Multiple sequence alignment - TraesCS2D01G198100

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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 TraesCS2D01G198100 chr2D 100.000 9157 0 0 1 9157 145884591 145893747 0.000000e+00 16910.0
1 TraesCS2D01G198100 chr2D 98.113 53 1 0 7312 7364 145891872 145891924 9.790000e-15 93.5
2 TraesCS2D01G198100 chr2D 98.113 53 1 0 7282 7334 145891902 145891954 9.790000e-15 93.5
3 TraesCS2D01G198100 chr2B 95.701 8653 230 55 186 8768 206109083 206117663 0.000000e+00 13788.0
4 TraesCS2D01G198100 chr2B 93.506 77 5 0 2039 2115 206111007 206111083 2.090000e-21 115.0
5 TraesCS2D01G198100 chr2B 88.889 45 4 1 3800 3844 97371019 97370976 5.000000e-03 54.7
6 TraesCS2D01G198100 chr2A 95.428 6408 196 41 234 6568 156375991 156369608 0.000000e+00 10120.0
7 TraesCS2D01G198100 chr2A 92.173 1878 72 38 7312 9157 156368611 156366777 0.000000e+00 2584.0
8 TraesCS2D01G198100 chr2A 95.719 654 22 4 6561 7212 156369412 156368763 0.000000e+00 1048.0
9 TraesCS2D01G198100 chr2A 95.968 124 1 2 7213 7334 156368680 156368559 2.020000e-46 198.0
10 TraesCS2D01G198100 chr2A 97.872 47 0 1 7007 7052 632952952 632952998 7.620000e-11 80.5
11 TraesCS2D01G198100 chr6D 90.654 107 7 3 4942 5046 84938438 84938543 1.240000e-28 139.0
12 TraesCS2D01G198100 chr6D 92.708 96 4 3 4962 5055 84938543 84938449 1.600000e-27 135.0
13 TraesCS2D01G198100 chr6D 89.362 94 10 0 4953 5046 301102143 301102236 1.620000e-22 119.0
14 TraesCS2D01G198100 chr6D 88.000 75 5 2 5307 5377 26243081 26243007 1.640000e-12 86.1
15 TraesCS2D01G198100 chr7B 92.000 100 5 2 5811 5907 539218276 539218375 4.460000e-28 137.0
16 TraesCS2D01G198100 chr7B 90.625 96 9 0 4962 5057 156955452 156955547 2.680000e-25 128.0
17 TraesCS2D01G198100 chr3A 94.118 85 5 0 4962 5046 213131980 213131896 7.460000e-26 130.0
18 TraesCS2D01G198100 chr3A 92.000 50 4 0 5338 5387 600084555 600084506 4.590000e-08 71.3
19 TraesCS2D01G198100 chr3A 93.182 44 1 2 5338 5379 495012108 495012065 7.680000e-06 63.9
20 TraesCS2D01G198100 chr3D 91.398 93 6 1 5817 5907 305448661 305448569 9.650000e-25 126.0
21 TraesCS2D01G198100 chr3D 96.296 54 1 1 6996 7048 611532957 611532904 4.550000e-13 87.9
22 TraesCS2D01G198100 chr3D 96.154 52 1 1 6997 7047 19538006 19538057 5.890000e-12 84.2
23 TraesCS2D01G198100 chr5D 87.963 108 10 3 4945 5049 362406774 362406667 3.470000e-24 124.0
24 TraesCS2D01G198100 chr5D 85.849 106 13 1 5817 5920 556009426 556009321 2.700000e-20 111.0
25 TraesCS2D01G198100 chr5D 94.545 55 2 1 6994 7047 416973234 416973288 5.890000e-12 84.2
26 TraesCS2D01G198100 chr4A 89.474 95 10 0 4962 5056 47630472 47630566 4.490000e-23 121.0
27 TraesCS2D01G198100 chr4A 85.000 60 4 4 6997 7052 387126062 387126120 1.000000e-03 56.5
28 TraesCS2D01G198100 chr5B 89.247 93 8 1 5817 5907 544610570 544610478 2.090000e-21 115.0
29 TraesCS2D01G198100 chr5B 89.130 92 9 1 5817 5907 34252088 34252179 7.510000e-21 113.0
30 TraesCS2D01G198100 chr5B 94.545 55 2 1 6994 7047 222375777 222375831 5.890000e-12 84.2
31 TraesCS2D01G198100 chr5B 92.593 54 2 2 6997 7048 611540077 611540130 9.860000e-10 76.8
32 TraesCS2D01G198100 chr6B 88.172 93 9 1 5817 5907 560191852 560191944 9.720000e-20 110.0
33 TraesCS2D01G198100 chr6B 94.340 53 2 1 6997 7048 7144747 7144799 7.620000e-11 80.5
34 TraesCS2D01G198100 chr6B 88.679 53 1 4 6995 7047 118215849 118215896 9.930000e-05 60.2
35 TraesCS2D01G198100 chr6A 84.906 106 12 3 5817 5920 500508984 500508881 4.520000e-18 104.0
36 TraesCS2D01G198100 chr6A 94.737 38 0 2 5304 5339 529567117 529567080 3.570000e-04 58.4
37 TraesCS2D01G198100 chr7D 86.022 93 9 3 5810 5899 261818690 261818599 7.570000e-16 97.1
38 TraesCS2D01G198100 chr7D 95.122 41 2 0 7008 7048 47326998 47327038 2.130000e-06 65.8
39 TraesCS2D01G198100 chr1D 90.541 74 4 1 5309 5379 331917701 331917628 2.720000e-15 95.3
40 TraesCS2D01G198100 chr1D 84.884 86 4 5 5302 5379 298637798 298637714 2.740000e-10 78.7
41 TraesCS2D01G198100 chr1D 92.500 40 2 1 7014 7052 345812414 345812453 1.000000e-03 56.5
42 TraesCS2D01G198100 chr1B 90.541 74 4 1 5309 5379 446029277 446029204 2.720000e-15 95.3
43 TraesCS2D01G198100 chr1B 92.593 54 1 3 7008 7059 115751942 115751994 3.550000e-09 75.0
44 TraesCS2D01G198100 chr5A 98.077 52 0 1 6997 7047 482768156 482768105 1.270000e-13 89.8
45 TraesCS2D01G198100 chr7A 92.593 54 4 0 5326 5379 473011837 473011784 2.740000e-10 78.7
46 TraesCS2D01G198100 chr1A 94.118 51 1 2 5338 5387 575209905 575209954 9.860000e-10 76.8
47 TraesCS2D01G198100 chr1A 82.955 88 3 8 5302 5379 372532630 372532545 1.650000e-07 69.4
48 TraesCS2D01G198100 chr4B 86.667 60 3 4 6997 7052 315738093 315738151 2.760000e-05 62.1
49 TraesCS2D01G198100 chr4D 89.796 49 2 3 7007 7052 484399551 484399503 9.930000e-05 60.2
50 TraesCS2D01G198100 chr4D 100.000 30 0 0 7023 7052 220325824 220325795 1.000000e-03 56.5


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 TraesCS2D01G198100 chr2D 145884591 145893747 9156 False 5699.0 16910 98.742 1 9157 3 chr2D.!!$F1 9156
1 TraesCS2D01G198100 chr2B 206109083 206117663 8580 False 13788.0 13788 95.701 186 8768 1 chr2B.!!$F1 8582
2 TraesCS2D01G198100 chr2A 156366777 156375991 9214 True 3487.5 10120 94.822 234 9157 4 chr2A.!!$R1 8923

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
163 164 0.096454 GCCGGACTAAATTGTGTCGC 59.904 55.000 5.05 1.91 34.31 5.19 F
