Multiple sequence alignment - TraesCS5A01G226900

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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 TraesCS5A01G226900 chr5A 100.000 4511 0 0 1 4511 442703884 442699374 0.000000e+00 8331
1 TraesCS5A01G226900 chr5A 86.726 113 12 3 1 110 563414162 563414274 6.130000e-24 122
2 TraesCS5A01G226900 chr5D 93.768 4461 188 52 104 4511 341568951 341564528 0.000000e+00 6615
3 TraesCS5A01G226900 chr5D 86.087 115 9 6 1 110 363327310 363327422 2.850000e-22 117
4 TraesCS5A01G226900 chr5B 93.736 4470 174 35 109 4511 401012615 401008185 0.000000e+00 6606
5 TraesCS5A01G226900 chr3A 87.611 113 12 2 1 111 523540081 523539969 3.660000e-26 130
6 TraesCS5A01G226900 chr1B 87.273 110 12 2 2 109 441508002 441507893 1.700000e-24 124
7 TraesCS5A01G226900 chr6B 86.207 116 13 3 1 114 288287895 288288009 6.130000e-24 122
8 TraesCS5A01G226900 chr3B 86.842 114 9 5 1 110 31124879 31124990 6.130000e-24 122
9 TraesCS5A01G226900 chr7D 85.841 113 13 3 1 110 82851246 82851134 2.850000e-22 117
10 TraesCS5A01G226900 chr3D 85.841 113 13 3 1 110 287339559 287339671 2.850000e-22 117
11 TraesCS5A01G226900 chr2B 85.586 111 14 2 1 109 37969513 37969623 1.030000e-21 115


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 TraesCS5A01G226900 chr5A 442699374 442703884 4510 True 8331 8331 100.000 1 4511 1 chr5A.!!$R1 4510
1 TraesCS5A01G226900 chr5D 341564528 341568951 4423 True 6615 6615 93.768 104 4511 1 chr5D.!!$R1 4407
2 TraesCS5A01G226900 chr5B 401008185 401012615 4430 True 6606 6606 93.736 109 4511 1 chr5B.!!$R1 4402

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
30 31 0.032515 TTCGGAGGTGCTCATAGGGA 60.033 55.0 0.00 0.00 31.08 4.20 F
52 53 0.093026 GAGTGTGCATGTACGCGTTC 59.907 55.0 20.78 14.31 36.24 3.95 F
99 100 0.109689 GAGCGCTTCGTCTGTACTGT 60.110 55.0 13.26 0.00 0.00 3.55 F
101 102 0.386858 GCGCTTCGTCTGTACTGTGA 60.387 55.0 0.00 0.00 0.00 3.58 F
1380 1450 0.957362 AAGAAAAGCTGCACTGCCTC 59.043 50.0 1.02 0.00 0.00 4.70 F
2996 3068 0.918983 CCTGGGGGCTGTTTATGAGA 59.081 55.0 0.00 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 1600 1.004918 GAACTGTGTCCCTCCACCG 60.005 63.158 0.0 0.0 34.35 4.94 R
1608 1678 1.021390 CCAATGCAGTCCTGACGGTC 61.021 60.000 0.0 0.0 36.20 4.79 R
1957 2027 6.101650 TGCACAGTATAGAAGGATACATGG 57.898 41.667 0.0 0.0 35.16 3.66 R
2311 2383 0.741915 GCCTAGAAGGACAGGACTCG 59.258 60.000 0.0 0.0 37.67 4.18 R
3097 3169 0.603707 ACGCTTCACACCTGACATGG 60.604 55.000 0.0 0.0 0.00 3.66 R
4241 4317 0.035439 GGCCCTTCCGACAAGAATCA 60.035 55.000 0.0 0.0 0.00 2.57 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
17 18 4.485554 CGGCTGAGTCTTTCGGAG 57.514 61.111 0.00 0.00 33.75 4.63
18 19 1.153745 CGGCTGAGTCTTTCGGAGG 60.154 63.158 0.00 0.00 33.75 4.30
19 20 1.878656 CGGCTGAGTCTTTCGGAGGT 61.879 60.000 0.00 0.00 33.75 3.85
20 21 0.390472 GGCTGAGTCTTTCGGAGGTG 60.390 60.000 0.00 0.00 33.75 4.00
21 22 1.016653 GCTGAGTCTTTCGGAGGTGC 61.017 60.000 0.00 0.00 33.75 5.01
22 23 0.605589 CTGAGTCTTTCGGAGGTGCT 59.394 55.000 0.00 0.00 33.75 4.40
23 24 0.603569 TGAGTCTTTCGGAGGTGCTC 59.396 55.000 0.00 0.00 0.00 4.26
24 25 0.603569 GAGTCTTTCGGAGGTGCTCA 59.396 55.000 0.00 0.00 31.08 4.26
25 26 1.205893 GAGTCTTTCGGAGGTGCTCAT 59.794 52.381 0.00 0.00 31.08 2.90
26 27 2.427453 GAGTCTTTCGGAGGTGCTCATA 59.573 50.000 0.00 0.00 31.08 2.15
27 28 2.428890 AGTCTTTCGGAGGTGCTCATAG 59.571 50.000 0.00 0.00 31.08 2.23
28 29 1.757118 TCTTTCGGAGGTGCTCATAGG 59.243 52.381 0.00 0.00 31.08 2.57
29 30 0.830648 TTTCGGAGGTGCTCATAGGG 59.169 55.000 0.00 0.00 31.08 3.53
30 31 0.032515 TTCGGAGGTGCTCATAGGGA 60.033 55.000 0.00 0.00 31.08 4.20
31 32 0.188587 TCGGAGGTGCTCATAGGGAT 59.811 55.000 0.00 0.00 31.08 3.85
32 33 1.427753 TCGGAGGTGCTCATAGGGATA 59.572 52.381 0.00 0.00 31.08 2.59
33 34 1.821753 CGGAGGTGCTCATAGGGATAG 59.178 57.143 0.00 0.00 31.08 2.08
34 35 2.555448 CGGAGGTGCTCATAGGGATAGA 60.555 54.545 0.00 0.00 31.08 1.98
35 36 3.096092 GGAGGTGCTCATAGGGATAGAG 58.904 54.545 0.00 0.00 31.08 2.43
