Multiple sequence alignment - TraesCS6D01G165900

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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 TraesCS6D01G165900 chr6D 100.000 3970 0 0 1 3970 146505726 146509695 0.000000e+00 7332.0
1 TraesCS6D01G165900 chr6D 98.312 3080 39 4 893 3970 131032865 131029797 0.000000e+00 5387.0
2 TraesCS6D01G165900 chr6D 95.625 3040 76 16 376 3391 130214175 130211169 0.000000e+00 4824.0
3 TraesCS6D01G165900 chr6D 87.409 548 44 12 333 863 131033406 131032867 1.220000e-169 606.0
4 TraesCS6D01G165900 chr6D 85.235 596 33 19 3378 3970 130211154 130210611 2.680000e-156 562.0
5 TraesCS6D01G165900 chr6B 97.471 3638 64 7 335 3970 257783583 257779972 0.000000e+00 6183.0
6 TraesCS6D01G165900 chr6B 92.201 3667 168 41 335 3970 228758106 228754527 0.000000e+00 5079.0
7 TraesCS6D01G165900 chr6B 93.109 3149 159 29 831 3970 230602352 230605451 0.000000e+00 4560.0
8 TraesCS6D01G165900 chr6B 89.486 1265 104 9 991 2249 213521302 213522543 0.000000e+00 1572.0
9 TraesCS6D01G165900 chr6A 94.360 2163 75 11 813 2962 171738696 171740824 0.000000e+00 3275.0
10 TraesCS6D01G165900 chr6A 94.232 1907 70 19 641 2529 169226964 169225080 0.000000e+00 2876.0
11 TraesCS6D01G165900 chr6A 94.154 1454 58 15 2525 3970 169221052 169219618 0.000000e+00 2189.0
12 TraesCS6D01G165900 chr6A 92.893 999 43 15 2979 3970 171740812 171741789 0.000000e+00 1426.0
13 TraesCS6D01G165900 chr6A 89.252 1163 54 29 968 2123 162911123 162912221 0.000000e+00 1389.0
14 TraesCS6D01G165900 chr6A 87.472 878 77 17 2979 3853 162913640 162914487 0.000000e+00 981.0
15 TraesCS6D01G165900 chr6A 93.226 620 29 2 2354 2962 162913035 162913652 0.000000e+00 900.0
16 TraesCS6D01G165900 chr6A 85.168 654 70 17 377 1015 169254958 169254317 0.000000e+00 645.0
17 TraesCS6D01G165900 chr6A 93.069 101 4 2 781 880 171738604 171738702 1.150000e-30 145.0
18 TraesCS6D01G165900 chr6A 93.333 75 5 0 3896 3970 162914481 162914555 1.170000e-20 111.0
19 TraesCS6D01G165900 chr6A 75.686 255 39 14 687 928 162909448 162909692 5.430000e-19 106.0
20 TraesCS6D01G165900 chr5B 94.616 1133 51 4 1842 2965 84884569 84883438 0.000000e+00 1746.0
21 TraesCS6D01G165900 chr5B 91.863 848 47 7 3125 3970 84883226 84882399 0.000000e+00 1164.0
22 TraesCS6D01G165900 chr5B 94.702 151 5 2 2979 3128 84883453 84883305 8.580000e-57 231.0
23 TraesCS6D01G165900 chr7D 94.675 338 17 1 1 337 382328834 382328497 1.260000e-144 523.0
24 TraesCS6D01G165900 chr7D 94.910 334 15 2 1 334 287990636 287990305 4.550000e-144 521.0
25 TraesCS6D01G165900 chr3D 94.643 336 17 1 1 336 123557151 123557485 1.640000e-143 520.0
26 TraesCS6D01G165900 chr3D 94.012 334 19 1 1 334 502600570 502600902 4.580000e-139 505.0
27 TraesCS6D01G165900 chr2D 94.611 334 17 1 1 334 440955370 440955702 2.120000e-142 516.0
28 TraesCS6D01G165900 chr4D 94.328 335 18 1 1 335 68643421 68643754 2.740000e-141 512.0
29 TraesCS6D01G165900 chr1D 94.328 335 17 2 1 335 389154560 389154892 2.740000e-141 512.0
30 TraesCS6D01G165900 chr1D 94.065 337 19 1 1 337 190088735 190088400 9.840000e-141 510.0
31 TraesCS6D01G165900 chr1D 87.218 133 11 4 641 768 266787784 266787653 3.200000e-31 147.0
32 TraesCS6D01G165900 chr5D 94.311 334 16 3 1 334 111549442 111549772 3.540000e-140 508.0
33 TraesCS6D01G165900 chr5D 78.491 265 33 11 374 632 449127787 449128033 6.870000e-33 152.0
34 TraesCS6D01G165900 chr5D 100.000 29 0 0 626 654 199164307 199164279 2.000000e-03 54.7


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 TraesCS6D01G165900 chr6D 146505726 146509695 3969 False 7332.000000 7332 100.000000 1 3970 1 chr6D.!!$F1 3969
1 TraesCS6D01G165900 chr6D 131029797 131033406 3609 True 2996.500000 5387 92.860500 333 3970 2 chr6D.!!$R2 3637
2 TraesCS6D01G165900 chr6D 130210611 130214175 3564 True 2693.000000 4824 90.430000 376 3970 2 chr6D.!!$R1 3594
3 TraesCS6D01G165900 chr6B 257779972 257783583 3611 True 6183.000000 6183 97.471000 335 3970 1 chr6B.!!$R2 3635
4 TraesCS6D01G165900 chr6B 228754527 228758106 3579 True 5079.000000 5079 92.201000 335 3970 1 chr6B.!!$R1 3635