1509 1542 0.241213 GAACTTCCTTTTCTGCGGGC 59.759 55.000 0.00 0.00 0.00 6.13 F
1708 1742 0.687920 GGGCTCTGTAGGGCCTTATC 59.312 60.000 21.36 3.53 46.80 1.75 F
1921 1957 1.002134 TTGCTTGCTGGGCCTAGTC 60.002 57.895 18.47 10.54 0.00 2.59 F
1922 1958 1.778017 TTGCTTGCTGGGCCTAGTCA 61.778 55.000 18.47 13.08 0.00 3.41 F
1937 1985 3.693085 CCTAGTCACTTGCAGCATCATTT 59.307 43.478 0.00 0.00 0.00 2.32 F
2963 3013 4.580855 TGCATATTTTGTTTTGCATCGC 57.419 36.364 0.00 0.00 39.98 4.58 F
4919 4980 0.823356 TTGAAGGCCGCTCAAAGCTT 60.823 50.000 17.90 0.00 39.60 3.74 F
6890 7190 1.609783 CGCTCCCTCCTTCCCAATT 59.390 57.895 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1742 1.153429 CGAGGGGGCGTTTCCTTAG 60.153 63.158 0.00 0.00 32.74 2.18 R
2605 2653 2.711542 ACAATTCAAGAACCTAGCCGG 58.288 47.619 0.00 0.00 39.35 6.13 R
2638 2686 9.590451 AAACATTTACAAATGATAGGCAAGATG 57.410 29.630 18.95 0.00 46.72 2.90 R
3840 3896 5.833667 TCGACTCAGGGAAACTCATATGTAT 59.166 40.000 1.90 0.00 0.00 2.29 R
4877 4938 5.982356 AGACACATGTGCTGATTGTAGTAT 58.018 37.500 25.68 0.78 0.00 2.12 R
4919 4980 0.669619 TGACAGACTAAACGCGGTCA 59.330 50.000 12.47 8.85 35.18 4.02 R
5561 5655 2.943199 GCTTGTCTTTCCTCCCTCATGG 60.943 54.545 0.00 0.00 0.00 3.66 R
7355 7741 0.744874 GCATGCTCATGTGGCTCATT 59.255 50.000 11.37 0.00 40.80 2.57 R
8825 9233 0.109735 GCTTTTGAAGTAGGTGCCGC 60.110 55.000 0.00 0.00 0.00 6.53 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 3.304251 GTGAGCCAGAGGGAGGAC 58.696 66.667 0.00 0.00 35.59 3.85
18 19 1.610673 GTGAGCCAGAGGGAGGACA 60.611 63.158 0.00 0.00 35.59 4.02
19 20 1.158466 TGAGCCAGAGGGAGGACAA 59.842 57.895 0.00 0.00 35.59 3.18
20 21 0.473694 TGAGCCAGAGGGAGGACAAA 60.474 55.000 0.00 0.00 35.59 2.83
21 22 0.251634 GAGCCAGAGGGAGGACAAAG 59.748 60.000 0.00 0.00 35.59 2.77
22 23 1.204113 AGCCAGAGGGAGGACAAAGG 61.204 60.000 0.00 0.00 35.59 3.11
23 24 1.201429 GCCAGAGGGAGGACAAAGGA 61.201 60.000 0.00 0.00 35.59 3.36
24 25 1.362224 CCAGAGGGAGGACAAAGGAA 58.638 55.000 0.00 0.00 35.59 3.36
25 26 1.280421 CCAGAGGGAGGACAAAGGAAG 59.720 57.143 0.00 0.00 35.59 3.46
26 27 0.988063 AGAGGGAGGACAAAGGAAGC 59.012 55.000 0.00 0.00 0.00 3.86
27 28 0.693049 GAGGGAGGACAAAGGAAGCA 59.307 55.000 0.00 0.00 0.00 3.91
28 29 0.402121 AGGGAGGACAAAGGAAGCAC 59.598 55.000 0.00 0.00 0.00 4.40
29 30 0.609406 GGGAGGACAAAGGAAGCACC 60.609 60.000 0.00 0.00 39.35 5.01
30 31 0.609406 GGAGGACAAAGGAAGCACCC 60.609 60.000 0.00 0.00 40.05 4.61
31 32 0.955919 GAGGACAAAGGAAGCACCCG 60.956 60.000 0.00 0.00 40.05 5.28
32 33 1.072505 GGACAAAGGAAGCACCCGA 59.927 57.895 0.00 0.00 40.05 5.14
33 34 0.955919 GGACAAAGGAAGCACCCGAG 60.956 60.000 0.00 0.00 40.05 4.63
34 35 0.250338 GACAAAGGAAGCACCCGAGT 60.250 55.000 0.00 0.00 40.05 4.18
35 36 0.250338 ACAAAGGAAGCACCCGAGTC 60.250 55.000 0.00 0.00 40.05 3.36
36 37 0.955919 CAAAGGAAGCACCCGAGTCC 60.956 60.000 0.00 0.00 40.05 3.85
37 38 1.415672 AAAGGAAGCACCCGAGTCCA 61.416 55.000 0.00 0.00 40.05 4.02
38 39 1.201429 AAGGAAGCACCCGAGTCCAT 61.201 55.000 0.00 0.00 40.05 3.41
39 40 1.450312 GGAAGCACCCGAGTCCATG 60.450 63.158 0.00 0.00 0.00 3.66
40 41 2.045926 AAGCACCCGAGTCCATGC 60.046 61.111 0.68 0.68 38.39 4.06
41 42 3.628646 AAGCACCCGAGTCCATGCC 62.629 63.158 4.70 0.00 38.92 4.40
42 43 4.101448 GCACCCGAGTCCATGCCT 62.101 66.667 0.00 0.00 31.71 4.75
43 44 2.671070 CACCCGAGTCCATGCCTT 59.329 61.111 0.00 0.00 0.00 4.35
44 45 1.746615 CACCCGAGTCCATGCCTTG 60.747 63.158 0.00 0.00 0.00 3.61
45 46 2.224159 ACCCGAGTCCATGCCTTGT 61.224 57.895 0.00 0.00 0.00 3.16
46 47 1.450312 CCCGAGTCCATGCCTTGTC 60.450 63.158 0.00 0.00 0.00 3.18
47 48 1.450312 CCGAGTCCATGCCTTGTCC 60.450 63.158 0.00 0.00 0.00 4.02
48 49 1.811266 CGAGTCCATGCCTTGTCCG 60.811 63.158 0.00 0.00 0.00 4.79
49 50 1.296715 GAGTCCATGCCTTGTCCGT 59.703 57.895 0.00 0.00 0.00 4.69
50 51 0.321653 GAGTCCATGCCTTGTCCGTT 60.322 55.000 0.00 0.00 0.00 4.44
51 52 0.110486 AGTCCATGCCTTGTCCGTTT 59.890 50.000 0.00 0.00 0.00 3.60
52 53 0.521735 GTCCATGCCTTGTCCGTTTC 59.478 55.000 0.00 0.00 0.00 2.78
53 54 0.109532 TCCATGCCTTGTCCGTTTCA 59.890 50.000 0.00 0.00 0.00 2.69
54 55 0.523072 CCATGCCTTGTCCGTTTCAG 59.477 55.000 0.00 0.00 0.00 3.02
55 56 0.109597 CATGCCTTGTCCGTTTCAGC 60.110 55.000 0.00 0.00 0.00 4.26
56 57 1.577328 ATGCCTTGTCCGTTTCAGCG 61.577 55.000 0.00 0.00 0.00 5.18
57 58 2.556287 CCTTGTCCGTTTCAGCGC 59.444 61.111 0.00 0.00 0.00 5.92
58 59 2.250939 CCTTGTCCGTTTCAGCGCA 61.251 57.895 11.47 0.00 0.00 6.09
59 60 1.646540 CTTGTCCGTTTCAGCGCAA 59.353 52.632 11.47 0.00 0.00 4.85
60 61 0.657368 CTTGTCCGTTTCAGCGCAAC 60.657 55.000 11.47 4.33 0.00 4.17
61 62 1.369839 TTGTCCGTTTCAGCGCAACA 61.370 50.000 11.47 0.00 0.00 3.33
62 63 1.368850 GTCCGTTTCAGCGCAACAC 60.369 57.895 11.47 0.00 0.00 3.32
64 65 2.425124 CGTTTCAGCGCAACACGG 60.425 61.111 11.47 0.00 43.93 4.94
75 76 4.540238 GCGCAACACGGTTTAAATTTAG 57.460 40.909 0.30 0.00 43.93 1.85
76 77 4.220572 GCGCAACACGGTTTAAATTTAGA 58.779 39.130 0.30 0.00 43.93 2.10
77 78 4.087507 GCGCAACACGGTTTAAATTTAGAC 59.912 41.667 0.30 9.79 43.93 2.59
78 79 4.613866 CGCAACACGGTTTAAATTTAGACC 59.386 41.667 22.30 22.30 38.44 3.85
88 89 7.823665 GGTTTAAATTTAGACCGGAAATGAGT 58.176 34.615 19.02 0.00 29.65 3.41
89 90 7.753580 GGTTTAAATTTAGACCGGAAATGAGTG 59.246 37.037 19.02 0.00 29.65 3.51
90 91 8.508875 GTTTAAATTTAGACCGGAAATGAGTGA 58.491 33.333 9.46 0.00 0.00 3.41
