Multiple sequence alignment - TraesCS1A01G236200

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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 TraesCS1A01G236200 chr1A 100.000 2709 0 0 1 2709 418602211 418604919 0.000000e+00 5003.0
1 TraesCS1A01G236200 chr1B 89.940 1332 70 22 301 1598 438061441 438060140 0.000000e+00 1659.0
2 TraesCS1A01G236200 chr1B 76.056 781 181 5 1933 2709 624993418 624992640 4.200000e-108 401.0
3 TraesCS1A01G236200 chr1B 93.562 233 5 6 1692 1918 438059654 438059426 3.340000e-89 339.0
4 TraesCS1A01G236200 chr2B 98.992 794 7 1 1916 2709 545184248 545185040 0.000000e+00 1421.0
5 TraesCS1A01G236200 chr2B 97.862 795 17 0 1915 2709 714209366 714208572 0.000000e+00 1375.0
6 TraesCS1A01G236200 chr1D 88.935 967 42 15 973 1918 325629576 325628654 0.000000e+00 1133.0
7 TraesCS1A01G236200 chr1D 81.143 525 56 17 301 797 325630085 325629576 5.470000e-102 381.0
8 TraesCS1A01G236200 chr5B 88.651 793 88 2 1918 2709 9587909 9587118 0.000000e+00 965.0
9 TraesCS1A01G236200 chr5B 85.217 230 31 3 1 228 229081051 229081279 1.620000e-57 233.0
10 TraesCS1A01G236200 chr6B 82.997 794 129 4 1921 2709 680101085 680100293 0.000000e+00 713.0
11 TraesCS1A01G236200 chr6B 77.888 805 162 13 1915 2709 52812303 52811505 1.130000e-133 486.0
12 TraesCS1A01G236200 chr2A 88.210 229 24 2 3 228 725599110 725598882 1.240000e-68 270.0
13 TraesCS1A01G236200 chr2A 88.210 229 24 2 3 228 725664494 725664266 1.240000e-68 270.0
14 TraesCS1A01G236200 chr2A 98.148 108 2 0 1918 2025 90518837 90518944 3.560000e-44 189.0
15 TraesCS1A01G236200 chr3D 87.554 233 24 4 1 229 458888365 458888134 5.750000e-67 265.0
16 TraesCS1A01G236200 chr3A 87.336 229 27 2 2 228 156205835 156206063 7.440000e-66 261.0
17 TraesCS1A01G236200 chr4B 85.837 233 29 4 1 230 489301064 489300833 7.490000e-61 244.0
18 TraesCS1A01G236200 chr3B 85.345 232 29 4 1 228 668790866 668790636 4.510000e-58 235.0
19 TraesCS1A01G236200 chr7B 80.269 223 39 4 1 220 585783446 585783666 2.160000e-36 163.0
20 TraesCS1A01G236200 chr5D 89.130 46 5 0 2261 2306 16121552 16121597 1.050000e-04 58.4
21 TraesCS1A01G236200 chr5A 92.500 40 2 1 233 271 559025236 559025197 3.770000e-04 56.5
22 TraesCS1A01G236200 chr2D 100.000 30 0 0 2617 2646 540963183 540963154 3.770000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G236200 chr1A 418602211 418604919 2708 False 5003 5003 100.000 1 2709 1 chr1A.!!$F1 2708
1 TraesCS1A01G236200 chr1B 438059426 438061441 2015 True 999 1659 91.751 301 1918 2 chr1B.!!$R2 1617
2 TraesCS1A01G236200 chr1B 624992640 624993418 778 True 401 401 76.056 1933 2709 1 chr1B.!!$R1 776
3 TraesCS1A01G236200 chr2B 545184248 545185040 792 False 1421 1421 98.992 1916 2709 1 chr2B.!!$F1 793