5 TraesCS6D01G165900 chr6B 230602352 230605451 3099 False 4560.000000 4560 93.109000 831 3970 1 chr6B.!!$F2 3139
6 TraesCS6D01G165900 chr6B 213521302 213522543 1241 False 1572.000000 1572 89.486000 991 2249 1 chr6B.!!$F1 1258
7 TraesCS6D01G165900 chr6A 169225080 169226964 1884 True 2876.000000 2876 94.232000 641 2529 1 chr6A.!!$R2 1888
8 TraesCS6D01G165900 chr6A 169219618 169221052 1434 True 2189.000000 2189 94.154000 2525 3970 1 chr6A.!!$R1 1445
9 TraesCS6D01G165900 chr6A 171738604 171741789 3185 False 1615.333333 3275 93.440667 781 3970 3 chr6A.!!$F2 3189
10 TraesCS6D01G165900 chr6A 162909448 162914555 5107 False 697.400000 1389 87.793800 687 3970 5 chr6A.!!$F1 3283
11 TraesCS6D01G165900 chr6A 169254317 169254958 641 True 645.000000 645 85.168000 377 1015 1 chr6A.!!$R3 638
12 TraesCS6D01G165900 chr5B 84882399 84884569 2170 True 1047.000000 1746 93.727000 1842 3970 3 chr5B.!!$R1 2128

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
79 80 0.033504 TGCTTCCTTGACGTCCACTC 59.966 55.0 14.12 0.0 0.0 3.51 F
89 90 0.178958 ACGTCCACTCCAAGTCTCCT 60.179 55.0 0.00 0.0 0.0 3.69 F
90 91 0.244994 CGTCCACTCCAAGTCTCCTG 59.755 60.0 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 3628 1.597854 CCAAGTTGTCCTCGCTGCA 60.598 57.895 1.45 0.00 0.00 4.41 R
2635 4939 3.557264 GGTCCTTTGAGTCGAGGTTGATT 60.557 47.826 11.04 0.00 34.57 2.57 R
3932 6386 7.331934 TGAGTTCCATATCAAGAAAGACTTTCG 59.668 37.037 19.67 8.92 44.29 3.46 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
30 31 4.514577 CGCGCCTACCTCACTGGG 62.515 72.222 0.00 0.00 41.11 4.45
31 32 4.840005 GCGCCTACCTCACTGGGC 62.840 72.222 0.00 0.00 41.11 5.36
33 34 4.840005 GCCTACCTCACTGGGCGC 62.840 72.222 0.00 0.00 41.11 6.53
34 35 4.514577 CCTACCTCACTGGGCGCG 62.515 72.222 0.00 0.00 41.11 6.86
53 54 3.905678 CCTCCTACCTCGCGGCTG 61.906 72.222 6.13 0.00 0.00 4.85
54 55 4.577246 CTCCTACCTCGCGGCTGC 62.577 72.222 7.70 7.70 37.91 5.25
57 58 4.577246 CTACCTCGCGGCTGCCTC 62.577 72.222 17.92 8.04 38.08 4.70
65 66 3.793144 CGGCTGCCTCGTTGCTTC 61.793 66.667 17.92 0.00 0.00 3.86
66 67 3.435186 GGCTGCCTCGTTGCTTCC 61.435 66.667 12.43 0.00 0.00 3.46
67 68 2.359230 GCTGCCTCGTTGCTTCCT 60.359 61.111 0.00 0.00 0.00 3.36
68 69 1.968540 GCTGCCTCGTTGCTTCCTT 60.969 57.895 0.00 0.00 0.00 3.36
69 70 1.871772 CTGCCTCGTTGCTTCCTTG 59.128 57.895 1.05 0.00 0.00 3.61
70 71 0.603707 CTGCCTCGTTGCTTCCTTGA 60.604 55.000 1.05 0.00 0.00 3.02
71 72 0.884704 TGCCTCGTTGCTTCCTTGAC 60.885 55.000 1.05 0.00 0.00 3.18
72 73 1.901650 GCCTCGTTGCTTCCTTGACG 61.902 60.000 0.00 0.00 36.89 4.35
73 74 0.600255 CCTCGTTGCTTCCTTGACGT 60.600 55.000 0.00 0.00 36.89 4.34
74 75 0.784778 CTCGTTGCTTCCTTGACGTC 59.215 55.000 9.11 9.11 36.89 4.34
75 76 0.599204 TCGTTGCTTCCTTGACGTCC 60.599 55.000 14.12 0.00 36.89 4.79
76 77 0.878523 CGTTGCTTCCTTGACGTCCA 60.879 55.000 14.12 0.00 0.00 4.02
77 78 0.586802 GTTGCTTCCTTGACGTCCAC 59.413 55.000 14.12 0.00 0.00 4.02
78 79 0.468226 TTGCTTCCTTGACGTCCACT 59.532 50.000 14.12 0.00 0.00 4.00
79 80 0.033504 TGCTTCCTTGACGTCCACTC 59.966 55.000 14.12 0.00 0.00 3.51
80 81 0.670854 GCTTCCTTGACGTCCACTCC 60.671 60.000 14.12 0.00 0.00 3.85
81 82 0.679505 CTTCCTTGACGTCCACTCCA 59.320 55.000 14.12 0.00 0.00 3.86
82 83 1.070134 CTTCCTTGACGTCCACTCCAA 59.930 52.381 14.12 0.00 0.00 3.53
83 84 0.679505 TCCTTGACGTCCACTCCAAG 59.320 55.000 14.12 9.17 36.64 3.61
84 85 0.393077 CCTTGACGTCCACTCCAAGT 59.607 55.000 14.12 0.00 35.50 3.16
85 86 1.605712 CCTTGACGTCCACTCCAAGTC 60.606 57.143 14.12 0.00 35.50 3.01
86 87 1.341531 CTTGACGTCCACTCCAAGTCT 59.658 52.381 14.12 0.00 33.34 3.24
87 88 0.959553 TGACGTCCACTCCAAGTCTC 59.040 55.000 14.12 0.00 33.40 3.36
88 89 0.244178 GACGTCCACTCCAAGTCTCC 59.756 60.000 3.51 0.00 0.00 3.71
89 90 0.178958 ACGTCCACTCCAAGTCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
90 91 0.244994 CGTCCACTCCAAGTCTCCTG 59.755 60.000 0.00 0.00 0.00 3.86
91 92 0.610687 GTCCACTCCAAGTCTCCTGG 59.389 60.000 0.00 0.00 0.00 4.45
92 93 0.487325 TCCACTCCAAGTCTCCTGGA 59.513 55.000 0.00 0.00 0.00 3.86
93 94 1.079490 TCCACTCCAAGTCTCCTGGAT 59.921 52.381 0.00 0.00 0.00 3.41