91 92 8.624367 TTAAATTTAGACCGGAAATGAGTGAA 57.376 30.769 9.46 0.00 0.00 3.18
92 93 6.496338 AATTTAGACCGGAAATGAGTGAAC 57.504 37.500 9.46 0.00 0.00 3.18
93 94 2.080286 AGACCGGAAATGAGTGAACG 57.920 50.000 9.46 0.00 0.00 3.95
94 95 1.076332 GACCGGAAATGAGTGAACGG 58.924 55.000 9.46 0.00 46.16 4.44
95 96 0.953960 ACCGGAAATGAGTGAACGGC 60.954 55.000 9.46 0.00 44.73 5.68
96 97 1.419922 CGGAAATGAGTGAACGGCG 59.580 57.895 4.80 4.80 0.00 6.46
97 98 1.794222 GGAAATGAGTGAACGGCGG 59.206 57.895 13.24 0.00 0.00 6.13
98 99 1.644786 GGAAATGAGTGAACGGCGGG 61.645 60.000 13.24 0.00 0.00 6.13
99 100 0.672401 GAAATGAGTGAACGGCGGGA 60.672 55.000 13.24 0.00 0.00 5.14
100 101 0.250553 AAATGAGTGAACGGCGGGAA 60.251 50.000 13.24 0.00 0.00 3.97
101 102 0.250553 AATGAGTGAACGGCGGGAAA 60.251 50.000 13.24 0.00 0.00 3.13
102 103 0.250553 ATGAGTGAACGGCGGGAAAA 60.251 50.000 13.24 0.00 0.00 2.29
103 104 0.464013 TGAGTGAACGGCGGGAAAAA 60.464 50.000 13.24 0.00 0.00 1.94
123 124 4.737353 AAAAAGACATCCGTCCGTTTAC 57.263 40.909 0.00 0.00 43.73 2.01
124 125 3.389925 AAAGACATCCGTCCGTTTACA 57.610 42.857 0.00 0.00 43.73 2.41
125 126 2.649331 AGACATCCGTCCGTTTACAG 57.351 50.000 0.00 0.00 43.73 2.74
126 127 2.165167 AGACATCCGTCCGTTTACAGA 58.835 47.619 0.00 0.00 43.73 3.41
127 128 2.163815 AGACATCCGTCCGTTTACAGAG 59.836 50.000 0.00 0.00 43.73 3.35
128 129 2.163010 GACATCCGTCCGTTTACAGAGA 59.837 50.000 0.00 0.00 36.02 3.10
129 130 2.094854 ACATCCGTCCGTTTACAGAGAC 60.095 50.000 0.00 0.00 0.00 3.36
131 132 2.346884 CGTCCGTTTACAGAGACGC 58.653 57.895 0.00 0.00 44.61 5.19
132 133 1.393597 CGTCCGTTTACAGAGACGCG 61.394 60.000 3.53 3.53 44.61 6.01
133 134 0.386478 GTCCGTTTACAGAGACGCGT 60.386 55.000 13.85 13.85 37.91 6.01
134 135 0.386352 TCCGTTTACAGAGACGCGTG 60.386 55.000 20.70 4.21 37.91 5.34
135 136 0.662374 CCGTTTACAGAGACGCGTGT 60.662 55.000 20.70 14.93 37.91 4.49
136 137 1.126079 CGTTTACAGAGACGCGTGTT 58.874 50.000 20.70 3.95 32.11 3.32
137 138 2.309693 CGTTTACAGAGACGCGTGTTA 58.690 47.619 20.70 0.00 32.11 2.41
138 139 2.720578 CGTTTACAGAGACGCGTGTTAA 59.279 45.455 20.70 5.58 32.11 2.01
139 140 3.180189 CGTTTACAGAGACGCGTGTTAAA 59.820 43.478 20.70 12.18 32.11 1.52
140 141 4.440068 GTTTACAGAGACGCGTGTTAAAC 58.560 43.478 20.70 20.03 0.00 2.01
149 150 3.043121 GTGTTAAACGCGGCCGGA 61.043 61.111 29.38 0.00 39.22 5.14
150 151 3.043121 TGTTAAACGCGGCCGGAC 61.043 61.111 29.38 10.39 39.22 4.79
151 152 2.739671 GTTAAACGCGGCCGGACT 60.740 61.111 29.38 11.56 39.22 3.85
152 153 1.445926 GTTAAACGCGGCCGGACTA 60.446 57.895 29.38 10.62 39.22 2.59
153 154 1.013524 GTTAAACGCGGCCGGACTAA 61.014 55.000 29.38 15.34 39.22 2.24
154 155 0.320247 TTAAACGCGGCCGGACTAAA 60.320 50.000 29.38 8.86 39.22 1.85
155 156 0.108233 TAAACGCGGCCGGACTAAAT 60.108 50.000 29.38 0.00 39.22 1.40
156 157 0.956902 AAACGCGGCCGGACTAAATT 60.957 50.000 29.38 3.28 39.22 1.82
157 158 1.641123 AACGCGGCCGGACTAAATTG 61.641 55.000 29.38 0.00 39.22 2.32
158 159 2.104253 CGCGGCCGGACTAAATTGT 61.104 57.895 29.38 0.00 0.00 2.71
159 160 1.427819 GCGGCCGGACTAAATTGTG 59.572 57.895 29.38 0.00 0.00 3.33
160 161 1.303091 GCGGCCGGACTAAATTGTGT 61.303 55.000 29.38 0.00 0.00 3.72
161 162 0.725117 CGGCCGGACTAAATTGTGTC 59.275 55.000 20.10 3.32 0.00 3.67
162 163 0.725117 GGCCGGACTAAATTGTGTCG 59.275 55.000 5.05 0.00 34.31 4.35
163 164 0.096454 GCCGGACTAAATTGTGTCGC 59.904 55.000 5.05 1.91 34.31 5.19
164 165 0.368907 CCGGACTAAATTGTGTCGCG 59.631 55.000 0.00 0.00 34.31 5.87
165 166 1.065358 CGGACTAAATTGTGTCGCGT 58.935 50.000 5.77 0.00 34.31 6.01
166 167 1.201769 CGGACTAAATTGTGTCGCGTG 60.202 52.381 5.77 0.00 34.31 5.34
167 168 1.796459 GGACTAAATTGTGTCGCGTGT 59.204 47.619 5.77 0.00 34.31 4.49
168 169 2.222445 GGACTAAATTGTGTCGCGTGTT 59.778 45.455 5.77 0.00 34.31 3.32
169 170 3.215244 GACTAAATTGTGTCGCGTGTTG 58.785 45.455 5.77 0.00 0.00 3.33
170 171 2.032377 ACTAAATTGTGTCGCGTGTTGG 60.032 45.455 5.77 0.00 0.00 3.77
171 172 1.018148 AAATTGTGTCGCGTGTTGGA 58.982 45.000 5.77 0.00 0.00 3.53
172 173 0.586319 AATTGTGTCGCGTGTTGGAG 59.414 50.000 5.77 0.00 0.00 3.86
173 174 0.531974 ATTGTGTCGCGTGTTGGAGT 60.532 50.000 5.77 0.00 0.00 3.85
174 175 0.741574 TTGTGTCGCGTGTTGGAGTT 60.742 50.000 5.77 0.00 0.00 3.01
175 176 1.275657 GTGTCGCGTGTTGGAGTTG 59.724 57.895 5.77 0.00 0.00 3.16
176 177 1.885388 TGTCGCGTGTTGGAGTTGG 60.885 57.895 5.77 0.00 0.00 3.77
177 178 1.593209 GTCGCGTGTTGGAGTTGGA 60.593 57.895 5.77 0.00 0.00 3.53
178 179 1.300620 TCGCGTGTTGGAGTTGGAG 60.301 57.895 5.77 0.00 0.00 3.86
179 180 1.594293 CGCGTGTTGGAGTTGGAGT 60.594 57.895 0.00 0.00 0.00 3.85
180 181 1.157870 CGCGTGTTGGAGTTGGAGTT 61.158 55.000 0.00 0.00 0.00 3.01
181 182 0.307760 GCGTGTTGGAGTTGGAGTTG 59.692 55.000 0.00 0.00 0.00 3.16
182 183 0.944386 CGTGTTGGAGTTGGAGTTGG 59.056 55.000 0.00 0.00 0.00 3.77
183 184 0.668535 GTGTTGGAGTTGGAGTTGGC 59.331 55.000 0.00 0.00 0.00 4.52
184 185 0.257328 TGTTGGAGTTGGAGTTGGCA 59.743 50.000 0.00 0.00 0.00 4.92
249 251 4.718961 AGCAGATATCCCAATACACAACC 58.281 43.478 0.00 0.00 0.00 3.77
287 289 1.663702 ACGTTACACTGTCGCCAGC 60.664 57.895 0.00 0.00 42.81 4.85
303 305 0.883833 CAGCCGTCCATGCTTTTCTT 59.116 50.000 0.00 0.00 36.81 2.52
304 306 1.135575 CAGCCGTCCATGCTTTTCTTC 60.136 52.381 0.00 0.00 36.81 2.87
305 307 1.168714 GCCGTCCATGCTTTTCTTCT 58.831 50.000 0.00 0.00 0.00 2.85
325 327 2.981859 ACCCTGCGTAGATTTGGTAG 57.018 50.000 0.53 0.00 0.00 3.18
326 328 2.185387 ACCCTGCGTAGATTTGGTAGT 58.815 47.619 0.53 0.00 0.00 2.73