4 TraesCS1A01G236200 chr2B 714208572 714209366 794 True 1375 1375 97.862 1915 2709 1 chr2B.!!$R1 794
5 TraesCS1A01G236200 chr1D 325628654 325630085 1431 True 757 1133 85.039 301 1918 2 chr1D.!!$R1 1617
6 TraesCS1A01G236200 chr5B 9587118 9587909 791 True 965 965 88.651 1918 2709 1 chr5B.!!$R1 791
7 TraesCS1A01G236200 chr6B 680100293 680101085 792 True 713 713 82.997 1921 2709 1 chr6B.!!$R2 788
8 TraesCS1A01G236200 chr6B 52811505 52812303 798 True 486 486 77.888 1915 2709 1 chr6B.!!$R1 794

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
96 97 0.030638 CGTGTTGTTTTGGGGCTGAG 59.969 55.0 0.00 0.0 0.00 3.35 F
139 140 0.032952 TTGTAGCTTCGTCAACGCCT 59.967 50.0 0.00 0.0 39.60 5.52 F
148 149 0.109458 CGTCAACGCCTGCTAGTGTA 60.109 55.0 0.00 0.0 0.00 2.90 F
1337 1407 0.587285 CCGTCGTCGAGGATAAGGAG 59.413 60.0 16.16 0.0 39.71 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 1502 0.179129 CATGTTGGATTTCGGCAGCC 60.179 55.000 0.00 0.0 0.00 4.85 R
1583 1653 0.670239 TAGTGCGAGACGTACCACGA 60.670 55.000 5.61 0.0 46.05 4.35 R
1692 2186 3.437395 TGTTGCACAAGTGTCGTTAACTT 59.563 39.130 3.71 0.0 38.40 2.66 R
2665 3172 1.473257 GCCGCTGAATGATGTAGGACA 60.473 52.381 0.00 0.0 0.00 4.02 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 4.409342 CGAGCATCAAGGACGAGG 57.591 61.111 0.00 0.00 33.17 4.63
18 19 1.880340 CGAGCATCAAGGACGAGGC 60.880 63.158 0.00 0.00 42.88 4.70
19 20 1.522580 GAGCATCAAGGACGAGGCC 60.523 63.158 0.00 0.00 43.57 5.19
20 21 2.514824 GCATCAAGGACGAGGCCC 60.515 66.667 0.00 0.00 36.72 5.80
21 22 2.202932 CATCAAGGACGAGGCCCG 60.203 66.667 11.48 11.48 45.44 6.13
22 23 3.470888 ATCAAGGACGAGGCCCGG 61.471 66.667 16.44 0.00 43.93 5.73
40 41 4.504916 CGCTGGGACGAGCTGGAG 62.505 72.222 1.44 0.00 36.77 3.86
41 42 4.828925 GCTGGGACGAGCTGGAGC 62.829 72.222 1.44 0.00 42.49 4.70
53 54 2.162319 GCTGGAGCTGTAGGATTAGC 57.838 55.000 0.00 0.00 40.18 3.09
54 55 1.414181 GCTGGAGCTGTAGGATTAGCA 59.586 52.381 0.00 0.00 42.29 3.49
55 56 2.038295 GCTGGAGCTGTAGGATTAGCAT 59.962 50.000 0.00 0.00 42.29 3.79
56 57 3.864160 GCTGGAGCTGTAGGATTAGCATC 60.864 52.174 0.00 0.00 42.29 3.91
57 58 2.297315 TGGAGCTGTAGGATTAGCATCG 59.703 50.000 0.00 0.00 42.29 3.84
58 59 2.558795 GGAGCTGTAGGATTAGCATCGA 59.441 50.000 0.00 0.00 42.29 3.59
59 60 3.194542 GGAGCTGTAGGATTAGCATCGAT 59.805 47.826 0.00 0.00 42.29 3.59
60 61 4.420168 GAGCTGTAGGATTAGCATCGATC 58.580 47.826 0.00 0.00 42.29 3.69
61 62 3.829026 AGCTGTAGGATTAGCATCGATCA 59.171 43.478 0.00 0.00 42.29 2.92
62 63 4.465660 AGCTGTAGGATTAGCATCGATCAT 59.534 41.667 0.00 0.00 42.29 2.45
63 64 4.803088 GCTGTAGGATTAGCATCGATCATC 59.197 45.833 0.00 0.00 39.67 2.92