94 95 1.912043 CCACTCCAAGTCTCCTGGATT 59.088 52.381 0.00 0.00 0.00 3.01
95 96 2.355513 CCACTCCAAGTCTCCTGGATTG 60.356 54.545 0.00 0.00 33.75 2.67
96 97 1.280421 ACTCCAAGTCTCCTGGATTGC 59.720 52.381 0.00 0.00 0.00 3.56
97 98 1.280133 CTCCAAGTCTCCTGGATTGCA 59.720 52.381 0.00 0.00 0.00 4.08
98 99 1.918262 TCCAAGTCTCCTGGATTGCAT 59.082 47.619 0.00 0.00 0.00 3.96
99 100 2.309755 TCCAAGTCTCCTGGATTGCATT 59.690 45.455 0.00 0.00 0.00 3.56
100 101 3.094572 CCAAGTCTCCTGGATTGCATTT 58.905 45.455 0.00 0.00 0.00 2.32
101 102 3.119245 CCAAGTCTCCTGGATTGCATTTG 60.119 47.826 0.00 0.00 0.00 2.32
102 103 3.446442 AGTCTCCTGGATTGCATTTGT 57.554 42.857 0.00 0.00 0.00 2.83
103 104 3.771216 AGTCTCCTGGATTGCATTTGTT 58.229 40.909 0.00 0.00 0.00 2.83
104 105 3.760684 AGTCTCCTGGATTGCATTTGTTC 59.239 43.478 0.00 0.00 0.00 3.18
105 106 3.760684 GTCTCCTGGATTGCATTTGTTCT 59.239 43.478 0.00 0.00 0.00 3.01
106 107 4.943705 GTCTCCTGGATTGCATTTGTTCTA 59.056 41.667 0.00 0.00 0.00 2.10
107 108 5.415701 GTCTCCTGGATTGCATTTGTTCTAA 59.584 40.000 0.00 0.00 0.00 2.10
108 109 6.009589 TCTCCTGGATTGCATTTGTTCTAAA 58.990 36.000 0.00 0.00 0.00 1.85
109 110 6.493115 TCTCCTGGATTGCATTTGTTCTAAAA 59.507 34.615 0.00 0.00 0.00 1.52
110 111 7.015098 TCTCCTGGATTGCATTTGTTCTAAAAA 59.985 33.333 0.00 0.00 0.00 1.94
111 112 6.928492 TCCTGGATTGCATTTGTTCTAAAAAC 59.072 34.615 0.00 0.00 0.00 2.43
112 113 6.705381 CCTGGATTGCATTTGTTCTAAAAACA 59.295 34.615 0.00 0.00 0.00 2.83
113 114 7.226325 CCTGGATTGCATTTGTTCTAAAAACAA 59.774 33.333 0.00 0.00 38.26 2.83
114 115 7.914465 TGGATTGCATTTGTTCTAAAAACAAC 58.086 30.769 3.00 0.00 39.57 3.32
115 116 7.768120 TGGATTGCATTTGTTCTAAAAACAACT 59.232 29.630 3.00 0.00 39.57 3.16
116 117 8.275632 GGATTGCATTTGTTCTAAAAACAACTC 58.724 33.333 3.00 0.00 39.57 3.01
117 118 8.947055 ATTGCATTTGTTCTAAAAACAACTCT 57.053 26.923 3.00 0.00 39.57 3.24
118 119 7.985634 TGCATTTGTTCTAAAAACAACTCTC 57.014 32.000 3.00 0.00 39.57 3.20
119 120 6.978080 TGCATTTGTTCTAAAAACAACTCTCC 59.022 34.615 3.00 0.00 39.57 3.71
120 121 6.420903 GCATTTGTTCTAAAAACAACTCTCCC 59.579 38.462 3.00 0.00 39.57 4.30
121 122 5.744666 TTGTTCTAAAAACAACTCTCCCG 57.255 39.130 0.00 0.00 35.45 5.14
122 123 5.026038 TGTTCTAAAAACAACTCTCCCGA 57.974 39.130 0.00 0.00 0.00 5.14
123 124 5.430007 TGTTCTAAAAACAACTCTCCCGAA 58.570 37.500 0.00 0.00 0.00 4.30
124 125 5.526111 TGTTCTAAAAACAACTCTCCCGAAG 59.474 40.000 0.00 0.00 0.00 3.79
125 126 8.805918 TTGTTCTAAAAACAACTCTCCCGAAGG 61.806 40.741 0.00 0.00 40.56 3.46
140 141 2.928694 CGAAGGTTTCATTCCGTTTGG 58.071 47.619 0.00 0.00 0.00 3.28
141 142 2.550606 CGAAGGTTTCATTCCGTTTGGA 59.449 45.455 0.00 0.00 44.61 3.53
142 143 3.190535 CGAAGGTTTCATTCCGTTTGGAT 59.809 43.478 0.00 0.00 45.91 3.41
143 144 4.320935 CGAAGGTTTCATTCCGTTTGGATT 60.321 41.667 0.00 0.00 45.91 3.01
144 145 4.783764 AGGTTTCATTCCGTTTGGATTC 57.216 40.909 0.00 0.00 45.91 2.52
145 146 3.509967 AGGTTTCATTCCGTTTGGATTCC 59.490 43.478 0.00 0.00 45.91 3.01
146 147 3.498082 GTTTCATTCCGTTTGGATTCCG 58.502 45.455 0.00 0.00 45.91 4.30
147 148 2.483014 TCATTCCGTTTGGATTCCGT 57.517 45.000 0.00 0.00 45.91 4.69
148 149 2.785562 TCATTCCGTTTGGATTCCGTT 58.214 42.857 0.00 0.00 45.91 4.44
149 150 3.150767 TCATTCCGTTTGGATTCCGTTT 58.849 40.909 0.00 0.00 45.91 3.60
150 151 3.057876 TCATTCCGTTTGGATTCCGTTTG 60.058 43.478 0.00 0.00 45.91 2.93
151 152 2.257691 TCCGTTTGGATTCCGTTTGA 57.742 45.000 0.00 0.00 40.17 2.69
152 153 2.785562 TCCGTTTGGATTCCGTTTGAT 58.214 42.857 0.00 0.00 40.17 2.57
153 154 3.940319 TCCGTTTGGATTCCGTTTGATA 58.060 40.909 0.00 0.00 40.17 2.15
154 155 4.519213 TCCGTTTGGATTCCGTTTGATAT 58.481 39.130 0.00 0.00 40.17 1.63
155 156 4.944930 TCCGTTTGGATTCCGTTTGATATT 59.055 37.500 0.00 0.00 40.17 1.28
156 157 5.065474 TCCGTTTGGATTCCGTTTGATATTC 59.935 40.000 0.00 0.00 40.17 1.75
157 158 5.270853 CGTTTGGATTCCGTTTGATATTCC 58.729 41.667 0.00 0.00 0.00 3.01
158 159 5.065988 CGTTTGGATTCCGTTTGATATTCCT 59.934 40.000 0.00 0.00 0.00 3.36
159 160 6.404293 CGTTTGGATTCCGTTTGATATTCCTT 60.404 38.462 0.00 0.00 0.00 3.36
160 161 7.320399 GTTTGGATTCCGTTTGATATTCCTTT 58.680 34.615 0.00 0.00 0.00 3.11
