Multiple sequence alignment - TraesCS2D01G519600

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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 TraesCS2D01G519600 chr2D 100.000 2393 0 0 1 2393 609424079 609426471 0.000000e+00 4420.0
1 TraesCS2D01G519600 chr2A 86.960 1365 72 30 171 1447 741372186 741373532 0.000000e+00 1437.0
2 TraesCS2D01G519600 chr2B 90.909 473 25 7 987 1447 743695111 743695577 9.400000e-174 619.0
3 TraesCS2D01G519600 chr2B 86.726 565 21 21 207 726 743694353 743694908 1.590000e-161 579.0
4 TraesCS2D01G519600 chr2B 80.851 282 42 6 2123 2393 743698483 743698763 6.700000e-51 211.0
5 TraesCS2D01G519600 chr2B 91.111 90 6 1 1756 1843 743698075 743698164 1.160000e-23 121.0
6 TraesCS2D01G519600 chr2B 92.857 42 2 1 1761 1802 743695773 743695813 2.570000e-05 60.2
7 TraesCS2D01G519600 chr7A 87.629 97 9 3 2213 2307 731163852 731163757 2.510000e-20 110.0
8 TraesCS2D01G519600 chr7A 85.567 97 9 4 2213 2307 731102115 731102022 1.960000e-16 97.1
9 TraesCS2D01G519600 chr7A 85.567 97 9 4 2213 2307 731134141 731134048 1.960000e-16 97.1
10 TraesCS2D01G519600 chr7A 85.567 97 9 4 2213 2307 731192809 731192716 1.960000e-16 97.1
11 TraesCS2D01G519600 chr5D 87.356 87 9 2 1658 1743 383629083 383629168 5.440000e-17 99.0
12 TraesCS2D01G519600 chr5A 87.356 87 9 2 1658 1743 483550234 483550319 5.440000e-17 99.0
13 TraesCS2D01G519600 chr1D 77.419 186 24 12 2217 2393 910390 910214 7.040000e-16 95.3
14 TraesCS2D01G519600 chr7D 92.188 64 5 0 1198 1261 422106760 422106697 9.110000e-15 91.6
15 TraesCS2D01G519600 chr7D 84.211 95 11 3 2214 2307 634722396 634722487 3.280000e-14 89.8
16 TraesCS2D01G519600 chr1B 83.838 99 10 5 2222 2318 3663469 3663375 3.280000e-14 89.8
17 TraesCS2D01G519600 chr1B 90.323 62 6 0 1656 1717 563443598 563443659 5.480000e-12 82.4
18 TraesCS2D01G519600 chr4A 92.982 57 4 0 1198 1254 685738558 685738502 1.520000e-12 84.2
19 TraesCS2D01G519600 chr6B 100.000 43 0 0 1212 1254 21012797 21012839 1.970000e-11 80.5
20 TraesCS2D01G519600 chr6A 83.516 91 9 3 2217 2307 583012363 583012447 1.970000e-11 80.5
21 TraesCS2D01G519600 chr6D 83.750 80 11 2 2217 2296 78818607 78818684 9.170000e-10 75.0
22 TraesCS2D01G519600 chr3B 89.655 58 6 0 1198 1255 819985117 819985174 9.170000e-10 75.0


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 TraesCS2D01G519600 chr2D 609424079 609426471 2392 False 4420.00 4420 100.0000 1 2393 1 chr2D.!!$F1 2392
1 TraesCS2D01G519600 chr2A 741372186 741373532 1346 False 1437.00 1437 86.9600 171 1447 1 chr2A.!!$F1 1276
2 TraesCS2D01G519600 chr2B 743694353 743698763 4410 False 318.04 619 88.4908 207 2393 5 chr2B.!!$F1 2186

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
671 731 0.039256 TGGTTGGCTCACGTACGTAC 60.039 55.0 22.34 15.9 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 4546 0.165944 CTCAATTGTCCGAACGCCAC 59.834 55.0 5.13 0.0 0.0 5.01 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 4.994744 GCATTTTGTGGGGTGCTC 57.005 55.556 0.00 0.00 34.85 4.26
18 19 2.048601 GCATTTTGTGGGGTGCTCA 58.951 52.632 0.00 0.00 34.85 4.26
19 20 0.609662 GCATTTTGTGGGGTGCTCAT 59.390 50.000 0.00 0.00 34.85 2.90
20 21 1.824230 GCATTTTGTGGGGTGCTCATA 59.176 47.619 0.00 0.00 34.85 2.15
21 22 2.159198 GCATTTTGTGGGGTGCTCATAG 60.159 50.000 0.00 0.00 34.85 2.23
22 23 3.355378 CATTTTGTGGGGTGCTCATAGA 58.645 45.455 0.00 0.00 0.00 1.98
23 24 2.787473 TTTGTGGGGTGCTCATAGAG 57.213 50.000 0.00 0.00 0.00 2.43
24 25 1.951209 TTGTGGGGTGCTCATAGAGA 58.049 50.000 0.00 0.00 0.00 3.10
25 26 2.180946 TGTGGGGTGCTCATAGAGAT 57.819 50.000 0.00 0.00 0.00 2.75
26 27 3.328535 TGTGGGGTGCTCATAGAGATA 57.671 47.619 0.00 0.00 0.00 1.98
27 28 3.234353 TGTGGGGTGCTCATAGAGATAG 58.766 50.000 0.00 0.00 0.00 2.08
28 29 2.564947 GTGGGGTGCTCATAGAGATAGG 59.435 54.545 0.00 0.00 0.00 2.57
29 30 2.183679 GGGGTGCTCATAGAGATAGGG 58.816 57.143 0.00 0.00 0.00 3.53
30 31 2.493687 GGGGTGCTCATAGAGATAGGGT 60.494 54.545 0.00 0.00 0.00 4.34
31 32 2.564947 GGGTGCTCATAGAGATAGGGTG 59.435 54.545 0.00 0.00 0.00 4.61
32 33 3.235200 GGTGCTCATAGAGATAGGGTGT 58.765 50.000 0.00 0.00 0.00 4.16
33 34 3.006323 GGTGCTCATAGAGATAGGGTGTG 59.994 52.174 0.00 0.00 0.00 3.82
34 35 2.630098 TGCTCATAGAGATAGGGTGTGC 59.370 50.000 0.00 0.00 0.00 4.57
35 36 2.028567 GCTCATAGAGATAGGGTGTGCC 60.029 54.545 0.00 0.00 0.00 5.01
36 37 2.230025 CTCATAGAGATAGGGTGTGCCG 59.770 54.545 0.00 0.00 34.97 5.69
37 38 1.964223 CATAGAGATAGGGTGTGCCGT 59.036 52.381 0.00 0.00 36.71 5.68
38 39 1.399714 TAGAGATAGGGTGTGCCGTG 58.600 55.000 0.00 0.00 34.32 4.94
39 40 0.614979 AGAGATAGGGTGTGCCGTGT 60.615 55.000 0.00 0.00 34.32 4.49
40 41 0.460284 GAGATAGGGTGTGCCGTGTG 60.460 60.000 0.00 0.00 34.32 3.82
41 42 1.192146 AGATAGGGTGTGCCGTGTGT 61.192 55.000 0.00 0.00 34.32 3.72
42 43 0.321298 GATAGGGTGTGCCGTGTGTT 60.321 55.000 0.00 0.00 34.32 3.32
43 44 0.321298 ATAGGGTGTGCCGTGTGTTC 60.321 55.000 0.00 0.00 34.32 3.18
44 45 1.687297 TAGGGTGTGCCGTGTGTTCA 61.687 55.000 0.00 0.00 34.32 3.18
45 46 1.896660 GGGTGTGCCGTGTGTTCAT 60.897 57.895 0.00 0.00 34.97 2.57