64 65 5.330455 TGTAGGATTAGCATCGATCATCC 57.670 43.478 11.90 11.90 34.64 3.51
65 66 5.019470 TGTAGGATTAGCATCGATCATCCT 58.981 41.667 20.74 20.74 44.87 3.24
66 67 5.481824 TGTAGGATTAGCATCGATCATCCTT 59.518 40.000 21.57 11.58 40.84 3.36
67 68 4.829968 AGGATTAGCATCGATCATCCTTG 58.170 43.478 14.96 0.00 40.84 3.61
68 69 4.285517 AGGATTAGCATCGATCATCCTTGT 59.714 41.667 14.96 0.56 40.84 3.16
69 70 5.481824 AGGATTAGCATCGATCATCCTTGTA 59.518 40.000 14.96 0.00 40.84 2.41
70 71 6.014242 AGGATTAGCATCGATCATCCTTGTAA 60.014 38.462 14.96 0.80 40.84 2.41
71 72 6.091441 GGATTAGCATCGATCATCCTTGTAAC 59.909 42.308 12.32 0.00 32.10 2.50
72 73 3.733337 AGCATCGATCATCCTTGTAACC 58.267 45.455 0.00 0.00 0.00 2.85
73 74 3.389329 AGCATCGATCATCCTTGTAACCT 59.611 43.478 0.00 0.00 0.00 3.50
74 75 3.496130 GCATCGATCATCCTTGTAACCTG 59.504 47.826 0.00 0.00 0.00 4.00
75 76 4.740634 GCATCGATCATCCTTGTAACCTGA 60.741 45.833 0.00 0.00 0.00 3.86
76 77 4.386867 TCGATCATCCTTGTAACCTGAC 57.613 45.455 0.00 0.00 0.00 3.51
77 78 3.132289 TCGATCATCCTTGTAACCTGACC 59.868 47.826 0.00 0.00 0.00 4.02
78 79 3.458189 GATCATCCTTGTAACCTGACCG 58.542 50.000 0.00 0.00 0.00 4.79
79 80 2.253610 TCATCCTTGTAACCTGACCGT 58.746 47.619 0.00 0.00 0.00 4.83
80 81 2.028476 TCATCCTTGTAACCTGACCGTG 60.028 50.000 0.00 0.00 0.00 4.94
81 82 1.416243 TCCTTGTAACCTGACCGTGT 58.584 50.000 0.00 0.00 0.00 4.49
82 83 1.764134 TCCTTGTAACCTGACCGTGTT 59.236 47.619 0.00 0.00 0.00 3.32
83 84 1.871039 CCTTGTAACCTGACCGTGTTG 59.129 52.381 0.00 0.00 0.00 3.33
84 85 2.557317 CTTGTAACCTGACCGTGTTGT 58.443 47.619 0.00 0.00 0.00 3.32
85 86 2.695127 TGTAACCTGACCGTGTTGTT 57.305 45.000 0.00 0.00 0.00 2.83
86 87 2.988570 TGTAACCTGACCGTGTTGTTT 58.011 42.857 0.00 0.00 0.00 2.83
87 88 3.345414 TGTAACCTGACCGTGTTGTTTT 58.655 40.909 0.00 0.00 0.00 2.43
88 89 2.931512 AACCTGACCGTGTTGTTTTG 57.068 45.000 0.00 0.00 0.00 2.44
89 90 1.099689 ACCTGACCGTGTTGTTTTGG 58.900 50.000 0.00 0.00 0.00 3.28
90 91 0.383949 CCTGACCGTGTTGTTTTGGG 59.616 55.000 0.00 0.00 0.00 4.12
91 92 0.383949 CTGACCGTGTTGTTTTGGGG 59.616 55.000 0.00 0.00 0.00 4.96
92 93 1.066752 GACCGTGTTGTTTTGGGGC 59.933 57.895 0.00 0.00 0.00 5.80
93 94 1.380650 ACCGTGTTGTTTTGGGGCT 60.381 52.632 0.00 0.00 0.00 5.19
94 95 1.067250 CCGTGTTGTTTTGGGGCTG 59.933 57.895 0.00 0.00 0.00 4.85
95 96 1.388065 CCGTGTTGTTTTGGGGCTGA 61.388 55.000 0.00 0.00 0.00 4.26
96 97 0.030638 CGTGTTGTTTTGGGGCTGAG 59.969 55.000 0.00 0.00 0.00 3.35
97 98 0.249447 GTGTTGTTTTGGGGCTGAGC 60.249 55.000 0.00 0.00 0.00 4.26
98 99 0.685785 TGTTGTTTTGGGGCTGAGCA 60.686 50.000 6.82 0.00 0.00 4.26
99 100 0.463620 GTTGTTTTGGGGCTGAGCAA 59.536 50.000 6.82 0.00 0.00 3.91
100 101 0.463620 TTGTTTTGGGGCTGAGCAAC 59.536 50.000 6.82 1.90 0.00 4.17
