Multiple sequence alignment - TraesCS4D01G248800

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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 TraesCS4D01G248800 chr4D 100.000 2173 0 0 815 2987 417813336 417815508 0.000000e+00 4013.0
1 TraesCS4D01G248800 chr4D 98.729 1889 19 2 815 2702 401417281 401419165 0.000000e+00 3350.0
2 TraesCS4D01G248800 chr4D 100.000 724 0 0 1 724 417812522 417813245 0.000000e+00 1338.0
3 TraesCS4D01G248800 chr4D 92.621 393 13 11 348 724 401416858 401417250 4.350000e-153 551.0
4 TraesCS4D01G248800 chr4D 98.258 287 5 0 2701 2987 401419582 401419868 1.240000e-138 503.0
5 TraesCS4D01G248800 chr4D 90.000 320 32 0 26 345 484062884 484062565 5.960000e-112 414.0
6 TraesCS4D01G248800 chr4B 95.097 1856 70 5 847 2702 496463545 496465379 0.000000e+00 2904.0
7 TraesCS4D01G248800 chr4B 94.167 360 6 9 380 724 496462885 496463244 4.380000e-148 534.0
8 TraesCS4D01G248800 chr4B 89.136 359 36 3 3 358 496426407 496426765 7.600000e-121 444.0
9 TraesCS4D01G248800 chr4B 93.214 280 19 0 2708 2987 496465803 496466082 2.140000e-111 412.0
10 TraesCS4D01G248800 chr4A 94.340 1855 83 10 864 2702 59244562 59246410 0.000000e+00 2824.0
11 TraesCS4D01G248800 chr4A 100.000 414 0 0 815 1228 59244120 59244533 0.000000e+00 765.0
12 TraesCS4D01G248800 chr4A 92.287 376 8 11 364 724 59243696 59244065 5.710000e-142 514.0
13 TraesCS4D01G248800 chr4A 90.747 281 23 3 2705 2984 59246836 59247114 3.640000e-99 372.0
14 TraesCS4D01G248800 chr7D 98.258 287 4 1 2701 2987 340168392 340168677 4.450000e-138 501.0
15 TraesCS4D01G248800 chr7D 97.297 74 2 0 2629 2702 340167902 340167975 3.130000e-25 126.0
16 TraesCS4D01G248800 chr3D 89.521 334 31 2 26 356 580128183 580128515 1.280000e-113 420.0
17 TraesCS4D01G248800 chr3D 88.218 331 37 2 26 356 156729685 156729357 7.760000e-106 394.0
18 TraesCS4D01G248800 chr5B 88.822 331 36 1 26 356 512940559 512940888 3.590000e-109 405.0
19 TraesCS4D01G248800 chr5B 86.486 74 10 0 2708 2781 551422078 551422005 6.860000e-12 82.4
20 TraesCS4D01G248800 chr2D 88.657 335 35 2 26 357 14521540 14521874 3.590000e-109 405.0
21 TraesCS4D01G248800 chr1D 88.358 335 38 1 26 359 9867966 9867632 4.640000e-108 401.0
22 TraesCS4D01G248800 chr5D 88.485 330 37 1 26 355 42067639 42067967 6.000000e-107 398.0
23 TraesCS4D01G248800 chr3B 87.798 336 36 5 26 358 650808785 650808452 3.610000e-104 388.0
24 TraesCS4D01G248800 chr2A 84.672 137 18 3 2713 2848 748694844 748694978 1.870000e-27 134.0
25 TraesCS4D01G248800 chr1B 84.127 126 18 2 2719 2843 623885213 623885089 1.450000e-23 121.0


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 TraesCS4D01G248800 chr4D 417812522 417815508 2986 False 2675.500000 4013 100.000000 1 2987 2 chr4D.!!$F2 2986
1 TraesCS4D01G248800 chr4D 401416858 401419868 3010 False 1468.000000 3350 96.536000 348 2987 3 chr4D.!!$F1 2639
2 TraesCS4D01G248800 chr4B 496462885 496466082 3197 False 1283.333333 2904 94.159333 380 2987 3 chr4B.!!$F2 2607
3 TraesCS4D01G248800 chr4A 59243696 59247114 3418 False 1118.750000 2824 94.343500 364 2984 4 chr4A.!!$F1 2620
4 TraesCS4D01G248800 chr7D 340167902 340168677 775 False 313.500000 501 97.777500 2629 2987 2 chr7D.!!$F1 358

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
185 186 0.037326 GGCTGTCATCGACAAGGTCA 60.037 55.0 0.0 0.0 42.26 4.02 F
269 270 0.313043 GTCGTTCGGTGGTCTCAGAA 59.687 55.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2561 0.671781 ACAGCGACATCACTTCAGGC 60.672 55.000 0.00 0.0 0.00 4.85 R
2093 2689 3.549471 CAGATCGTGCAATCTACTCACAC 59.451 47.826 0.56 0.0 34.21 3.82 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
33 34 6.840780 ATATGAACTTGAAAACTCCTTGGG 57.159 37.500 0.00 0.00 0.00 4.12
34 35 4.243793 TGAACTTGAAAACTCCTTGGGA 57.756 40.909 0.00 0.00 0.00 4.37
35 36 3.951680 TGAACTTGAAAACTCCTTGGGAC 59.048 43.478 0.00 0.00 0.00 4.46
36 37 2.572290 ACTTGAAAACTCCTTGGGACG 58.428 47.619 0.00 0.00 0.00 4.79
37 38 1.880027 CTTGAAAACTCCTTGGGACGG 59.120 52.381 0.00 0.00 0.00 4.79
38 39 0.841289 TGAAAACTCCTTGGGACGGT 59.159 50.000 0.00 0.00 0.00 4.83
39 40 1.235724 GAAAACTCCTTGGGACGGTG 58.764 55.000 0.00 0.00 0.00 4.94
40 41 0.841289 AAAACTCCTTGGGACGGTGA 59.159 50.000 0.00 0.00 0.00 4.02
41 42 0.396811 AAACTCCTTGGGACGGTGAG 59.603 55.000 0.00 0.00 0.00 3.51
42 43 1.481056 AACTCCTTGGGACGGTGAGG 61.481 60.000 0.00 0.00 0.00 3.86
43 44 1.913762 CTCCTTGGGACGGTGAGGT 60.914 63.158 0.00 0.00 0.00 3.85
44 45 1.460689 TCCTTGGGACGGTGAGGTT 60.461 57.895 0.00 0.00 0.00 3.50
45 46 0.178926 TCCTTGGGACGGTGAGGTTA 60.179 55.000 0.00 0.00 0.00 2.85
46 47 0.249398 CCTTGGGACGGTGAGGTTAG 59.751 60.000 0.00 0.00 0.00 2.34
47 48 0.249398 CTTGGGACGGTGAGGTTAGG 59.751 60.000 0.00 0.00 0.00 2.69
48 49 1.196104 TTGGGACGGTGAGGTTAGGG 61.196 60.000 0.00 0.00 0.00 3.53
49 50 1.611556 GGGACGGTGAGGTTAGGGT 60.612 63.158 0.00 0.00 0.00 4.34
50 51 1.196766 GGGACGGTGAGGTTAGGGTT 61.197 60.000 0.00 0.00 0.00 4.11
51 52 0.689055 GGACGGTGAGGTTAGGGTTT 59.311 55.000 0.00 0.00 0.00 3.27
52 53 1.338484 GGACGGTGAGGTTAGGGTTTC 60.338 57.143 0.00 0.00 0.00 2.78