46 47 0.604243 GGGTGTGCCGTGTGTTCATA 60.604 55.000 0.00 0.00 34.97 2.15
47 48 1.231221 GGTGTGCCGTGTGTTCATAA 58.769 50.000 0.00 0.00 0.00 1.90
48 49 1.196808 GGTGTGCCGTGTGTTCATAAG 59.803 52.381 0.00 0.00 0.00 1.73
49 50 2.139917 GTGTGCCGTGTGTTCATAAGA 58.860 47.619 0.00 0.00 0.00 2.10
50 51 2.742053 GTGTGCCGTGTGTTCATAAGAT 59.258 45.455 0.00 0.00 0.00 2.40
51 52 3.188460 GTGTGCCGTGTGTTCATAAGATT 59.812 43.478 0.00 0.00 0.00 2.40
52 53 3.188254 TGTGCCGTGTGTTCATAAGATTG 59.812 43.478 0.00 0.00 0.00 2.67
53 54 3.435327 GTGCCGTGTGTTCATAAGATTGA 59.565 43.478 0.00 0.00 0.00 2.57
54 55 3.684305 TGCCGTGTGTTCATAAGATTGAG 59.316 43.478 0.00 0.00 0.00 3.02
55 56 3.684788 GCCGTGTGTTCATAAGATTGAGT 59.315 43.478 0.00 0.00 0.00 3.41
56 57 4.436050 GCCGTGTGTTCATAAGATTGAGTG 60.436 45.833 0.00 0.00 0.00 3.51
57 58 4.690748 CCGTGTGTTCATAAGATTGAGTGT 59.309 41.667 0.00 0.00 0.00 3.55
58 59 5.867174 CCGTGTGTTCATAAGATTGAGTGTA 59.133 40.000 0.00 0.00 0.00 2.90
59 60 6.535150 CCGTGTGTTCATAAGATTGAGTGTAT 59.465 38.462 0.00 0.00 0.00 2.29
60 61 7.394099 CGTGTGTTCATAAGATTGAGTGTATG 58.606 38.462 0.00 0.00 0.00 2.39
61 62 7.063426 CGTGTGTTCATAAGATTGAGTGTATGT 59.937 37.037 0.00 0.00 0.00 2.29
62 63 8.171196 GTGTGTTCATAAGATTGAGTGTATGTG 58.829 37.037 0.00 0.00 0.00 3.21
63 64 7.148423 TGTGTTCATAAGATTGAGTGTATGTGC 60.148 37.037 0.00 0.00 0.00 4.57
64 65 6.035975 TGTTCATAAGATTGAGTGTATGTGCG 59.964 38.462 0.00 0.00 0.00 5.34
65 66 5.660460 TCATAAGATTGAGTGTATGTGCGT 58.340 37.500 0.00 0.00 0.00 5.24
66 67 5.519927 TCATAAGATTGAGTGTATGTGCGTG 59.480 40.000 0.00 0.00 0.00 5.34
67 68 3.592898 AGATTGAGTGTATGTGCGTGA 57.407 42.857 0.00 0.00 0.00 4.35
68 69 3.925379 AGATTGAGTGTATGTGCGTGAA 58.075 40.909 0.00 0.00 0.00 3.18
69 70 4.314961 AGATTGAGTGTATGTGCGTGAAA 58.685 39.130 0.00 0.00 0.00 2.69
70 71 4.389992 AGATTGAGTGTATGTGCGTGAAAG 59.610 41.667 0.00 0.00 0.00 2.62
71 72 3.378911 TGAGTGTATGTGCGTGAAAGA 57.621 42.857 0.00 0.00 0.00 2.52
72 73 3.723260 TGAGTGTATGTGCGTGAAAGAA 58.277 40.909 0.00 0.00 0.00 2.52
73 74 4.314961 TGAGTGTATGTGCGTGAAAGAAT 58.685 39.130 0.00 0.00 0.00 2.40
74 75 5.474825 TGAGTGTATGTGCGTGAAAGAATA 58.525 37.500 0.00 0.00 0.00 1.75
75 76 5.929415 TGAGTGTATGTGCGTGAAAGAATAA 59.071 36.000 0.00 0.00 0.00 1.40
76 77 6.128661 TGAGTGTATGTGCGTGAAAGAATAAC 60.129 38.462 0.00 0.00 0.00 1.89
77 78 5.013236 GTGTATGTGCGTGAAAGAATAACG 58.987 41.667 0.00 0.00 40.22 3.18
78 79 3.740044 ATGTGCGTGAAAGAATAACGG 57.260 42.857 0.00 0.00 37.77 4.44
79 80 2.756829 TGTGCGTGAAAGAATAACGGA 58.243 42.857 0.00 0.00 37.77 4.69
80 81 3.132160 TGTGCGTGAAAGAATAACGGAA 58.868 40.909 0.00 0.00 39.36 4.30
81 82 3.560481 TGTGCGTGAAAGAATAACGGAAA 59.440 39.130 0.00 0.00 39.36 3.13
82 83 4.214545 TGTGCGTGAAAGAATAACGGAAAT 59.785 37.500 0.00 0.00 39.36 2.17
83 84 5.408909 TGTGCGTGAAAGAATAACGGAAATA 59.591 36.000 0.00 0.00 39.36 1.40
84 85 5.731263 GTGCGTGAAAGAATAACGGAAATAC 59.269 40.000 0.00 0.00 39.36 1.89
85 86 4.953814 GCGTGAAAGAATAACGGAAATACG 59.046 41.667 0.00 0.00 37.77 3.06
86 87 5.220265 GCGTGAAAGAATAACGGAAATACGA 60.220 40.000 0.00 0.00 37.77 3.43
87 88 6.670452 GCGTGAAAGAATAACGGAAATACGAA 60.670 38.462 0.00 0.00 37.77 3.85
88 89 7.396419 CGTGAAAGAATAACGGAAATACGAAT 58.604 34.615 0.00 0.00 37.61 3.34
89 90 8.533965 CGTGAAAGAATAACGGAAATACGAATA 58.466 33.333 0.00 0.00 37.61 1.75
100 101 5.349809 GGAAATACGAATATCCGGATCTCC 58.650 45.833 23.08 9.91 30.71 3.71
101 102 5.127356 GGAAATACGAATATCCGGATCTCCT 59.873 44.000 23.08 11.11 30.71 3.69
102 103 5.584253 AATACGAATATCCGGATCTCCTG 57.416 43.478 23.08 10.95 30.71 3.86
103 104 2.171840 ACGAATATCCGGATCTCCTGG 58.828 52.381 23.08 9.27 0.00 4.45
104 105 1.478510 CGAATATCCGGATCTCCTGGG 59.521 57.143 23.08 2.73 32.84 4.45
105 106 1.208293 GAATATCCGGATCTCCTGGGC 59.792 57.143 23.08 0.00 32.84 5.36
106 107 0.972983 ATATCCGGATCTCCTGGGCG 60.973 60.000 23.08 0.00 32.84 6.13
107 108 2.076597 TATCCGGATCTCCTGGGCGA 62.077 60.000 23.08 0.00 32.84 5.54
108 109 3.610669 CCGGATCTCCTGGGCGAG 61.611 72.222 0.00 0.00 0.00 5.03
109 110 3.610669 CGGATCTCCTGGGCGAGG 61.611 72.222 9.61 9.61 44.45 4.63
115 116 4.932060 TCCTGGGCGAGGAGATAG 57.068 61.111 14.88 0.00 46.96 2.08
116 117 1.931296 TCCTGGGCGAGGAGATAGT 59.069 57.895 14.88 0.00 46.96 2.12
117 118 1.146452 TCCTGGGCGAGGAGATAGTA 58.854 55.000 14.88 0.00 46.96 1.82
118 119 1.074084 TCCTGGGCGAGGAGATAGTAG 59.926 57.143 14.88 0.00 46.96 2.57
119 120 1.074084 CCTGGGCGAGGAGATAGTAGA 59.926 57.143 10.44 0.00 46.33 2.59
120 121 2.291282 CCTGGGCGAGGAGATAGTAGAT 60.291 54.545 10.44 0.00 46.33 1.98
121 122 2.752354 CTGGGCGAGGAGATAGTAGATG 59.248 54.545 0.00 0.00 0.00 2.90
122 123 2.108425 TGGGCGAGGAGATAGTAGATGT 59.892 50.000 0.00 0.00 0.00 3.06
123 124 2.490115 GGGCGAGGAGATAGTAGATGTG 59.510 54.545 0.00 0.00 0.00 3.21
124 125 2.094957 GGCGAGGAGATAGTAGATGTGC 60.095 54.545 0.00 0.00 0.00 4.57
125 126 2.817258 GCGAGGAGATAGTAGATGTGCT 59.183 50.000 0.00 0.00 0.00 4.40
126 127 3.254657 GCGAGGAGATAGTAGATGTGCTT 59.745 47.826 0.00 0.00 0.00 3.91
127 128 4.793071 CGAGGAGATAGTAGATGTGCTTG 58.207 47.826 0.00 0.00 0.00 4.01