101 102 1.367471 GTTTTGGGGCTGAGCAACC 59.633 57.895 6.82 8.73 0.00 3.77
102 103 1.836604 TTTTGGGGCTGAGCAACCC 60.837 57.895 11.37 11.37 46.24 4.11
106 107 4.432741 GGGCTGAGCAACCCCCTC 62.433 72.222 6.82 0.00 40.56 4.30
107 108 3.334054 GGCTGAGCAACCCCCTCT 61.334 66.667 6.82 0.00 0.00 3.69
108 109 2.759795 GCTGAGCAACCCCCTCTT 59.240 61.111 0.00 0.00 0.00 2.85
109 110 1.377856 GCTGAGCAACCCCCTCTTC 60.378 63.158 0.00 0.00 0.00 2.87
110 111 1.846712 GCTGAGCAACCCCCTCTTCT 61.847 60.000 0.00 0.00 0.00 2.85
111 112 0.695347 CTGAGCAACCCCCTCTTCTT 59.305 55.000 0.00 0.00 0.00 2.52
112 113 0.693049 TGAGCAACCCCCTCTTCTTC 59.307 55.000 0.00 0.00 0.00 2.87
113 114 0.988063 GAGCAACCCCCTCTTCTTCT 59.012 55.000 0.00 0.00 0.00 2.85
114 115 0.695347 AGCAACCCCCTCTTCTTCTG 59.305 55.000 0.00 0.00 0.00 3.02
115 116 0.962855 GCAACCCCCTCTTCTTCTGC 60.963 60.000 0.00 0.00 0.00 4.26
116 117 0.695347 CAACCCCCTCTTCTTCTGCT 59.305 55.000 0.00 0.00 0.00 4.24
117 118 0.988063 AACCCCCTCTTCTTCTGCTC 59.012 55.000 0.00 0.00 0.00 4.26
118 119 0.912006 ACCCCCTCTTCTTCTGCTCC 60.912 60.000 0.00 0.00 0.00 4.70
119 120 0.620121 CCCCCTCTTCTTCTGCTCCT 60.620 60.000 0.00 0.00 0.00 3.69
120 121 1.284313 CCCCTCTTCTTCTGCTCCTT 58.716 55.000 0.00 0.00 0.00 3.36
121 122 1.632920 CCCCTCTTCTTCTGCTCCTTT 59.367 52.381 0.00 0.00 0.00 3.11
122 123 2.617532 CCCCTCTTCTTCTGCTCCTTTG 60.618 54.545 0.00 0.00 0.00 2.77
123 124 2.039613 CCCTCTTCTTCTGCTCCTTTGT 59.960 50.000 0.00 0.00 0.00 2.83
124 125 3.261897 CCCTCTTCTTCTGCTCCTTTGTA 59.738 47.826 0.00 0.00 0.00 2.41
125 126 4.502962 CCTCTTCTTCTGCTCCTTTGTAG 58.497 47.826 0.00 0.00 0.00 2.74
126 127 3.931578 TCTTCTTCTGCTCCTTTGTAGC 58.068 45.455 0.00 0.00 40.50 3.58
127 128 3.580458 TCTTCTTCTGCTCCTTTGTAGCT 59.420 43.478 0.00 0.00 40.73 3.32
128 129 4.040952 TCTTCTTCTGCTCCTTTGTAGCTT 59.959 41.667 0.00 0.00 40.73 3.74
129 130 3.931578 TCTTCTGCTCCTTTGTAGCTTC 58.068 45.455 0.00 0.00 40.73 3.86
130 131 2.370281 TCTGCTCCTTTGTAGCTTCG 57.630 50.000 0.00 0.00 40.73 3.79
131 132 1.618837 TCTGCTCCTTTGTAGCTTCGT 59.381 47.619 0.00 0.00 40.73 3.85
132 133 1.996191 CTGCTCCTTTGTAGCTTCGTC 59.004 52.381 0.00 0.00 40.73 4.20
133 134 1.343142 TGCTCCTTTGTAGCTTCGTCA 59.657 47.619 0.00 0.00 40.73 4.35
134 135 2.224185 TGCTCCTTTGTAGCTTCGTCAA 60.224 45.455 0.00 0.00 40.73 3.18
135 136 2.157863 GCTCCTTTGTAGCTTCGTCAAC 59.842 50.000 0.00 0.00 37.01 3.18
136 137 2.400399 TCCTTTGTAGCTTCGTCAACG 58.600 47.619 0.00 0.00 41.45 4.10
137 138 1.136336 CCTTTGTAGCTTCGTCAACGC 60.136 52.381 0.00 0.00 39.60 4.84
138 139 0.863144 TTTGTAGCTTCGTCAACGCC 59.137 50.000 0.00 0.00 39.60 5.68
139 140 0.032952 TTGTAGCTTCGTCAACGCCT 59.967 50.000 0.00 0.00 39.60 5.52