53 54 1.622312 GACGGTGAGGTTAGGGTTTCT 59.378 52.381 0.00 0.00 0.00 2.52
54 55 1.622312 ACGGTGAGGTTAGGGTTTCTC 59.378 52.381 0.00 0.00 0.00 2.87
55 56 1.403780 CGGTGAGGTTAGGGTTTCTCG 60.404 57.143 0.00 0.00 0.00 4.04
56 57 1.622312 GGTGAGGTTAGGGTTTCTCGT 59.378 52.381 0.00 0.00 0.00 4.18
57 58 2.353505 GGTGAGGTTAGGGTTTCTCGTC 60.354 54.545 0.00 0.00 0.00 4.20
58 59 2.298163 GTGAGGTTAGGGTTTCTCGTCA 59.702 50.000 0.00 0.00 0.00 4.35
59 60 3.056035 GTGAGGTTAGGGTTTCTCGTCAT 60.056 47.826 0.00 0.00 0.00 3.06
60 61 4.159135 GTGAGGTTAGGGTTTCTCGTCATA 59.841 45.833 0.00 0.00 0.00 2.15
61 62 4.960469 TGAGGTTAGGGTTTCTCGTCATAT 59.040 41.667 0.00 0.00 0.00 1.78
62 63 5.163447 TGAGGTTAGGGTTTCTCGTCATATG 60.163 44.000 0.00 0.00 0.00 1.78
63 64 4.101119 AGGTTAGGGTTTCTCGTCATATGG 59.899 45.833 2.13 0.00 0.00 2.74
64 65 2.622064 AGGGTTTCTCGTCATATGGC 57.378 50.000 2.13 0.00 0.00 4.40
65 66 1.202533 AGGGTTTCTCGTCATATGGCG 60.203 52.381 23.43 23.43 45.75 5.69
66 67 1.217882 GGTTTCTCGTCATATGGCGG 58.782 55.000 27.91 18.63 44.30 6.13
67 68 1.217882 GTTTCTCGTCATATGGCGGG 58.782 55.000 27.91 25.85 46.55 6.13
72 73 1.877637 TCGTCATATGGCGGGATTTG 58.122 50.000 27.91 0.00 44.30 2.32
73 74 0.874390 CGTCATATGGCGGGATTTGG 59.126 55.000 21.82 0.00 39.84 3.28
74 75 1.813862 CGTCATATGGCGGGATTTGGT 60.814 52.381 21.82 0.00 39.84 3.67
75 76 1.608590 GTCATATGGCGGGATTTGGTG 59.391 52.381 2.13 0.00 0.00 4.17
76 77 1.214175 TCATATGGCGGGATTTGGTGT 59.786 47.619 2.13 0.00 0.00 4.16
77 78 1.608590 CATATGGCGGGATTTGGTGTC 59.391 52.381 0.00 0.00 0.00 3.67
78 79 0.621082 TATGGCGGGATTTGGTGTCA 59.379 50.000 0.00 0.00 0.00 3.58
79 80 0.680921 ATGGCGGGATTTGGTGTCAG 60.681 55.000 0.00 0.00 0.00 3.51
80 81 2.046285 GGCGGGATTTGGTGTCAGG 61.046 63.158 0.00 0.00 0.00 3.86
81 82 1.303317 GCGGGATTTGGTGTCAGGT 60.303 57.895 0.00 0.00 0.00 4.00
82 83 1.586154 GCGGGATTTGGTGTCAGGTG 61.586 60.000 0.00 0.00 0.00 4.00
83 84 0.250727 CGGGATTTGGTGTCAGGTGT 60.251 55.000 0.00 0.00 0.00 4.16
84 85 1.817740 CGGGATTTGGTGTCAGGTGTT 60.818 52.381 0.00 0.00 0.00 3.32
85 86 2.316108 GGGATTTGGTGTCAGGTGTTT 58.684 47.619 0.00 0.00 0.00 2.83
86 87 2.296190 GGGATTTGGTGTCAGGTGTTTC 59.704 50.000 0.00 0.00 0.00 2.78
87 88 2.955660 GGATTTGGTGTCAGGTGTTTCA 59.044 45.455 0.00 0.00 0.00 2.69
88 89 3.004734 GGATTTGGTGTCAGGTGTTTCAG 59.995 47.826 0.00 0.00 0.00 3.02
89 90 3.358111 TTTGGTGTCAGGTGTTTCAGA 57.642 42.857 0.00 0.00 0.00 3.27
90 91 3.576078 TTGGTGTCAGGTGTTTCAGAT 57.424 42.857 0.00 0.00 0.00 2.90
91 92 3.126001 TGGTGTCAGGTGTTTCAGATC 57.874 47.619 0.00 0.00 0.00 2.75
92 93 2.705658 TGGTGTCAGGTGTTTCAGATCT 59.294 45.455 0.00 0.00 0.00 2.75
93 94 3.901222 TGGTGTCAGGTGTTTCAGATCTA 59.099 43.478 0.00 0.00 0.00 1.98
94 95 4.532126 TGGTGTCAGGTGTTTCAGATCTAT 59.468 41.667 0.00 0.00 0.00 1.98
95 96 5.013079 TGGTGTCAGGTGTTTCAGATCTATT 59.987 40.000 0.00 0.00 0.00 1.73
96 97 5.582665 GGTGTCAGGTGTTTCAGATCTATTC 59.417 44.000 0.00 0.00 0.00 1.75
97 98 6.166279 GTGTCAGGTGTTTCAGATCTATTCA 58.834 40.000 0.00 0.00 0.00 2.57
98 99 6.312426 GTGTCAGGTGTTTCAGATCTATTCAG 59.688 42.308 0.00 0.00 0.00 3.02
99 100 5.814705 GTCAGGTGTTTCAGATCTATTCAGG 59.185 44.000 0.00 0.00 0.00 3.86
100 101 5.104776 TCAGGTGTTTCAGATCTATTCAGGG 60.105 44.000 0.00 0.00 0.00 4.45
101 102 4.164988 AGGTGTTTCAGATCTATTCAGGGG 59.835 45.833 0.00 0.00 0.00 4.79
102 103 4.080299 GGTGTTTCAGATCTATTCAGGGGT 60.080 45.833 0.00 0.00 0.00 4.95
103 104 5.501156 GTGTTTCAGATCTATTCAGGGGTT 58.499 41.667 0.00 0.00 0.00 4.11
104 105 5.586643 GTGTTTCAGATCTATTCAGGGGTTC 59.413 44.000 0.00 0.00 0.00 3.62
105 106 5.250543 TGTTTCAGATCTATTCAGGGGTTCA 59.749 40.000 0.00 0.00 0.00 3.18
106 107 6.180472 GTTTCAGATCTATTCAGGGGTTCAA 58.820 40.000 0.00 0.00 0.00 2.69
107 108 5.359194 TCAGATCTATTCAGGGGTTCAAC 57.641 43.478 0.00 0.00 0.00 3.18
108 109 4.122776 CAGATCTATTCAGGGGTTCAACG 58.877 47.826 0.00 0.00 0.00 4.10
109 110 4.030913 AGATCTATTCAGGGGTTCAACGA 58.969 43.478 0.00 0.00 0.00 3.85
110 111 3.604875 TCTATTCAGGGGTTCAACGAC 57.395 47.619 0.00 0.00 0.00 4.34
111 112 2.094390 TCTATTCAGGGGTTCAACGACG 60.094 50.000 0.00 0.00 0.00 5.12
112 113 0.682852 ATTCAGGGGTTCAACGACGA 59.317 50.000 0.00 0.00 0.00 4.20
113 114 0.249573 TTCAGGGGTTCAACGACGAC 60.250 55.000 0.00 0.00 0.00 4.34
114 115 2.019951 CAGGGGTTCAACGACGACG 61.020 63.158 5.58 5.58 45.75 5.12
115 116 2.195567 AGGGGTTCAACGACGACGA 61.196 57.895 15.32 0.00 42.66 4.20
116 117 2.018324 GGGGTTCAACGACGACGAC 61.018 63.158 15.32 1.03 42.66 4.34
117 118 1.008079 GGGTTCAACGACGACGACT 60.008 57.895 15.32 0.00 42.66 4.18
118 119 1.273455 GGGTTCAACGACGACGACTG 61.273 60.000 15.32 10.64 42.66 3.51
119 120 1.481683 GTTCAACGACGACGACTGC 59.518 57.895 15.32 0.00 42.66 4.40
120 121 2.007114 TTCAACGACGACGACTGCG 61.007 57.895 15.32 2.20 42.66 5.18
121 122 4.104633 CAACGACGACGACTGCGC 62.105 66.667 15.32 0.00 42.48 6.09
124 125 4.156622 CGACGACGACTGCGCCTA 62.157 66.667 4.18 0.00 42.48 3.93
125 126 2.576317 GACGACGACTGCGCCTAC 60.576 66.667 4.18 0.00 42.48 3.18
126 127 3.318539 GACGACGACTGCGCCTACA 62.319 63.158 4.18 0.00 42.48 2.74
127 128 2.102357 CGACGACTGCGCCTACAT 59.898 61.111 4.18 0.00 42.48 2.29