327 329 3.368248 ACCCTGCGTAGATTTGGTAGTA 58.632 45.455 0.53 0.00 0.00 1.82
328 330 3.965347 ACCCTGCGTAGATTTGGTAGTAT 59.035 43.478 0.53 0.00 0.00 2.12
329 331 5.142639 ACCCTGCGTAGATTTGGTAGTATA 58.857 41.667 0.53 0.00 0.00 1.47
397 399 2.186125 GGTAGAAACTCCCCGCGG 59.814 66.667 21.04 21.04 0.00 6.46
622 630 1.109323 GCAGCCACACCCAGAAAAGT 61.109 55.000 0.00 0.00 0.00 2.66
1024 1053 1.594564 GATTCGCCGAACCCTAGCC 60.595 63.158 0.00 0.00 0.00 3.93
1212 1241 2.522193 GCCCTCCTAGACTCCCCG 60.522 72.222 0.00 0.00 0.00 5.73
1224 1253 4.316823 TCCCCGGTGCTCCTCACT 62.317 66.667 0.00 0.00 44.98 3.41
1238 1267 4.323104 GCTCCTCACTAACTTCAAGGTGAT 60.323 45.833 0.00 0.00 37.92 3.06
1271 1300 3.211865 TGTACTGTACCTATCGCCTCTG 58.788 50.000 14.91 0.00 0.00 3.35
1306 1335 2.588034 GTTACCGCGGGATCTGCC 60.588 66.667 31.76 5.76 0.00 4.85
1509 1542 0.241213 GAACTTCCTTTTCTGCGGGC 59.759 55.000 0.00 0.00 0.00 6.13
1648 1682 3.818210 TGTTAGTTATGCACACACTTGGG 59.182 43.478 0.00 0.00 0.00 4.12
1708 1742 0.687920 GGGCTCTGTAGGGCCTTATC 59.312 60.000 21.36 3.53 46.80 1.75
1799 1835 5.982890 AGGAAATCACCAAGTAATTGTGG 57.017 39.130 1.80 3.74 41.00 4.17
1839 1875 5.183228 GTTGTTATTCTTCCTCGGGATTGA 58.817 41.667 0.00 0.00 0.00 2.57
1889 1925 1.357258 CTCTTGCTGGCAGCGTACAG 61.357 60.000 32.12 23.75 46.26 2.74
1921 1957 1.002134 TTGCTTGCTGGGCCTAGTC 60.002 57.895 18.47 10.54 0.00 2.59
1922 1958 1.778017 TTGCTTGCTGGGCCTAGTCA 61.778 55.000 18.47 13.08 0.00 3.41
1937 1985 3.693085 CCTAGTCACTTGCAGCATCATTT 59.307 43.478 0.00 0.00 0.00 2.32
2183 2231 7.811236 ATGTACTTCATATATGCAATTTGCAGC 59.189 33.333 26.44 0.29 45.31 5.25
2203 2251 5.411669 GCAGCCTATAGTGTTGTTGTACTTT 59.588 40.000 0.00 0.00 0.00 2.66
2231 2279 7.901874 TTTTGCGTTCACAAGTAAAGTATTC 57.098 32.000 0.00 0.00 0.00 1.75
2232 2280 6.606234 TTGCGTTCACAAGTAAAGTATTCA 57.394 33.333 0.00 0.00 0.00 2.57
2233 2281 6.223138 TGCGTTCACAAGTAAAGTATTCAG 57.777 37.500 0.00 0.00 0.00 3.02
2234 2282 5.986741 TGCGTTCACAAGTAAAGTATTCAGA 59.013 36.000 0.00 0.00 0.00 3.27
2235 2283 6.649141 TGCGTTCACAAGTAAAGTATTCAGAT 59.351 34.615 0.00 0.00 0.00 2.90
2274 2322 9.968743 GGTAGACATCGAAAATAGTTAACAAAG 57.031 33.333 8.61 0.00 0.00 2.77
2486 2534 8.542953 CACAACCTTTAATTTTCTTTTCTCTGC 58.457 33.333 0.00 0.00 0.00 4.26
2798 2846 5.779806 AGCATTACGTCTTTCACATGTAC 57.220 39.130 0.00 0.00 0.00 2.90
2963 3013 4.580855 TGCATATTTTGTTTTGCATCGC 57.419 36.364 0.00 0.00 39.98 4.58
3630 3680 7.933577 CCTGCATTCTTGTATCTAGTATGGAAA 59.066 37.037 0.00 0.00 0.00 3.13
4148 4204 4.954089 ACAGAGGAGGAGGATTTAGAGTT 58.046 43.478 0.00 0.00 0.00 3.01
4919 4980 0.823356 TTGAAGGCCGCTCAAAGCTT 60.823 50.000 17.90 0.00 39.60 3.74
5060 5122 2.160813 GGGCGTATTATTTATGTGGGCG 59.839 50.000 0.00 0.00 0.00 6.13
5181 5268 9.102757 ACATATAATGCAAAACAAAAACACACA 57.897 25.926 0.00 0.00 0.00 3.72
5184 5271 5.876612 ATGCAAAACAAAAACACACACAT 57.123 30.435 0.00 0.00 0.00 3.21
5205 5292 8.358895 ACACATTTCATTTATGTCATGACACAA 58.641 29.630 30.09 22.86 45.05 3.33
5362 5452 9.601971 GTTGAACTGCAAAAACGTCTTATATTA 57.398 29.630 0.00 0.00 38.44 0.98
5416 5506 4.843728 TCCCTAAGCATACAAAGTGAAGG 58.156 43.478 0.00 0.00 0.00 3.46
5561 5655 1.732809 GCTAGTCAAAGACGCCCTTTC 59.267 52.381 0.97 0.00 42.88 2.62
5883 5978 5.700402 AAAGGACATTGTATAGAGGCTGT 57.300 39.130 0.00 0.00 0.00 4.40
5907 6002 3.074412 CAATTAATTCGGATCGGAGGGG 58.926 50.000 0.00 0.00 0.00 4.79
5908 6003 1.797320 TTAATTCGGATCGGAGGGGT 58.203 50.000 2.99 0.00 0.00 4.95
5926 6021 6.072119 GGAGGGGTTACTTCATTTTGTAAGTG 60.072 42.308 0.00 0.00 36.62 3.16
5936 6031 9.308318 ACTTCATTTTGTAAGTGCGTTAAAATT 57.692 25.926 0.00 0.00 34.70 1.82
6450 6546 6.803154 AAAAGCTCACCTTGTAACATACTC 57.197 37.500 0.00 0.00 33.01 2.59
6490 6586 1.949525 CACAACTCCCACTTGTTCCAG 59.050 52.381 0.00 0.00 29.02 3.86
6508 6604 4.326826 TCCAGTAAAAGAATGTGGCTCAG 58.673 43.478 0.00 0.00 0.00 3.35
6890 7190 1.609783 CGCTCCCTCCTTCCCAATT 59.390 57.895 0.00 0.00 0.00 2.32
6926 7226 6.467339 GGCCTCCCAGTATCCATTTATAGTTT 60.467 42.308 0.00 0.00 0.00 2.66
7005 7305 6.949463 ACTGCTACTAATCTAATACTCCCTCC 59.051 42.308 0.00 0.00 0.00 4.30
7136 7438 5.169992 AGATGGGATCATTCGAATGCATA 57.830 39.130 29.32 15.65 36.36 3.14
7329 7715 9.845740 ATAACATACAGCACCAAGTAATAATGA 57.154 29.630 0.00 0.00 0.00 2.57
7332 7718 5.897377 ACAGCACCAAGTAATAATGAACC 57.103 39.130 0.00 0.00 0.00 3.62
7355 7741 7.570132 ACCATAACATACAGCACCAAGTAATA 58.430 34.615 0.00 0.00 0.00 0.98
7452 7839 5.518812 TGGTGATTGATGTTTCGAAAAGTG 58.481 37.500 13.10 0.00 0.00 3.16
7518 7905 6.483307 TGTGAATGGATTTGTATGTAGCTAGC 59.517 38.462 6.62 6.62 0.00 3.42
7519 7906 6.483307 GTGAATGGATTTGTATGTAGCTAGCA 59.517 38.462 18.83 0.00 0.00 3.49
7520 7907 6.707608 TGAATGGATTTGTATGTAGCTAGCAG 59.292 38.462 18.83 0.00 0.00 4.24
7521 7908 4.380531 TGGATTTGTATGTAGCTAGCAGC 58.619 43.478 18.83 9.54 42.84 5.25
7577 7973 8.874744 AGCCATTGCACTCTTATATATTTGAT 57.125 30.769 0.00 0.00 41.13 2.57
7730 8126 3.285484 GAATGCAACCCATGAGATGTCT 58.715 45.455 0.00 0.00 33.49 3.41
7733 8129 1.951895 GCAACCCATGAGATGTCTGCA 60.952 52.381 0.00 0.00 31.47 4.41
7763 8159 3.867493 TGAAGAATGTCGTGCATCAGATC 59.133 43.478 0.00 0.00 36.67 2.75
7844 8240 3.689161 TCACCAACCAATATTCTCAAGCG 59.311 43.478 0.00 0.00 0.00 4.68
7977 8373 2.154854 ATCCATGGCTTCGATGTACG 57.845 50.000 6.96 0.00 44.09 3.67