140 141 0.666274 TGTAGCTTCGTCAACGCCTG 60.666 55.000 0.00 0.00 39.60 4.85
141 142 1.736645 TAGCTTCGTCAACGCCTGC 60.737 57.895 0.00 2.39 39.60 4.85
142 143 2.154798 TAGCTTCGTCAACGCCTGCT 62.155 55.000 16.18 16.18 40.03 4.24
143 144 1.736645 GCTTCGTCAACGCCTGCTA 60.737 57.895 0.00 0.00 39.60 3.49
144 145 1.687494 GCTTCGTCAACGCCTGCTAG 61.687 60.000 0.00 0.00 39.60 3.42
145 146 0.388649 CTTCGTCAACGCCTGCTAGT 60.389 55.000 0.00 0.00 39.60 2.57
146 147 0.666274 TTCGTCAACGCCTGCTAGTG 60.666 55.000 0.00 0.00 39.60 2.74
147 148 1.372997 CGTCAACGCCTGCTAGTGT 60.373 57.895 0.00 0.00 0.00 3.55
148 149 0.109458 CGTCAACGCCTGCTAGTGTA 60.109 55.000 0.00 0.00 0.00 2.90
149 150 1.469251 CGTCAACGCCTGCTAGTGTAT 60.469 52.381 0.00 0.00 0.00 2.29
150 151 2.223409 CGTCAACGCCTGCTAGTGTATA 60.223 50.000 0.00 0.00 0.00 1.47
151 152 3.550233 CGTCAACGCCTGCTAGTGTATAT 60.550 47.826 0.00 0.00 0.00 0.86
152 153 3.736252 GTCAACGCCTGCTAGTGTATATG 59.264 47.826 0.00 0.00 0.00 1.78
153 154 3.059884 CAACGCCTGCTAGTGTATATGG 58.940 50.000 0.00 0.00 0.00 2.74
154 155 2.594131 ACGCCTGCTAGTGTATATGGA 58.406 47.619 0.00 0.00 0.00 3.41
155 156 3.165875 ACGCCTGCTAGTGTATATGGAT 58.834 45.455 0.00 0.00 0.00 3.41
156 157 3.578716 ACGCCTGCTAGTGTATATGGATT 59.421 43.478 0.00 0.00 0.00 3.01
157 158 3.928992 CGCCTGCTAGTGTATATGGATTG 59.071 47.826 0.00 0.00 0.00 2.67
158 159 4.321974 CGCCTGCTAGTGTATATGGATTGA 60.322 45.833 0.00 0.00 0.00 2.57
159 160 5.174395 GCCTGCTAGTGTATATGGATTGAG 58.826 45.833 0.00 0.00 0.00 3.02
160 161 5.728471 CCTGCTAGTGTATATGGATTGAGG 58.272 45.833 0.00 0.00 0.00 3.86
161 162 5.247110 CCTGCTAGTGTATATGGATTGAGGT 59.753 44.000 0.00 0.00 0.00 3.85
162 163 6.239714 CCTGCTAGTGTATATGGATTGAGGTT 60.240 42.308 0.00 0.00 0.00 3.50
163 164 6.524734 TGCTAGTGTATATGGATTGAGGTTG 58.475 40.000 0.00 0.00 0.00 3.77
164 165 5.409826 GCTAGTGTATATGGATTGAGGTTGC 59.590 44.000 0.00 0.00 0.00 4.17
165 166 5.372343 AGTGTATATGGATTGAGGTTGCA 57.628 39.130 0.00 0.00 0.00 4.08
166 167 5.754782 AGTGTATATGGATTGAGGTTGCAA 58.245 37.500 0.00 0.00 0.00 4.08
167 168 5.590259 AGTGTATATGGATTGAGGTTGCAAC 59.410 40.000 21.59 21.59 0.00 4.17
182 183 5.853936 GGTTGCAACCCTTTATTTTCTTCT 58.146 37.500 34.36 0.00 43.43 2.85
183 184 6.988522 GGTTGCAACCCTTTATTTTCTTCTA 58.011 36.000 34.36 0.00 43.43 2.10
184 185 6.866770 GGTTGCAACCCTTTATTTTCTTCTAC 59.133 38.462 34.36 5.75 43.43 2.59
185 186 6.584185 TGCAACCCTTTATTTTCTTCTACC 57.416 37.500 0.00 0.00 0.00 3.18
186 187 6.311735 TGCAACCCTTTATTTTCTTCTACCT 58.688 36.000 0.00 0.00 0.00 3.08
187 188 7.463431 TGCAACCCTTTATTTTCTTCTACCTA 58.537 34.615 0.00 0.00 0.00 3.08
188 189 8.113462 TGCAACCCTTTATTTTCTTCTACCTAT 58.887 33.333 0.00 0.00 0.00 2.57