128 129 4.277174 CGAGGAGATAGTAGATGTGCTTGT 59.723 45.833 0.00 0.00 0.00 3.16
129 130 5.527951 GAGGAGATAGTAGATGTGCTTGTG 58.472 45.833 0.00 0.00 0.00 3.33
130 131 5.204292 AGGAGATAGTAGATGTGCTTGTGA 58.796 41.667 0.00 0.00 0.00 3.58
131 132 5.301551 AGGAGATAGTAGATGTGCTTGTGAG 59.698 44.000 0.00 0.00 0.00 3.51
132 133 5.508825 GGAGATAGTAGATGTGCTTGTGAGG 60.509 48.000 0.00 0.00 0.00 3.86
133 134 2.393271 AGTAGATGTGCTTGTGAGGC 57.607 50.000 0.00 0.00 0.00 4.70
134 135 1.065854 AGTAGATGTGCTTGTGAGGCC 60.066 52.381 0.00 0.00 0.00 5.19
135 136 0.108186 TAGATGTGCTTGTGAGGCCG 60.108 55.000 0.00 0.00 0.00 6.13
136 137 2.360350 ATGTGCTTGTGAGGCCGG 60.360 61.111 0.00 0.00 0.00 6.13
159 160 3.053896 GGTTGCCCGTGTAGCCAC 61.054 66.667 0.00 0.00 38.27 5.01
160 161 2.032071 GTTGCCCGTGTAGCCACT 59.968 61.111 0.00 0.00 39.55 4.00
161 162 1.294138 GTTGCCCGTGTAGCCACTA 59.706 57.895 0.00 0.00 39.55 2.74
162 163 0.739813 GTTGCCCGTGTAGCCACTAG 60.740 60.000 0.00 0.00 39.55 2.57
163 164 2.202892 GCCCGTGTAGCCACTAGC 60.203 66.667 0.00 0.00 39.55 3.42
164 165 2.499685 CCCGTGTAGCCACTAGCC 59.500 66.667 0.00 0.00 45.47 3.93
165 166 2.355986 CCCGTGTAGCCACTAGCCA 61.356 63.158 0.00 0.00 45.47 4.75
166 167 1.141881 CCGTGTAGCCACTAGCCAG 59.858 63.158 0.00 0.00 45.47 4.85
167 168 1.519455 CGTGTAGCCACTAGCCAGC 60.519 63.158 0.00 0.00 45.47 4.85
168 169 1.519455 GTGTAGCCACTAGCCAGCG 60.519 63.158 0.00 0.00 45.47 5.18
169 170 2.586357 GTAGCCACTAGCCAGCGC 60.586 66.667 0.00 0.00 45.47 5.92
177 178 3.932580 CTAGCCAGCGCCGTGAACA 62.933 63.158 2.29 0.00 34.57 3.18
218 223 1.168714 GTTGAACTTGGCAGGCTAGG 58.831 55.000 10.15 0.00 0.00 3.02
236 241 1.415672 GGTGTCTGGAAGGTGGACCA 61.416 60.000 0.00 0.00 38.89 4.02
239 247 3.081554 CTGGAAGGTGGACCAGGG 58.918 66.667 0.00 0.00 46.76 4.45
423 432 1.208293 GATCGGAACTCTTCTGCCCTT 59.792 52.381 0.00 0.00 35.98 3.95
424 433 0.321671 TCGGAACTCTTCTGCCCTTG 59.678 55.000 0.00 0.00 35.98 3.61
425 434 1.301677 CGGAACTCTTCTGCCCTTGC 61.302 60.000 0.00 0.00 38.26 4.01
426 435 0.962855 GGAACTCTTCTGCCCTTGCC 60.963 60.000 0.00 0.00 36.33 4.52
644 704 1.374947 CCCATACCCCATACGGCAG 59.625 63.158 0.00 0.00 0.00 4.85
645 705 1.302511 CCATACCCCATACGGCAGC 60.303 63.158 0.00 0.00 0.00 5.25
646 706 1.449782 CATACCCCATACGGCAGCA 59.550 57.895 0.00 0.00 0.00 4.41
668 728 2.380410 GCTGGTTGGCTCACGTACG 61.380 63.158 15.01 15.01 0.00 3.67
669 729 1.006571 CTGGTTGGCTCACGTACGT 60.007 57.895 16.72 16.72 0.00 3.57
670 730 0.241749 CTGGTTGGCTCACGTACGTA 59.758 55.000 22.34 8.85 0.00 3.57
671 731 0.039256 TGGTTGGCTCACGTACGTAC 60.039 55.000 22.34 15.90 0.00 3.67
768 840 3.427098 CCAGTCACACATCATGCAATGTC 60.427 47.826 0.90 0.00 46.80 3.06
771 843 3.057386 GTCACACATCATGCAATGTCCAA 60.057 43.478 0.90 0.00 46.80 3.53
772 844 3.573110 TCACACATCATGCAATGTCCAAA 59.427 39.130 0.90 0.00 46.80 3.28
775 847 4.464951 ACACATCATGCAATGTCCAAATCT 59.535 37.500 0.90 0.00 46.80 2.40
786 858 3.674997 TGTCCAAATCTAACACAGCCTC 58.325 45.455 0.00 0.00 0.00 4.70
790 862 3.125316 CCAAATCTAACACAGCCTCGAAC 59.875 47.826 0.00 0.00 0.00 3.95
839 911 4.481463 GCATGCACACCGTAAAAGTAAAT 58.519 39.130 14.21 0.00 0.00 1.40
866 938 1.465689 GGAATTGCGGAATCGTGTGTG 60.466 52.381 1.48 0.00 38.89 3.82
910 988 4.393155 ACCCGCGATCTGCTGCAA 62.393 61.111 8.23 0.00 43.27 4.08
911 989 2.898840 CCCGCGATCTGCTGCAAT 60.899 61.111 8.23 0.24 43.27 3.56
913 991 0.952497 CCCGCGATCTGCTGCAATAT 60.952 55.000 8.23 0.00 43.27 1.28
924 1021 1.860676 CTGCAATATGGTGGCAATGC 58.139 50.000 0.00 0.00 37.06 3.56
973 1070 1.212751 GTGGCAACGGCTCCAAATC 59.787 57.895 0.00 0.00 40.87 2.17
1163 1263 2.654877 GGAGGCCGTCAAGTTCGA 59.345 61.111 0.00 0.00 0.00 3.71
1410 1518 3.191581 TGTGACATTGTTTCGTTTGGTGT 59.808 39.130 0.00 0.00 0.00 4.16
1462 3684 1.858458 TCTGTGTGTCGAAGCGAAAAG 59.142 47.619 0.00 0.00 37.72 2.27
1465 3687 3.644823 TGTGTGTCGAAGCGAAAAGATA 58.355 40.909 0.00 0.00 37.72 1.98
1469 3691 3.000575 GTGTCGAAGCGAAAAGATAGCTC 60.001 47.826 0.00 0.00 40.78 4.09
1471 3693 3.241784 GTCGAAGCGAAAAGATAGCTCAG 59.758 47.826 0.00 0.00 40.78 3.35
1486 3708 8.072321 AGATAGCTCAGTTTCATTGACTTCTA 57.928 34.615 0.00 0.00 0.00 2.10
1490 3712 5.698545 GCTCAGTTTCATTGACTTCTACTGT 59.301 40.000 0.00 0.00 34.62 3.55
1491 3713 6.868864 GCTCAGTTTCATTGACTTCTACTGTA 59.131 38.462 0.00 0.00 34.62 2.74
1492 3714 7.385205 GCTCAGTTTCATTGACTTCTACTGTAA 59.615 37.037 0.00 0.00 34.62 2.41
1493 3715 9.261180 CTCAGTTTCATTGACTTCTACTGTAAA 57.739 33.333 0.00 0.00 34.62 2.01
1494 3716 9.042008 TCAGTTTCATTGACTTCTACTGTAAAC 57.958 33.333 0.00 0.00 34.62 2.01
1495 3717 8.826710 CAGTTTCATTGACTTCTACTGTAAACA 58.173 33.333 0.00 0.00 0.00 2.83
1496 3718 9.561069 AGTTTCATTGACTTCTACTGTAAACAT 57.439 29.630 0.00 0.00 0.00 2.71
1532 3754 9.830975 ATTTTTACTGTAAACATTTTGCTTCCT 57.169 25.926 12.27 0.00 0.00 3.36
1596 3826 6.487668 TGGACTATACATGAATCAATGCCAAG 59.512 38.462 0.00 0.00 0.00 3.61
1617 3847 7.201350 GCCAAGTTAATTTCTTTGCTTGATACG 60.201 37.037 0.00 0.00 35.47 3.06
1629 3859 6.954487 TTGCTTGATACGAAGGAGATACTA 57.046 37.500 0.00 0.00 0.00 1.82