128 129 2.224217 CGACGACTGCGCCTACATG 61.224 63.158 4.18 0.00 42.48 3.21
129 130 1.878522 GACGACTGCGCCTACATGG 60.879 63.158 4.18 0.00 42.48 3.66
130 131 2.184322 CGACTGCGCCTACATGGT 59.816 61.111 4.18 0.00 38.35 3.55
136 137 2.268920 CGCCTACATGGTGCTGGT 59.731 61.111 0.00 0.00 39.73 4.00
137 138 1.815421 CGCCTACATGGTGCTGGTC 60.815 63.158 0.00 0.00 39.73 4.02
138 139 1.452108 GCCTACATGGTGCTGGTCC 60.452 63.158 0.00 0.00 38.35 4.46
139 140 1.915078 GCCTACATGGTGCTGGTCCT 61.915 60.000 0.00 0.00 38.35 3.85
140 141 0.620556 CCTACATGGTGCTGGTCCTT 59.379 55.000 0.00 0.00 0.00 3.36
141 142 1.837439 CCTACATGGTGCTGGTCCTTA 59.163 52.381 0.00 0.00 0.00 2.69
142 143 2.158900 CCTACATGGTGCTGGTCCTTAG 60.159 54.545 0.00 0.00 0.00 2.18
143 144 1.656587 ACATGGTGCTGGTCCTTAGA 58.343 50.000 0.00 0.00 0.00 2.10
144 145 1.556911 ACATGGTGCTGGTCCTTAGAG 59.443 52.381 0.00 0.00 0.00 2.43
145 146 1.134280 CATGGTGCTGGTCCTTAGAGG 60.134 57.143 0.00 0.00 36.46 3.69
146 147 1.222113 GGTGCTGGTCCTTAGAGGC 59.778 63.158 0.00 0.00 34.61 4.70
147 148 1.553690 GGTGCTGGTCCTTAGAGGCA 61.554 60.000 0.00 0.00 34.61 4.75
148 149 0.391793 GTGCTGGTCCTTAGAGGCAC 60.392 60.000 0.00 0.00 42.04 5.01
149 150 1.153549 GCTGGTCCTTAGAGGCACG 60.154 63.158 0.00 0.00 34.61 5.34
150 151 1.889530 GCTGGTCCTTAGAGGCACGT 61.890 60.000 0.00 0.00 34.61 4.49
151 152 0.108615 CTGGTCCTTAGAGGCACGTG 60.109 60.000 12.28 12.28 34.61 4.49
152 153 1.448013 GGTCCTTAGAGGCACGTGC 60.448 63.158 32.15 32.15 34.61 5.34
153 154 1.292223 GTCCTTAGAGGCACGTGCA 59.708 57.895 38.60 18.47 44.36 4.57
154 155 1.014564 GTCCTTAGAGGCACGTGCAC 61.015 60.000 38.60 30.08 44.36 4.57
155 156 2.094659 CCTTAGAGGCACGTGCACG 61.095 63.158 38.60 35.99 44.36 5.34
156 157 1.080772 CTTAGAGGCACGTGCACGA 60.081 57.895 42.94 25.03 44.36 4.35
157 158 0.666274 CTTAGAGGCACGTGCACGAA 60.666 55.000 42.94 29.03 44.36 3.85
158 159 0.666274 TTAGAGGCACGTGCACGAAG 60.666 55.000 42.94 32.60 44.36 3.79
159 160 1.520600 TAGAGGCACGTGCACGAAGA 61.521 55.000 42.94 18.39 44.36 2.87
160 161 2.658707 GAGGCACGTGCACGAAGAC 61.659 63.158 42.94 33.95 44.36 3.01
161 162 2.661866 GGCACGTGCACGAAGACT 60.662 61.111 42.94 19.98 44.36 3.24
162 163 2.244651 GGCACGTGCACGAAGACTT 61.245 57.895 42.94 19.18 44.36 3.01
163 164 1.201825 GCACGTGCACGAAGACTTC 59.798 57.895 42.94 19.21 43.02 3.01
164 165 1.853319 CACGTGCACGAAGACTTCC 59.147 57.895 42.94 0.00 43.02 3.46
165 166 1.300697 ACGTGCACGAAGACTTCCC 60.301 57.895 42.94 0.00 43.02 3.97
166 167 2.372690 CGTGCACGAAGACTTCCCG 61.373 63.158 34.93 1.26 43.02 5.14
167 168 2.027625 GTGCACGAAGACTTCCCGG 61.028 63.158 9.63 0.00 0.00 5.73
168 169 3.119096 GCACGAAGACTTCCCGGC 61.119 66.667 9.63 7.06 0.00 6.13
169 170 2.657237 CACGAAGACTTCCCGGCT 59.343 61.111 9.63 0.00 0.00 5.52
170 171 1.738099 CACGAAGACTTCCCGGCTG 60.738 63.158 9.63 0.00 0.00 4.85
171 172 2.207924 ACGAAGACTTCCCGGCTGT 61.208 57.895 9.63 0.00 0.00 4.40
172 173 1.446272 CGAAGACTTCCCGGCTGTC 60.446 63.158 9.63 3.58 0.00 3.51
173 174 1.671742 GAAGACTTCCCGGCTGTCA 59.328 57.895 17.64 0.00 33.56 3.58
174 175 0.250513 GAAGACTTCCCGGCTGTCAT 59.749 55.000 17.64 9.04 33.56 3.06
175 176 0.250513 AAGACTTCCCGGCTGTCATC 59.749 55.000 17.64 2.48 33.56 2.92
176 177 1.519455 GACTTCCCGGCTGTCATCG 60.519 63.158 12.68 0.00 0.00 3.84
177 178 1.945354 GACTTCCCGGCTGTCATCGA 61.945 60.000 12.68 0.00 0.00 3.59
178 179 1.519455 CTTCCCGGCTGTCATCGAC 60.519 63.158 0.00 0.00 0.00 4.20
179 180 2.225791 CTTCCCGGCTGTCATCGACA 62.226 60.000 0.00 0.00 40.50 4.35
180 181 1.822114 TTCCCGGCTGTCATCGACAA 61.822 55.000 0.00 0.00 42.26 3.18
181 182 1.811266 CCCGGCTGTCATCGACAAG 60.811 63.158 0.00 0.00 42.26 3.16
182 183 1.811266 CCGGCTGTCATCGACAAGG 60.811 63.158 0.00 0.00 42.26 3.61
183 184 1.079819 CGGCTGTCATCGACAAGGT 60.080 57.895 0.00 0.00 42.26 3.50
184 185 1.078759 CGGCTGTCATCGACAAGGTC 61.079 60.000 0.00 0.00 42.26 3.85
185 186 0.037326 GGCTGTCATCGACAAGGTCA 60.037 55.000 0.00 0.00 42.26 4.02
186 187 1.608025 GGCTGTCATCGACAAGGTCAA 60.608 52.381 0.00 0.00 42.26 3.18
187 188 1.728971 GCTGTCATCGACAAGGTCAAG 59.271 52.381 0.00 0.00 42.26 3.02
188 189 1.728971 CTGTCATCGACAAGGTCAAGC 59.271 52.381 0.00 0.00 42.26 4.01
189 190 1.079503 GTCATCGACAAGGTCAAGCC 58.920 55.000 0.00 0.00 32.09 4.35
190 191 0.389817 TCATCGACAAGGTCAAGCCG 60.390 55.000 0.00 0.00 43.70 5.52
191 192 1.079127 ATCGACAAGGTCAAGCCGG 60.079 57.895 0.00 0.00 43.70 6.13
192 193 3.423154 CGACAAGGTCAAGCCGGC 61.423 66.667 21.89 21.89 43.70 6.13
193 194 2.032681 GACAAGGTCAAGCCGGCT 59.967 61.111 27.08 27.08 43.70 5.52
194 195 2.032681 ACAAGGTCAAGCCGGCTC 59.967 61.111 32.93 18.07 43.70 4.70
195 196 2.747855 CAAGGTCAAGCCGGCTCC 60.748 66.667 32.93 26.75 43.70 4.70
196 197 4.394712 AAGGTCAAGCCGGCTCCG 62.395 66.667 32.93 24.15 43.70 4.63
214 215 4.424566 GTACGGGAGCGGCGACAA 62.425 66.667 12.98 0.00 0.00 3.18
215 216 4.424566 TACGGGAGCGGCGACAAC 62.425 66.667 12.98 0.00 0.00 3.32
237 238 3.257561 CATCGCCGGCTCGTTCTG 61.258 66.667 26.68 6.92 0.00 3.02
238 239 3.449227 ATCGCCGGCTCGTTCTGA 61.449 61.111 26.68 12.96 0.00 3.27
239 240 3.701604 ATCGCCGGCTCGTTCTGAC 62.702 63.158 26.68 0.00 0.00 3.51