161 162 7.475137 TTGGATTCCGTTTGATATTCCTTTT 57.525 32.000 0.00 0.00 0.00 2.27
162 163 7.095695 TGGATTCCGTTTGATATTCCTTTTC 57.904 36.000 0.00 0.00 0.00 2.29
163 164 6.889722 TGGATTCCGTTTGATATTCCTTTTCT 59.110 34.615 0.00 0.00 0.00 2.52
164 165 7.148086 TGGATTCCGTTTGATATTCCTTTTCTG 60.148 37.037 0.00 0.00 0.00 3.02
165 166 5.560966 TCCGTTTGATATTCCTTTTCTGC 57.439 39.130 0.00 0.00 0.00 4.26
166 167 4.094294 TCCGTTTGATATTCCTTTTCTGCG 59.906 41.667 0.00 0.00 0.00 5.18
167 168 4.094294 CCGTTTGATATTCCTTTTCTGCGA 59.906 41.667 0.00 0.00 0.00 5.10
168 169 5.391523 CCGTTTGATATTCCTTTTCTGCGAA 60.392 40.000 0.00 0.00 0.00 4.70
169 170 6.083630 CGTTTGATATTCCTTTTCTGCGAAA 58.916 36.000 0.00 0.55 0.00 3.46
170 171 6.032460 CGTTTGATATTCCTTTTCTGCGAAAC 59.968 38.462 3.71 0.00 0.00 2.78
171 172 6.567687 TTGATATTCCTTTTCTGCGAAACA 57.432 33.333 3.71 0.00 0.00 2.83
172 173 5.938322 TGATATTCCTTTTCTGCGAAACAC 58.062 37.500 3.71 0.00 0.00 3.32
173 174 5.705441 TGATATTCCTTTTCTGCGAAACACT 59.295 36.000 3.71 0.00 0.00 3.55
174 175 3.691049 TTCCTTTTCTGCGAAACACTG 57.309 42.857 3.71 0.00 0.00 3.66
175 176 2.912771 TCCTTTTCTGCGAAACACTGA 58.087 42.857 3.71 0.00 0.00 3.41
176 177 3.275143 TCCTTTTCTGCGAAACACTGAA 58.725 40.909 3.71 0.00 0.00 3.02
177 178 3.692101 TCCTTTTCTGCGAAACACTGAAA 59.308 39.130 3.71 0.00 34.44 2.69
178 179 4.338118 TCCTTTTCTGCGAAACACTGAAAT 59.662 37.500 3.71 0.00 35.68 2.17
179 180 5.529430 TCCTTTTCTGCGAAACACTGAAATA 59.471 36.000 3.71 0.00 35.68 1.40
180 181 5.853282 CCTTTTCTGCGAAACACTGAAATAG 59.147 40.000 3.71 0.00 35.68 1.73
181 182 5.356882 TTTCTGCGAAACACTGAAATAGG 57.643 39.130 0.00 0.00 32.25 2.57
182 183 4.265904 TCTGCGAAACACTGAAATAGGA 57.734 40.909 0.00 0.00 0.00 2.94
183 184 4.637276 TCTGCGAAACACTGAAATAGGAA 58.363 39.130 0.00 0.00 0.00 3.36
184 185 5.060506 TCTGCGAAACACTGAAATAGGAAA 58.939 37.500 0.00 0.00 0.00 3.13
185 186 5.529430 TCTGCGAAACACTGAAATAGGAAAA 59.471 36.000 0.00 0.00 0.00 2.29
186 187 6.038825 TCTGCGAAACACTGAAATAGGAAAAA 59.961 34.615 0.00 0.00 0.00 1.94
212 213 2.749280 GCAATTTGCACTAGGCCTTT 57.251 45.000 12.58 0.00 44.26 3.11
213 214 2.340337 GCAATTTGCACTAGGCCTTTG 58.660 47.619 12.58 10.50 44.26 2.77
214 215 2.932187 GCAATTTGCACTAGGCCTTTGG 60.932 50.000 12.58 4.33 44.26 3.28
215 216 2.299867 CAATTTGCACTAGGCCTTTGGT 59.700 45.455 12.58 5.08 43.89 3.67
216 217 2.080654 TTTGCACTAGGCCTTTGGTT 57.919 45.000 12.58 0.00 43.89 3.67
217 218 2.961531 TTGCACTAGGCCTTTGGTTA 57.038 45.000 12.58 0.00 43.89 2.85
218 219 2.489938 TGCACTAGGCCTTTGGTTAG 57.510 50.000 12.58 2.76 43.89 2.34
219 220 1.702957 TGCACTAGGCCTTTGGTTAGT 59.297 47.619 12.58 3.59 43.89 2.24
220 221 2.907696 TGCACTAGGCCTTTGGTTAGTA 59.092 45.455 12.58 0.00 43.89 1.82
221 222 3.055385 TGCACTAGGCCTTTGGTTAGTAG 60.055 47.826 12.58 0.00 43.89 2.57
222 223 3.681874 GCACTAGGCCTTTGGTTAGTAGG 60.682 52.174 12.58 0.00 36.11 3.18
223 224 3.518303 CACTAGGCCTTTGGTTAGTAGGT 59.482 47.826 12.58 0.00 0.00 3.08
224 225 4.019591 CACTAGGCCTTTGGTTAGTAGGTT 60.020 45.833 12.58 0.00 0.00 3.50
225 226 5.188359 CACTAGGCCTTTGGTTAGTAGGTTA 59.812 44.000 12.58 0.00 0.00 2.85
226 227 4.838904 AGGCCTTTGGTTAGTAGGTTAG 57.161 45.455 0.00 0.00 0.00 2.34
227 228 4.173594 AGGCCTTTGGTTAGTAGGTTAGT 58.826 43.478 0.00 0.00 0.00 2.24
228 229 4.224594 AGGCCTTTGGTTAGTAGGTTAGTC 59.775 45.833 0.00 0.00 0.00 2.59
229 230 4.511527 GCCTTTGGTTAGTAGGTTAGTCC 58.488 47.826 0.00 0.00 0.00 3.85
230 231 4.624843 GCCTTTGGTTAGTAGGTTAGTCCC 60.625 50.000 0.00 0.00 36.75 4.46
231 232 4.533311 CCTTTGGTTAGTAGGTTAGTCCCA 59.467 45.833 0.00 0.00 36.75 4.37
232 233 5.013391 CCTTTGGTTAGTAGGTTAGTCCCAA 59.987 44.000 0.00 0.00 36.75 4.12
233 234 6.466182 CCTTTGGTTAGTAGGTTAGTCCCAAA 60.466 42.308 0.00 0.00 38.12 3.28
234 235 6.512514 TTGGTTAGTAGGTTAGTCCCAAAA 57.487 37.500 0.00 0.00 36.75 2.44
235 236 6.512514 TGGTTAGTAGGTTAGTCCCAAAAA 57.487 37.500 0.00 0.00 36.75 1.94
236 237 6.536447 TGGTTAGTAGGTTAGTCCCAAAAAG 58.464 40.000 0.00 0.00 36.75 2.27
237 238 6.329723 TGGTTAGTAGGTTAGTCCCAAAAAGA 59.670 38.462 0.00 0.00 36.75 2.52