189 190 8.622157 GCAACCCTTTATTTTCTTCTACCTATC 58.378 37.037 0.00 0.00 0.00 2.08
190 191 9.681062 CAACCCTTTATTTTCTTCTACCTATCA 57.319 33.333 0.00 0.00 0.00 2.15
203 204 8.577296 TCTTCTACCTATCAATGGAAAGATACG 58.423 37.037 0.00 0.00 0.00 3.06
204 205 6.688578 TCTACCTATCAATGGAAAGATACGC 58.311 40.000 0.00 0.00 0.00 4.42
205 206 5.552870 ACCTATCAATGGAAAGATACGCT 57.447 39.130 0.00 0.00 0.00 5.07
206 207 5.542779 ACCTATCAATGGAAAGATACGCTC 58.457 41.667 0.00 0.00 0.00 5.03
207 208 5.305644 ACCTATCAATGGAAAGATACGCTCT 59.694 40.000 0.00 0.00 34.96 4.09
208 209 6.493802 ACCTATCAATGGAAAGATACGCTCTA 59.506 38.462 0.00 0.00 32.41 2.43
209 210 7.015292 ACCTATCAATGGAAAGATACGCTCTAA 59.985 37.037 0.00 0.00 32.41 2.10
210 211 7.872993 CCTATCAATGGAAAGATACGCTCTAAA 59.127 37.037 0.00 0.00 32.41 1.85
211 212 7.721286 ATCAATGGAAAGATACGCTCTAAAG 57.279 36.000 0.00 0.00 32.41 1.85
212 213 5.523916 TCAATGGAAAGATACGCTCTAAAGC 59.476 40.000 0.00 0.00 45.56 3.51
295 296 9.825972 AAACGTTCACATCACTATTTTATTGAG 57.174 29.630 0.00 0.00 0.00 3.02
296 297 7.974675 ACGTTCACATCACTATTTTATTGAGG 58.025 34.615 0.00 0.00 0.00 3.86
297 298 7.065803 ACGTTCACATCACTATTTTATTGAGGG 59.934 37.037 0.00 0.00 0.00 4.30
298 299 7.279981 CGTTCACATCACTATTTTATTGAGGGA 59.720 37.037 0.00 0.00 0.00 4.20
299 300 8.616076 GTTCACATCACTATTTTATTGAGGGAG 58.384 37.037 0.00 0.00 0.00 4.30
356 357 6.348540 GGAGTGCATAGACCAGTTTAACTTTG 60.349 42.308 0.00 0.00 0.00 2.77
380 381 9.429109 TTGAGGACTGTGTATATATAACTTGGA 57.571 33.333 0.00 0.00 0.00 3.53
420 423 4.525487 CGGAGGCTACCAATGGTTAGTATA 59.475 45.833 11.41 0.00 37.09 1.47
421 424 5.011329 CGGAGGCTACCAATGGTTAGTATAA 59.989 44.000 11.41 0.00 37.09 0.98
459 479 8.753133 AGAGGAGAAACAAAATCAGAAAAGTTT 58.247 29.630 0.00 0.00 32.48 2.66
480 500 7.709947 AGTTTATGCATGGATGTAGTCAATTG 58.290 34.615 10.16 0.00 0.00 2.32
623 668 2.478879 CGCCGGGGAACAATAAACATTC 60.479 50.000 14.46 0.00 0.00 2.67
627 672 3.936453 CGGGGAACAATAAACATTCGAGA 59.064 43.478 0.00 0.00 0.00 4.04
628 673 4.393680 CGGGGAACAATAAACATTCGAGAA 59.606 41.667 0.00 0.00 0.00 2.87
660 705 1.000274 CAAGCTGGTGGCAACTAAACC 60.000 52.381 3.27 0.00 44.79 3.27
679 732 1.021390 CAACAGAATTCCGGCGAGCT 61.021 55.000 9.30 0.00 0.00 4.09
737 790 1.944024 CACCTGTCAGCCGTTACAAAA 59.056 47.619 0.00 0.00 0.00 2.44
752 805 5.048991 CGTTACAAAACTAGGCTGGAAATGT 60.049 40.000 4.33 8.43 33.15 2.71
761 814 7.961326 ACTAGGCTGGAAATGTTATCAAAAT 57.039 32.000 4.33 0.00 0.00 1.82
808 861 3.312736 AAAGAAGGCTTCTGGTTTGGA 57.687 42.857 29.19 0.00 40.59 3.53
823 876 4.894201 GGACATCATGGCCTCCTG 57.106 61.111 0.47 0.00 44.12 3.86
863 916 0.606673 GCTCCGGGCTTGACTTTTCT 60.607 55.000 0.00 0.00 38.06 2.52