248 249 2.564975 CGTTCTGACGGCGGTAGT 59.435 61.111 13.24 0.00 45.32 2.73
249 250 1.800315 CGTTCTGACGGCGGTAGTG 60.800 63.158 13.24 0.00 45.32 2.74
250 251 1.445582 GTTCTGACGGCGGTAGTGG 60.446 63.158 13.24 0.00 0.00 4.00
251 252 1.904865 TTCTGACGGCGGTAGTGGT 60.905 57.895 13.24 0.00 0.00 4.16
252 253 1.870055 TTCTGACGGCGGTAGTGGTC 61.870 60.000 13.24 0.00 0.00 4.02
253 254 3.678717 CTGACGGCGGTAGTGGTCG 62.679 68.421 13.24 0.00 32.17 4.79
254 255 3.741476 GACGGCGGTAGTGGTCGT 61.741 66.667 13.24 0.00 36.74 4.34
255 256 3.273080 GACGGCGGTAGTGGTCGTT 62.273 63.158 13.24 0.00 34.06 3.85
256 257 2.505557 CGGCGGTAGTGGTCGTTC 60.506 66.667 0.00 0.00 0.00 3.95
257 258 2.505557 GGCGGTAGTGGTCGTTCG 60.506 66.667 0.00 0.00 0.00 3.95
258 259 2.505557 GCGGTAGTGGTCGTTCGG 60.506 66.667 0.00 0.00 0.00 4.30
259 260 2.956987 CGGTAGTGGTCGTTCGGT 59.043 61.111 0.00 0.00 0.00 4.69
260 261 1.443194 CGGTAGTGGTCGTTCGGTG 60.443 63.158 0.00 0.00 0.00 4.94
261 262 1.080298 GGTAGTGGTCGTTCGGTGG 60.080 63.158 0.00 0.00 0.00 4.61
262 263 1.662044 GTAGTGGTCGTTCGGTGGT 59.338 57.895 0.00 0.00 0.00 4.16
263 264 0.387750 GTAGTGGTCGTTCGGTGGTC 60.388 60.000 0.00 0.00 0.00 4.02
264 265 0.538057 TAGTGGTCGTTCGGTGGTCT 60.538 55.000 0.00 0.00 0.00 3.85
265 266 1.372623 GTGGTCGTTCGGTGGTCTC 60.373 63.158 0.00 0.00 0.00 3.36
266 267 1.829096 TGGTCGTTCGGTGGTCTCA 60.829 57.895 0.00 0.00 0.00 3.27
267 268 1.080705 GGTCGTTCGGTGGTCTCAG 60.081 63.158 0.00 0.00 0.00 3.35
268 269 1.521450 GGTCGTTCGGTGGTCTCAGA 61.521 60.000 0.00 0.00 0.00 3.27
269 270 0.313043 GTCGTTCGGTGGTCTCAGAA 59.687 55.000 0.00 0.00 0.00 3.02
270 271 1.067776 GTCGTTCGGTGGTCTCAGAAT 60.068 52.381 0.00 0.00 0.00 2.40
271 272 1.201647 TCGTTCGGTGGTCTCAGAATC 59.798 52.381 0.00 0.00 0.00 2.52
272 273 1.202582 CGTTCGGTGGTCTCAGAATCT 59.797 52.381 0.00 0.00 0.00 2.40
273 274 2.732597 CGTTCGGTGGTCTCAGAATCTC 60.733 54.545 0.00 0.00 0.00 2.75
274 275 1.095600 TCGGTGGTCTCAGAATCTCG 58.904 55.000 0.00 0.00 0.00 4.04
275 276 1.095600 CGGTGGTCTCAGAATCTCGA 58.904 55.000 0.00 0.00 0.00 4.04
276 277 1.678627 CGGTGGTCTCAGAATCTCGAT 59.321 52.381 0.00 0.00 0.00 3.59
277 278 2.542618 CGGTGGTCTCAGAATCTCGATG 60.543 54.545 0.00 0.00 0.00 3.84
278 279 2.428890 GGTGGTCTCAGAATCTCGATGT 59.571 50.000 0.00 0.00 0.00 3.06
279 280 3.632604 GGTGGTCTCAGAATCTCGATGTA 59.367 47.826 0.00 0.00 0.00 2.29
280 281 4.098044 GGTGGTCTCAGAATCTCGATGTAA 59.902 45.833 0.00 0.00 0.00 2.41
281 282 5.221342 GGTGGTCTCAGAATCTCGATGTAAT 60.221 44.000 0.00 0.00 0.00 1.89
282 283 6.276847 GTGGTCTCAGAATCTCGATGTAATT 58.723 40.000 0.00 0.00 0.00 1.40
283 284 6.758886 GTGGTCTCAGAATCTCGATGTAATTT 59.241 38.462 0.00 0.00 0.00 1.82
284 285 7.278868 GTGGTCTCAGAATCTCGATGTAATTTT 59.721 37.037 0.00 0.00 0.00 1.82
285 286 7.824289 TGGTCTCAGAATCTCGATGTAATTTTT 59.176 33.333 0.00 0.00 0.00 1.94
286 287 9.314321 GGTCTCAGAATCTCGATGTAATTTTTA 57.686 33.333 0.00 0.00 0.00 1.52
312 313 8.621532 TTATGTTTGAGATGCTTTGTACTTCT 57.378 30.769 0.00 0.00 0.00 2.85
313 314 6.304356 TGTTTGAGATGCTTTGTACTTCTG 57.696 37.500 0.00 0.00 0.00 3.02
314 315 5.239306 TGTTTGAGATGCTTTGTACTTCTGG 59.761 40.000 0.00 0.00 0.00 3.86
315 316 3.338249 TGAGATGCTTTGTACTTCTGGC 58.662 45.455 0.00 0.00 0.00 4.85
316 317 2.349886 GAGATGCTTTGTACTTCTGGCG 59.650 50.000 0.00 0.00 0.00 5.69
317 318 2.028112 AGATGCTTTGTACTTCTGGCGA 60.028 45.455 0.00 0.00 0.00 5.54
318 319 2.248280 TGCTTTGTACTTCTGGCGAA 57.752 45.000 0.00 0.00 0.00 4.70
319 320 1.871039 TGCTTTGTACTTCTGGCGAAC 59.129 47.619 0.00 0.00 0.00 3.95
320 321 2.143925 GCTTTGTACTTCTGGCGAACT 58.856 47.619 0.00 0.00 0.00 3.01
321 322 2.548480 GCTTTGTACTTCTGGCGAACTT 59.452 45.455 0.00 0.00 0.00 2.66
322 323 3.003378 GCTTTGTACTTCTGGCGAACTTT 59.997 43.478 0.00 0.00 0.00 2.66
323 324 4.527564 CTTTGTACTTCTGGCGAACTTTG 58.472 43.478 0.00 0.00 0.00 2.77
324 325 3.462483 TGTACTTCTGGCGAACTTTGA 57.538 42.857 0.00 0.00 0.00 2.69
325 326 4.002906 TGTACTTCTGGCGAACTTTGAT 57.997 40.909 0.00 0.00 0.00 2.57
326 327 5.142061 TGTACTTCTGGCGAACTTTGATA 57.858 39.130 0.00 0.00 0.00 2.15
327 328 5.543714 TGTACTTCTGGCGAACTTTGATAA 58.456 37.500 0.00 0.00 0.00 1.75
328 329 6.170506 TGTACTTCTGGCGAACTTTGATAAT 58.829 36.000 0.00 0.00 0.00 1.28
329 330 7.324935 TGTACTTCTGGCGAACTTTGATAATA 58.675 34.615 0.00 0.00 0.00 0.98
330 331 6.910536 ACTTCTGGCGAACTTTGATAATAG 57.089 37.500 0.00 0.00 0.00 1.73
331 332 6.640518 ACTTCTGGCGAACTTTGATAATAGA 58.359 36.000 0.00 0.00 0.00 1.98
332 333 7.275920 ACTTCTGGCGAACTTTGATAATAGAT 58.724 34.615 0.00 0.00 0.00 1.98
333 334 7.770897 ACTTCTGGCGAACTTTGATAATAGATT 59.229 33.333 0.00 0.00 0.00 2.40
334 335 8.506168 TTCTGGCGAACTTTGATAATAGATTT 57.494 30.769 0.00 0.00 0.00 2.17
335 336 7.919690 TCTGGCGAACTTTGATAATAGATTTG 58.080 34.615 0.00 0.00 0.00 2.32
336 337 7.012327 TCTGGCGAACTTTGATAATAGATTTGG 59.988 37.037 0.00 0.00 0.00 3.28
337 338 6.826231 TGGCGAACTTTGATAATAGATTTGGA 59.174 34.615 0.00 0.00 0.00 3.53
338 339 7.502226 TGGCGAACTTTGATAATAGATTTGGAT 59.498 33.333 0.00 0.00 0.00 3.41
339 340 8.017946 GGCGAACTTTGATAATAGATTTGGATC 58.982 37.037 0.00 0.00 0.00 3.36