8177 8573 5.760131 TGAGAGGAATGATGAGAGTGTCTA 58.240 41.667 0.00 0.00 0.00 2.59
8353 8750 3.304391 GCATGTGTCTTTTTAAGTGCGGA 60.304 43.478 0.00 0.00 0.00 5.54
8522 8921 6.207221 TGGTAATTTTCTTTCCCGTTAAGACC 59.793 38.462 0.00 0.00 31.68 3.85
8577 8976 5.040635 GCTTAGTCTCTGTGCTTACATCTC 58.959 45.833 0.00 0.00 0.00 2.75
8613 9018 6.869913 TGATTGGGTTTACTTTGTACTACTCG 59.130 38.462 0.00 0.00 0.00 4.18
8614 9019 4.559153 TGGGTTTACTTTGTACTACTCGC 58.441 43.478 0.00 0.00 0.00 5.03
8632 9040 2.633967 TCGCTTACAAGTTCCAACCCTA 59.366 45.455 0.00 0.00 0.00 3.53
8662 9070 3.094386 TGGACAACCAGAAGTGCAC 57.906 52.632 9.40 9.40 41.77 4.57
8696 9104 1.203013 TGGTCGAAACCTCCTGAGAGA 60.203 52.381 0.00 0.00 46.60 3.10
8738 9146 0.037303 CTGCCTTCAGCCTTCAGGAA 59.963 55.000 0.00 0.00 42.71 3.36
8774 9182 4.887071 ACTGGAGTACTGATCAGAGATGAC 59.113 45.833 29.27 16.44 0.00 3.06
8818 9226 6.144175 GGCGAGTAACAGTAGAATAGATCAC 58.856 44.000 0.00 0.00 0.00 3.06
8837 9245 1.338389 ACGTAAATGCGGCACCTACTT 60.338 47.619 4.03 0.54 35.98 2.24
8856 9264 7.773690 ACCTACTTCAAAAGCTAGAACTTTCAA 59.226 33.333 0.00 0.00 38.92 2.69
8932 9341 4.127171 CGGATGTATGGAAGTGGTTTAGG 58.873 47.826 0.00 0.00 0.00 2.69
8942 9351 3.652057 AGTGGTTTAGGCTATGCATGT 57.348 42.857 10.16 0.00 0.00 3.21
8944 9353 4.344104 AGTGGTTTAGGCTATGCATGTTT 58.656 39.130 10.16 0.00 0.00 2.83
8945 9354 4.399303 AGTGGTTTAGGCTATGCATGTTTC 59.601 41.667 10.16 0.00 0.00 2.78
8952 9367 3.127548 AGGCTATGCATGTTTCTTCAACG 59.872 43.478 10.16 0.00 38.36 4.10
8959 9374 4.202101 TGCATGTTTCTTCAACGACCAAAT 60.202 37.500 0.00 0.00 38.36 2.32
9008 9423 4.631813 GCTCTTAGCGAGGAATTTTTCTCA 59.368 41.667 0.00 0.00 40.25 3.27
9128 9553 3.782992 AGAAATCTCCAAAGGCACCAAT 58.217 40.909 0.00 0.00 0.00 3.16
9135 9560 2.187100 CCAAAGGCACCAATACCCATT 58.813 47.619 0.00 0.00 0.00 3.16
9148 9573 8.517878 CACCAATACCCATTATCTCAAATCATC 58.482 37.037 0.00 0.00 0.00 2.92
9153 9578 7.592885 ACCCATTATCTCAAATCATCTTTGG 57.407 36.000 0.00 0.00 0.00 3.28
9155 9580 7.620888 ACCCATTATCTCAAATCATCTTTGGTT 59.379 33.333 0.00 0.00 0.00 3.67
9156 9581 9.135189 CCCATTATCTCAAATCATCTTTGGTTA 57.865 33.333 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.194781 TTGTCCTCCCTCTGGCTCAC 61.195 60.000 0.00 0.00 0.00 3.51
1 2 0.473694 TTTGTCCTCCCTCTGGCTCA 60.474 55.000 0.00 0.00 0.00 4.26
2 3 0.251634 CTTTGTCCTCCCTCTGGCTC 59.748 60.000 0.00 0.00 0.00 4.70
3 4 1.204113 CCTTTGTCCTCCCTCTGGCT 61.204 60.000 0.00 0.00 0.00 4.75
4 5 1.201429 TCCTTTGTCCTCCCTCTGGC 61.201 60.000 0.00 0.00 0.00 4.85
5 6 1.280421 CTTCCTTTGTCCTCCCTCTGG 59.720 57.143 0.00 0.00 0.00 3.86
6 7 1.339535 GCTTCCTTTGTCCTCCCTCTG 60.340 57.143 0.00 0.00 0.00 3.35
7 8 0.988063 GCTTCCTTTGTCCTCCCTCT 59.012 55.000 0.00 0.00 0.00 3.69
8 9 0.693049 TGCTTCCTTTGTCCTCCCTC 59.307 55.000 0.00 0.00 0.00 4.30
9 10 0.402121 GTGCTTCCTTTGTCCTCCCT 59.598 55.000 0.00 0.00 0.00 4.20
10 11 0.609406 GGTGCTTCCTTTGTCCTCCC 60.609 60.000 0.00 0.00 0.00 4.30
11 12 0.609406 GGGTGCTTCCTTTGTCCTCC 60.609 60.000 0.00 0.00 36.25 4.30
12 13 0.955919 CGGGTGCTTCCTTTGTCCTC 60.956 60.000 0.00 0.00 36.25 3.71
13 14 1.073199 CGGGTGCTTCCTTTGTCCT 59.927 57.895 0.00 0.00 36.25 3.85
14 15 0.955919 CTCGGGTGCTTCCTTTGTCC 60.956 60.000 0.00 0.00 36.25 4.02
15 16 0.250338 ACTCGGGTGCTTCCTTTGTC 60.250 55.000 0.00 0.00 36.25 3.18
16 17 0.250338 GACTCGGGTGCTTCCTTTGT 60.250 55.000 0.00 0.00 36.25 2.83
17 18 0.955919 GGACTCGGGTGCTTCCTTTG 60.956 60.000 0.00 0.00 36.25 2.77
18 19 1.375326 GGACTCGGGTGCTTCCTTT 59.625 57.895 0.00 0.00 36.25 3.11
19 20 1.201429 ATGGACTCGGGTGCTTCCTT 61.201 55.000 8.88 0.00 34.78 3.36
20 21 1.613630 ATGGACTCGGGTGCTTCCT 60.614 57.895 8.88 0.00 34.78 3.36
21 22 1.450312 CATGGACTCGGGTGCTTCC 60.450 63.158 8.88 0.00 34.78 3.46
22 23 2.109126 GCATGGACTCGGGTGCTTC 61.109 63.158 8.88 0.00 34.78 3.86
23 24 2.045926 GCATGGACTCGGGTGCTT 60.046 61.111 8.88 0.00 34.78 3.91
24 25 4.101448 GGCATGGACTCGGGTGCT 62.101 66.667 8.88 0.00 37.70 4.40
25 26 3.628646 AAGGCATGGACTCGGGTGC 62.629 63.158 0.00 0.00 36.88 5.01
26 27 1.746615 CAAGGCATGGACTCGGGTG 60.747 63.158 0.00 0.00 0.00 4.61
27 28 2.185310 GACAAGGCATGGACTCGGGT 62.185 60.000 0.00 0.00 0.00 5.28
28 29 1.450312 GACAAGGCATGGACTCGGG 60.450 63.158 0.00 0.00 0.00 5.14
29 30 1.450312 GGACAAGGCATGGACTCGG 60.450 63.158 0.00 0.00 0.00 4.63
30 31 1.811266 CGGACAAGGCATGGACTCG 60.811 63.158 0.00 0.00 0.00 4.18
31 32 0.321653 AACGGACAAGGCATGGACTC 60.322 55.000 0.00 0.00 0.00 3.36
32 33 0.110486 AAACGGACAAGGCATGGACT 59.890 50.000 0.00 0.00 0.00 3.85
33 34 0.521735 GAAACGGACAAGGCATGGAC 59.478 55.000 0.00 0.00 0.00 4.02
34 35 0.109532 TGAAACGGACAAGGCATGGA 59.890 50.000 0.00 0.00 0.00 3.41
35 36 0.523072 CTGAAACGGACAAGGCATGG 59.477 55.000 0.00 0.00 0.00 3.66
36 37 0.109597 GCTGAAACGGACAAGGCATG 60.110 55.000 0.00 0.00 0.00 4.06
37 38 1.577328 CGCTGAAACGGACAAGGCAT 61.577 55.000 0.00 0.00 0.00 4.40
38 39 2.250939 CGCTGAAACGGACAAGGCA 61.251 57.895 0.00 0.00 0.00 4.75
39 40 2.556287 CGCTGAAACGGACAAGGC 59.444 61.111 0.00 0.00 0.00 4.35
40 41 1.781025 TTGCGCTGAAACGGACAAGG 61.781 55.000 9.73 0.00 31.24 3.61
41 42 0.657368 GTTGCGCTGAAACGGACAAG 60.657 55.000 9.73 0.00 31.24 3.16
42 43 1.353804 GTTGCGCTGAAACGGACAA 59.646 52.632 9.73 0.00 31.24 3.18
43 44 1.815840 TGTTGCGCTGAAACGGACA 60.816 52.632 9.73 0.00 31.24 4.02
44 45 1.368850 GTGTTGCGCTGAAACGGAC 60.369 57.895 9.73 0.00 31.24 4.79
45 46 2.876879 CGTGTTGCGCTGAAACGGA 61.877 57.895 9.73 0.00 0.00 4.69