36 37 3.501385 GGAGGTGCTCATAGGGATAGAGT 60.501 52.174 0.00 0.00 31.08 3.24
37 38 3.505386 AGGTGCTCATAGGGATAGAGTG 58.495 50.000 0.00 0.00 0.00 3.51
38 39 3.116939 AGGTGCTCATAGGGATAGAGTGT 60.117 47.826 0.00 0.00 0.00 3.55
39 40 3.006323 GGTGCTCATAGGGATAGAGTGTG 59.994 52.174 0.00 0.00 0.00 3.82
40 41 2.630098 TGCTCATAGGGATAGAGTGTGC 59.370 50.000 0.00 0.00 0.00 4.57
41 42 2.630098 GCTCATAGGGATAGAGTGTGCA 59.370 50.000 0.00 0.00 31.69 4.57
42 43 3.260380 GCTCATAGGGATAGAGTGTGCAT 59.740 47.826 0.00 0.00 31.69 3.96
43 44 4.818642 CTCATAGGGATAGAGTGTGCATG 58.181 47.826 0.00 0.00 0.00 4.06
44 45 4.226384 TCATAGGGATAGAGTGTGCATGT 58.774 43.478 0.00 0.00 0.00 3.21
45 46 5.393866 TCATAGGGATAGAGTGTGCATGTA 58.606 41.667 0.00 0.00 0.00 2.29
46 47 5.243954 TCATAGGGATAGAGTGTGCATGTAC 59.756 44.000 7.03 7.03 0.00 2.90
47 48 2.362397 AGGGATAGAGTGTGCATGTACG 59.638 50.000 9.48 0.00 0.00 3.67
48 49 2.128035 GGATAGAGTGTGCATGTACGC 58.872 52.381 18.46 18.46 0.00 4.42
49 50 1.781429 GATAGAGTGTGCATGTACGCG 59.219 52.381 19.67 3.53 36.24 6.01
50 51 0.524414 TAGAGTGTGCATGTACGCGT 59.476 50.000 19.17 19.17 36.24 6.01
51 52 0.319555 AGAGTGTGCATGTACGCGTT 60.320 50.000 20.78 10.59 36.24 4.84
52 53 0.093026 GAGTGTGCATGTACGCGTTC 59.907 55.000 20.78 14.31 36.24 3.95
53 54 0.598942 AGTGTGCATGTACGCGTTCA 60.599 50.000 20.78 20.85 36.24 3.18
54 55 0.442310 GTGTGCATGTACGCGTTCAT 59.558 50.000 23.47 23.47 33.35 2.57
55 56 1.656594 GTGTGCATGTACGCGTTCATA 59.343 47.619 27.44 13.26 33.35 2.15
56 57 1.656594 TGTGCATGTACGCGTTCATAC 59.343 47.619 27.44 22.98 33.35 2.39
57 58 1.005347 GTGCATGTACGCGTTCATACC 60.005 52.381 27.44 21.20 33.35 2.73
58 59 0.228742 GCATGTACGCGTTCATACCG 59.771 55.000 27.44 17.84 0.00 4.02
59 60 0.850217 CATGTACGCGTTCATACCGG 59.150 55.000 27.44 13.87 0.00 5.28
60 61 0.249155 ATGTACGCGTTCATACCGGG 60.249 55.000 26.94 0.00 43.05 5.73
61 62 1.311651 TGTACGCGTTCATACCGGGA 61.312 55.000 20.78 0.00 40.27 5.14
62 63 0.593263 GTACGCGTTCATACCGGGAG 60.593 60.000 20.78 0.00 40.27 4.30
80 81 6.392625 CGGGAGGGTATGTGAGTATATATG 57.607 45.833 0.00 0.00 0.00 1.78
81 82 6.127101 CGGGAGGGTATGTGAGTATATATGA 58.873 44.000 0.00 0.00 0.00 2.15
82 83 6.263392 CGGGAGGGTATGTGAGTATATATGAG 59.737 46.154 0.00 0.00 0.00 2.90
83 84 6.041069 GGGAGGGTATGTGAGTATATATGAGC 59.959 46.154 0.00 0.00 0.00 4.26
84 85 6.238786 GGAGGGTATGTGAGTATATATGAGCG 60.239 46.154 0.00 0.00 0.00 5.03
85 86 5.067936 AGGGTATGTGAGTATATATGAGCGC 59.932 44.000 0.00 0.00 0.00 5.92
86 87 5.067936 GGGTATGTGAGTATATATGAGCGCT 59.932 44.000 11.27 11.27 0.00 5.92
87 88 6.405953 GGGTATGTGAGTATATATGAGCGCTT 60.406 42.308 13.26 0.00 0.00 4.68
88 89 6.693545 GGTATGTGAGTATATATGAGCGCTTC 59.306 42.308 13.26 5.55 0.00 3.86
89 90 4.723248 TGTGAGTATATATGAGCGCTTCG 58.277 43.478 13.26 0.00 0.00 3.79
90 91 4.215613 TGTGAGTATATATGAGCGCTTCGT 59.784 41.667 13.26 9.09 0.00 3.85
91 92 4.789119 GTGAGTATATATGAGCGCTTCGTC 59.211 45.833 13.26 0.00 0.00 4.20
92 93 4.695928 TGAGTATATATGAGCGCTTCGTCT 59.304 41.667 13.26 2.46 0.00 4.18
93 94 4.975788 AGTATATATGAGCGCTTCGTCTG 58.024 43.478 13.26 0.00 0.00 3.51
94 95 3.924918 ATATATGAGCGCTTCGTCTGT 57.075 42.857 13.26 0.00 0.00 3.41
95 96 5.642491 AGTATATATGAGCGCTTCGTCTGTA 59.358 40.000 13.26 0.00 0.00 2.74
96 97 2.470196 TATGAGCGCTTCGTCTGTAC 57.530 50.000 13.26 0.00 0.00 2.90
97 98 0.811915 ATGAGCGCTTCGTCTGTACT 59.188 50.000 13.26 0.00 0.00 2.73
98 99 0.109735 TGAGCGCTTCGTCTGTACTG 60.110 55.000 13.26 0.00 0.00 2.74
99 100 0.109689 GAGCGCTTCGTCTGTACTGT 60.110 55.000 13.26 0.00 0.00 3.55
100 101 0.387367 AGCGCTTCGTCTGTACTGTG 60.387 55.000 2.64 0.00 0.00 3.66
101 102 0.386858 GCGCTTCGTCTGTACTGTGA 60.387 55.000 0.00 0.00 0.00 3.58
102 103 1.732732 GCGCTTCGTCTGTACTGTGAT 60.733 52.381 0.00 0.00 0.00 3.06
103 104 2.477357 GCGCTTCGTCTGTACTGTGATA 60.477 50.000 0.00 0.00 0.00 2.15
104 105 3.754955 CGCTTCGTCTGTACTGTGATAA 58.245 45.455 0.00 0.00 0.00 1.75
105 106 4.163552 CGCTTCGTCTGTACTGTGATAAA 58.836 43.478 0.00 0.00 0.00 1.40