340 341 7.742089 GCGAACTTTGATAATAGATTTGGATCG 59.258 37.037 0.00 0.00 37.37 3.69
341 342 8.765219 CGAACTTTGATAATAGATTTGGATCGT 58.235 33.333 0.00 0.00 37.37 3.73
346 347 9.929722 TTTGATAATAGATTTGGATCGTTTTCG 57.070 29.630 0.00 0.00 45.64 3.46
1790 2378 5.361857 TCTGTGATTCTGATGTCTATGCTGA 59.638 40.000 0.00 0.00 0.00 4.26
1871 2459 4.228237 AGGTCATGGATAGGGGAATACA 57.772 45.455 0.00 0.00 0.00 2.29
1965 2561 6.090493 CACATGTATTAGGATTGAGCAGATCG 59.910 42.308 0.00 0.00 0.00 3.69
2093 2689 5.432885 AGGACCTGTTGTTTTTACATTCG 57.567 39.130 0.00 0.00 0.00 3.34
2373 2969 5.006552 GCATTGAGACATAGAGAACTTCTGC 59.993 44.000 0.00 0.00 36.61 4.26
2546 3143 6.991938 ACAAGCAACTGCAAAAGGATAATTA 58.008 32.000 4.22 0.00 45.16 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.508977 TCCCAAGGAGTTTTCAAGTTCATATTT 59.491 33.333 0.00 0.00 0.00 1.40
9 10 7.010160 TCCCAAGGAGTTTTCAAGTTCATATT 58.990 34.615 0.00 0.00 0.00 1.28
10 11 6.434340 GTCCCAAGGAGTTTTCAAGTTCATAT 59.566 38.462 0.00 0.00 29.39 1.78
11 12 5.768164 GTCCCAAGGAGTTTTCAAGTTCATA 59.232 40.000 0.00 0.00 29.39 2.15
12 13 4.584743 GTCCCAAGGAGTTTTCAAGTTCAT 59.415 41.667 0.00 0.00 29.39 2.57
13 14 3.951680 GTCCCAAGGAGTTTTCAAGTTCA 59.048 43.478 0.00 0.00 29.39 3.18
14 15 3.003378 CGTCCCAAGGAGTTTTCAAGTTC 59.997 47.826 0.00 0.00 29.39 3.01
15 16 2.949644 CGTCCCAAGGAGTTTTCAAGTT 59.050 45.455 0.00 0.00 29.39 2.66
16 17 2.572290 CGTCCCAAGGAGTTTTCAAGT 58.428 47.619 0.00 0.00 29.39 3.16
17 18 1.880027 CCGTCCCAAGGAGTTTTCAAG 59.120 52.381 0.00 0.00 29.39 3.02
18 19 1.213430 ACCGTCCCAAGGAGTTTTCAA 59.787 47.619 0.00 0.00 29.39 2.69
19 20 0.841289 ACCGTCCCAAGGAGTTTTCA 59.159 50.000 0.00 0.00 29.39 2.69
20 21 1.202722 TCACCGTCCCAAGGAGTTTTC 60.203 52.381 0.00 0.00 29.39 2.29
21 22 0.841289 TCACCGTCCCAAGGAGTTTT 59.159 50.000 0.00 0.00 29.39 2.43
22 23 0.396811 CTCACCGTCCCAAGGAGTTT 59.603 55.000 0.00 0.00 29.39 2.66
23 24 1.481056 CCTCACCGTCCCAAGGAGTT 61.481 60.000 0.00 0.00 29.39 3.01
24 25 1.913762 CCTCACCGTCCCAAGGAGT 60.914 63.158 0.00 0.00 29.39 3.85
25 26 1.481056 AACCTCACCGTCCCAAGGAG 61.481 60.000 0.00 0.00 32.99 3.69
26 27 0.178926 TAACCTCACCGTCCCAAGGA 60.179 55.000 0.00 0.00 32.99 3.36
27 28 0.249398 CTAACCTCACCGTCCCAAGG 59.751 60.000 0.00 0.00 34.94 3.61
28 29 0.249398 CCTAACCTCACCGTCCCAAG 59.751 60.000 0.00 0.00 0.00 3.61
29 30 1.196104 CCCTAACCTCACCGTCCCAA 61.196 60.000 0.00 0.00 0.00 4.12
30 31 1.611261 CCCTAACCTCACCGTCCCA 60.611 63.158 0.00 0.00 0.00 4.37
31 32 1.196766 AACCCTAACCTCACCGTCCC 61.197 60.000 0.00 0.00 0.00 4.46
32 33 0.689055 AAACCCTAACCTCACCGTCC 59.311 55.000 0.00 0.00 0.00 4.79
33 34 1.622312 AGAAACCCTAACCTCACCGTC 59.378 52.381 0.00 0.00 0.00 4.79
34 35 1.622312 GAGAAACCCTAACCTCACCGT 59.378 52.381 0.00 0.00 0.00 4.83
35 36 1.403780 CGAGAAACCCTAACCTCACCG 60.404 57.143 0.00 0.00 0.00 4.94
36 37 1.622312 ACGAGAAACCCTAACCTCACC 59.378 52.381 0.00 0.00 0.00 4.02
37 38 2.298163 TGACGAGAAACCCTAACCTCAC 59.702 50.000 0.00 0.00 0.00 3.51
38 39 2.600790 TGACGAGAAACCCTAACCTCA 58.399 47.619 0.00 0.00 0.00 3.86
39 40 3.889520 ATGACGAGAAACCCTAACCTC 57.110 47.619 0.00 0.00 0.00 3.85
40 41 4.101119 CCATATGACGAGAAACCCTAACCT 59.899 45.833 3.65 0.00 0.00 3.50
41 42 4.377897 CCATATGACGAGAAACCCTAACC 58.622 47.826 3.65 0.00 0.00 2.85
42 43 3.808174 GCCATATGACGAGAAACCCTAAC 59.192 47.826 3.65 0.00 0.00 2.34
43 44 3.491964 CGCCATATGACGAGAAACCCTAA 60.492 47.826 5.37 0.00 0.00 2.69
44 45 2.035449 CGCCATATGACGAGAAACCCTA 59.965 50.000 5.37 0.00 0.00 3.53
45 46 1.202533 CGCCATATGACGAGAAACCCT 60.203 52.381 5.37 0.00 0.00 4.34
46 47 1.217882 CGCCATATGACGAGAAACCC 58.782 55.000 5.37 0.00 0.00 4.11
47 48 1.217882 CCGCCATATGACGAGAAACC 58.782 55.000 13.40 0.00 0.00 3.27
48 49 1.202486 TCCCGCCATATGACGAGAAAC 60.202 52.381 13.40 0.00 0.00 2.78
49 50 1.116308 TCCCGCCATATGACGAGAAA 58.884 50.000 13.40 0.00 0.00 2.52
50 51 1.338107 ATCCCGCCATATGACGAGAA 58.662 50.000 13.40 0.00 0.00 2.87
51 52 1.338107 AATCCCGCCATATGACGAGA 58.662 50.000 13.40 5.44 0.00 4.04
52 53 1.800586 CAAATCCCGCCATATGACGAG 59.199 52.381 13.40 0.00 0.00 4.18
53 54 1.542328 CCAAATCCCGCCATATGACGA 60.542 52.381 13.40 0.00 0.00 4.20
54 55 0.874390 CCAAATCCCGCCATATGACG 59.126 55.000 3.65 3.96 0.00 4.35
55 56 1.608590 CACCAAATCCCGCCATATGAC 59.391 52.381 3.65 0.00 0.00 3.06
56 57 1.214175 ACACCAAATCCCGCCATATGA 59.786 47.619 3.65 0.00 0.00 2.15
57 58 1.608590 GACACCAAATCCCGCCATATG 59.391 52.381 0.00 0.00 0.00 1.78
58 59 1.214175 TGACACCAAATCCCGCCATAT 59.786 47.619 0.00 0.00 0.00 1.78
59 60 0.621082 TGACACCAAATCCCGCCATA 59.379 50.000 0.00 0.00 0.00 2.74
60 61 0.680921 CTGACACCAAATCCCGCCAT 60.681 55.000 0.00 0.00 0.00 4.40
61 62 1.303236 CTGACACCAAATCCCGCCA 60.303 57.895 0.00 0.00 0.00 5.69
62 63 2.046285 CCTGACACCAAATCCCGCC 61.046 63.158 0.00 0.00 0.00 6.13
63 64 1.303317 ACCTGACACCAAATCCCGC 60.303 57.895 0.00 0.00 0.00 6.13
64 65 0.250727 ACACCTGACACCAAATCCCG 60.251 55.000 0.00 0.00 0.00 5.14
65 66 1.995376 AACACCTGACACCAAATCCC 58.005 50.000 0.00 0.00 0.00 3.85
66 67 2.955660 TGAAACACCTGACACCAAATCC 59.044 45.455 0.00 0.00 0.00 3.01