1632 3862 6.320418 TGCTTGATACGAAGGAGATACTACAA 59.680 38.462 0.00 0.00 0.00 2.41
1636 3866 9.745880 TTGATACGAAGGAGATACTACAATTTC 57.254 33.333 0.00 0.00 0.00 2.17
1673 3903 6.650120 TGTTTGAGTAATACTCCCTCCATTC 58.350 40.000 16.89 1.66 44.44 2.67
1688 3918 5.259632 CCTCCATTCTCAAAAGGAAGACAT 58.740 41.667 0.00 0.00 32.12 3.06
1730 3960 5.350914 TCAAACTGTGCAAAATTTGACCAAG 59.649 36.000 9.38 3.64 36.42 3.61
1763 4088 6.709018 AAAACTGCCAACAACTACAATACT 57.291 33.333 0.00 0.00 0.00 2.12
1771 4096 6.979238 GCCAACAACTACAATACTAGAGTAGG 59.021 42.308 0.00 0.00 39.54 3.18
1798 4125 5.180117 TGCTCTCATTTGAAGACAGTAAAGC 59.820 40.000 0.00 0.00 0.00 3.51
1807 4134 0.796927 GACAGTAAAGCTTGCCGGTC 59.203 55.000 1.90 6.44 0.00 4.79
1843 4170 3.439129 CGACCATCTTTTCTTTACCCACC 59.561 47.826 0.00 0.00 0.00 4.61
1844 4171 3.762288 GACCATCTTTTCTTTACCCACCC 59.238 47.826 0.00 0.00 0.00 4.61
1845 4172 3.141272 ACCATCTTTTCTTTACCCACCCA 59.859 43.478 0.00 0.00 0.00 4.51
1846 4173 3.509967 CCATCTTTTCTTTACCCACCCAC 59.490 47.826 0.00 0.00 0.00 4.61
1847 4174 3.232720 TCTTTTCTTTACCCACCCACC 57.767 47.619 0.00 0.00 0.00 4.61
1848 4175 2.514582 TCTTTTCTTTACCCACCCACCA 59.485 45.455 0.00 0.00 0.00 4.17
1849 4176 3.141272 TCTTTTCTTTACCCACCCACCAT 59.859 43.478 0.00 0.00 0.00 3.55
1853 4180 2.167662 CTTTACCCACCCACCATTGTC 58.832 52.381 0.00 0.00 0.00 3.18
1864 4191 3.391965 CCACCATTGTCACCACAAAATG 58.608 45.455 0.00 0.00 45.78 2.32
1872 4199 3.391098 CCACAAAATGGGCAGGGG 58.609 61.111 0.00 0.00 45.95 4.79
1874 4201 1.672898 CACAAAATGGGCAGGGGTG 59.327 57.895 0.00 0.00 0.00 4.61
1876 4203 0.485099 ACAAAATGGGCAGGGGTGTA 59.515 50.000 0.00 0.00 0.00 2.90
1877 4204 1.185315 CAAAATGGGCAGGGGTGTAG 58.815 55.000 0.00 0.00 0.00 2.74
1878 4205 0.783850 AAAATGGGCAGGGGTGTAGT 59.216 50.000 0.00 0.00 0.00 2.73
1879 4206 0.039618 AAATGGGCAGGGGTGTAGTG 59.960 55.000 0.00 0.00 0.00 2.74
1881 4208 1.562672 ATGGGCAGGGGTGTAGTGTC 61.563 60.000 0.00 0.00 0.00 3.67
1940 4304 5.538433 TGTTTTTGTCCCTCAAATTCCCTAG 59.462 40.000 0.00 0.00 44.15 3.02
1948 4312 7.290248 TGTCCCTCAAATTCCCTAGAAGTATAG 59.710 40.741 0.00 0.00 34.86 1.31
1950 4314 8.242325 TCCCTCAAATTCCCTAGAAGTATAGAT 58.758 37.037 0.00 0.00 34.86 1.98
1951 4315 8.885346 CCCTCAAATTCCCTAGAAGTATAGATT 58.115 37.037 0.00 0.00 34.86 2.40
1960 4324 9.810870 TCCCTAGAAGTATAGATTTAGTCCTTC 57.189 37.037 0.00 0.00 0.00 3.46
1961 4325 9.589461 CCCTAGAAGTATAGATTTAGTCCTTCA 57.411 37.037 0.00 0.00 31.55 3.02
1973 4337 9.067986 AGATTTAGTCCTTCAAAAGAATTTCGT 57.932 29.630 0.00 0.00 37.28 3.85
1979 4343 7.913821 AGTCCTTCAAAAGAATTTCGTAAACAC 59.086 33.333 0.00 0.00 37.28 3.32
1990 4354 1.000060 TCGTAAACACTTGGTCCCTCG 60.000 52.381 0.00 0.00 0.00 4.63
2005 4369 1.014564 CCTCGAGTCTCAAAACCGGC 61.015 60.000 12.31 0.00 0.00 6.13
2010 4374 1.732809 GAGTCTCAAAACCGGCTAAGC 59.267 52.381 0.00 0.00 0.00 3.09
2014 4378 1.128692 CTCAAAACCGGCTAAGCTTCG 59.871 52.381 0.00 0.00 0.00 3.79
2016 4380 1.136057 CAAAACCGGCTAAGCTTCGTC 60.136 52.381 0.00 0.00 0.00 4.20
2025 4389 2.095718 GCTAAGCTTCGTCCAAAACCAG 60.096 50.000 0.00 0.00 0.00 4.00
2027 4391 1.594331 AGCTTCGTCCAAAACCAGAC 58.406 50.000 0.00 0.00 0.00 3.51
2028 4392 0.591659 GCTTCGTCCAAAACCAGACC 59.408 55.000 0.00 0.00 0.00 3.85
2029 4393 1.961793 CTTCGTCCAAAACCAGACCA 58.038 50.000 0.00 0.00 0.00 4.02
2031 4395 2.178912 TCGTCCAAAACCAGACCATC 57.821 50.000 0.00 0.00 0.00 3.51
2032 4396 1.697432 TCGTCCAAAACCAGACCATCT 59.303 47.619 0.00 0.00 0.00 2.90
2033 4397 2.105821 TCGTCCAAAACCAGACCATCTT 59.894 45.455 0.00 0.00 0.00 2.40
2034 4398 2.884639 CGTCCAAAACCAGACCATCTTT 59.115 45.455 0.00 0.00 0.00 2.52
2039 4408 2.185004 AACCAGACCATCTTTGACCG 57.815 50.000 0.00 0.00 0.00 4.79
2057 4426 2.477880 GGGTTTGACCGCCACATAG 58.522 57.895 0.00 0.00 39.83 2.23
2075 4444 6.005583 ACATAGTTTGTGCTTCATGAACAG 57.994 37.500 3.38 0.00 35.26 3.16
2076 4445 5.532406 ACATAGTTTGTGCTTCATGAACAGT 59.468 36.000 3.38 0.00 35.26 3.55
2077 4446 6.710295 ACATAGTTTGTGCTTCATGAACAGTA 59.290 34.615 3.38 0.00 35.26 2.74
2078 4447 7.228507 ACATAGTTTGTGCTTCATGAACAGTAA 59.771 33.333 3.38 4.35 35.26 2.24
2079 4448 6.449635 AGTTTGTGCTTCATGAACAGTAAA 57.550 33.333 3.38 9.26 35.26 2.01
2080 4449 7.042797 AGTTTGTGCTTCATGAACAGTAAAT 57.957 32.000 3.38 2.65 35.26 1.40
2081 4450 7.491682 AGTTTGTGCTTCATGAACAGTAAATT 58.508 30.769 3.38 6.86 35.26 1.82
2083 4452 9.243637 GTTTGTGCTTCATGAACAGTAAATTTA 57.756 29.630 3.38 0.00 35.26 1.40
2084 4453 9.809096 TTTGTGCTTCATGAACAGTAAATTTAA 57.191 25.926 3.38 0.00 35.26 1.52
2085 4454 9.809096 TTGTGCTTCATGAACAGTAAATTTAAA 57.191 25.926 3.38 0.00 35.26 1.52
2136 4524 4.122776 AGCTTCCAATATGCTCAAGTACG 58.877 43.478 0.00 0.00 33.49 3.67
2137 4525 3.248602 GCTTCCAATATGCTCAAGTACGG 59.751 47.826 0.00 0.00 0.00 4.02
2138 4526 4.693283 CTTCCAATATGCTCAAGTACGGA 58.307 43.478 0.00 0.00 0.00 4.69
2156 4544 3.634283 CGGAAAGGTGCGTACAAATTTT 58.366 40.909 5.86 0.48 33.27 1.82
2157 4545 4.045783 CGGAAAGGTGCGTACAAATTTTT 58.954 39.130 5.86 0.00 33.27 1.94
2158 4546 4.085312 CGGAAAGGTGCGTACAAATTTTTG 60.085 41.667 5.86 1.56 37.72 2.44