46 47 2.425124 CGTGTTGCGCTGAAACGG 60.425 61.111 9.73 0.00 0.00 4.44
47 48 2.425124 CCGTGTTGCGCTGAAACG 60.425 61.111 16.70 16.70 39.71 3.60
48 49 0.524604 AAACCGTGTTGCGCTGAAAC 60.525 50.000 9.73 5.43 39.71 2.78
49 50 1.015109 TAAACCGTGTTGCGCTGAAA 58.985 45.000 9.73 0.00 39.71 2.69
50 51 1.015109 TTAAACCGTGTTGCGCTGAA 58.985 45.000 9.73 0.00 39.71 3.02
51 52 1.015109 TTTAAACCGTGTTGCGCTGA 58.985 45.000 9.73 0.00 39.71 4.26
52 53 2.044888 ATTTAAACCGTGTTGCGCTG 57.955 45.000 9.73 0.00 39.71 5.18
53 54 2.785713 AATTTAAACCGTGTTGCGCT 57.214 40.000 9.73 0.00 39.71 5.92
54 55 4.087507 GTCTAAATTTAAACCGTGTTGCGC 59.912 41.667 0.00 0.00 39.71 6.09
55 56 4.613866 GGTCTAAATTTAAACCGTGTTGCG 59.386 41.667 4.96 0.00 40.95 4.85
63 64 7.753580 CACTCATTTCCGGTCTAAATTTAAACC 59.246 37.037 10.25 10.25 0.00 3.27
64 65 8.508875 TCACTCATTTCCGGTCTAAATTTAAAC 58.491 33.333 0.00 0.00 0.00 2.01
65 66 8.624367 TCACTCATTTCCGGTCTAAATTTAAA 57.376 30.769 0.00 0.00 0.00 1.52
66 67 8.508875 GTTCACTCATTTCCGGTCTAAATTTAA 58.491 33.333 0.00 0.00 0.00 1.52
67 68 7.148540 CGTTCACTCATTTCCGGTCTAAATTTA 60.149 37.037 0.00 0.00 0.00 1.40
68 69 6.348213 CGTTCACTCATTTCCGGTCTAAATTT 60.348 38.462 0.00 0.00 0.00 1.82
69 70 5.121768 CGTTCACTCATTTCCGGTCTAAATT 59.878 40.000 0.00 0.00 0.00 1.82
70 71 4.630069 CGTTCACTCATTTCCGGTCTAAAT 59.370 41.667 0.00 0.00 0.00 1.40
71 72 3.991773 CGTTCACTCATTTCCGGTCTAAA 59.008 43.478 0.00 0.00 0.00 1.85
72 73 3.581755 CGTTCACTCATTTCCGGTCTAA 58.418 45.455 0.00 0.00 0.00 2.10
73 74 2.094390 CCGTTCACTCATTTCCGGTCTA 60.094 50.000 0.00 0.00 0.00 2.59
74 75 1.337823 CCGTTCACTCATTTCCGGTCT 60.338 52.381 0.00 0.00 0.00 3.85
75 76 1.076332 CCGTTCACTCATTTCCGGTC 58.924 55.000 0.00 0.00 0.00 4.79
76 77 0.953960 GCCGTTCACTCATTTCCGGT 60.954 55.000 0.00 0.00 37.76 5.28
77 78 1.794222 GCCGTTCACTCATTTCCGG 59.206 57.895 0.00 0.00 38.45 5.14
78 79 1.419922 CGCCGTTCACTCATTTCCG 59.580 57.895 0.00 0.00 0.00 4.30
79 80 1.644786 CCCGCCGTTCACTCATTTCC 61.645 60.000 0.00 0.00 0.00 3.13
80 81 0.672401 TCCCGCCGTTCACTCATTTC 60.672 55.000 0.00 0.00 0.00 2.17
81 82 0.250553 TTCCCGCCGTTCACTCATTT 60.251 50.000 0.00 0.00 0.00 2.32
82 83 0.250553 TTTCCCGCCGTTCACTCATT 60.251 50.000 0.00 0.00 0.00 2.57
83 84 0.250553 TTTTCCCGCCGTTCACTCAT 60.251 50.000 0.00 0.00 0.00 2.90
84 85 0.464013 TTTTTCCCGCCGTTCACTCA 60.464 50.000 0.00 0.00 0.00 3.41
85 86 2.323213 TTTTTCCCGCCGTTCACTC 58.677 52.632 0.00 0.00 0.00 3.51
86 87 4.563404 TTTTTCCCGCCGTTCACT 57.437 50.000 0.00 0.00 0.00 3.41
102 103 4.128643 TGTAAACGGACGGATGTCTTTTT 58.871 39.130 0.00 0.00 44.83 1.94
103 104 3.731089 TGTAAACGGACGGATGTCTTTT 58.269 40.909 0.00 0.00 44.83 2.27
104 105 3.006110 TCTGTAAACGGACGGATGTCTTT 59.994 43.478 0.00 0.00 44.83 2.52
105 106 2.559668 TCTGTAAACGGACGGATGTCTT 59.440 45.455 0.00 0.00 44.83 3.01
106 107 2.163815 CTCTGTAAACGGACGGATGTCT 59.836 50.000 0.00 0.00 44.83 3.41
107 108 2.163010 TCTCTGTAAACGGACGGATGTC 59.837 50.000 0.00 0.00 44.72 3.06
108 109 2.094854 GTCTCTGTAAACGGACGGATGT 60.095 50.000 0.00 0.00 34.22 3.06
109 110 2.527100 GTCTCTGTAAACGGACGGATG 58.473 52.381 0.00 0.00 34.22 3.51
110 111 1.131883 CGTCTCTGTAAACGGACGGAT 59.868 52.381 0.00 0.00 44.92 4.18
111 112 0.518636 CGTCTCTGTAAACGGACGGA 59.481 55.000 0.00 0.00 44.92 4.69
112 113 3.011513 CGTCTCTGTAAACGGACGG 57.988 57.895 0.00 0.00 44.92 4.79
114 115 0.386478 ACGCGTCTCTGTAAACGGAC 60.386 55.000 5.58 0.00 39.24 4.79
115 116 0.386352 CACGCGTCTCTGTAAACGGA 60.386 55.000 9.86 0.00 39.24 4.69
116 117 0.662374 ACACGCGTCTCTGTAAACGG 60.662 55.000 9.86 0.00 39.24 4.44
117 118 1.126079 AACACGCGTCTCTGTAAACG 58.874 50.000 9.86 0.00 41.68 3.60
118 119 4.440068 GTTTAACACGCGTCTCTGTAAAC 58.560 43.478 9.86 14.93 0.00 2.01
119 120 3.180189 CGTTTAACACGCGTCTCTGTAAA 59.820 43.478 9.86 7.00 43.37 2.01
120 121 2.720578 CGTTTAACACGCGTCTCTGTAA 59.279 45.455 9.86 0.36 43.37 2.41
121 122 2.309693 CGTTTAACACGCGTCTCTGTA 58.690 47.619 9.86 0.00 43.37 2.74
122 123 1.126079 CGTTTAACACGCGTCTCTGT 58.874 50.000 9.86 0.07 43.37 3.41
123 124 3.901225 CGTTTAACACGCGTCTCTG 57.099 52.632 9.86 0.00 43.37 3.35
132 133 3.043121 TCCGGCCGCGTTTAACAC 61.043 61.111 22.85 0.00 0.00 3.32
133 134 2.152297 TAGTCCGGCCGCGTTTAACA 62.152 55.000 22.85 0.00 0.00 2.41
134 135 1.013524 TTAGTCCGGCCGCGTTTAAC 61.014 55.000 22.85 10.10 0.00 2.01
135 136 0.320247 TTTAGTCCGGCCGCGTTTAA 60.320 50.000 22.85 12.24 0.00 1.52
136 137 0.108233 ATTTAGTCCGGCCGCGTTTA 60.108 50.000 22.85 6.19 0.00 2.01
137 138 0.956902 AATTTAGTCCGGCCGCGTTT 60.957 50.000 22.85 7.30 0.00 3.60
138 139 1.376295 AATTTAGTCCGGCCGCGTT 60.376 52.632 22.85 9.33 0.00 4.84
139 140 2.104253 CAATTTAGTCCGGCCGCGT 61.104 57.895 22.85 8.66 0.00 6.01
140 141 2.104253 ACAATTTAGTCCGGCCGCG 61.104 57.895 22.85 13.93 0.00 6.46
141 142 1.303091 ACACAATTTAGTCCGGCCGC 61.303 55.000 22.85 7.25 0.00 6.53
142 143 0.725117 GACACAATTTAGTCCGGCCG 59.275 55.000 21.04 21.04 0.00 6.13
143 144 0.725117 CGACACAATTTAGTCCGGCC 59.275 55.000 0.00 0.00 0.00 6.13
144 145 0.096454 GCGACACAATTTAGTCCGGC 59.904 55.000 0.00 0.00 0.00 6.13
145 146 0.368907 CGCGACACAATTTAGTCCGG 59.631 55.000 0.00 0.00 0.00 5.14
146 147 1.065358 ACGCGACACAATTTAGTCCG 58.935 50.000 15.93 12.29 35.79 4.79
147 148 1.796459 ACACGCGACACAATTTAGTCC 59.204 47.619 15.93 0.00 0.00 3.85
148 149 3.215244 CAACACGCGACACAATTTAGTC 58.785 45.455 15.93 0.00 0.00 2.59
