 10162 3.521947 AAATAGTACAGCCGAGTCACC 57.478 47.619 0.00 0.00 0.00 4.02
3947 10228 1.816074 TTAGGCCGACATTTCACACC 58.184 50.000 0.00 0.00 0.00 4.16
4141 10461 0.879400 CAGTCTCATCATCTGCCGGC 60.879 60.000 22.73 22.73 0.00 6.13
4159 10479 2.655090 TGACTTCTGCCAATCAACCA 57.345 45.000 0.00 0.00 0.00 3.67
4229 10550 8.957466 GCAATTTCTGGAGTAGGTTTATACTTT 58.043 33.333 0.00 0.00 36.13 2.66
4230 10551 8.329502 AGCAATTTCTGGAGTAGGTTTATACTT 58.670 33.333 0.00 0.00 36.13 2.24
4345 10744 2.615447 CGTGCATTGTGCCTTCATCTAT 59.385 45.455 0.00 0.00 44.23 1.98
4346 10745 2.009051 CGTGCATTGTGCCTTCATCTA 58.991 47.619 0.00 0.00 44.23 1.98
4382 10781 5.774690 ACAGCCCTCATTTCAACTTATTTCA 59.225 36.000 0.00 0.00 0.00 2.69
4804 11688 8.102484 ACCATGTACTCCATTAAATCCTTACT 57.898 34.615 0.00 0.00 0.00 2.24
4810 11694 8.190784 CCTTGAAACCATGTACTCCATTAAATC 58.809 37.037 0.00 0.00 0.00 2.17
4914 11802 2.941720 CTGCTGTTTATGGCCTCTCTTC 59.058 50.000 3.32 0.00 0.00 2.87
4923 11811 5.353956 TGTGTGCTAATACTGCTGTTTATGG 59.646 40.000 0.09 0.00 0.00 2.74
4958 11846 1.126846 GAGAAAATGCAGTCGTGGACG 59.873 52.381 0.00 0.00 37.67 4.79
4998 11886 3.616379 GTGAGTAGTCTTGAAGCATCAGC 59.384 47.826 0.00 0.00 36.78 4.26
4999 11887 4.814147 TGTGAGTAGTCTTGAAGCATCAG 58.186 43.478 0.00 0.00 36.78 2.90
5000 11888 4.814147 CTGTGAGTAGTCTTGAAGCATCA 58.186 43.478 0.00 0.00 0.00 3.07
5001 11889 3.616379 GCTGTGAGTAGTCTTGAAGCATC 59.384 47.826 0.00 0.00 0.00 3.91
5002 11890 3.260380 AGCTGTGAGTAGTCTTGAAGCAT 59.740 43.478 13.24 0.00 31.85 3.79
5003 11891 2.630098 AGCTGTGAGTAGTCTTGAAGCA 59.370 45.455 13.24 0.00 31.85 3.91
5004 11892 3.311486 AGCTGTGAGTAGTCTTGAAGC 57.689 47.619 0.00 3.23 0.00 3.86


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

AutoCloner maintained by Alex Coulton.