2178 4566 0.034198 TGGCGTTCGGACAATTGAGA 59.966 50.000 13.59 5.72 0.00 3.27
2183 4571 2.092838 CGTTCGGACAATTGAGAAGCTC 59.907 50.000 13.59 0.00 0.00 4.09
2187 4575 1.129437 GGACAATTGAGAAGCTCGTGC 59.871 52.381 13.59 0.07 40.05 5.34
2191 4579 1.896220 ATTGAGAAGCTCGTGCCAAA 58.104 45.000 5.73 0.00 40.80 3.28
2193 4581 1.229428 TGAGAAGCTCGTGCCAAAAG 58.771 50.000 5.73 0.00 40.80 2.27
2194 4582 1.230324 GAGAAGCTCGTGCCAAAAGT 58.770 50.000 5.73 0.00 40.80 2.66
2199 4587 4.278419 AGAAGCTCGTGCCAAAAGTAAAAT 59.722 37.500 5.73 0.00 40.80 1.82
2296 4687 4.874534 CCAAGATGCTTGGTTGCG 57.125 55.556 16.18 0.00 34.92 4.85
2318 4709 2.485266 AGGTGCGTACAAAGTTTTGC 57.515 45.000 5.86 0.00 41.79 3.68
2320 4711 2.164624 AGGTGCGTACAAAGTTTTGCAA 59.835 40.909 5.86 0.00 41.79 4.08
2321 4712 2.924290 GGTGCGTACAAAGTTTTGCAAA 59.076 40.909 8.05 8.05 41.79 3.68
2322 4713 3.553917 GGTGCGTACAAAGTTTTGCAAAT 59.446 39.130 13.65 0.00 41.79 2.32
2323 4714 4.033472 GGTGCGTACAAAGTTTTGCAAATT 59.967 37.500 13.65 2.09 41.79 1.82
2327 4724 6.920758 TGCGTACAAAGTTTTGCAAATTATCT 59.079 30.769 13.65 6.77 41.79 1.98
2336 4733 7.994194 AGTTTTGCAAATTATCTGAGGATCTC 58.006 34.615 13.65 0.00 34.92 2.75
2339 4736 9.857656 TTTTGCAAATTATCTGAGGATCTCTAT 57.142 29.630 13.65 0.00 34.92 1.98
2341 4738 8.198807 TGCAAATTATCTGAGGATCTCTATCA 57.801 34.615 0.00 0.00 34.92 2.15
2342 4739 8.312564 TGCAAATTATCTGAGGATCTCTATCAG 58.687 37.037 9.88 9.88 41.47 2.90
2343 4740 8.313292 GCAAATTATCTGAGGATCTCTATCAGT 58.687 37.037 13.58 7.36 41.01 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.609662 ATGAGCACCCCACAAAATGC 59.390 50.000 0.00 0.00 38.39 3.56
1 2 3.355378 TCTATGAGCACCCCACAAAATG 58.645 45.455 0.00 0.00 0.00 2.32
2 3 3.266772 TCTCTATGAGCACCCCACAAAAT 59.733 43.478 0.00 0.00 0.00 1.82
3 4 2.642311 TCTCTATGAGCACCCCACAAAA 59.358 45.455 0.00 0.00 0.00 2.44
4 5 2.265367 TCTCTATGAGCACCCCACAAA 58.735 47.619 0.00 0.00 0.00 2.83
5 6 1.951209 TCTCTATGAGCACCCCACAA 58.049 50.000 0.00 0.00 0.00 3.33
6 7 2.180946 ATCTCTATGAGCACCCCACA 57.819 50.000 0.00 0.00 0.00 4.17
7 8 2.564947 CCTATCTCTATGAGCACCCCAC 59.435 54.545 0.00 0.00 0.00 4.61
8 9 2.493500 CCCTATCTCTATGAGCACCCCA 60.494 54.545 0.00 0.00 0.00 4.96
9 10 2.183679 CCCTATCTCTATGAGCACCCC 58.816 57.143 0.00 0.00 0.00 4.95
10 11 2.564947 CACCCTATCTCTATGAGCACCC 59.435 54.545 0.00 0.00 0.00 4.61
11 12 3.006323 CACACCCTATCTCTATGAGCACC 59.994 52.174 0.00 0.00 0.00 5.01
12 13 3.553922 GCACACCCTATCTCTATGAGCAC 60.554 52.174 0.00 0.00 0.00 4.40
13 14 2.630098 GCACACCCTATCTCTATGAGCA 59.370 50.000 0.00 0.00 0.00 4.26
14 15 2.028567 GGCACACCCTATCTCTATGAGC 60.029 54.545 0.00 0.00 0.00 4.26
15 16 2.230025 CGGCACACCCTATCTCTATGAG 59.770 54.545 0.00 0.00 0.00 2.90
16 17 2.239400 CGGCACACCCTATCTCTATGA 58.761 52.381 0.00 0.00 0.00 2.15
17 18 1.964223 ACGGCACACCCTATCTCTATG 59.036 52.381 0.00 0.00 0.00 2.23
18 19 1.964223 CACGGCACACCCTATCTCTAT 59.036 52.381 0.00 0.00 0.00 1.98
19 20 1.341679 ACACGGCACACCCTATCTCTA 60.342 52.381 0.00 0.00 0.00 2.43
20 21 0.614979 ACACGGCACACCCTATCTCT 60.615 55.000 0.00 0.00 0.00 3.10
21 22 0.460284 CACACGGCACACCCTATCTC 60.460 60.000 0.00 0.00 0.00 2.75
22 23 1.192146 ACACACGGCACACCCTATCT 61.192 55.000 0.00 0.00 0.00 1.98
23 24 0.321298 AACACACGGCACACCCTATC 60.321 55.000 0.00 0.00 0.00 2.08
24 25 0.321298 GAACACACGGCACACCCTAT 60.321 55.000 0.00 0.00 0.00 2.57
25 26 1.070105 GAACACACGGCACACCCTA 59.930 57.895 0.00 0.00 0.00 3.53
26 27 2.203153 GAACACACGGCACACCCT 60.203 61.111 0.00 0.00 0.00 4.34
27 28 0.604243 TATGAACACACGGCACACCC 60.604 55.000 0.00 0.00 0.00 4.61
28 29 1.196808 CTTATGAACACACGGCACACC 59.803 52.381 0.00 0.00 0.00 4.16
29 30 2.139917 TCTTATGAACACACGGCACAC 58.860 47.619 0.00 0.00 0.00 3.82
30 31 2.535012 TCTTATGAACACACGGCACA 57.465 45.000 0.00 0.00 0.00 4.57
31 32 3.435327 TCAATCTTATGAACACACGGCAC 59.565 43.478 0.00 0.00 0.00 5.01
32 33 3.669536 TCAATCTTATGAACACACGGCA 58.330 40.909 0.00 0.00 0.00 5.69
33 34 3.684788 ACTCAATCTTATGAACACACGGC 59.315 43.478 0.00 0.00 0.00 5.68
34 35 4.690748 ACACTCAATCTTATGAACACACGG 59.309 41.667 0.00 0.00 0.00 4.94
35 36 5.845985 ACACTCAATCTTATGAACACACG 57.154 39.130 0.00 0.00 0.00 4.49
36 37 8.171196 CACATACACTCAATCTTATGAACACAC 58.829 37.037 0.00 0.00 0.00 3.82
37 38 7.148423 GCACATACACTCAATCTTATGAACACA 60.148 37.037 0.00 0.00 0.00 3.72
38 39 7.182761 GCACATACACTCAATCTTATGAACAC 58.817 38.462 0.00 0.00 0.00 3.32
39 40 6.035975 CGCACATACACTCAATCTTATGAACA 59.964 38.462 0.00 0.00 0.00 3.18
40 41 6.036083 ACGCACATACACTCAATCTTATGAAC 59.964 38.462 0.00 0.00 0.00 3.18
41 42 6.035975 CACGCACATACACTCAATCTTATGAA 59.964 38.462 0.00 0.00 0.00 2.57
42 43 5.519927 CACGCACATACACTCAATCTTATGA 59.480 40.000 0.00 0.00 0.00 2.15
43 44 5.519927 TCACGCACATACACTCAATCTTATG 59.480 40.000 0.00 0.00 0.00 1.90
44 45 5.660460 TCACGCACATACACTCAATCTTAT 58.340 37.500 0.00 0.00 0.00 1.73
45 46 5.066968 TCACGCACATACACTCAATCTTA 57.933 39.130 0.00 0.00 0.00 2.10
46 47 3.925379 TCACGCACATACACTCAATCTT 58.075 40.909 0.00 0.00 0.00 2.40