149 150 2.032377 CCAACACGCGACACAATTTAGT 60.032 45.455 15.93 0.00 0.00 2.24
150 151 2.222213 TCCAACACGCGACACAATTTAG 59.778 45.455 15.93 0.00 0.00 1.85
151 152 2.210961 TCCAACACGCGACACAATTTA 58.789 42.857 15.93 0.00 0.00 1.40
152 153 1.002900 CTCCAACACGCGACACAATTT 60.003 47.619 15.93 0.00 0.00 1.82
153 154 0.586319 CTCCAACACGCGACACAATT 59.414 50.000 15.93 0.00 0.00 2.32
154 155 0.531974 ACTCCAACACGCGACACAAT 60.532 50.000 15.93 0.00 0.00 2.71
155 156 0.741574 AACTCCAACACGCGACACAA 60.742 50.000 15.93 0.00 0.00 3.33
156 157 1.153529 AACTCCAACACGCGACACA 60.154 52.632 15.93 0.00 0.00 3.72
157 158 1.275657 CAACTCCAACACGCGACAC 59.724 57.895 15.93 0.00 0.00 3.67
158 159 1.885388 CCAACTCCAACACGCGACA 60.885 57.895 15.93 0.00 0.00 4.35
159 160 1.557443 CTCCAACTCCAACACGCGAC 61.557 60.000 15.93 0.00 0.00 5.19
160 161 1.300620 CTCCAACTCCAACACGCGA 60.301 57.895 15.93 0.00 0.00 5.87
161 162 1.157870 AACTCCAACTCCAACACGCG 61.158 55.000 3.53 3.53 0.00 6.01
162 163 0.307760 CAACTCCAACTCCAACACGC 59.692 55.000 0.00 0.00 0.00 5.34
163 164 0.944386 CCAACTCCAACTCCAACACG 59.056 55.000 0.00 0.00 0.00 4.49
164 165 0.668535 GCCAACTCCAACTCCAACAC 59.331 55.000 0.00 0.00 0.00 3.32
165 166 0.257328 TGCCAACTCCAACTCCAACA 59.743 50.000 0.00 0.00 0.00 3.33
166 167 1.620822 ATGCCAACTCCAACTCCAAC 58.379 50.000 0.00 0.00 0.00 3.77
167 168 2.380064 AATGCCAACTCCAACTCCAA 57.620 45.000 0.00 0.00 0.00 3.53
168 169 2.642311 TCTAATGCCAACTCCAACTCCA 59.358 45.455 0.00 0.00 0.00 3.86
169 170 3.350219 TCTAATGCCAACTCCAACTCC 57.650 47.619 0.00 0.00 0.00 3.85
170 171 4.513318 GCTATCTAATGCCAACTCCAACTC 59.487 45.833 0.00 0.00 0.00 3.01
171 172 4.455606 GCTATCTAATGCCAACTCCAACT 58.544 43.478 0.00 0.00 0.00 3.16
172 173 4.820284 GCTATCTAATGCCAACTCCAAC 57.180 45.455 0.00 0.00 0.00 3.77
181 182 4.598062 GAAAAACACGGCTATCTAATGCC 58.402 43.478 0.00 0.00 45.25 4.40
182 183 4.201783 ACGAAAAACACGGCTATCTAATGC 60.202 41.667 0.00 0.00 34.93 3.56
183 184 5.464965 ACGAAAAACACGGCTATCTAATG 57.535 39.130 0.00 0.00 34.93 1.90
184 185 6.072893 ACAAACGAAAAACACGGCTATCTAAT 60.073 34.615 0.00 0.00 34.93 1.73
201 202 0.741915 GCACCAAAGGGACAAACGAA 59.258 50.000 0.00 0.00 38.05 3.85
287 289 2.678336 GGTAGAAGAAAAGCATGGACGG 59.322 50.000 0.00 0.00 0.00 4.79
305 307 3.368248 ACTACCAAATCTACGCAGGGTA 58.632 45.455 0.00 0.00 0.00 3.69
325 327 6.034683 CGACTCTTTTTGGCTACACTGTATAC 59.965 42.308 0.00 0.00 0.00 1.47
326 328 6.097356 CGACTCTTTTTGGCTACACTGTATA 58.903 40.000 0.00 0.00 0.00 1.47
327 329 4.929808 CGACTCTTTTTGGCTACACTGTAT 59.070 41.667 0.00 0.00 0.00 2.29
328 330 4.202182 ACGACTCTTTTTGGCTACACTGTA 60.202 41.667 0.00 0.00 0.00 2.74
329 331 3.131396 CGACTCTTTTTGGCTACACTGT 58.869 45.455 0.00 0.00 0.00 3.55
397 399 2.549926 CGGGCCTGGATTTTAAAATGC 58.450 47.619 21.64 21.64 37.27 3.56
602 609 0.825010 CTTTTCTGGGTGTGGCTGCT 60.825 55.000 0.00 0.00 0.00 4.24
603 610 1.109323 ACTTTTCTGGGTGTGGCTGC 61.109 55.000 0.00 0.00 0.00 5.25
622 630 3.161450 GGAGGCACCGATGGGCTA 61.161 66.667 0.00 0.00 41.74 3.93
795 824 2.044451 TGGATGGCGCCCGAAATT 60.044 55.556 26.77 0.79 0.00 1.82
837 866 3.066203 CGTGTGGACTTAATTAATGGGGC 59.934 47.826 0.00 0.00 0.00 5.80
1203 1232 3.966930 GAGGAGCACCGGGGAGTCT 62.967 68.421 8.67 0.00 41.83 3.24
1224 1253 1.810151 GCGGCAATCACCTTGAAGTTA 59.190 47.619 0.00 0.00 36.97 2.24
1238 1267 2.606519 AGTACAGGGAGGCGGCAA 60.607 61.111 13.08 0.00 0.00 4.52
1271 1300 3.697619 AACAAGTAGTAACAGGAGGCC 57.302 47.619 0.00 0.00 0.00 5.19
1276 1305 2.919229 CGCGGTAACAAGTAGTAACAGG 59.081 50.000 0.00 0.00 0.00 4.00
1648 1682 3.531538 TGATGATTTGTTCTCGTAGCCC 58.468 45.455 0.00 0.00 0.00 5.19
1708 1742 1.153429 CGAGGGGGCGTTTCCTTAG 60.153 63.158 0.00 0.00 32.74 2.18
1811 1847 4.705023 CCCGAGGAAGAATAACAACCAAAT 59.295 41.667 0.00 0.00 0.00 2.32
1839 1875 9.010029 CAGGTAAACAAATACCACTTCTACAAT 57.990 33.333 6.30 0.00 46.48 2.71
1861 1897 1.835927 GCCAGCAAGAGGACTCAGGT 61.836 60.000 1.75 0.00 0.00 4.00
1921 1957 6.643770 AGAAAGTAAAAATGATGCTGCAAGTG 59.356 34.615 6.36 0.00 35.30 3.16
1922 1958 6.752168 AGAAAGTAAAAATGATGCTGCAAGT 58.248 32.000 6.36 0.00 35.30 3.16
1937 1985 7.094377 ACAACAGAGCAAGACAAAGAAAGTAAA 60.094 33.333 0.00 0.00 0.00 2.01
2134 2182 3.941483 CGCCCTCTGAAATAAATGTCACT 59.059 43.478 0.00 0.00 0.00 3.41
2224 2272 6.313905 CCACGCTTTAAGACATCTGAATACTT 59.686 38.462 0.00 0.00 0.00 2.24
2225 2273 5.812642 CCACGCTTTAAGACATCTGAATACT 59.187 40.000 0.00 0.00 0.00 2.12
2226 2274 5.581085 ACCACGCTTTAAGACATCTGAATAC 59.419 40.000 0.00 0.00 0.00 1.89
2227 2275 5.730550 ACCACGCTTTAAGACATCTGAATA 58.269 37.500 0.00 0.00 0.00 1.75
2228 2276 4.579869 ACCACGCTTTAAGACATCTGAAT 58.420 39.130 0.00 0.00 0.00 2.57
2229 2277 4.002906 ACCACGCTTTAAGACATCTGAA 57.997 40.909 0.00 0.00 0.00 3.02
2230 2278 3.678056 ACCACGCTTTAAGACATCTGA 57.322 42.857 0.00 0.00 0.00 3.27
2231 2279 4.563184 GTCTACCACGCTTTAAGACATCTG 59.437 45.833 0.00 0.00 37.20 2.90
2232 2280 4.219944 TGTCTACCACGCTTTAAGACATCT 59.780 41.667 0.00 0.00 41.09 2.90
2233 2281 4.491676 TGTCTACCACGCTTTAAGACATC 58.508 43.478 0.00 0.00 41.09 3.06
2234 2282 4.530710 TGTCTACCACGCTTTAAGACAT 57.469 40.909 0.00 0.00 41.09 3.06
2605 2653 2.711542 ACAATTCAAGAACCTAGCCGG 58.288 47.619 0.00 0.00 39.35 6.13
2638 2686 9.590451 AAACATTTACAAATGATAGGCAAGATG 57.410 29.630 18.95 0.00 46.72 2.90
3840 3896 5.833667 TCGACTCAGGGAAACTCATATGTAT 59.166 40.000 1.90 0.00 0.00 2.29