106 107 4.619760 CGCTTCGTCTGTACTGTGATAAAA 59.380 41.667 0.00 0.00 0.00 1.52
107 108 5.118050 CGCTTCGTCTGTACTGTGATAAAAA 59.882 40.000 0.00 0.00 0.00 1.94
136 137 9.938670 GTGTTTGGGTTTTAAATTTAAATGGTC 57.061 29.630 20.98 12.78 33.12 4.02
281 290 2.369394 CCCACAGCCCAAGATTTCTAC 58.631 52.381 0.00 0.00 0.00 2.59
579 629 2.352032 CCGAGCTCCGTCCTTCCTT 61.352 63.158 8.47 0.00 36.31 3.36
583 633 2.184579 CTCCGTCCTTCCTTCCGC 59.815 66.667 0.00 0.00 0.00 5.54
786 850 6.149973 GGTAAAGTTTGGTGGTTAGGATACAC 59.850 42.308 0.00 0.00 41.41 2.90
863 927 6.767902 GTCTATGATTGCCTCAGGTGAAATTA 59.232 38.462 0.00 0.00 37.28 1.40
997 1064 4.458989 GTGTGCAATTCTCAGGATAAACCA 59.541 41.667 0.00 0.00 42.04 3.67
998 1065 5.126061 GTGTGCAATTCTCAGGATAAACCAT 59.874 40.000 0.00 0.00 42.04 3.55
999 1066 6.318648 GTGTGCAATTCTCAGGATAAACCATA 59.681 38.462 0.00 0.00 42.04 2.74
1167 1237 1.741770 GAAGCGGACCGATTGCACT 60.742 57.895 24.10 2.42 35.04 4.40
1173 1243 1.860950 CGGACCGATTGCACTATCTTG 59.139 52.381 8.64 0.00 0.00 3.02
1251 1321 2.836262 TCGCCGGTGAAGAAGTTTAAA 58.164 42.857 17.09 0.00 0.00 1.52
1299 1369 6.891908 ACTATACACCTTGCCAAGATCAAAAT 59.108 34.615 5.89 0.00 0.00 1.82
1380 1450 0.957362 AAGAAAAGCTGCACTGCCTC 59.043 50.000 1.02 0.00 0.00 4.70
1530 1600 1.087501 GCAACGTCTTCAGATTCCCC 58.912 55.000 0.00 0.00 0.00 4.81
1703 1773 3.643763 TCGTGAGCTTCTTCTGACTTTC 58.356 45.455 0.00 0.00 0.00 2.62
1724 1794 9.525826 ACTTTCTTCATGTCCTAAAATTCTGAT 57.474 29.630 0.00 0.00 0.00 2.90
1887 1957 5.067805 GGCACAATTAAACTCCCTTATCCAG 59.932 44.000 0.00 0.00 0.00 3.86
1957 2027 3.879892 GGAATGAATGGTGAGCCTCTAAC 59.120 47.826 0.00 0.00 35.27 2.34
2040 2110 4.741321 ATACCTTGTGCCATTTTGATGG 57.259 40.909 1.05 1.05 44.44 3.51
2311 2383 8.568794 GCAATATGGAGGAAAAGAGTAAATACC 58.431 37.037 0.00 0.00 0.00 2.73
2524 2596 7.701539 ACTGTCTGGTCAATGCATTATTTTA 57.298 32.000 12.53 0.00 0.00 1.52
2577 2649 7.504924 TTAACATGTTGTTAGAAGTTCTGGG 57.495 36.000 21.42 0.00 42.93 4.45
2785 2857 4.402616 AATTCCAGGGGTTTCATCTCAA 57.597 40.909 0.00 0.00 0.00 3.02
2792 2864 4.277672 CAGGGGTTTCATCTCAAGCATATG 59.722 45.833 0.00 0.00 0.00 1.78
2996 3068 0.918983 CCTGGGGGCTGTTTATGAGA 59.081 55.000 0.00 0.00 0.00 3.27
3051 3123 2.289002 GCTTGTTATGCCTGAATCTCGG 59.711 50.000 0.00 0.00 0.00 4.63
3083 3155 7.807977 AAGTTGTTGTCATGAACTTACTGAT 57.192 32.000 7.76 0.00 37.99 2.90
3085 3157 9.507329 AAGTTGTTGTCATGAACTTACTGATAT 57.493 29.630 7.76 0.00 37.99 1.63
3097 3169 9.371136 TGAACTTACTGATATGTCTCACAATTC 57.629 33.333 0.00 0.00 0.00 2.17
3115 3187 0.320683 TCCATGTCAGGTGTGAAGCG 60.321 55.000 0.00 0.00 33.27 4.68
3151 3223 6.334296 TCCAAGGACCTATGATCTTATCCAT 58.666 40.000 0.00 0.00 0.00 3.41
3177 3249 4.993028 AGTGGCCTTTTCACCTTGTATAA 58.007 39.130 3.32 0.00 35.87 0.98
3202 3274 0.545309 AGTAAGCTGCTCCTGTCCCA 60.545 55.000 1.00 0.00 0.00 4.37
3223 3295 1.271001 TGGCATCAGTTCTGTCACCTG 60.271 52.381 0.00 0.00 0.00 4.00
3234 3306 7.179516 TCAGTTCTGTCACCTGGTATAACAATA 59.820 37.037 0.00 0.00 0.00 1.90
3248 3320 9.116067 TGGTATAACAATAAGTAAGATTGCCAC 57.884 33.333 0.00 0.00 37.74 5.01
3261 3333 3.767673 AGATTGCCACTGCTGATTCATTT 59.232 39.130 0.00 0.00 38.71 2.32
3560 3632 0.407139 ATCCACCTTTGAAGCTGGCT 59.593 50.000 0.00 0.00 32.82 4.75
3668 3740 7.363431 TGATCGAGAGCAGTATATTGTTGTAG 58.637 38.462 0.00 0.00 0.00 2.74
3736 3808 8.738645 ACTCTGGTTAATTGAAGGATGTATTC 57.261 34.615 0.00 0.00 0.00 1.75
3802 3874 4.362279 TGCAACTTCTGAATGTTTGCTTC 58.638 39.130 21.84 5.23 0.00 3.86
3809 3881 5.295431 TCTGAATGTTTGCTTCATTACCG 57.705 39.130 0.00 0.00 35.94 4.02
3820 3892 3.751698 GCTTCATTACCGGTAATCCCATC 59.248 47.826 32.34 18.22 33.79 3.51
3821 3893 4.745478 GCTTCATTACCGGTAATCCCATCA 60.745 45.833 32.34 14.22 33.79 3.07
3833 3905 4.766404 AATCCCATCACTTCGTTGTTTC 57.234 40.909 0.00 0.00 0.00 2.78
3835 3907 3.815809 TCCCATCACTTCGTTGTTTCTT 58.184 40.909 0.00 0.00 0.00 2.52
3836 3908 4.963373 TCCCATCACTTCGTTGTTTCTTA 58.037 39.130 0.00 0.00 0.00 2.10