47 48 3.592898 TCACGCACATACACTCAATCT 57.407 42.857 0.00 0.00 0.00 2.40
48 49 4.388773 TCTTTCACGCACATACACTCAATC 59.611 41.667 0.00 0.00 0.00 2.67
49 50 4.314961 TCTTTCACGCACATACACTCAAT 58.685 39.130 0.00 0.00 0.00 2.57
50 51 3.723260 TCTTTCACGCACATACACTCAA 58.277 40.909 0.00 0.00 0.00 3.02
51 52 3.378911 TCTTTCACGCACATACACTCA 57.621 42.857 0.00 0.00 0.00 3.41
52 53 4.928661 ATTCTTTCACGCACATACACTC 57.071 40.909 0.00 0.00 0.00 3.51
53 54 5.163992 CGTTATTCTTTCACGCACATACACT 60.164 40.000 0.00 0.00 0.00 3.55
54 55 5.013236 CGTTATTCTTTCACGCACATACAC 58.987 41.667 0.00 0.00 0.00 2.90
55 56 4.092237 CCGTTATTCTTTCACGCACATACA 59.908 41.667 0.00 0.00 32.43 2.29
56 57 4.327898 TCCGTTATTCTTTCACGCACATAC 59.672 41.667 0.00 0.00 32.43 2.39
57 58 4.496360 TCCGTTATTCTTTCACGCACATA 58.504 39.130 0.00 0.00 32.43 2.29
58 59 3.331150 TCCGTTATTCTTTCACGCACAT 58.669 40.909 0.00 0.00 32.43 3.21
59 60 2.756829 TCCGTTATTCTTTCACGCACA 58.243 42.857 0.00 0.00 32.43 4.57
60 61 3.799137 TTCCGTTATTCTTTCACGCAC 57.201 42.857 0.00 0.00 32.43 5.34
61 62 5.444877 CGTATTTCCGTTATTCTTTCACGCA 60.445 40.000 0.00 0.00 32.43 5.24
62 63 4.953814 CGTATTTCCGTTATTCTTTCACGC 59.046 41.667 0.00 0.00 32.43 5.34
63 64 6.321873 TCGTATTTCCGTTATTCTTTCACG 57.678 37.500 0.00 0.00 0.00 4.35
67 68 8.706035 CGGATATTCGTATTTCCGTTATTCTTT 58.294 33.333 20.40 0.00 45.01 2.52
68 69 8.236084 CGGATATTCGTATTTCCGTTATTCTT 57.764 34.615 20.40 0.00 45.01 2.52
69 70 7.807687 CGGATATTCGTATTTCCGTTATTCT 57.192 36.000 20.40 0.00 45.01 2.40
77 78 5.127356 AGGAGATCCGGATATTCGTATTTCC 59.873 44.000 19.15 9.78 42.08 3.13
78 79 6.037098 CAGGAGATCCGGATATTCGTATTTC 58.963 44.000 19.15 0.95 42.08 2.17
79 80 5.105310 CCAGGAGATCCGGATATTCGTATTT 60.105 44.000 19.15 0.00 42.08 1.40
80 81 4.402793 CCAGGAGATCCGGATATTCGTATT 59.597 45.833 19.15 0.00 42.08 1.89
81 82 3.954904 CCAGGAGATCCGGATATTCGTAT 59.045 47.826 19.15 5.43 42.08 3.06
82 83 3.353557 CCAGGAGATCCGGATATTCGTA 58.646 50.000 19.15 0.00 42.08 3.43
83 84 2.171840 CCAGGAGATCCGGATATTCGT 58.828 52.381 19.15 16.26 42.08 3.85
84 85 1.478510 CCCAGGAGATCCGGATATTCG 59.521 57.143 19.15 9.44 42.08 3.34
85 86 1.208293 GCCCAGGAGATCCGGATATTC 59.792 57.143 19.15 14.10 42.08 1.75
86 87 1.280457 GCCCAGGAGATCCGGATATT 58.720 55.000 19.15 8.98 42.08 1.28
87 88 0.972983 CGCCCAGGAGATCCGGATAT 60.973 60.000 19.15 15.76 42.08 1.63
88 89 1.606601 CGCCCAGGAGATCCGGATA 60.607 63.158 19.15 0.00 42.08 2.59
89 90 2.919856 CGCCCAGGAGATCCGGAT 60.920 66.667 19.21 19.21 42.08 4.18
90 91 4.137615 TCGCCCAGGAGATCCGGA 62.138 66.667 6.61 6.61 42.08 5.14
91 92 3.610669 CTCGCCCAGGAGATCCGG 61.611 72.222 0.00 0.00 42.08 5.14
99 100 1.074084 TCTACTATCTCCTCGCCCAGG 59.926 57.143 0.00 0.00 45.15 4.45
100 101 2.570415 TCTACTATCTCCTCGCCCAG 57.430 55.000 0.00 0.00 0.00 4.45
101 102 2.108425 ACATCTACTATCTCCTCGCCCA 59.892 50.000 0.00 0.00 0.00 5.36
102 103 2.490115 CACATCTACTATCTCCTCGCCC 59.510 54.545 0.00 0.00 0.00 6.13
103 104 2.094957 GCACATCTACTATCTCCTCGCC 60.095 54.545 0.00 0.00 0.00 5.54
104 105 2.817258 AGCACATCTACTATCTCCTCGC 59.183 50.000 0.00 0.00 0.00 5.03
105 106 4.277174 ACAAGCACATCTACTATCTCCTCG 59.723 45.833 0.00 0.00 0.00 4.63
106 107 5.300539 TCACAAGCACATCTACTATCTCCTC 59.699 44.000 0.00 0.00 0.00 3.71
107 108 5.204292 TCACAAGCACATCTACTATCTCCT 58.796 41.667 0.00 0.00 0.00 3.69
108 109 5.508825 CCTCACAAGCACATCTACTATCTCC 60.509 48.000 0.00 0.00 0.00 3.71
109 110 5.527951 CCTCACAAGCACATCTACTATCTC 58.472 45.833 0.00 0.00 0.00 2.75
110 111 4.202202 GCCTCACAAGCACATCTACTATCT 60.202 45.833 0.00 0.00 0.00 1.98
111 112 4.054671 GCCTCACAAGCACATCTACTATC 58.945 47.826 0.00 0.00 0.00 2.08
112 113 3.181461 GGCCTCACAAGCACATCTACTAT 60.181 47.826 0.00 0.00 0.00 2.12
113 114 2.168521 GGCCTCACAAGCACATCTACTA 59.831 50.000 0.00 0.00 0.00 1.82
114 115 1.065854 GGCCTCACAAGCACATCTACT 60.066 52.381 0.00 0.00 0.00 2.57
115 116 1.373570 GGCCTCACAAGCACATCTAC 58.626 55.000 0.00 0.00 0.00 2.59
116 117 0.108186 CGGCCTCACAAGCACATCTA 60.108 55.000 0.00 0.00 0.00 1.98
117 118 1.376424 CGGCCTCACAAGCACATCT 60.376 57.895 0.00 0.00 0.00 2.90
118 119 2.401766 CCGGCCTCACAAGCACATC 61.402 63.158 0.00 0.00 0.00 3.06
119 120 2.360350 CCGGCCTCACAAGCACAT 60.360 61.111 0.00 0.00 0.00 3.21
151 152 2.892640 CGCTGGCTAGTGGCTACA 59.107 61.111 2.02 0.00 41.46 2.74
152 153 2.586357 GCGCTGGCTAGTGGCTAC 60.586 66.667 12.91 0.00 41.46 3.58
157 158 3.932580 TTCACGGCGCTGGCTAGTG 62.933 63.158 22.44 9.41 43.69 2.74
158 159 3.691342 TTCACGGCGCTGGCTAGT 61.691 61.111 22.44 0.00 39.81 2.57
159 160 3.188786 GTTCACGGCGCTGGCTAG 61.189 66.667 22.44 7.53 39.81 3.42
160 161 3.932580 CTGTTCACGGCGCTGGCTA 62.933 63.158 22.44 1.81 39.81 3.93
163 164 3.414700 GTCTGTTCACGGCGCTGG 61.415 66.667 22.44 9.81 0.00 4.85
164 165 3.414700 GGTCTGTTCACGGCGCTG 61.415 66.667 16.39 16.39 0.00 5.18
165 166 4.681978 GGGTCTGTTCACGGCGCT 62.682 66.667 6.90 0.00 0.00 5.92
192 193 1.204312 GCCAAGTTCAACGAGCGAC 59.796 57.895 0.00 0.00 0.00 5.19
193 194 1.221466 CTGCCAAGTTCAACGAGCGA 61.221 55.000 0.00 0.00 0.00 4.93
194 195 1.205064 CTGCCAAGTTCAACGAGCG 59.795 57.895 0.00 0.00 0.00 5.03