864 917 1.897560 CTCCGGGCTTGACTTTTCTT 58.102 50.000 0.00 0.00 0.00 2.52
865 918 2.230660 CTCCGGGCTTGACTTTTCTTT 58.769 47.619 0.00 0.00 0.00 2.52
866 919 2.226674 CTCCGGGCTTGACTTTTCTTTC 59.773 50.000 0.00 0.00 0.00 2.62
867 920 1.269723 CCGGGCTTGACTTTTCTTTCC 59.730 52.381 0.00 0.00 0.00 3.13
875 928 2.293122 TGACTTTTCTTTCCCGTGCATG 59.707 45.455 0.00 0.00 0.00 4.06
878 931 3.383185 ACTTTTCTTTCCCGTGCATGAAA 59.617 39.130 7.72 8.04 0.00 2.69
904 957 2.731721 CCACGCACGCACGTAGAA 60.732 61.111 2.78 0.00 46.34 2.10
906 959 2.430244 ACGCACGCACGTAGAAGG 60.430 61.111 0.96 0.00 46.19 3.46
907 960 2.430244 CGCACGCACGTAGAAGGT 60.430 61.111 0.00 0.00 0.00 3.50
916 972 2.582978 GTAGAAGGTCGTGGGGGC 59.417 66.667 0.00 0.00 0.00 5.80
937 993 1.345415 GGAGGGCGATATAAAACCGGA 59.655 52.381 9.46 0.00 0.00 5.14
939 995 1.071228 AGGGCGATATAAAACCGGACC 59.929 52.381 9.46 0.00 0.00 4.46
968 1024 2.650116 GCTTCTCCTCGCCTCCACA 61.650 63.158 0.00 0.00 0.00 4.17
970 1026 2.570582 CTTCTCCTCGCCTCCACAGC 62.571 65.000 0.00 0.00 0.00 4.40
974 1030 3.385384 CTCGCCTCCACAGCTCCA 61.385 66.667 0.00 0.00 0.00 3.86
975 1031 3.655810 CTCGCCTCCACAGCTCCAC 62.656 68.421 0.00 0.00 0.00 4.02
976 1032 3.699894 CGCCTCCACAGCTCCACT 61.700 66.667 0.00 0.00 0.00 4.00
1015 1071 4.796231 CGCCCGACGGTTCCTCTG 62.796 72.222 13.94 0.00 38.44 3.35
1224 1294 2.745100 CCTCCTCGTCCGACGACA 60.745 66.667 19.51 8.39 46.73 4.35
1238 1308 4.773117 GACACCTCCGTCGCCGTC 62.773 72.222 0.00 0.00 0.00 4.79
1240 1310 4.351938 CACCTCCGTCGCCGTCAA 62.352 66.667 0.00 0.00 0.00 3.18
1241 1311 4.052229 ACCTCCGTCGCCGTCAAG 62.052 66.667 0.00 0.00 0.00 3.02
1242 1312 4.796231 CCTCCGTCGCCGTCAAGG 62.796 72.222 0.00 0.00 44.97 3.61
1243 1313 3.744719 CTCCGTCGCCGTCAAGGA 61.745 66.667 0.00 0.00 45.00 3.36
1337 1407 0.587285 CCGTCGTCGAGGATAAGGAG 59.413 60.000 16.16 0.00 39.71 3.69
1345 1415 1.639722 GAGGATAAGGAGGAGGAGGC 58.360 60.000 0.00 0.00 0.00 4.70
1371 1441 1.726853 GGTCAAGAAGGATGTCACCG 58.273 55.000 0.00 0.00 34.73 4.94
1373 1443 1.002087 GTCAAGAAGGATGTCACCGGT 59.998 52.381 0.00 0.00 34.73 5.28
1432 1502 1.078143 CTTTGAAGGAGGAGGGCGG 60.078 63.158 0.00 0.00 0.00 6.13
1447 1517 2.749839 CGGGCTGCCGAAATCCAA 60.750 61.111 13.40 0.00 34.88 3.53
1487 1557 0.617820 TGGTGGAGGAGGCTAAGGTC 60.618 60.000 0.00 0.00 0.00 3.85
1534 1604 2.168106 CACTCATCAAGGAGGAGACCAG 59.832 54.545 14.05 0.00 42.19 4.00
1583 1653 1.347707 TCTCCTGCTTCCACAAACGAT 59.652 47.619 0.00 0.00 0.00 3.73
1621 2115 9.056005 TCGCACTAATTTGAATTTAGCATCTAT 57.944 29.630 6.73 0.00 0.00 1.98
1791 2286 1.192428 AGGTCACCTCGGTGGAATAC 58.808 55.000 15.58 6.67 45.43 1.89
1868 2368 5.443283 GAACGGGTTTTATCCCCTCTAATT 58.557 41.667 0.00 0.00 44.32 1.40