3846 3918 8.757789 CACTTCGTTGTTTCTTAGTTATGTACA 58.242 33.333 0.00 0.00 0.00 2.90
3885 3957 6.062095 AGCTTTACTGTGTTGTTACCTGAAT 58.938 36.000 0.00 0.00 0.00 2.57
3888 3960 7.468084 GCTTTACTGTGTTGTTACCTGAATGAA 60.468 37.037 0.00 0.00 0.00 2.57
3912 3984 9.604626 GAACTGAATGTTTTCTACTCAAGAATG 57.395 33.333 0.00 0.00 43.75 2.67
3974 4046 6.909076 AGAGATATTTTCTTCCTGCTTGGAT 58.091 36.000 0.09 0.00 45.68 3.41
4022 4096 1.211703 TCTTGGTGTTGTTCCTGCTCA 59.788 47.619 0.00 0.00 0.00 4.26
4025 4099 2.229792 TGGTGTTGTTCCTGCTCAATC 58.770 47.619 0.00 0.00 0.00 2.67
4029 4103 2.225091 TGTTGTTCCTGCTCAATCCCAT 60.225 45.455 0.00 0.00 0.00 4.00
4049 4123 6.050432 CCCATTATGTGCATGCTAAATGTTT 58.950 36.000 20.33 0.00 0.00 2.83
4053 4127 5.657826 ATGTGCATGCTAAATGTTTGGTA 57.342 34.783 20.33 0.00 0.00 3.25
4054 4128 5.657826 TGTGCATGCTAAATGTTTGGTAT 57.342 34.783 20.33 0.00 0.00 2.73
4071 4146 2.576615 GTATTCCTGCTCCATTCCACC 58.423 52.381 0.00 0.00 0.00 4.61
4082 4157 1.067425 CCATTCCACCATGTGCAGTTG 60.067 52.381 0.00 0.00 31.34 3.16
4091 4166 2.738846 CCATGTGCAGTTGTGAGTAGTC 59.261 50.000 0.00 0.00 0.00 2.59
4105 4180 7.526142 TGTGAGTAGTCTAAAGAGTTGATGT 57.474 36.000 0.00 0.00 0.00 3.06
4148 4224 4.623167 GCTGCATATCTACTGTTACATCCG 59.377 45.833 0.00 0.00 0.00 4.18
4175 4251 9.559958 GAAATAAAATACAGATTGATATGCCGG 57.440 33.333 0.00 0.00 0.00 6.13
4206 4282 5.644644 CCTATGCTTTAGGTTGCTTTCTTG 58.355 41.667 5.42 0.00 0.00 3.02
4210 4286 3.858503 GCTTTAGGTTGCTTTCTTGCTGG 60.859 47.826 0.00 0.00 0.00 4.85
4215 4291 3.507622 AGGTTGCTTTCTTGCTGGATTAC 59.492 43.478 0.00 0.00 0.00 1.89
4223 4299 3.954200 TCTTGCTGGATTACATTGCAGA 58.046 40.909 0.00 0.00 37.24 4.26
4228 4304 6.321848 TGCTGGATTACATTGCAGATAATG 57.678 37.500 4.46 0.01 42.38 1.90
4233 4309 8.165239 TGGATTACATTGCAGATAATGTTACC 57.835 34.615 7.04 8.76 46.18 2.85
4237 4313 4.574828 ACATTGCAGATAATGTTACCGTCC 59.425 41.667 0.00 0.00 46.18 4.79
4240 4316 4.188462 TGCAGATAATGTTACCGTCCTTG 58.812 43.478 0.00 0.00 0.00 3.61
4241 4317 4.189231 GCAGATAATGTTACCGTCCTTGT 58.811 43.478 0.00 0.00 0.00 3.16
4242 4318 4.034048 GCAGATAATGTTACCGTCCTTGTG 59.966 45.833 0.00 0.00 0.00 3.33
4243 4319 5.416083 CAGATAATGTTACCGTCCTTGTGA 58.584 41.667 0.00 0.00 0.00 3.58
4244 4320 6.049149 CAGATAATGTTACCGTCCTTGTGAT 58.951 40.000 0.00 0.00 0.00 3.06
4246 4322 6.761714 AGATAATGTTACCGTCCTTGTGATTC 59.238 38.462 0.00 0.00 0.00 2.52
4247 4323 4.553330 ATGTTACCGTCCTTGTGATTCT 57.447 40.909 0.00 0.00 0.00 2.40
4248 4324 4.345859 TGTTACCGTCCTTGTGATTCTT 57.654 40.909 0.00 0.00 0.00 2.52
4249 4325 4.062293 TGTTACCGTCCTTGTGATTCTTG 58.938 43.478 0.00 0.00 0.00 3.02
4250 4326 2.930826 ACCGTCCTTGTGATTCTTGT 57.069 45.000 0.00 0.00 0.00 3.16
4251 4327 2.767505 ACCGTCCTTGTGATTCTTGTC 58.232 47.619 0.00 0.00 0.00 3.18
4252 4328 1.726791 CCGTCCTTGTGATTCTTGTCG 59.273 52.381 0.00 0.00 0.00 4.35
4253 4329 1.726791 CGTCCTTGTGATTCTTGTCGG 59.273 52.381 0.00 0.00 0.00 4.79
4254 4330 2.609491 CGTCCTTGTGATTCTTGTCGGA 60.609 50.000 0.00 0.00 0.00 4.55
4255 4331 3.399330 GTCCTTGTGATTCTTGTCGGAA 58.601 45.455 0.00 0.00 0.00 4.30
4256 4332 3.433615 GTCCTTGTGATTCTTGTCGGAAG 59.566 47.826 0.00 0.00 0.00 3.46
4257 4333 2.744202 CCTTGTGATTCTTGTCGGAAGG 59.256 50.000 0.00 0.00 0.00 3.46
4258 4334 2.472695 TGTGATTCTTGTCGGAAGGG 57.527 50.000 0.00 0.00 0.00 3.95
4259 4335 1.087501 GTGATTCTTGTCGGAAGGGC 58.912 55.000 0.00 0.00 0.00 5.19
4260 4336 0.035439 TGATTCTTGTCGGAAGGGCC 60.035 55.000 0.00 0.00 0.00 5.80
4261 4337 0.253327 GATTCTTGTCGGAAGGGCCT 59.747 55.000 0.00 0.00 0.00 5.19
4262 4338 1.485066 GATTCTTGTCGGAAGGGCCTA 59.515 52.381 6.41 0.00 0.00 3.93
4309 4385 6.514048 GCCTTCATTACCATTCATAGCTTCAC 60.514 42.308 0.00 0.00 0.00 3.18
4334 4410 1.610522 CAGGCAAGACCAAAGGTTCAG 59.389 52.381 0.00 0.00 43.14 3.02
4338 4414 3.191371 GGCAAGACCAAAGGTTCAGTATG 59.809 47.826 0.00 0.00 35.25 2.39
4366 4442 3.028850 CGGTATGTTCCTACTTCCTCCA 58.971 50.000 0.00 0.00 0.00 3.86
4378 4454 6.273730 TCCTACTTCCTCCAAAAATTGACCTA 59.726 38.462 0.00 0.00 0.00 3.08