67 68 3.882888 TCTGAAACACCTGACACCAAATC 59.117 43.478 0.00 0.00 0.00 2.17
68 69 3.897239 TCTGAAACACCTGACACCAAAT 58.103 40.909 0.00 0.00 0.00 2.32
69 70 3.358111 TCTGAAACACCTGACACCAAA 57.642 42.857 0.00 0.00 0.00 3.28
70 71 3.136443 AGATCTGAAACACCTGACACCAA 59.864 43.478 0.00 0.00 0.00 3.67
71 72 2.705658 AGATCTGAAACACCTGACACCA 59.294 45.455 0.00 0.00 0.00 4.17
72 73 3.409026 AGATCTGAAACACCTGACACC 57.591 47.619 0.00 0.00 0.00 4.16
73 74 6.166279 TGAATAGATCTGAAACACCTGACAC 58.834 40.000 5.18 0.00 0.00 3.67
74 75 6.358974 TGAATAGATCTGAAACACCTGACA 57.641 37.500 5.18 0.00 0.00 3.58
75 76 5.814705 CCTGAATAGATCTGAAACACCTGAC 59.185 44.000 5.18 0.00 0.00 3.51
76 77 5.104776 CCCTGAATAGATCTGAAACACCTGA 60.105 44.000 5.18 0.00 0.00 3.86
77 78 5.121811 CCCTGAATAGATCTGAAACACCTG 58.878 45.833 5.18 0.00 0.00 4.00
78 79 4.164988 CCCCTGAATAGATCTGAAACACCT 59.835 45.833 5.18 0.00 0.00 4.00
79 80 4.080299 ACCCCTGAATAGATCTGAAACACC 60.080 45.833 5.18 0.00 0.00 4.16
80 81 5.104259 ACCCCTGAATAGATCTGAAACAC 57.896 43.478 5.18 0.00 0.00 3.32
81 82 5.250543 TGAACCCCTGAATAGATCTGAAACA 59.749 40.000 5.18 0.00 0.00 2.83
82 83 5.745227 TGAACCCCTGAATAGATCTGAAAC 58.255 41.667 5.18 0.00 0.00 2.78
83 84 6.180472 GTTGAACCCCTGAATAGATCTGAAA 58.820 40.000 5.18 0.00 0.00 2.69
84 85 5.626809 CGTTGAACCCCTGAATAGATCTGAA 60.627 44.000 5.18 0.00 0.00 3.02
85 86 4.141937 CGTTGAACCCCTGAATAGATCTGA 60.142 45.833 5.18 0.00 0.00 3.27
86 87 4.122776 CGTTGAACCCCTGAATAGATCTG 58.877 47.826 5.18 0.00 0.00 2.90
87 88 4.030913 TCGTTGAACCCCTGAATAGATCT 58.969 43.478 0.00 0.00 0.00 2.75
88 89 4.120589 GTCGTTGAACCCCTGAATAGATC 58.879 47.826 0.00 0.00 0.00 2.75
89 90 3.430374 CGTCGTTGAACCCCTGAATAGAT 60.430 47.826 0.00 0.00 0.00 1.98
90 91 2.094390 CGTCGTTGAACCCCTGAATAGA 60.094 50.000 0.00 0.00 0.00 1.98
91 92 2.094390 TCGTCGTTGAACCCCTGAATAG 60.094 50.000 0.00 0.00 0.00 1.73
92 93 1.894466 TCGTCGTTGAACCCCTGAATA 59.106 47.619 0.00 0.00 0.00 1.75
93 94 0.682852 TCGTCGTTGAACCCCTGAAT 59.317 50.000 0.00 0.00 0.00 2.57
94 95 0.249573 GTCGTCGTTGAACCCCTGAA 60.250 55.000 0.00 0.00 0.00 3.02
95 96 1.364901 GTCGTCGTTGAACCCCTGA 59.635 57.895 0.00 0.00 0.00 3.86
96 97 2.019951 CGTCGTCGTTGAACCCCTG 61.020 63.158 0.00 0.00 0.00 4.45
97 98 2.195567 TCGTCGTCGTTGAACCCCT 61.196 57.895 1.33 0.00 38.33 4.79
98 99 2.018324 GTCGTCGTCGTTGAACCCC 61.018 63.158 1.33 0.00 38.33 4.95
99 100 1.008079 AGTCGTCGTCGTTGAACCC 60.008 57.895 1.33 0.00 38.33 4.11
100 101 1.873355 GCAGTCGTCGTCGTTGAACC 61.873 60.000 1.33 0.00 38.33 3.62
101 102 1.481683 GCAGTCGTCGTCGTTGAAC 59.518 57.895 1.33 0.00 38.33 3.18
102 103 2.007114 CGCAGTCGTCGTCGTTGAA 61.007 57.895 1.33 0.00 38.33 2.69
103 104 2.426261 CGCAGTCGTCGTCGTTGA 60.426 61.111 1.33 0.00 38.33 3.18
104 105 4.104633 GCGCAGTCGTCGTCGTTG 62.105 66.667 0.30 3.79 38.14 4.10
107 108 4.156622 TAGGCGCAGTCGTCGTCG 62.157 66.667 10.83 0.00 46.46 5.12
108 109 2.576317 GTAGGCGCAGTCGTCGTC 60.576 66.667 10.83 0.00 46.46 4.20
109 110 2.697761 ATGTAGGCGCAGTCGTCGT 61.698 57.895 10.83 0.00 46.46 4.34
110 111 2.102357 ATGTAGGCGCAGTCGTCG 59.898 61.111 10.83 0.00 46.46 5.12
111 112 1.878522 CCATGTAGGCGCAGTCGTC 60.879 63.158 10.83 0.00 41.36 4.20
112 113 2.184322 CCATGTAGGCGCAGTCGT 59.816 61.111 10.83 0.00 36.95 4.34
113 114 2.167219 CACCATGTAGGCGCAGTCG 61.167 63.158 10.83 0.00 43.14 4.18
114 115 2.464459 GCACCATGTAGGCGCAGTC 61.464 63.158 10.83 0.00 45.00 3.51
115 116 2.436646 GCACCATGTAGGCGCAGT 60.437 61.111 10.83 0.00 45.00 4.40
118 119 3.204827 CCAGCACCATGTAGGCGC 61.205 66.667 0.00 0.00 46.03 6.53
119 120 1.815421 GACCAGCACCATGTAGGCG 60.815 63.158 0.00 0.00 43.14 5.52
120 121 1.452108 GGACCAGCACCATGTAGGC 60.452 63.158 0.00 0.00 43.14 3.93
121 122 0.620556 AAGGACCAGCACCATGTAGG 59.379 55.000 0.00 0.00 45.67 3.18
122 123 2.766263 TCTAAGGACCAGCACCATGTAG 59.234 50.000 0.00 0.00 0.00 2.74
123 124 2.766263 CTCTAAGGACCAGCACCATGTA 59.234 50.000 0.00 0.00 0.00 2.29
124 125 1.556911 CTCTAAGGACCAGCACCATGT 59.443 52.381 0.00 0.00 0.00 3.21
125 126 1.134280 CCTCTAAGGACCAGCACCATG 60.134 57.143 0.00 0.00 37.67 3.66
126 127 1.207791 CCTCTAAGGACCAGCACCAT 58.792 55.000 0.00 0.00 37.67 3.55
127 128 1.553690 GCCTCTAAGGACCAGCACCA 61.554 60.000 0.00 0.00 37.67 4.17
128 129 1.222113 GCCTCTAAGGACCAGCACC 59.778 63.158 0.00 0.00 37.67 5.01
129 130 0.391793 GTGCCTCTAAGGACCAGCAC 60.392 60.000 0.00 0.00 43.14 4.40
130 131 1.888436 CGTGCCTCTAAGGACCAGCA 61.888 60.000 0.00 0.00 37.67 4.41
131 132 1.153549 CGTGCCTCTAAGGACCAGC 60.154 63.158 0.00 0.00 37.67 4.85
132 133 0.108615 CACGTGCCTCTAAGGACCAG 60.109 60.000 0.82 0.00 37.67 4.00
133 134 1.972198 CACGTGCCTCTAAGGACCA 59.028 57.895 0.82 0.00 37.67 4.02
134 135 1.448013 GCACGTGCCTCTAAGGACC 60.448 63.158 30.12 0.00 37.67 4.46
135 136 1.014564 GTGCACGTGCCTCTAAGGAC 61.015 60.000 35.72 21.17 37.67 3.85
136 137 1.292223 GTGCACGTGCCTCTAAGGA 59.708 57.895 35.72 13.53 37.67 3.36
137 138 2.094659 CGTGCACGTGCCTCTAAGG 61.095 63.158 35.72 19.12 41.18 2.69
138 139 0.666274 TTCGTGCACGTGCCTCTAAG 60.666 55.000 35.72 19.99 41.18 2.18
139 140 0.666274 CTTCGTGCACGTGCCTCTAA 60.666 55.000 35.72 23.53 41.18 2.10