238 239 7.147337 TGGTTAGTAGGTTAGTCCCAAAAAGAA 60.147 37.037 0.00 0.00 36.75 2.52
239 240 7.886970 GGTTAGTAGGTTAGTCCCAAAAAGAAT 59.113 37.037 0.00 0.00 36.75 2.40
240 241 9.948964 GTTAGTAGGTTAGTCCCAAAAAGAATA 57.051 33.333 0.00 0.00 36.75 1.75
279 280 9.863845 ATAAAACCCGTTAAATATCCAAAACAG 57.136 29.630 0.00 0.00 0.00 3.16
280 281 7.527568 AAACCCGTTAAATATCCAAAACAGA 57.472 32.000 0.00 0.00 0.00 3.41
281 282 7.712204 AACCCGTTAAATATCCAAAACAGAT 57.288 32.000 0.00 0.00 0.00 2.90
282 283 8.810990 AACCCGTTAAATATCCAAAACAGATA 57.189 30.769 0.00 0.00 0.00 1.98
283 284 8.810990 ACCCGTTAAATATCCAAAACAGATAA 57.189 30.769 0.00 0.00 30.31 1.75
284 285 9.416284 ACCCGTTAAATATCCAAAACAGATAAT 57.584 29.630 0.00 0.00 30.31 1.28
519 533 4.476361 GGCAAAATCGGGCGAAAG 57.524 55.556 0.00 0.00 0.00 2.62
534 548 1.378531 GAAAGCCCGCACATATGACA 58.621 50.000 10.38 0.00 0.00 3.58
634 649 3.841870 GGATGGATCCGCAAACCC 58.158 61.111 7.39 0.00 37.19 4.11
635 650 1.227383 GGATGGATCCGCAAACCCT 59.773 57.895 7.39 0.00 37.19 4.34
673 688 3.708220 CTCTTCGGAGGCTCGGTGC 62.708 68.421 19.85 0.33 38.36 5.01
674 689 4.069232 CTTCGGAGGCTCGGTGCA 62.069 66.667 19.85 6.58 45.15 4.57
681 696 0.391661 GAGGCTCGGTGCAGATTTGA 60.392 55.000 0.00 0.00 45.15 2.69
1017 2555 1.450312 CCGCCAAATCGAGCTCCTT 60.450 57.895 8.47 0.00 0.00 3.36
3100 5420 8.748380 ATGCAACTTTTACTGCTTATTTTCTC 57.252 30.769 0.00 0.00 39.38 2.87
3623 6064 1.134159 GGAGCATGACATGAAGCCTCT 60.134 52.381 19.76 5.21 0.00 3.69
3624 6065 2.641305 GAGCATGACATGAAGCCTCTT 58.359 47.619 19.76 0.00 0.00 2.85
3625 6066 3.015327 GAGCATGACATGAAGCCTCTTT 58.985 45.455 19.76 0.00 0.00 2.52
3626 6067 4.194640 GAGCATGACATGAAGCCTCTTTA 58.805 43.478 19.76 0.00 0.00 1.85
3627 6068 4.789807 AGCATGACATGAAGCCTCTTTAT 58.210 39.130 19.76 0.00 0.00 1.40
3863 6317 9.415544 GAATCTTGGTTTATGAATTATGATGCC 57.584 33.333 0.00 0.00 0.00 4.40
3932 6386 4.725790 ATTAGCTGGAAACATCTTTGGC 57.274 40.909 0.00 0.00 41.51 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.514577 CCCAGTGAGGTAGGCGCG 62.515 72.222 0.00 0.00 34.66 6.86
14 15 4.840005 GCCCAGTGAGGTAGGCGC 62.840 72.222 0.00 0.00 35.30 6.53
16 17 4.840005 GCGCCCAGTGAGGTAGGC 62.840 72.222 0.00 0.00 42.18 3.93
17 18 4.514577 CGCGCCCAGTGAGGTAGG 62.515 72.222 0.00 0.00 34.66 3.18
48 49 3.793144 GAAGCAACGAGGCAGCCG 61.793 66.667 5.55 0.00 35.83 5.52
49 50 3.435186 GGAAGCAACGAGGCAGCC 61.435 66.667 1.84 1.84 35.83 4.85
50 51 1.968540 AAGGAAGCAACGAGGCAGC 60.969 57.895 5.91 0.00 35.83 5.25
51 52 0.603707 TCAAGGAAGCAACGAGGCAG 60.604 55.000 5.91 0.00 35.83 4.85
52 53 0.884704 GTCAAGGAAGCAACGAGGCA 60.885 55.000 5.91 0.00 35.83 4.75
53 54 1.869690 GTCAAGGAAGCAACGAGGC 59.130 57.895 0.00 0.00 0.00 4.70
54 55 0.600255 ACGTCAAGGAAGCAACGAGG 60.600 55.000 0.31 0.00 38.44 4.63
55 56 0.784778 GACGTCAAGGAAGCAACGAG 59.215 55.000 11.55 0.00 38.44 4.18
56 57 0.599204 GGACGTCAAGGAAGCAACGA 60.599 55.000 18.91 0.00 38.44 3.85
57 58 0.878523 TGGACGTCAAGGAAGCAACG 60.879 55.000 18.91 0.00 40.77 4.10
58 59 0.586802 GTGGACGTCAAGGAAGCAAC 59.413 55.000 18.91 0.00 0.00 4.17
59 60 0.468226 AGTGGACGTCAAGGAAGCAA 59.532 50.000 18.91 0.00 0.00 3.91
60 61 0.033504 GAGTGGACGTCAAGGAAGCA 59.966 55.000 18.91 0.65 0.00 3.91
61 62 0.670854 GGAGTGGACGTCAAGGAAGC 60.671 60.000 18.91 0.00 0.00 3.86
62 63 0.679505 TGGAGTGGACGTCAAGGAAG 59.320 55.000 18.91 0.00 0.00 3.46
63 64 1.070134 CTTGGAGTGGACGTCAAGGAA 59.930 52.381 18.91 1.14 34.61 3.36
64 65 0.679505 CTTGGAGTGGACGTCAAGGA 59.320 55.000 18.91 0.00 34.61 3.36
65 66 0.393077 ACTTGGAGTGGACGTCAAGG 59.607 55.000 18.91 0.91 40.41 3.61
66 67 1.341531 AGACTTGGAGTGGACGTCAAG 59.658 52.381 18.91 13.77 41.46 3.02
67 68 1.340248 GAGACTTGGAGTGGACGTCAA 59.660 52.381 18.91 2.10 0.00 3.18
68 69 0.959553 GAGACTTGGAGTGGACGTCA 59.040 55.000 18.91 0.27 0.00 4.35
69 70 0.244178 GGAGACTTGGAGTGGACGTC 59.756 60.000 7.13 7.13 0.00 4.34
70 71 0.178958 AGGAGACTTGGAGTGGACGT 60.179 55.000 0.00 0.00 37.44 4.34
71 72 0.244994 CAGGAGACTTGGAGTGGACG 59.755 60.000 0.00 0.00 40.21 4.79
72 73 0.610687 CCAGGAGACTTGGAGTGGAC 59.389 60.000 0.00 0.00 40.21 4.02