218 223 2.142220 TGGTCCACCTTCCAGACAC 58.858 57.895 0.00 0.00 36.82 3.67
225 230 4.048470 GCCCCCTGGTCCACCTTC 62.048 72.222 0.00 0.00 36.82 3.46
246 254 2.926779 AGAGGGCAGCTGCTCACA 60.927 61.111 38.55 0.00 46.01 3.58
257 265 3.745803 GCAACAGCAGCAGAGGGC 61.746 66.667 0.00 0.00 45.30 5.19
370 379 0.904865 TCTGTTCGTCCATGGCTCCT 60.905 55.000 6.96 0.00 0.00 3.69
423 432 0.459489 GTTTTTGTGTGGAGCAGGCA 59.541 50.000 0.00 0.00 0.00 4.75
424 433 0.746659 AGTTTTTGTGTGGAGCAGGC 59.253 50.000 0.00 0.00 0.00 4.85
425 434 2.948979 TGTAGTTTTTGTGTGGAGCAGG 59.051 45.455 0.00 0.00 0.00 4.85
426 435 3.876914 TCTGTAGTTTTTGTGTGGAGCAG 59.123 43.478 0.00 0.00 0.00 4.24
644 704 2.334946 TGAGCCAACCAGCGAATGC 61.335 57.895 0.00 0.00 43.24 3.56
645 705 1.503542 GTGAGCCAACCAGCGAATG 59.496 57.895 0.00 0.00 38.01 2.67
646 706 2.034879 CGTGAGCCAACCAGCGAAT 61.035 57.895 0.00 0.00 38.01 3.34
668 728 4.580551 CGTCCCGGGCGATGGTAC 62.581 72.222 26.75 13.09 0.00 3.34
768 840 2.972625 TCGAGGCTGTGTTAGATTTGG 58.027 47.619 0.00 0.00 0.00 3.28
771 843 2.607187 CGTTCGAGGCTGTGTTAGATT 58.393 47.619 0.00 0.00 0.00 2.40
772 844 1.736032 GCGTTCGAGGCTGTGTTAGAT 60.736 52.381 0.00 0.00 0.00 1.98
775 847 0.666274 CTGCGTTCGAGGCTGTGTTA 60.666 55.000 11.18 0.00 0.00 2.41
786 858 2.567470 ATTGCACGATGCTGCGTTCG 62.567 55.000 19.09 19.09 45.31 3.95
790 862 1.458220 CGAAATTGCACGATGCTGCG 61.458 55.000 10.54 0.00 45.31 5.18
807 879 1.884926 TGTGCATGCGTGTGTTCGA 60.885 52.632 14.09 0.00 0.00 3.71
839 911 1.946768 GATTCCGCAATTCCCGATTGA 59.053 47.619 3.12 0.00 46.59 2.57
866 938 3.840763 CGTGAAAAAGTAAAGCGAGATGC 59.159 43.478 0.00 0.00 46.98 3.91
897 975 1.069432 CACCATATTGCAGCAGATCGC 60.069 52.381 0.00 1.92 42.91 4.58
898 976 1.534163 CCACCATATTGCAGCAGATCG 59.466 52.381 0.00 0.00 0.00 3.69
924 1021 4.355543 ACGTGCATTTTTATACTGGCAG 57.644 40.909 14.16 14.16 31.10 4.85
927 1024 6.521821 GTGTGTTACGTGCATTTTTATACTGG 59.478 38.462 0.00 0.00 0.00 4.00
1365 1465 1.815421 CTTGAAGCCGTCGGGGATG 60.815 63.158 14.38 0.00 38.47 3.51
1410 1518 3.755526 ATGCATGGGCGCTCGCTTA 62.756 57.895 7.64 4.04 45.35 3.09
1437 3659 1.880601 GCTTCGACACACAGACAGCG 61.881 60.000 0.00 0.00 0.00 5.18
1462 3684 7.978975 AGTAGAAGTCAATGAAACTGAGCTATC 59.021 37.037 0.00 0.00 0.00 2.08
1465 3687 5.931146 CAGTAGAAGTCAATGAAACTGAGCT 59.069 40.000 0.00 0.00 0.00 4.09
1469 3691 8.826710 TGTTTACAGTAGAAGTCAATGAAACTG 58.173 33.333 0.00 0.00 0.00 3.16
1506 3728 9.830975 AGGAAGCAAAATGTTTACAGTAAAAAT 57.169 25.926 7.35 5.13 0.00 1.82
1508 3730 9.959749 CTAGGAAGCAAAATGTTTACAGTAAAA 57.040 29.630 7.35 0.00 0.00 1.52
1509 3731 9.127277 ACTAGGAAGCAAAATGTTTACAGTAAA 57.873 29.630 1.26 1.26 0.00 2.01
1510 3732 8.685838 ACTAGGAAGCAAAATGTTTACAGTAA 57.314 30.769 0.00 0.00 0.00 2.24
1511 3733 8.685838 AACTAGGAAGCAAAATGTTTACAGTA 57.314 30.769 0.00 0.00 0.00 2.74
1512 3734 7.255486 GGAACTAGGAAGCAAAATGTTTACAGT 60.255 37.037 0.00 0.00 0.00 3.55
1513 3735 7.084486 GGAACTAGGAAGCAAAATGTTTACAG 58.916 38.462 0.00 0.00 0.00 2.74
1514 3736 6.015772 GGGAACTAGGAAGCAAAATGTTTACA 60.016 38.462 0.00 0.00 0.00 2.41
1515 3737 6.015772 TGGGAACTAGGAAGCAAAATGTTTAC 60.016 38.462 0.00 0.00 0.00 2.01
1532 3754 3.694072 GCATTTGCATACACTGGGAACTA 59.306 43.478 0.00 0.00 41.59 2.24
1562 3784 7.338957 TGATTCATGTATAGTCCATGCAAAACA 59.661 33.333 0.00 0.00 39.60 2.83
1580 3802 8.712285 AGAAATTAACTTGGCATTGATTCATG 57.288 30.769 0.00 0.00 0.00 3.07
1596 3826 8.234546 TCCTTCGTATCAAGCAAAGAAATTAAC 58.765 33.333 0.00 0.00 0.00 2.01
1629 3859 9.921637 TCAAACAAAGTCAAGTAAAGAAATTGT 57.078 25.926 0.00 0.00 31.42 2.71
1647 3877 6.442541 TGGAGGGAGTATTACTCAAACAAA 57.557 37.500 22.10 3.91 46.79 2.83
1663 3893 3.916349 TCTTCCTTTTGAGAATGGAGGGA 59.084 43.478 0.00 0.00 39.45 4.20
1673 3903 9.846248 CCAAAAGTTATATGTCTTCCTTTTGAG 57.154 33.333 18.91 9.19 45.69 3.02
1688 3918 7.284489 ACAGTTTGACTTGAGCCAAAAGTTATA 59.716 33.333 0.00 0.00 37.98 0.98
1699 3929 2.849880 TTGCACAGTTTGACTTGAGC 57.150 45.000 0.00 0.00 0.00 4.26
1712 3942 4.999950 ACAAACTTGGTCAAATTTTGCACA 59.000 33.333 4.19 3.34 31.53 4.57
1751 3981 6.697892 GCAAGCCTACTCTAGTATTGTAGTTG 59.302 42.308 0.00 0.00 33.75 3.16
1754 3984 6.488683 AGAGCAAGCCTACTCTAGTATTGTAG 59.511 42.308 0.00 0.00 41.44 2.74
1763 4088 4.711846 TCAAATGAGAGCAAGCCTACTCTA 59.288 41.667 0.36 2.08 43.26 2.43
1771 4096 3.501445 ACTGTCTTCAAATGAGAGCAAGC 59.499 43.478 0.00 0.00 0.00 4.01
1798 4125 0.591236 CAACACAAACGACCGGCAAG 60.591 55.000 0.00 0.00 0.00 4.01
1838 4165 1.606313 GGTGACAATGGTGGGTGGG 60.606 63.158 0.00 0.00 0.00 4.61
1843 4170 3.391965 CATTTTGTGGTGACAATGGTGG 58.608 45.455 0.00 0.00 46.06 4.61
1844 4171 3.391965 CCATTTTGTGGTGACAATGGTG 58.608 45.455 4.06 0.00 46.06 4.17
1845 4172 3.749665 CCATTTTGTGGTGACAATGGT 57.250 42.857 4.06 0.00 46.06 3.55
1864 4191 1.774894 TTGACACTACACCCCTGCCC 61.775 60.000 0.00 0.00 0.00 5.36
1887 4251 5.700832 CAGTATGTCCCATAATGCAATACGT 59.299 40.000 0.00 0.00 0.00 3.57
1888 4252 5.931724 TCAGTATGTCCCATAATGCAATACG 59.068 40.000 6.77 0.00 37.40 3.06