4379 4455 6.374613 CCTACTTCCTCCAAAAATTGACCTAC 59.625 42.308 0.00 0.00 0.00 3.18
4380 4456 5.953571 ACTTCCTCCAAAAATTGACCTACT 58.046 37.500 0.00 0.00 0.00 2.57
4381 4457 5.770162 ACTTCCTCCAAAAATTGACCTACTG 59.230 40.000 0.00 0.00 0.00 2.74
4397 4473 7.794041 TGACCTACTGTTTTTACTTACTTGGA 58.206 34.615 0.00 0.00 0.00 3.53
4438 4514 4.844998 TTGCTTTACTGCAGTGCATAAA 57.155 36.364 29.57 19.23 44.27 1.40
4446 4522 5.824904 ACTGCAGTGCATAAATTCTTAGG 57.175 39.130 20.97 4.59 38.13 2.69
4451 4527 5.529060 GCAGTGCATAAATTCTTAGGTAGCT 59.471 40.000 11.09 0.00 0.00 3.32
4468 4544 0.746204 GCTAAGCTTCCTCACAGGCC 60.746 60.000 0.00 0.00 34.61 5.19
4471 4547 0.407139 AAGCTTCCTCACAGGCCAAT 59.593 50.000 5.01 0.00 34.61 3.16
4473 4549 1.203100 AGCTTCCTCACAGGCCAATTT 60.203 47.619 5.01 0.00 34.61 1.82
4474 4550 1.203287 GCTTCCTCACAGGCCAATTTC 59.797 52.381 5.01 0.00 34.61 2.17
4476 4552 0.322456 TCCTCACAGGCCAATTTCGG 60.322 55.000 5.01 0.00 34.61 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153745 CCTCCGAAAGACTCAGCCG 60.154 63.158 0.00 0.00 0.00 5.52
1 2 0.390472 CACCTCCGAAAGACTCAGCC 60.390 60.000 0.00 0.00 0.00 4.85
2 3 1.016653 GCACCTCCGAAAGACTCAGC 61.017 60.000 0.00 0.00 0.00 4.26
3 4 0.605589 AGCACCTCCGAAAGACTCAG 59.394 55.000 0.00 0.00 0.00 3.35
4 5 0.603569 GAGCACCTCCGAAAGACTCA 59.396 55.000 0.00 0.00 0.00 3.41
5 6 0.603569 TGAGCACCTCCGAAAGACTC 59.396 55.000 0.00 0.00 0.00 3.36
6 7 1.270907 ATGAGCACCTCCGAAAGACT 58.729 50.000 0.00 0.00 0.00 3.24
7 8 2.482142 CCTATGAGCACCTCCGAAAGAC 60.482 54.545 0.00 0.00 0.00 3.01
8 9 1.757118 CCTATGAGCACCTCCGAAAGA 59.243 52.381 0.00 0.00 0.00 2.52
9 10 1.202580 CCCTATGAGCACCTCCGAAAG 60.203 57.143 0.00 0.00 0.00 2.62
10 11 0.830648 CCCTATGAGCACCTCCGAAA 59.169 55.000 0.00 0.00 0.00 3.46
11 12 0.032515 TCCCTATGAGCACCTCCGAA 60.033 55.000 0.00 0.00 0.00 4.30
12 13 0.188587 ATCCCTATGAGCACCTCCGA 59.811 55.000 0.00 0.00 0.00 4.55
13 14 1.821753 CTATCCCTATGAGCACCTCCG 59.178 57.143 0.00 0.00 0.00 4.63
14 15 3.096092 CTCTATCCCTATGAGCACCTCC 58.904 54.545 0.00 0.00 0.00 4.30
15 16 3.509575 CACTCTATCCCTATGAGCACCTC 59.490 52.174 0.00 0.00 0.00 3.85
16 17 3.116939 ACACTCTATCCCTATGAGCACCT 60.117 47.826 0.00 0.00 0.00 4.00
17 18 3.006323 CACACTCTATCCCTATGAGCACC 59.994 52.174 0.00 0.00 0.00 5.01
18 19 3.553922 GCACACTCTATCCCTATGAGCAC 60.554 52.174 0.00 0.00 0.00 4.40
19 20 2.630098 GCACACTCTATCCCTATGAGCA 59.370 50.000 0.00 0.00 0.00 4.26
20 21 2.630098 TGCACACTCTATCCCTATGAGC 59.370 50.000 0.00 0.00 0.00 4.26
21 22 4.282957 ACATGCACACTCTATCCCTATGAG 59.717 45.833 0.00 0.00 0.00 2.90
22 23 4.226384 ACATGCACACTCTATCCCTATGA 58.774 43.478 0.00 0.00 0.00 2.15
23 24 4.613925 ACATGCACACTCTATCCCTATG 57.386 45.455 0.00 0.00 0.00 2.23
24 25 4.218635 CGTACATGCACACTCTATCCCTAT 59.781 45.833 0.00 0.00 0.00 2.57
25 26 3.568430 CGTACATGCACACTCTATCCCTA 59.432 47.826 0.00 0.00 0.00 3.53
26 27 2.362397 CGTACATGCACACTCTATCCCT 59.638 50.000 0.00 0.00 0.00 4.20
27 28 2.743938 CGTACATGCACACTCTATCCC 58.256 52.381 0.00 0.00 0.00 3.85
28 29 2.128035 GCGTACATGCACACTCTATCC 58.872 52.381 0.00 0.00 34.15 2.59
29 30 1.781429 CGCGTACATGCACACTCTATC 59.219 52.381 0.00 0.00 34.15 2.08
30 31 1.134367 ACGCGTACATGCACACTCTAT 59.866 47.619 11.67 0.00 34.15 1.98
31 32 0.524414 ACGCGTACATGCACACTCTA 59.476 50.000 11.67 0.00 34.15 2.43
32 33 0.319555 AACGCGTACATGCACACTCT 60.320 50.000 14.46 0.00 34.15 3.24
33 34 0.093026 GAACGCGTACATGCACACTC 59.907 55.000 14.46 0.00 34.15 3.51
34 35 0.598942 TGAACGCGTACATGCACACT 60.599 50.000 14.46 0.00 34.15 3.55
35 36 0.442310 ATGAACGCGTACATGCACAC 59.558 50.000 14.46 0.00 34.15 3.82
36 37 1.656594 GTATGAACGCGTACATGCACA 59.343 47.619 14.46 5.04 36.67 4.57
37 38 1.005347 GGTATGAACGCGTACATGCAC 60.005 52.381 14.46 6.12 38.08 4.57
38 39 1.282817 GGTATGAACGCGTACATGCA 58.717 50.000 14.46 6.66 38.08 3.96
39 40 0.228742 CGGTATGAACGCGTACATGC 59.771 55.000 14.46 3.07 38.08 4.06
40 41 0.850217 CCGGTATGAACGCGTACATG 59.150 55.000 14.46 3.22 38.08 3.21