73 74 0.487325 TCCAGGAGACTTGGAGTGGA 59.513 55.000 0.00 0.00 40.21 4.02
74 75 1.577736 ATCCAGGAGACTTGGAGTGG 58.422 55.000 8.43 0.00 39.78 4.00
75 76 2.938756 GCAATCCAGGAGACTTGGAGTG 60.939 54.545 20.22 20.22 46.73 3.51
76 77 1.280421 GCAATCCAGGAGACTTGGAGT 59.720 52.381 8.43 3.28 39.78 3.85
77 78 1.280133 TGCAATCCAGGAGACTTGGAG 59.720 52.381 8.43 0.00 39.78 3.86
78 79 1.361204 TGCAATCCAGGAGACTTGGA 58.639 50.000 5.16 5.16 40.21 3.53
79 80 2.431954 ATGCAATCCAGGAGACTTGG 57.568 50.000 0.00 0.00 40.21 3.61
80 81 3.508793 ACAAATGCAATCCAGGAGACTTG 59.491 43.478 0.00 0.00 40.21 3.16
81 82 3.771216 ACAAATGCAATCCAGGAGACTT 58.229 40.909 0.00 0.00 40.21 3.01
82 83 3.446442 ACAAATGCAATCCAGGAGACT 57.554 42.857 0.00 0.00 46.44 3.24
83 84 3.760684 AGAACAAATGCAATCCAGGAGAC 59.239 43.478 0.00 0.00 0.00 3.36
84 85 4.038271 AGAACAAATGCAATCCAGGAGA 57.962 40.909 0.00 0.00 0.00 3.71
85 86 5.902613 TTAGAACAAATGCAATCCAGGAG 57.097 39.130 0.00 0.00 0.00 3.69
86 87 6.662865 TTTTAGAACAAATGCAATCCAGGA 57.337 33.333 0.00 0.00 0.00 3.86
87 88 6.705381 TGTTTTTAGAACAAATGCAATCCAGG 59.295 34.615 0.00 0.00 0.00 4.45
88 89 7.712264 TGTTTTTAGAACAAATGCAATCCAG 57.288 32.000 0.00 0.00 0.00 3.86
89 90 7.768120 AGTTGTTTTTAGAACAAATGCAATCCA 59.232 29.630 2.61 0.00 41.23 3.41
90 91 8.141835 AGTTGTTTTTAGAACAAATGCAATCC 57.858 30.769 2.61 0.00 41.23 3.01
91 92 9.034544 AGAGTTGTTTTTAGAACAAATGCAATC 57.965 29.630 6.07 0.00 41.23 2.67
92 93 8.947055 AGAGTTGTTTTTAGAACAAATGCAAT 57.053 26.923 6.07 0.00 41.23 3.56
93 94 7.491048 GGAGAGTTGTTTTTAGAACAAATGCAA 59.509 33.333 6.07 0.00 41.23 4.08
94 95 6.978080 GGAGAGTTGTTTTTAGAACAAATGCA 59.022 34.615 6.07 0.00 41.23 3.96
95 96 6.420903 GGGAGAGTTGTTTTTAGAACAAATGC 59.579 38.462 6.07 0.65 41.23 3.56
96 97 6.636850 CGGGAGAGTTGTTTTTAGAACAAATG 59.363 38.462 6.07 0.00 41.23 2.32
97 98 6.544564 TCGGGAGAGTTGTTTTTAGAACAAAT 59.455 34.615 2.61 1.86 41.23 2.32
98 99 5.881443 TCGGGAGAGTTGTTTTTAGAACAAA 59.119 36.000 2.61 0.00 41.23 2.83
99 100 5.430007 TCGGGAGAGTTGTTTTTAGAACAA 58.570 37.500 0.00 0.00 37.76 2.83
100 101 5.026038 TCGGGAGAGTTGTTTTTAGAACA 57.974 39.130 0.00 0.00 0.00 3.18
101 102 5.049612 CCTTCGGGAGAGTTGTTTTTAGAAC 60.050 44.000 0.00 0.00 41.75 3.01
102 103 5.061179 CCTTCGGGAGAGTTGTTTTTAGAA 58.939 41.667 0.00 0.00 41.75 2.10
103 104 4.102054 ACCTTCGGGAGAGTTGTTTTTAGA 59.898 41.667 0.00 0.00 41.75 2.10
104 105 4.386711 ACCTTCGGGAGAGTTGTTTTTAG 58.613 43.478 0.00 0.00 41.75 1.85
105 106 4.426736 ACCTTCGGGAGAGTTGTTTTTA 57.573 40.909 0.00 0.00 41.75 1.52
106 107 3.292492 ACCTTCGGGAGAGTTGTTTTT 57.708 42.857 0.00 0.00 41.75 1.94
107 108 3.292492 AACCTTCGGGAGAGTTGTTTT 57.708 42.857 0.00 0.00 41.75 2.43
108 109 3.211865 GAAACCTTCGGGAGAGTTGTTT 58.788 45.455 0.00 0.00 41.75 2.83
109 110 2.171870 TGAAACCTTCGGGAGAGTTGTT 59.828 45.455 0.00 0.00 41.75 2.83
110 111 1.766496 TGAAACCTTCGGGAGAGTTGT 59.234 47.619 0.00 0.00 41.75 3.32
111 112 2.543777 TGAAACCTTCGGGAGAGTTG 57.456 50.000 0.00 0.00 41.75 3.16
112 113 3.559384 GGAATGAAACCTTCGGGAGAGTT 60.559 47.826 0.00 0.00 41.75 3.01
113 114 2.027100 GGAATGAAACCTTCGGGAGAGT 60.027 50.000 0.00 0.00 41.75 3.24
114 115 2.633488 GGAATGAAACCTTCGGGAGAG 58.367 52.381 0.00 0.00 41.75 3.20
115 116 1.066430 CGGAATGAAACCTTCGGGAGA 60.066 52.381 0.00 0.00 38.77 3.71
116 117 1.338769 ACGGAATGAAACCTTCGGGAG 60.339 52.381 0.00 0.00 38.77 4.30
117 118 0.688487 ACGGAATGAAACCTTCGGGA 59.312 50.000 0.00 0.00 38.77 5.14
118 119 1.530323 AACGGAATGAAACCTTCGGG 58.470 50.000 0.00 0.00 41.87 5.14
119 120 2.351350 CCAAACGGAATGAAACCTTCGG 60.351 50.000 0.00 0.00 0.00 4.30
120 121 2.550606 TCCAAACGGAATGAAACCTTCG 59.449 45.455 0.00 0.00 0.00 3.79
121 122 4.783764 ATCCAAACGGAATGAAACCTTC 57.216 40.909 0.00 0.00 35.74 3.46
122 123 4.021456 GGAATCCAAACGGAATGAAACCTT 60.021 41.667 0.00 0.00 35.74 3.50
123 124 3.509967 GGAATCCAAACGGAATGAAACCT 59.490 43.478 0.00 0.00 35.74 3.50
124 125 3.672241 CGGAATCCAAACGGAATGAAACC 60.672 47.826 0.00 0.00 35.74 3.27
125 126 3.057806 ACGGAATCCAAACGGAATGAAAC 60.058 43.478 0.00 0.00 35.74 2.78
126 127 3.150767 ACGGAATCCAAACGGAATGAAA 58.849 40.909 0.00 0.00 35.74 2.69