140 141 1.080772 CTTCGTGCACGTGCCTCTA 60.081 57.895 35.72 16.34 41.18 2.43
141 142 2.356313 CTTCGTGCACGTGCCTCT 60.356 61.111 35.72 0.00 41.18 3.69
142 143 2.355837 TCTTCGTGCACGTGCCTC 60.356 61.111 35.72 26.19 41.18 4.70
143 144 2.644555 AAGTCTTCGTGCACGTGCCT 62.645 55.000 35.72 22.55 41.18 4.75
144 145 2.159272 GAAGTCTTCGTGCACGTGCC 62.159 60.000 35.72 25.12 41.18 5.01
145 146 1.201825 GAAGTCTTCGTGCACGTGC 59.798 57.895 35.74 33.11 40.80 5.34
146 147 1.557443 GGGAAGTCTTCGTGCACGTG 61.557 60.000 35.74 28.05 40.80 4.49
147 148 1.300697 GGGAAGTCTTCGTGCACGT 60.301 57.895 35.74 18.16 40.80 4.49
148 149 2.372690 CGGGAAGTCTTCGTGCACG 61.373 63.158 32.76 32.76 41.45 5.34
149 150 2.027625 CCGGGAAGTCTTCGTGCAC 61.028 63.158 6.82 6.82 0.00 4.57
150 151 2.342279 CCGGGAAGTCTTCGTGCA 59.658 61.111 6.50 0.00 0.00 4.57
151 152 3.119096 GCCGGGAAGTCTTCGTGC 61.119 66.667 2.18 5.37 0.00 5.34
152 153 1.738099 CAGCCGGGAAGTCTTCGTG 60.738 63.158 2.18 1.59 0.00 4.35
153 154 2.156051 GACAGCCGGGAAGTCTTCGT 62.156 60.000 2.18 0.00 0.00 3.85
154 155 1.446272 GACAGCCGGGAAGTCTTCG 60.446 63.158 2.18 0.00 0.00 3.79
155 156 0.250513 ATGACAGCCGGGAAGTCTTC 59.749 55.000 16.74 3.80 33.56 2.87
156 157 0.250513 GATGACAGCCGGGAAGTCTT 59.749 55.000 16.74 12.06 33.56 3.01
157 158 1.901085 GATGACAGCCGGGAAGTCT 59.099 57.895 16.74 6.11 33.56 3.24
158 159 1.519455 CGATGACAGCCGGGAAGTC 60.519 63.158 2.18 5.22 0.00 3.01
159 160 1.982395 TCGATGACAGCCGGGAAGT 60.982 57.895 2.18 0.00 0.00 3.01
160 161 1.519455 GTCGATGACAGCCGGGAAG 60.519 63.158 2.18 0.00 32.09 3.46
161 162 1.822114 TTGTCGATGACAGCCGGGAA 61.822 55.000 2.18 0.00 43.69 3.97
162 163 2.225791 CTTGTCGATGACAGCCGGGA 62.226 60.000 2.18 0.00 43.69 5.14
163 164 1.811266 CTTGTCGATGACAGCCGGG 60.811 63.158 2.18 0.00 43.69 5.73
164 165 1.811266 CCTTGTCGATGACAGCCGG 60.811 63.158 0.00 0.00 43.69 6.13
165 166 1.078759 GACCTTGTCGATGACAGCCG 61.079 60.000 0.00 0.00 43.69 5.52
166 167 0.037326 TGACCTTGTCGATGACAGCC 60.037 55.000 0.00 0.00 43.69 4.85
167 168 1.728971 CTTGACCTTGTCGATGACAGC 59.271 52.381 0.00 0.00 43.69 4.40
168 169 1.728971 GCTTGACCTTGTCGATGACAG 59.271 52.381 0.00 0.00 43.69 3.51
169 170 1.608025 GGCTTGACCTTGTCGATGACA 60.608 52.381 0.00 0.00 41.09 3.58
170 171 1.079503 GGCTTGACCTTGTCGATGAC 58.920 55.000 0.00 0.00 34.95 3.06
171 172 0.389817 CGGCTTGACCTTGTCGATGA 60.390 55.000 0.00 0.00 34.95 2.92
172 173 1.361668 CCGGCTTGACCTTGTCGATG 61.362 60.000 0.00 0.00 34.95 3.84
173 174 1.079127 CCGGCTTGACCTTGTCGAT 60.079 57.895 0.00 0.00 34.95 3.59
174 175 2.342279 CCGGCTTGACCTTGTCGA 59.658 61.111 0.00 0.00 34.95 4.20
175 176 3.423154 GCCGGCTTGACCTTGTCG 61.423 66.667 22.15 0.00 34.95 4.35
176 177 2.032681 AGCCGGCTTGACCTTGTC 59.967 61.111 27.08 0.00 35.61 3.18
177 178 2.032681 GAGCCGGCTTGACCTTGT 59.967 61.111 33.34 4.05 35.61 3.16
178 179 2.747855 GGAGCCGGCTTGACCTTG 60.748 66.667 33.34 0.00 35.61 3.61
179 180 4.394712 CGGAGCCGGCTTGACCTT 62.395 66.667 33.34 5.97 35.61 3.50
197 198 4.424566 TTGTCGCCGCTCCCGTAC 62.425 66.667 0.00 0.00 0.00 3.67
198 199 4.424566 GTTGTCGCCGCTCCCGTA 62.425 66.667 0.00 0.00 0.00 4.02
220 221 3.257561 CAGAACGAGCCGGCGATG 61.258 66.667 23.20 17.36 34.83 3.84
221 222 3.449227 TCAGAACGAGCCGGCGAT 61.449 61.111 23.20 3.63 34.83 4.58
222 223 4.415332 GTCAGAACGAGCCGGCGA 62.415 66.667 23.20 7.40 34.83 5.54
232 233 1.445582 CCACTACCGCCGTCAGAAC 60.446 63.158 0.00 0.00 0.00 3.01
233 234 1.870055 GACCACTACCGCCGTCAGAA 61.870 60.000 0.00 0.00 0.00 3.02
234 235 2.282674 ACCACTACCGCCGTCAGA 60.283 61.111 0.00 0.00 0.00 3.27
235 236 2.181021 GACCACTACCGCCGTCAG 59.819 66.667 0.00 0.00 0.00 3.51
236 237 3.740397 CGACCACTACCGCCGTCA 61.740 66.667 0.00 0.00 0.00 4.35
237 238 3.273080 AACGACCACTACCGCCGTC 62.273 63.158 0.00 0.00 32.64 4.79
238 239 3.273080 GAACGACCACTACCGCCGT 62.273 63.158 0.00 0.00 34.74 5.68
239 240 2.505557 GAACGACCACTACCGCCG 60.506 66.667 0.00 0.00 0.00 6.46
240 241 2.505557 CGAACGACCACTACCGCC 60.506 66.667 0.00 0.00 0.00 6.13
241 242 2.505557 CCGAACGACCACTACCGC 60.506 66.667 0.00 0.00 0.00 5.68
242 243 1.443194 CACCGAACGACCACTACCG 60.443 63.158 0.00 0.00 0.00 4.02
243 244 1.080298 CCACCGAACGACCACTACC 60.080 63.158 0.00 0.00 0.00 3.18
244 245 0.387750 GACCACCGAACGACCACTAC 60.388 60.000 0.00 0.00 0.00 2.73
245 246 0.538057 AGACCACCGAACGACCACTA 60.538 55.000 0.00 0.00 0.00 2.74
246 247 1.803366 GAGACCACCGAACGACCACT 61.803 60.000 0.00 0.00 0.00 4.00
247 248 1.372623 GAGACCACCGAACGACCAC 60.373 63.158 0.00 0.00 0.00 4.16
248 249 1.802337 CTGAGACCACCGAACGACCA 61.802 60.000 0.00 0.00 0.00 4.02
249 250 1.080705 CTGAGACCACCGAACGACC 60.081 63.158 0.00 0.00 0.00 4.79
250 251 0.313043 TTCTGAGACCACCGAACGAC 59.687 55.000 0.00 0.00 0.00 4.34
251 252 1.201647 GATTCTGAGACCACCGAACGA 59.798 52.381 0.00 0.00 0.00 3.85
252 253 1.202582 AGATTCTGAGACCACCGAACG 59.797 52.381 0.00 0.00 0.00 3.95
253 254 2.732597 CGAGATTCTGAGACCACCGAAC 60.733 54.545 0.00 0.00 0.00 3.95
254 255 1.472878 CGAGATTCTGAGACCACCGAA 59.527 52.381 0.00 0.00 0.00 4.30
255 256 1.095600 CGAGATTCTGAGACCACCGA 58.904 55.000 0.00 0.00 0.00 4.69