4877 4938 5.982356 AGACACATGTGCTGATTGTAGTAT 58.018 37.500 25.68 0.78 0.00 2.12
4919 4980 0.669619 TGACAGACTAAACGCGGTCA 59.330 50.000 12.47 8.85 35.18 4.02
5060 5122 4.838904 AAACTAATGGACCTCTGTACCC 57.161 45.455 0.00 0.00 0.00 3.69
5181 5268 9.761504 TTTTGTGTCATGACATAAATGAAATGT 57.238 25.926 36.08 0.00 46.55 2.71
5212 5299 5.401376 ACACGCGTATACATGATACATCAAC 59.599 40.000 13.44 0.00 40.58 3.18
5416 5506 3.119029 ACATACACCAGCCAATCAATTGC 60.119 43.478 0.00 0.00 36.48 3.56
5561 5655 2.943199 GCTTGTCTTTCCTCCCTCATGG 60.943 54.545 0.00 0.00 0.00 3.66
5883 5978 4.377021 CCTCCGATCCGAATTAATTGACA 58.623 43.478 5.17 0.00 0.00 3.58
5907 6002 8.770850 TTAACGCACTTACAAAATGAAGTAAC 57.229 30.769 0.00 0.00 34.13 2.50
5908 6003 9.784680 TTTTAACGCACTTACAAAATGAAGTAA 57.215 25.926 0.00 0.00 34.13 2.24
5926 6021 5.294248 CGTACAACATTGCAATTTTAACGC 58.706 37.500 21.97 9.94 0.00 4.84
5936 6031 3.004171 GGTGTATCCGTACAACATTGCA 58.996 45.455 0.00 0.00 45.81 4.08
6490 6586 4.479619 CTTGCTGAGCCACATTCTTTTAC 58.520 43.478 0.23 0.00 0.00 2.01
6508 6604 1.739067 ACGCTTGTAGGAATCCTTGC 58.261 50.000 7.30 6.66 34.61 4.01
6618 6918 3.240670 TGGGAGTGAACTCACCACT 57.759 52.632 10.15 0.00 45.64 4.00
7005 7305 8.951954 AAATATAGAGCGTTTAGATCACTACG 57.048 34.615 8.56 8.56 37.82 3.51
7136 7438 8.796475 TGCTCATAGCTTTGTTTTTAAGAAGAT 58.204 29.630 4.00 0.00 42.97 2.40
7329 7715 4.662278 ACTTGGTGCTGTATGTTATGGTT 58.338 39.130 0.00 0.00 0.00 3.67
7332 7718 9.882996 CATTATTACTTGGTGCTGTATGTTATG 57.117 33.333 0.00 0.00 0.00 1.90
7343 7729 3.694072 TGTGGCTCATTATTACTTGGTGC 59.306 43.478 0.00 0.00 0.00 5.01
7355 7741 0.744874 GCATGCTCATGTGGCTCATT 59.255 50.000 11.37 0.00 40.80 2.57
7452 7839 1.705337 CGGTGCGATCCATGTGGTTC 61.705 60.000 0.00 0.00 36.34 3.62
7478 7865 8.821686 ATCCATTCACAAGGTGATACAAATTA 57.178 30.769 0.00 0.00 42.40 1.40
7524 7911 7.815068 ACATAACAAACTGAGTAGCTAACTGAG 59.185 37.037 0.00 1.75 44.32 3.35
7525 7912 7.598869 CACATAACAAACTGAGTAGCTAACTGA 59.401 37.037 0.00 0.00 39.07 3.41
7526 7913 7.598869 TCACATAACAAACTGAGTAGCTAACTG 59.401 37.037 0.00 0.00 39.07 3.16
7527 7914 7.667557 TCACATAACAAACTGAGTAGCTAACT 58.332 34.615 0.00 0.00 42.80 2.24
7528 7915 7.412020 GCTCACATAACAAACTGAGTAGCTAAC 60.412 40.741 0.00 0.00 33.92 2.34
7529 7916 6.590292 GCTCACATAACAAACTGAGTAGCTAA 59.410 38.462 0.00 0.00 33.92 3.09
7577 7973 4.215399 GTGCATTTGTAGTAACTCCTGCAA 59.785 41.667 0.00 0.00 36.33 4.08
7730 8126 1.355381 ACATTCTTCATGGGAGGTGCA 59.645 47.619 0.00 0.00 37.17 4.57
7733 8129 1.909302 ACGACATTCTTCATGGGAGGT 59.091 47.619 0.00 0.00 37.17 3.85
7763 8159 0.818938 TGCTGGGCATATTGCTGTTG 59.181 50.000 0.00 0.00 44.28 3.33
7790 8186 0.952280 CACATGCTCTCATCATGCCC 59.048 55.000 0.00 0.00 43.71 5.36
7825 8221 2.223572 GCCGCTTGAGAATATTGGTTGG 60.224 50.000 0.00 0.00 0.00 3.77
7844 8240 2.280592 ACGGTGTCGGTTTCAGCC 60.281 61.111 0.00 0.00 41.39 4.85
7977 8373 2.646930 TGATGGATGTCTCATGTTGCC 58.353 47.619 0.00 0.00 0.00 4.52
8177 8573 6.774170 TGATTCATGGAGCTATAAGCATTTGT 59.226 34.615 1.22 0.00 45.56 2.83
8511 8909 6.037830 CCATAAATAACAGTGGTCTTAACGGG 59.962 42.308 0.00 0.00 0.00 5.28
8522 8921 5.991328 ACGAGCATCCATAAATAACAGTG 57.009 39.130 0.00 0.00 0.00 3.66
8606 9011 4.304939 GTTGGAACTTGTAAGCGAGTAGT 58.695 43.478 0.00 0.00 38.35 2.73
8613 9018 3.746940 TGTAGGGTTGGAACTTGTAAGC 58.253 45.455 0.00 0.00 0.00 3.09
8614 9019 6.702716 TTTTGTAGGGTTGGAACTTGTAAG 57.297 37.500 0.00 0.00 0.00 2.34
8632 9040 1.416030 GGTTGTCCATGCCCTTTTTGT 59.584 47.619 0.00 0.00 0.00 2.83
8662 9070 1.308069 CGACCACCCATGCTTCTTGG 61.308 60.000 0.00 0.00 0.00 3.61
8738 9146 2.826488 ACTCCAGTAGCACCAATCTCT 58.174 47.619 0.00 0.00 0.00 3.10
8774 9182 0.585838 GCAAAACAAAATGCCCACGG 59.414 50.000 0.00 0.00 36.56 4.94
8818 9226 1.326548 GAAGTAGGTGCCGCATTTACG 59.673 52.381 0.00 0.00 0.00 3.18
8824 9232 1.234821 CTTTTGAAGTAGGTGCCGCA 58.765 50.000 0.00 0.00 0.00 5.69
8825 9233 0.109735 GCTTTTGAAGTAGGTGCCGC 60.110 55.000 0.00 0.00 0.00 6.53
8837 9245 6.207417 CCATCCTTGAAAGTTCTAGCTTTTGA 59.793 38.462 0.00 0.00 38.64 2.69
8876 9284 0.976641 TTCTCGCATCCAACCTGTCT 59.023 50.000 0.00 0.00 0.00 3.41
8908 9316 1.874129 ACCACTTCCATACATCCGGA 58.126 50.000 6.61 6.61 0.00 5.14
8909 9317 2.710096 AACCACTTCCATACATCCGG 57.290 50.000 0.00 0.00 0.00 5.14
8932 9341 4.091424 GTCGTTGAAGAAACATGCATAGC 58.909 43.478 0.00 0.00 38.84 2.97
8942 9351 4.024387 CCGAAGATTTGGTCGTTGAAGAAA 60.024 41.667 0.00 0.00 35.48 2.52
8944 9353 3.064207 CCGAAGATTTGGTCGTTGAAGA 58.936 45.455 0.00 0.00 35.48 2.87
8945 9354 2.412847 GCCGAAGATTTGGTCGTTGAAG 60.413 50.000 0.87 0.00 35.48 3.02
8952 9367 4.095610 CGTAAATTGCCGAAGATTTGGTC 58.904 43.478 0.87 0.00 34.01 4.02
9027 9442 8.890472 TCCACCAGGCTAGATATACAAAATAAT 58.110 33.333 0.00 0.00 33.74 1.28
9030 9445 6.763715 TCCACCAGGCTAGATATACAAAAT 57.236 37.500 0.00 0.00 33.74 1.82
9101 9526 4.681483 GTGCCTTTGGAGATTTCTTTTTCG 59.319 41.667 0.00 0.00 0.00 3.46
9102 9527 4.991056 GGTGCCTTTGGAGATTTCTTTTTC 59.009 41.667 0.00 0.00 0.00 2.29
9108 9533 4.142160 GGTATTGGTGCCTTTGGAGATTTC 60.142 45.833 0.00 0.00 0.00 2.17
9109 9534 3.769300 GGTATTGGTGCCTTTGGAGATTT 59.231 43.478 0.00 0.00 0.00 2.17
9110 9535 3.365472 GGTATTGGTGCCTTTGGAGATT 58.635 45.455 0.00 0.00 0.00 2.40
9128 9553 8.281531 ACCAAAGATGATTTGAGATAATGGGTA 58.718 33.333 2.01 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.