41 42 0.249155 CCCGGTATGAACGCGTACAT 60.249 55.000 14.46 0.00 38.08 2.29
42 43 1.139308 CCCGGTATGAACGCGTACA 59.861 57.895 14.46 0.00 38.08 2.90
43 44 0.593263 CTCCCGGTATGAACGCGTAC 60.593 60.000 14.46 6.79 36.07 3.67
44 45 1.727511 CCTCCCGGTATGAACGCGTA 61.728 60.000 14.46 0.00 0.00 4.42
45 46 2.493030 CTCCCGGTATGAACGCGT 59.507 61.111 5.58 5.58 0.00 6.01
46 47 2.279252 CCTCCCGGTATGAACGCG 60.279 66.667 3.53 3.53 0.00 6.01
47 48 1.394266 TACCCTCCCGGTATGAACGC 61.394 60.000 0.00 0.00 45.97 4.84
48 49 2.811307 TACCCTCCCGGTATGAACG 58.189 57.895 0.00 0.00 45.97 3.95
56 57 2.011122 ATACTCACATACCCTCCCGG 57.989 55.000 0.00 0.00 37.81 5.73
57 58 6.127101 TCATATATACTCACATACCCTCCCG 58.873 44.000 0.00 0.00 0.00 5.14
58 59 6.041069 GCTCATATATACTCACATACCCTCCC 59.959 46.154 0.00 0.00 0.00 4.30
59 60 6.238786 CGCTCATATATACTCACATACCCTCC 60.239 46.154 0.00 0.00 0.00 4.30
60 61 6.730175 CGCTCATATATACTCACATACCCTC 58.270 44.000 0.00 0.00 0.00 4.30
61 62 5.067936 GCGCTCATATATACTCACATACCCT 59.932 44.000 0.00 0.00 0.00 4.34
62 63 5.067936 AGCGCTCATATATACTCACATACCC 59.932 44.000 2.64 0.00 0.00 3.69
63 64 6.137794 AGCGCTCATATATACTCACATACC 57.862 41.667 2.64 0.00 0.00 2.73
64 65 6.412362 CGAAGCGCTCATATATACTCACATAC 59.588 42.308 12.06 0.00 0.00 2.39
65 66 6.093633 ACGAAGCGCTCATATATACTCACATA 59.906 38.462 12.06 0.00 0.00 2.29
66 67 5.106118 ACGAAGCGCTCATATATACTCACAT 60.106 40.000 12.06 0.00 0.00 3.21
67 68 4.215613 ACGAAGCGCTCATATATACTCACA 59.784 41.667 12.06 0.00 0.00 3.58
68 69 4.724303 ACGAAGCGCTCATATATACTCAC 58.276 43.478 12.06 0.00 0.00 3.51
69 70 4.695928 AGACGAAGCGCTCATATATACTCA 59.304 41.667 12.06 0.00 0.00 3.41
70 71 5.025190 CAGACGAAGCGCTCATATATACTC 58.975 45.833 12.06 0.00 0.00 2.59
71 72 4.456222 ACAGACGAAGCGCTCATATATACT 59.544 41.667 12.06 0.00 0.00 2.12
72 73 4.724303 ACAGACGAAGCGCTCATATATAC 58.276 43.478 12.06 0.00 0.00 1.47
73 74 5.642491 AGTACAGACGAAGCGCTCATATATA 59.358 40.000 12.06 0.00 0.00 0.86
74 75 3.924918 ACAGACGAAGCGCTCATATAT 57.075 42.857 12.06 0.00 0.00 0.86
75 76 3.813724 AGTACAGACGAAGCGCTCATATA 59.186 43.478 12.06 0.00 0.00 0.86
76 77 2.619177 AGTACAGACGAAGCGCTCATAT 59.381 45.455 12.06 0.00 0.00 1.78
77 78 2.014857 AGTACAGACGAAGCGCTCATA 58.985 47.619 12.06 0.00 0.00 2.15
78 79 0.811915 AGTACAGACGAAGCGCTCAT 59.188 50.000 12.06 0.00 0.00 2.90
79 80 0.109735 CAGTACAGACGAAGCGCTCA 60.110 55.000 12.06 0.00 0.00 4.26
80 81 0.109689 ACAGTACAGACGAAGCGCTC 60.110 55.000 12.06 3.22 0.00 5.03
81 82 0.387367 CACAGTACAGACGAAGCGCT 60.387 55.000 2.64 2.64 0.00 5.92
82 83 0.386858 TCACAGTACAGACGAAGCGC 60.387 55.000 0.00 0.00 0.00 5.92
83 84 2.264109 ATCACAGTACAGACGAAGCG 57.736 50.000 0.00 0.00 0.00 4.68
84 85 6.462073 TTTTTATCACAGTACAGACGAAGC 57.538 37.500 0.00 0.00 0.00 3.86
136 137 8.592105 TGGAAGATACTTTTCTTTTTGCATTG 57.408 30.769 0.00 0.00 36.10 2.82
202 211 2.083835 CTACGGGGTTCGCGGATCAT 62.084 60.000 6.13 0.00 43.94 2.45
265 274 1.017387 GCGGTAGAAATCTTGGGCTG 58.983 55.000 0.00 0.00 0.00 4.85
272 281 1.742750 GCGGAAAGGCGGTAGAAATCT 60.743 52.381 0.00 0.00 0.00 2.40
281 290 1.330829 GAGAATAAAGCGGAAAGGCGG 59.669 52.381 0.00 0.00 38.18 6.13
483 507 3.019003 GCCAGCTCCTAGGCGAACA 62.019 63.158 2.96 0.00 41.70 3.18
539 563 3.929948 GCGGAAGAATGGCTCGCG 61.930 66.667 0.00 0.00 37.12 5.87
540 564 2.817423 CTGCGGAAGAATGGCTCGC 61.817 63.158 0.00 0.00 45.60 5.03
541 565 2.817423 GCTGCGGAAGAATGGCTCG 61.817 63.158 0.00 0.00 0.00 5.03
542 566 1.435408 GAGCTGCGGAAGAATGGCTC 61.435 60.000 0.00 0.00 39.14 4.70
543 567 1.451028 GAGCTGCGGAAGAATGGCT 60.451 57.895 0.00 0.00 0.00 4.75
544 568 2.476320 GGAGCTGCGGAAGAATGGC 61.476 63.158 0.00 0.00 0.00 4.40
545 569 2.176273 CGGAGCTGCGGAAGAATGG 61.176 63.158 21.08 0.00 0.00 3.16
546 570 1.150567 CTCGGAGCTGCGGAAGAATG 61.151 60.000 27.80 5.74 0.00 2.67
547 571 1.142748 CTCGGAGCTGCGGAAGAAT 59.857 57.895 27.80 0.00 0.00 2.40
549 573 4.135153 GCTCGGAGCTGCGGAAGA 62.135 66.667 27.80 7.21 38.45 2.87