127 128 2.785562 ACGGAATCCAAACGGAATGAA 58.214 42.857 0.00 0.00 35.74 2.57
128 129 2.483014 ACGGAATCCAAACGGAATGA 57.517 45.000 0.00 0.00 35.74 2.57
129 130 3.057876 TCAAACGGAATCCAAACGGAATG 60.058 43.478 0.00 0.00 35.74 2.67
130 131 3.150767 TCAAACGGAATCCAAACGGAAT 58.849 40.909 0.00 0.00 35.74 3.01
131 132 2.573369 TCAAACGGAATCCAAACGGAA 58.427 42.857 0.00 0.00 35.74 4.30
132 133 2.257691 TCAAACGGAATCCAAACGGA 57.742 45.000 0.00 0.00 36.85 4.69
133 134 4.893424 ATATCAAACGGAATCCAAACGG 57.107 40.909 0.00 0.00 0.00 4.44
134 135 5.065988 AGGAATATCAAACGGAATCCAAACG 59.934 40.000 0.00 0.00 32.27 3.60
135 136 6.451064 AGGAATATCAAACGGAATCCAAAC 57.549 37.500 0.00 0.00 32.27 2.93
136 137 7.475137 AAAGGAATATCAAACGGAATCCAAA 57.525 32.000 0.00 0.00 32.27 3.28
137 138 7.396055 AGAAAAGGAATATCAAACGGAATCCAA 59.604 33.333 0.00 0.00 32.27 3.53
138 139 6.889722 AGAAAAGGAATATCAAACGGAATCCA 59.110 34.615 0.00 0.00 32.27 3.41
139 140 7.196331 CAGAAAAGGAATATCAAACGGAATCC 58.804 38.462 0.00 0.00 0.00 3.01
140 141 6.693113 GCAGAAAAGGAATATCAAACGGAATC 59.307 38.462 0.00 0.00 0.00 2.52
141 142 6.564328 GCAGAAAAGGAATATCAAACGGAAT 58.436 36.000 0.00 0.00 0.00 3.01
142 143 5.391523 CGCAGAAAAGGAATATCAAACGGAA 60.392 40.000 0.00 0.00 0.00 4.30
143 144 4.094294 CGCAGAAAAGGAATATCAAACGGA 59.906 41.667 0.00 0.00 0.00 4.69
144 145 4.094294 TCGCAGAAAAGGAATATCAAACGG 59.906 41.667 0.00 0.00 0.00 4.44
145 146 5.216566 TCGCAGAAAAGGAATATCAAACG 57.783 39.130 0.00 0.00 0.00 3.60
146 147 6.861055 TGTTTCGCAGAAAAGGAATATCAAAC 59.139 34.615 5.51 0.00 45.90 2.93
147 148 6.861055 GTGTTTCGCAGAAAAGGAATATCAAA 59.139 34.615 5.51 0.00 45.90 2.69
148 149 6.206634 AGTGTTTCGCAGAAAAGGAATATCAA 59.793 34.615 5.51 0.00 45.90 2.57
149 150 5.705441 AGTGTTTCGCAGAAAAGGAATATCA 59.295 36.000 5.51 0.00 45.90 2.15
150 151 6.024049 CAGTGTTTCGCAGAAAAGGAATATC 58.976 40.000 5.51 0.00 45.90 1.63
151 152 5.705441 TCAGTGTTTCGCAGAAAAGGAATAT 59.295 36.000 5.51 0.00 45.90 1.28
152 153 5.060506 TCAGTGTTTCGCAGAAAAGGAATA 58.939 37.500 5.51 0.00 45.90 1.75
153 154 3.882888 TCAGTGTTTCGCAGAAAAGGAAT 59.117 39.130 5.51 0.00 45.90 3.01
154 155 3.275143 TCAGTGTTTCGCAGAAAAGGAA 58.725 40.909 5.51 0.00 45.90 3.36
155 156 2.912771 TCAGTGTTTCGCAGAAAAGGA 58.087 42.857 5.51 0.59 45.90 3.36
156 157 3.691049 TTCAGTGTTTCGCAGAAAAGG 57.309 42.857 5.51 0.00 45.90 3.11
157 158 5.853282 CCTATTTCAGTGTTTCGCAGAAAAG 59.147 40.000 5.51 5.08 45.90 2.27
158 159 5.529430 TCCTATTTCAGTGTTTCGCAGAAAA 59.471 36.000 5.51 0.00 45.90 2.29
159 160 5.060506 TCCTATTTCAGTGTTTCGCAGAAA 58.939 37.500 4.08 4.08 45.90 2.52
160 161 4.637276 TCCTATTTCAGTGTTTCGCAGAA 58.363 39.130 0.00 0.00 45.90 3.02
161 162 4.265904 TCCTATTTCAGTGTTTCGCAGA 57.734 40.909 0.00 0.00 0.00 4.26
162 163 5.356882 TTTCCTATTTCAGTGTTTCGCAG 57.643 39.130 0.00 0.00 0.00 5.18
163 164 5.759506 TTTTCCTATTTCAGTGTTTCGCA 57.240 34.783 0.00 0.00 0.00 5.10
186 187 3.809279 GCCTAGTGCAAATTGCTGTTTTT 59.191 39.130 19.34 1.34 45.31 1.94
187 188 3.392882 GCCTAGTGCAAATTGCTGTTTT 58.607 40.909 19.34 2.99 45.31 2.43
188 189 2.289010 GGCCTAGTGCAAATTGCTGTTT 60.289 45.455 19.34 4.67 45.31 2.83
189 190 1.273327 GGCCTAGTGCAAATTGCTGTT 59.727 47.619 19.34 7.05 45.31 3.16
190 191 0.890683 GGCCTAGTGCAAATTGCTGT 59.109 50.000 19.34 8.54 45.31 4.40
191 192 1.180029 AGGCCTAGTGCAAATTGCTG 58.820 50.000 19.34 6.68 45.31 4.41
192 193 1.928868 AAGGCCTAGTGCAAATTGCT 58.071 45.000 19.34 2.06 45.31 3.91
193 194 2.340337 CAAAGGCCTAGTGCAAATTGC 58.660 47.619 5.16 11.58 45.29 3.56
194 195 2.299867 ACCAAAGGCCTAGTGCAAATTG 59.700 45.455 5.16 3.81 43.89 2.32
195 196 2.608623 ACCAAAGGCCTAGTGCAAATT 58.391 42.857 5.16 0.00 43.89 1.82
196 197 2.309136 ACCAAAGGCCTAGTGCAAAT 57.691 45.000 5.16 0.00 43.89 2.32
197 198 2.080654 AACCAAAGGCCTAGTGCAAA 57.919 45.000 5.16 0.00 43.89 3.68
198 199 2.107552 ACTAACCAAAGGCCTAGTGCAA 59.892 45.455 5.16 0.00 43.89 4.08
199 200 1.702957 ACTAACCAAAGGCCTAGTGCA 59.297 47.619 5.16 0.00 43.89 4.57
200 201 2.491675 ACTAACCAAAGGCCTAGTGC 57.508 50.000 5.16 0.00 40.16 4.40