1889 4253 6.936900 ACTCAGTATGTCCCATAATGCAATAC 59.063 38.462 6.77 0.00 37.40 1.89
1891 4255 5.945310 ACTCAGTATGTCCCATAATGCAAT 58.055 37.500 6.77 0.00 37.40 3.56
1894 4258 6.974932 CATACTCAGTATGTCCCATAATGC 57.025 41.667 15.79 0.00 40.44 3.56
1906 4270 7.016153 TGAGGGACAAAAACATACTCAGTAT 57.984 36.000 0.00 0.00 0.00 2.12
1907 4271 6.428083 TGAGGGACAAAAACATACTCAGTA 57.572 37.500 0.00 0.00 0.00 2.74
1909 4273 6.633500 TTTGAGGGACAAAAACATACTCAG 57.367 37.500 0.00 0.00 44.16 3.35
1951 4315 9.940166 GTTTACGAAATTCTTTTGAAGGACTAA 57.060 29.630 0.00 0.00 42.30 2.24
1952 4316 9.111613 TGTTTACGAAATTCTTTTGAAGGACTA 57.888 29.630 0.00 0.00 42.30 2.59
1954 4318 7.913821 AGTGTTTACGAAATTCTTTTGAAGGAC 59.086 33.333 0.00 0.00 42.30 3.85
1955 4319 7.992008 AGTGTTTACGAAATTCTTTTGAAGGA 58.008 30.769 0.00 0.00 42.30 3.36
1956 4320 8.531530 CAAGTGTTTACGAAATTCTTTTGAAGG 58.468 33.333 0.00 0.00 42.30 3.46
1957 4321 8.531530 CCAAGTGTTTACGAAATTCTTTTGAAG 58.468 33.333 0.00 0.00 42.30 3.02
1959 4323 7.540299 ACCAAGTGTTTACGAAATTCTTTTGA 58.460 30.769 0.00 0.00 0.00 2.69
1960 4324 7.043656 GGACCAAGTGTTTACGAAATTCTTTTG 60.044 37.037 0.00 0.00 0.00 2.44
1961 4325 6.976349 GGACCAAGTGTTTACGAAATTCTTTT 59.024 34.615 0.00 0.00 0.00 2.27
1962 4326 6.460537 GGGACCAAGTGTTTACGAAATTCTTT 60.461 38.462 0.00 0.00 0.00 2.52
1963 4327 5.009310 GGGACCAAGTGTTTACGAAATTCTT 59.991 40.000 0.00 0.00 0.00 2.52
1964 4328 4.517832 GGGACCAAGTGTTTACGAAATTCT 59.482 41.667 0.00 0.00 0.00 2.40
1965 4329 4.517832 AGGGACCAAGTGTTTACGAAATTC 59.482 41.667 0.00 0.00 0.00 2.17
1966 4330 4.466827 AGGGACCAAGTGTTTACGAAATT 58.533 39.130 0.00 0.00 0.00 1.82
1967 4331 4.070009 GAGGGACCAAGTGTTTACGAAAT 58.930 43.478 0.00 0.00 0.00 2.17
1968 4332 3.469739 GAGGGACCAAGTGTTTACGAAA 58.530 45.455 0.00 0.00 0.00 3.46
1969 4333 2.546373 CGAGGGACCAAGTGTTTACGAA 60.546 50.000 0.00 0.00 0.00 3.85
1970 4334 1.000060 CGAGGGACCAAGTGTTTACGA 60.000 52.381 0.00 0.00 0.00 3.43
1971 4335 1.000060 TCGAGGGACCAAGTGTTTACG 60.000 52.381 0.00 0.00 0.00 3.18
1972 4336 2.036862 ACTCGAGGGACCAAGTGTTTAC 59.963 50.000 18.41 0.00 0.00 2.01
1973 4337 2.298163 GACTCGAGGGACCAAGTGTTTA 59.702 50.000 18.41 0.00 0.00 2.01
1974 4338 1.070289 GACTCGAGGGACCAAGTGTTT 59.930 52.381 18.41 0.00 0.00 2.83
1975 4339 0.680061 GACTCGAGGGACCAAGTGTT 59.320 55.000 18.41 0.00 0.00 3.32
1979 4343 1.257743 TTGAGACTCGAGGGACCAAG 58.742 55.000 18.41 0.00 0.00 3.61
1990 4354 1.732809 GCTTAGCCGGTTTTGAGACTC 59.267 52.381 1.90 0.00 0.00 3.36
2005 4369 3.186613 GTCTGGTTTTGGACGAAGCTTAG 59.813 47.826 0.00 0.68 0.00 2.18
2010 4374 1.961793 TGGTCTGGTTTTGGACGAAG 58.038 50.000 0.00 0.00 33.70 3.79
2014 4378 3.888930 TCAAAGATGGTCTGGTTTTGGAC 59.111 43.478 0.00 0.00 31.47 4.02
2016 4380 3.005791 GGTCAAAGATGGTCTGGTTTTGG 59.994 47.826 0.00 0.00 31.47 3.28
2025 4389 1.539827 CAAACCCGGTCAAAGATGGTC 59.460 52.381 0.00 0.00 0.00 4.02
2027 4391 1.539827 GTCAAACCCGGTCAAAGATGG 59.460 52.381 0.00 0.00 0.00 3.51
2028 4392 1.539827 GGTCAAACCCGGTCAAAGATG 59.460 52.381 0.00 0.00 30.04 2.90
2029 4393 1.880646 CGGTCAAACCCGGTCAAAGAT 60.881 52.381 0.00 0.00 44.32 2.40
2031 4395 1.946267 CGGTCAAACCCGGTCAAAG 59.054 57.895 0.00 0.00 44.32 2.77
2032 4396 4.144418 CGGTCAAACCCGGTCAAA 57.856 55.556 0.00 0.00 44.32 2.69
2039 4408 0.322187 ACTATGTGGCGGTCAAACCC 60.322 55.000 0.00 0.00 33.75 4.11
2054 4423 7.744087 TTACTGTTCATGAAGCACAAACTAT 57.256 32.000 8.80 0.00 0.00 2.12
2057 4426 7.698836 AATTTACTGTTCATGAAGCACAAAC 57.301 32.000 8.80 0.00 0.00 2.93
2109 4497 7.466746 ACTTGAGCATATTGGAAGCTAAAAA 57.533 32.000 0.00 0.00 39.02 1.94
2114 4502 4.122776 CGTACTTGAGCATATTGGAAGCT 58.877 43.478 0.00 0.00 42.17 3.74
2115 4503 3.248602 CCGTACTTGAGCATATTGGAAGC 59.751 47.826 0.00 0.00 0.00 3.86
2117 4505 4.746535 TCCGTACTTGAGCATATTGGAA 57.253 40.909 0.00 0.00 0.00 3.53
2120 4508 4.876107 ACCTTTCCGTACTTGAGCATATTG 59.124 41.667 0.00 0.00 0.00 1.90
2121 4509 4.876107 CACCTTTCCGTACTTGAGCATATT 59.124 41.667 0.00 0.00 0.00 1.28
2136 4524 5.323360 CAAAAATTTGTACGCACCTTTCC 57.677 39.130 0.00 0.00 33.59 3.13
2156 4544 0.309302 CAATTGTCCGAACGCCACAA 59.691 50.000 0.00 10.61 34.61 3.33
2157 4545 0.533085 TCAATTGTCCGAACGCCACA 60.533 50.000 5.13 0.00 0.00 4.17
2158 4546 0.165944 CTCAATTGTCCGAACGCCAC 59.834 55.000 5.13 0.00 0.00 5.01
2166 4554 1.391485 CACGAGCTTCTCAATTGTCCG 59.609 52.381 5.13 3.00 0.00 4.79
2178 4566 4.584327 ATTTTACTTTTGGCACGAGCTT 57.416 36.364 4.48 0.00 41.70 3.74
2260 4651 3.955471 TGGTTGCCACAAAATTTCCAAA 58.045 36.364 0.00 0.00 0.00 3.28
2262 4653 3.198635 TCTTGGTTGCCACAAAATTTCCA 59.801 39.130 0.00 0.00 30.78 3.53
2264 4655 4.319694 GCATCTTGGTTGCCACAAAATTTC 60.320 41.667 0.00 0.00 33.95 2.17
2266 4657 3.140623 GCATCTTGGTTGCCACAAAATT 58.859 40.909 0.00 0.00 33.95 1.82
2296 4687 3.551551 CAAAACTTTGTACGCACCTAGC 58.448 45.455 0.00 0.00 35.10 3.42
2307 4698 7.725251 TCCTCAGATAATTTGCAAAACTTTGT 58.275 30.769 17.19 4.43 40.24 2.83
2312 4703 7.994194 AGAGATCCTCAGATAATTTGCAAAAC 58.006 34.615 17.19 8.25 30.90 2.43


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

AutoCloner maintained by Alex Coulton.