256 257 1.095600 TCGAGATTCTGAGACCACCG 58.904 55.000 0.00 0.00 0.00 4.94
257 258 2.428890 ACATCGAGATTCTGAGACCACC 59.571 50.000 0.00 0.00 0.00 4.61
258 259 3.791973 ACATCGAGATTCTGAGACCAC 57.208 47.619 0.00 0.00 0.00 4.16
259 260 6.471233 AATTACATCGAGATTCTGAGACCA 57.529 37.500 0.00 0.00 0.00 4.02
260 261 7.778470 AAAATTACATCGAGATTCTGAGACC 57.222 36.000 0.00 0.00 0.00 3.85
286 287 9.236006 AGAAGTACAAAGCATCTCAAACATAAT 57.764 29.630 0.00 0.00 0.00 1.28
287 288 8.506437 CAGAAGTACAAAGCATCTCAAACATAA 58.494 33.333 0.00 0.00 0.00 1.90
288 289 7.119699 CCAGAAGTACAAAGCATCTCAAACATA 59.880 37.037 0.00 0.00 0.00 2.29
289 290 6.072286 CCAGAAGTACAAAGCATCTCAAACAT 60.072 38.462 0.00 0.00 0.00 2.71
290 291 5.239306 CCAGAAGTACAAAGCATCTCAAACA 59.761 40.000 0.00 0.00 0.00 2.83
291 292 5.693814 CCAGAAGTACAAAGCATCTCAAAC 58.306 41.667 0.00 0.00 0.00 2.93
292 293 4.216257 GCCAGAAGTACAAAGCATCTCAAA 59.784 41.667 0.00 0.00 0.00 2.69
293 294 3.753272 GCCAGAAGTACAAAGCATCTCAA 59.247 43.478 0.00 0.00 0.00 3.02
294 295 3.338249 GCCAGAAGTACAAAGCATCTCA 58.662 45.455 0.00 0.00 0.00 3.27
295 296 2.349886 CGCCAGAAGTACAAAGCATCTC 59.650 50.000 0.00 0.00 0.00 2.75
296 297 2.028112 TCGCCAGAAGTACAAAGCATCT 60.028 45.455 0.00 0.00 0.00 2.90
297 298 2.346803 TCGCCAGAAGTACAAAGCATC 58.653 47.619 0.00 0.00 0.00 3.91
298 299 2.472695 TCGCCAGAAGTACAAAGCAT 57.527 45.000 0.00 0.00 0.00 3.79
299 300 1.871039 GTTCGCCAGAAGTACAAAGCA 59.129 47.619 0.00 0.00 36.99 3.91
300 301 2.143925 AGTTCGCCAGAAGTACAAAGC 58.856 47.619 0.00 0.00 38.20 3.51
301 302 4.272504 TCAAAGTTCGCCAGAAGTACAAAG 59.727 41.667 0.00 0.00 38.98 2.77
302 303 4.193090 TCAAAGTTCGCCAGAAGTACAAA 58.807 39.130 0.00 0.00 38.98 2.83
303 304 3.799366 TCAAAGTTCGCCAGAAGTACAA 58.201 40.909 0.00 0.00 38.98 2.41
304 305 3.462483 TCAAAGTTCGCCAGAAGTACA 57.538 42.857 0.00 0.00 38.98 2.90
305 306 6.663944 ATTATCAAAGTTCGCCAGAAGTAC 57.336 37.500 0.00 0.00 38.98 2.73
306 307 7.778083 TCTATTATCAAAGTTCGCCAGAAGTA 58.222 34.615 0.00 0.00 38.98 2.24
307 308 6.640518 TCTATTATCAAAGTTCGCCAGAAGT 58.359 36.000 0.00 0.00 41.51 3.01
308 309 7.721286 ATCTATTATCAAAGTTCGCCAGAAG 57.279 36.000 0.00 0.00 36.99 2.85
309 310 8.397906 CAAATCTATTATCAAAGTTCGCCAGAA 58.602 33.333 0.00 0.00 0.00 3.02
310 311 7.012327 CCAAATCTATTATCAAAGTTCGCCAGA 59.988 37.037 0.00 0.00 0.00 3.86
311 312 7.012327 TCCAAATCTATTATCAAAGTTCGCCAG 59.988 37.037 0.00 0.00 0.00 4.85
312 313 6.826231 TCCAAATCTATTATCAAAGTTCGCCA 59.174 34.615 0.00 0.00 0.00 5.69
313 314 7.259290 TCCAAATCTATTATCAAAGTTCGCC 57.741 36.000 0.00 0.00 0.00 5.54
314 315 7.742089 CGATCCAAATCTATTATCAAAGTTCGC 59.258 37.037 0.00 0.00 0.00 4.70
315 316 8.765219 ACGATCCAAATCTATTATCAAAGTTCG 58.235 33.333 0.00 0.00 0.00 3.95
320 321 9.929722 CGAAAACGATCCAAATCTATTATCAAA 57.070 29.630 0.00 0.00 0.00 2.69
321 322 9.320352 TCGAAAACGATCCAAATCTATTATCAA 57.680 29.630 0.00 0.00 0.00 2.57
322 323 8.880878 TCGAAAACGATCCAAATCTATTATCA 57.119 30.769 0.00 0.00 0.00 2.15
325 326 9.982291 CTTTTCGAAAACGATCCAAATCTATTA 57.018 29.630 19.08 0.00 0.00 0.98
326 327 8.726988 TCTTTTCGAAAACGATCCAAATCTATT 58.273 29.630 19.08 0.00 0.00 1.73
327 328 8.263940 TCTTTTCGAAAACGATCCAAATCTAT 57.736 30.769 19.08 0.00 0.00 1.98
328 329 7.661127 TCTTTTCGAAAACGATCCAAATCTA 57.339 32.000 19.08 0.00 0.00 1.98
329 330 6.554334 TCTTTTCGAAAACGATCCAAATCT 57.446 33.333 19.08 0.00 0.00 2.40
330 331 7.617533 TTTCTTTTCGAAAACGATCCAAATC 57.382 32.000 19.08 0.00 38.62 2.17
331 332 7.995463 TTTTCTTTTCGAAAACGATCCAAAT 57.005 28.000 19.08 0.00 44.42 2.32
341 342 8.709386 TGTTGGATGATTTTTCTTTTCGAAAA 57.291 26.923 21.35 21.35 46.81 2.29
342 343 7.437862 CCTGTTGGATGATTTTTCTTTTCGAAA 59.562 33.333 6.47 6.47 36.22 3.46
343 344 6.922957 CCTGTTGGATGATTTTTCTTTTCGAA 59.077 34.615 0.00 0.00 34.57 3.71
344 345 6.446318 CCTGTTGGATGATTTTTCTTTTCGA 58.554 36.000 0.00 0.00 34.57 3.71
345 346 5.119125 GCCTGTTGGATGATTTTTCTTTTCG 59.881 40.000 0.00 0.00 34.57 3.46
346 347 5.990996 TGCCTGTTGGATGATTTTTCTTTTC 59.009 36.000 0.00 0.00 34.57 2.29
347 348 5.927819 TGCCTGTTGGATGATTTTTCTTTT 58.072 33.333 0.00 0.00 34.57 2.27
348 349 5.070847 ACTGCCTGTTGGATGATTTTTCTTT 59.929 36.000 0.00 0.00 34.57 2.52
349 350 4.590222 ACTGCCTGTTGGATGATTTTTCTT 59.410 37.500 0.00 0.00 34.57 2.52
350 351 4.154942 ACTGCCTGTTGGATGATTTTTCT 58.845 39.130 0.00 0.00 34.57 2.52
351 352 4.525912 ACTGCCTGTTGGATGATTTTTC 57.474 40.909 0.00 0.00 34.57 2.29
352 353 4.961438 AACTGCCTGTTGGATGATTTTT 57.039 36.364 0.00 0.00 37.52 1.94
357 358 3.010027 TCCATAAACTGCCTGTTGGATGA 59.990 43.478 9.71 0.00 39.13 2.92
511 514 2.741211 GGTTTGGACGACGGAGCC 60.741 66.667 0.00 0.00 0.00 4.70
1503 2091 6.407187 CCACATCATATGCCTTGGAAATCAAA 60.407 38.462 9.56 0.00 34.56 2.69
1790 2378 2.118404 CACAGCCCCAACAACACGT 61.118 57.895 0.00 0.00 0.00 4.49
1965 2561 0.671781 ACAGCGACATCACTTCAGGC 60.672 55.000 0.00 0.00 0.00 4.85
2093 2689 3.549471 CAGATCGTGCAATCTACTCACAC 59.451 47.826 0.56 0.00 34.21 3.82
2373 2969 3.418675 ACAGCGGTGACAGTATTCG 57.581 52.632 23.44 0.00 0.00 3.34
2702 3307 5.944007 ACTAAAAATGTACTTCTCCCGCATT 59.056 36.000 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.