201 202 3.518303 ACCTACTAACCAAAGGCCTAGTG 59.482 47.826 5.16 7.65 33.42 2.74
202 203 3.799719 ACCTACTAACCAAAGGCCTAGT 58.200 45.455 5.16 7.36 33.42 2.57
203 204 4.838904 AACCTACTAACCAAAGGCCTAG 57.161 45.455 5.16 0.00 33.42 3.02
204 205 5.344566 ACTAACCTACTAACCAAAGGCCTA 58.655 41.667 5.16 0.00 33.42 3.93
205 206 4.173594 ACTAACCTACTAACCAAAGGCCT 58.826 43.478 0.00 0.00 33.42 5.19
206 207 4.511527 GACTAACCTACTAACCAAAGGCC 58.488 47.826 0.00 0.00 33.42 5.19
207 208 4.511527 GGACTAACCTACTAACCAAAGGC 58.488 47.826 0.00 0.00 33.42 4.35
208 209 4.533311 TGGGACTAACCTACTAACCAAAGG 59.467 45.833 0.00 0.00 38.98 3.11
209 210 5.750352 TGGGACTAACCTACTAACCAAAG 57.250 43.478 0.00 0.00 38.98 2.77
210 211 6.512514 TTTGGGACTAACCTACTAACCAAA 57.487 37.500 0.00 0.00 42.49 3.28
211 212 6.512514 TTTTGGGACTAACCTACTAACCAA 57.487 37.500 0.00 0.00 38.98 3.67
212 213 6.329723 TCTTTTTGGGACTAACCTACTAACCA 59.670 38.462 0.00 0.00 38.98 3.67
213 214 6.772605 TCTTTTTGGGACTAACCTACTAACC 58.227 40.000 0.00 0.00 38.98 2.85
214 215 8.859236 ATTCTTTTTGGGACTAACCTACTAAC 57.141 34.615 0.00 0.00 38.98 2.34
253 254 9.863845 CTGTTTTGGATATTTAACGGGTTTTAT 57.136 29.630 0.00 0.00 0.00 1.40
254 255 9.075678 TCTGTTTTGGATATTTAACGGGTTTTA 57.924 29.630 0.00 0.00 0.00 1.52
255 256 7.953752 TCTGTTTTGGATATTTAACGGGTTTT 58.046 30.769 0.00 0.00 0.00 2.43
256 257 7.527568 TCTGTTTTGGATATTTAACGGGTTT 57.472 32.000 0.00 0.00 0.00 3.27
257 258 7.712204 ATCTGTTTTGGATATTTAACGGGTT 57.288 32.000 0.00 0.00 0.00 4.11
258 259 8.810990 TTATCTGTTTTGGATATTTAACGGGT 57.189 30.769 0.00 0.00 0.00 5.28
302 303 9.027129 CGTCTCCAACGTATCTATAATTTTTGA 57.973 33.333 0.00 0.00 46.42 2.69
319 320 0.172803 ACGCCTGATACGTCTCCAAC 59.827 55.000 0.00 0.00 40.28 3.77
320 321 1.753930 TACGCCTGATACGTCTCCAA 58.246 50.000 0.00 0.00 43.88 3.53
321 322 1.977056 ATACGCCTGATACGTCTCCA 58.023 50.000 0.00 0.00 43.88 3.86
322 323 3.332919 TCTATACGCCTGATACGTCTCC 58.667 50.000 0.00 0.00 43.88 3.71
323 324 3.181518 GCTCTATACGCCTGATACGTCTC 60.182 52.174 0.00 0.00 43.88 3.36
324 325 2.743126 GCTCTATACGCCTGATACGTCT 59.257 50.000 0.00 0.00 43.88 4.18
325 326 2.159544 GGCTCTATACGCCTGATACGTC 60.160 54.545 0.00 0.00 43.88 4.34
326 327 3.758831 CGGCTCTATACGCCTGATACGT 61.759 54.545 0.00 0.00 45.37 3.57
327 328 1.202043 CGGCTCTATACGCCTGATACG 60.202 57.143 6.71 0.00 45.37 3.06
328 329 2.546195 CGGCTCTATACGCCTGATAC 57.454 55.000 6.71 0.00 45.37 2.24
360 361 2.994699 CCCCCTGGTGCGTCATAA 59.005 61.111 0.00 0.00 0.00 1.90
519 533 1.597742 ATTCTGTCATATGTGCGGGC 58.402 50.000 1.90 0.00 0.00 6.13
534 548 1.524621 CATCCGCGAGCCCAATTCT 60.525 57.895 8.23 0.00 0.00 2.40
630 645 3.192944 GGTTAGGGTTAGGGTTAGGGTT 58.807 50.000 0.00 0.00 0.00 4.11
631 646 2.850833 GGTTAGGGTTAGGGTTAGGGT 58.149 52.381 0.00 0.00 0.00 4.34
632 647 1.764723 CGGTTAGGGTTAGGGTTAGGG 59.235 57.143 0.00 0.00 0.00 3.53
633 648 1.139654 GCGGTTAGGGTTAGGGTTAGG 59.860 57.143 0.00 0.00 0.00 2.69
634 649 2.102084 GAGCGGTTAGGGTTAGGGTTAG 59.898 54.545 0.00 0.00 0.00 2.34
635 650 2.110578 GAGCGGTTAGGGTTAGGGTTA 58.889 52.381 0.00 0.00 0.00 2.85
673 688 4.690748 TGTCGCCTTCTAACTTCAAATCTG 59.309 41.667 0.00 0.00 0.00 2.90
674 689 4.691216 GTGTCGCCTTCTAACTTCAAATCT 59.309 41.667 0.00 0.00 0.00 2.40
681 696 2.521105 AACGTGTCGCCTTCTAACTT 57.479 45.000 0.00 0.00 0.00 2.66
715 746 5.007724 TGGTTTTTGCAAAACGTGTTTTCTT 59.992 32.000 23.79 0.00 40.45 2.52
716 747 4.511826 TGGTTTTTGCAAAACGTGTTTTCT 59.488 33.333 23.79 0.00 40.45 2.52
717 748 4.773510 TGGTTTTTGCAAAACGTGTTTTC 58.226 34.783 23.79 8.16 40.45 2.29
814 850 0.472471 TTTTTCCCGAGTCAGGCTGT 59.528 50.000 15.27 0.00 0.00 4.40
872 976 0.594110 GGTCTCGATCGATCTGGGTC 59.406 60.000 19.78 13.13 0.00 4.46
1727 3277 2.747855 CTGAAGACCTTGGCGGCC 60.748 66.667 13.32 13.32 35.61 6.13
2078 3628 1.597854 CCAAGTTGTCCTCGCTGCA 60.598 57.895 1.45 0.00 0.00 4.41
2635 4939 3.557264 GGTCCTTTGAGTCGAGGTTGATT 60.557 47.826 11.04 0.00 34.57 2.57
3932 6386 7.331934 TGAGTTCCATATCAAGAAAGACTTTCG 59.668 37.037 19.67 8.92 44.29 3.46


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

AutoCloner maintained by Alex Coulton.