599 649 0.523072 CTCACAACCCAATGGCGAAG 59.477 55.000 0.00 0.00 33.59 3.79
705 763 1.521010 CATGTCGGCAGCAGGAGAG 60.521 63.158 0.00 0.00 0.00 3.20
764 828 5.074804 GGTGTATCCTAACCACCAAACTTT 58.925 41.667 3.28 0.00 46.33 2.66
786 850 2.609459 GGCTTTCGTGTATCACATCAGG 59.391 50.000 1.00 0.00 33.40 3.86
997 1064 1.536676 CCCCCTTGACGGCCATTAT 59.463 57.895 2.24 0.00 0.00 1.28
998 1065 3.003230 CCCCCTTGACGGCCATTA 58.997 61.111 2.24 0.00 0.00 1.90
1299 1369 4.899457 TCCCGAGGAAATTTCATAGCTCTA 59.101 41.667 19.49 3.52 0.00 2.43
1380 1450 1.397390 ATCCCTTAGGCGGTGGTACG 61.397 60.000 0.00 0.00 0.00 3.67
1530 1600 1.004918 GAACTGTGTCCCTCCACCG 60.005 63.158 0.00 0.00 34.35 4.94
1608 1678 1.021390 CCAATGCAGTCCTGACGGTC 61.021 60.000 0.00 0.00 36.20 4.79
1957 2027 6.101650 TGCACAGTATAGAAGGATACATGG 57.898 41.667 0.00 0.00 35.16 3.66
2311 2383 0.741915 GCCTAGAAGGACAGGACTCG 59.258 60.000 0.00 0.00 37.67 4.18
2524 2596 4.559862 ACACATCTAAGTAGGCAAAGCT 57.440 40.909 0.00 0.00 0.00 3.74
2609 2681 5.066634 TGGTGTTGCGAGAATAAGTGAAAAA 59.933 36.000 0.00 0.00 0.00 1.94
2624 2696 1.531149 CTTCTTGTACCTGGTGTTGCG 59.469 52.381 10.23 0.00 0.00 4.85
2785 2857 7.811236 CACATTTTGTTGTCTTTCTCATATGCT 59.189 33.333 0.00 0.00 0.00 3.79
2792 2864 6.795399 TCTTCCACATTTTGTTGTCTTTCTC 58.205 36.000 0.00 0.00 0.00 2.87
2996 3068 4.870636 TGGTAAATGCCAATCAATCCTCT 58.129 39.130 0.00 0.00 35.25 3.69
3051 3123 5.673337 TCATGACAACAACTTTACTGAGC 57.327 39.130 0.00 0.00 0.00 4.26
3083 3155 5.045651 ACCTGACATGGAATTGTGAGACATA 60.046 40.000 0.00 0.00 33.26 2.29
3085 3157 3.072915 ACCTGACATGGAATTGTGAGACA 59.927 43.478 0.00 0.00 33.26 3.41
3097 3169 0.603707 ACGCTTCACACCTGACATGG 60.604 55.000 0.00 0.00 0.00 3.66
3115 3187 7.506261 TCATAGGTCCTTGGATAAGTAGAGAAC 59.494 40.741 0.00 0.00 31.80 3.01
3151 3223 0.771127 AGGTGAAAAGGCCACTAGCA 59.229 50.000 5.01 0.00 46.50 3.49
3177 3249 4.508662 GACAGGAGCAGCTTACTTATTGT 58.491 43.478 0.00 0.00 0.00 2.71
3202 3274 1.632409 AGGTGACAGAACTGATGCCAT 59.368 47.619 8.87 0.00 0.00 4.40
3223 3295 9.338622 AGTGGCAATCTTACTTATTGTTATACC 57.661 33.333 0.00 0.00 36.82 2.73
3234 3306 3.423539 TCAGCAGTGGCAATCTTACTT 57.576 42.857 0.00 0.00 44.61 2.24
3447 3519 3.578282 TCACAGCATACAAGACCTTCTCA 59.422 43.478 0.00 0.00 0.00 3.27
3560 3632 5.667172 TGACTCCATATCTCAATTCCAGGAA 59.333 40.000 3.72 3.72 0.00 3.36
3564 3636 6.239800 CCTGATGACTCCATATCTCAATTCCA 60.240 42.308 0.00 0.00 32.09 3.53
3649 3721 6.227298 ACTGCTACAACAATATACTGCTCT 57.773 37.500 0.00 0.00 0.00 4.09
3650 3722 6.910536 AACTGCTACAACAATATACTGCTC 57.089 37.500 0.00 0.00 0.00 4.26
3802 3874 4.351874 AGTGATGGGATTACCGGTAATG 57.648 45.455 38.01 0.00 44.64 1.90
3809 3881 3.606687 ACAACGAAGTGATGGGATTACC 58.393 45.455 0.00 0.00 45.00 2.85
3820 3892 8.757789 TGTACATAACTAAGAAACAACGAAGTG 58.242 33.333 0.00 0.00 45.00 3.16
3857 3929 6.426937 CAGGTAACAACACAGTAAAGCTACAT 59.573 38.462 0.00 0.00 41.41 2.29
3858 3930 5.756347 CAGGTAACAACACAGTAAAGCTACA 59.244 40.000 0.00 0.00 41.41 2.74
3862 3934 5.744666 TTCAGGTAACAACACAGTAAAGC 57.255 39.130 0.00 0.00 41.41 3.51
3873 3945 7.581213 AACATTCAGTTCATTCAGGTAACAA 57.419 32.000 0.00 0.00 34.74 2.83
3885 3957 8.731275 TTCTTGAGTAGAAAACATTCAGTTCA 57.269 30.769 0.00 0.00 39.90 3.18
3888 3960 8.682936 ACATTCTTGAGTAGAAAACATTCAGT 57.317 30.769 0.00 0.00 45.62 3.41
3968 4040 7.431249 CATCCATTGTTCCATTAAGATCCAAG 58.569 38.462 0.00 0.00 0.00 3.61
3969 4041 6.324512 CCATCCATTGTTCCATTAAGATCCAA 59.675 38.462 0.00 0.00 0.00 3.53
3970 4042 5.834742 CCATCCATTGTTCCATTAAGATCCA 59.165 40.000 0.00 0.00 0.00 3.41
3974 4046 5.193527 TCTCCCATCCATTGTTCCATTAAGA 59.806 40.000 0.00 0.00 0.00 2.10
4011 4085 2.905415 AATGGGATTGAGCAGGAACA 57.095 45.000 0.00 0.00 0.00 3.18
4012 4086 4.037208 CACATAATGGGATTGAGCAGGAAC 59.963 45.833 0.00 0.00 0.00 3.62
4013 4087 4.209538 CACATAATGGGATTGAGCAGGAA 58.790 43.478 0.00 0.00 0.00 3.36
4022 4096 6.042322 ACATTTAGCATGCACATAATGGGATT 59.958 34.615 21.98 5.11 0.00 3.01
4025 4099 5.204409 ACATTTAGCATGCACATAATGGG 57.796 39.130 21.98 5.34 0.00 4.00
4029 4103 6.035368 ACCAAACATTTAGCATGCACATAA 57.965 33.333 21.98 7.14 0.00 1.90
4049 4123 2.092429 GTGGAATGGAGCAGGAATACCA 60.092 50.000 0.00 0.00 38.94 3.25
4053 4127 1.002069 TGGTGGAATGGAGCAGGAAT 58.998 50.000 0.00 0.00 0.00 3.01
4054 4128 1.002069 ATGGTGGAATGGAGCAGGAA 58.998 50.000 0.00 0.00 0.00 3.36
4071 4146 3.657634 AGACTACTCACAACTGCACATG 58.342 45.455 0.00 0.00 0.00 3.21
4148 4224 9.559958 CGGCATATCAATCTGTATTTTATTTCC 57.440 33.333 0.00 0.00 0.00 3.13
4159 4235 1.417517 TCAGCCGGCATATCAATCTGT 59.582 47.619 31.54 0.00 0.00 3.41
4175 4251 2.216898 CCTAAAGCATAGGCACTCAGC 58.783 52.381 0.67 0.00 44.61 4.26
4206 4282 6.323203 ACATTATCTGCAATGTAATCCAGC 57.677 37.500 0.00 0.00 45.13 4.85
4210 4286 7.861630 ACGGTAACATTATCTGCAATGTAATC 58.138 34.615 2.28 0.00 46.00 1.75
4215 4291 4.816385 AGGACGGTAACATTATCTGCAATG 59.184 41.667 0.00 0.00 40.93 2.82
4223 4299 6.650120 AGAATCACAAGGACGGTAACATTAT 58.350 36.000 0.00 0.00 0.00 1.28
4228 4304 4.062991 ACAAGAATCACAAGGACGGTAAC 58.937 43.478 0.00 0.00 0.00 2.50
4233 4309 1.726791 CCGACAAGAATCACAAGGACG 59.273 52.381 0.00 0.00 0.00 4.79
4237 4313 2.744202 CCCTTCCGACAAGAATCACAAG 59.256 50.000 0.00 0.00 0.00 3.16
4240 4316 1.087501 GCCCTTCCGACAAGAATCAC 58.912 55.000 0.00 0.00 0.00 3.06
4241 4317 0.035439 GGCCCTTCCGACAAGAATCA 60.035 55.000 0.00 0.00 0.00 2.57
4242 4318 0.253327 AGGCCCTTCCGACAAGAATC 59.747 55.000 0.00 0.00 40.77 2.52
4243 4319 1.580059 TAGGCCCTTCCGACAAGAAT 58.420 50.000 0.00 0.00 40.77 2.40
4244 4320 1.580059 ATAGGCCCTTCCGACAAGAA 58.420 50.000 0.00 0.00 40.77 2.52
4246 4322 2.420058 AAATAGGCCCTTCCGACAAG 57.580 50.000 0.00 0.00 40.77 3.16
4247 4323 2.040545 TCAAAATAGGCCCTTCCGACAA 59.959 45.455 0.00 0.00 40.77 3.18
4248 4324 1.631388 TCAAAATAGGCCCTTCCGACA 59.369 47.619 0.00 0.00 40.77 4.35
4249 4325 2.413310 TCAAAATAGGCCCTTCCGAC 57.587 50.000 0.00 0.00 40.77 4.79
4250 4326 2.574369 TCTTCAAAATAGGCCCTTCCGA 59.426 45.455 0.00 0.00 40.77 4.55
4251 4327 2.999331 TCTTCAAAATAGGCCCTTCCG 58.001 47.619 0.00 0.00 40.77 4.30
4252 4328 6.517362 GCATAATCTTCAAAATAGGCCCTTCC 60.517 42.308 0.00 0.00 0.00 3.46
4253 4329 6.266330 AGCATAATCTTCAAAATAGGCCCTTC 59.734 38.462 0.00 0.00 0.00 3.46
4254 4330 6.041296 CAGCATAATCTTCAAAATAGGCCCTT 59.959 38.462 0.00 0.00 0.00 3.95
4255 4331 5.537674 CAGCATAATCTTCAAAATAGGCCCT 59.462 40.000 0.00 0.00 0.00 5.19
4256 4332 5.279156 CCAGCATAATCTTCAAAATAGGCCC 60.279 44.000 0.00 0.00 0.00 5.80
4257 4333 5.776744 CCAGCATAATCTTCAAAATAGGCC 58.223 41.667 0.00 0.00 0.00 5.19
4258 4334 5.221303 TGCCAGCATAATCTTCAAAATAGGC 60.221 40.000 0.00 0.00 36.50 3.93
4259 4335 6.395426 TGCCAGCATAATCTTCAAAATAGG 57.605 37.500 0.00 0.00 0.00 2.57
4260 4336 6.420008 GCTTGCCAGCATAATCTTCAAAATAG 59.580 38.462 4.63 0.00 46.49 1.73
4261 4337 6.275335 GCTTGCCAGCATAATCTTCAAAATA 58.725 36.000 4.63 0.00 46.49 1.40
4262 4338 5.114081 GCTTGCCAGCATAATCTTCAAAAT 58.886 37.500 4.63 0.00 46.49 1.82
4309 4385 1.067516 CCTTTGGTCTTGCCTGTTGTG 59.932 52.381 0.00 0.00 38.35 3.33
4334 4410 7.710896 AGTAGGAACATACCGTTAACTCATAC 58.289 38.462 3.71 5.00 38.19 2.39
4338 4414 6.038985 GGAAGTAGGAACATACCGTTAACTC 58.961 44.000 3.71 0.00 38.19 3.01
4345 4421 3.028850 TGGAGGAAGTAGGAACATACCG 58.971 50.000 0.00 0.00 34.73 4.02
4418 4494 5.183713 AGAATTTATGCACTGCAGTAAAGCA 59.816 36.000 26.63 26.63 43.65 3.91
4446 4522 2.740256 GCCTGTGAGGAAGCTTAGCTAC 60.740 54.545 7.32 3.77 37.67 3.58
4451 4527 1.064003 TTGGCCTGTGAGGAAGCTTA 58.936 50.000 3.32 0.00 37.67 3.09
4468 4544 0.515127 TGCACGTACAGCCGAAATTG 59.485 50.000 5.00 0.00 0.00 2.32
4471 4547 1.666553 CCTGCACGTACAGCCGAAA 60.667 57.895 10.46 0.00 36.29 3.46
4473 4549 2.486636 CTTCCTGCACGTACAGCCGA 62.487 60.000 10.46 0.49 36.29 5.54
4474 4550 2.048597 TTCCTGCACGTACAGCCG 60.049 61.111 10.46 0.00 36.29 5.52
4476 4552 0.243907 TCTCTTCCTGCACGTACAGC 59.756 55.000 10.46 0.00 36.29 4.40


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

AutoCloner maintained by Alex Coulton.