1914 2415 3.823281 TTTCCACTTGTAGTTGTCCGA 57.177 42.857 0.00 0.00 0.00 4.55
1998 2500 7.043300 AGATACTATCTCCATCACCTCATCT 57.957 40.000 0.00 0.00 33.42 2.90
2421 2928 4.104086 TGAGTTTACTCCATCCCATCTGT 58.896 43.478 7.39 0.00 42.20 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.880340 GCCTCGTCCTTGATGCTCG 60.880 63.158 0.00 0.00 0.00 5.03
1 2 1.522580 GGCCTCGTCCTTGATGCTC 60.523 63.158 0.00 0.00 31.19 4.26
2 3 2.586792 GGCCTCGTCCTTGATGCT 59.413 61.111 0.00 0.00 31.19 3.79
3 4 2.514824 GGGCCTCGTCCTTGATGC 60.515 66.667 0.84 0.00 0.00 3.91
4 5 2.202932 CGGGCCTCGTCCTTGATG 60.203 66.667 0.84 0.00 0.00 3.07
5 6 3.470888 CCGGGCCTCGTCCTTGAT 61.471 66.667 0.84 0.00 37.11 2.57
23 24 4.504916 CTCCAGCTCGTCCCAGCG 62.505 72.222 0.00 0.00 44.82 5.18
24 25 4.828925 GCTCCAGCTCGTCCCAGC 62.829 72.222 0.00 0.00 39.99 4.85
34 35 1.414181 TGCTAATCCTACAGCTCCAGC 59.586 52.381 0.00 0.00 38.63 4.85
35 36 3.613671 CGATGCTAATCCTACAGCTCCAG 60.614 52.174 0.00 0.00 38.63 3.86
36 37 2.297315 CGATGCTAATCCTACAGCTCCA 59.703 50.000 0.00 0.00 38.63 3.86
37 38 2.558795 TCGATGCTAATCCTACAGCTCC 59.441 50.000 0.00 0.00 38.63 4.70
38 39 3.924918 TCGATGCTAATCCTACAGCTC 57.075 47.619 0.00 0.00 38.63 4.09
39 40 3.829026 TGATCGATGCTAATCCTACAGCT 59.171 43.478 0.54 0.00 38.63 4.24
40 41 4.179926 TGATCGATGCTAATCCTACAGC 57.820 45.455 0.54 0.00 38.31 4.40
41 42 5.126869 AGGATGATCGATGCTAATCCTACAG 59.873 44.000 19.54 0.00 44.19 2.74
42 43 5.019470 AGGATGATCGATGCTAATCCTACA 58.981 41.667 19.54 3.44 44.19 2.74
43 44 5.590530 AGGATGATCGATGCTAATCCTAC 57.409 43.478 19.54 0.00 44.19 3.18
44 45 5.481824 ACAAGGATGATCGATGCTAATCCTA 59.518 40.000 20.54 0.00 45.05 2.94
46 47 4.573900 ACAAGGATGATCGATGCTAATCC 58.426 43.478 0.54 10.00 37.63 3.01
47 48 6.091441 GGTTACAAGGATGATCGATGCTAATC 59.909 42.308 0.54 0.53 31.22 1.75
48 49 5.934625 GGTTACAAGGATGATCGATGCTAAT 59.065 40.000 0.54 0.00 31.22 1.73
49 50 5.070446 AGGTTACAAGGATGATCGATGCTAA 59.930 40.000 0.54 0.00 31.22 3.09
50 51 4.588951 AGGTTACAAGGATGATCGATGCTA 59.411 41.667 0.54 0.00 31.22 3.49
51 52 3.389329 AGGTTACAAGGATGATCGATGCT 59.611 43.478 0.54 0.00 33.26 3.79
52 53 3.496130 CAGGTTACAAGGATGATCGATGC 59.504 47.826 0.54 0.00 0.00 3.91
53 54 4.747108 GTCAGGTTACAAGGATGATCGATG 59.253 45.833 0.54 0.00 0.00 3.84
54 55 4.202264 GGTCAGGTTACAAGGATGATCGAT 60.202 45.833 0.00 0.00 0.00 3.59
55 56 3.132289 GGTCAGGTTACAAGGATGATCGA 59.868 47.826 0.00 0.00 0.00 3.59
56 57 3.458189 GGTCAGGTTACAAGGATGATCG 58.542 50.000 0.00 0.00 0.00 3.69
57 58 3.118738 ACGGTCAGGTTACAAGGATGATC 60.119 47.826 0.00 0.00 0.00 2.92
58 59 2.838202 ACGGTCAGGTTACAAGGATGAT 59.162 45.455 0.00 0.00 0.00 2.45
59 60 2.028476 CACGGTCAGGTTACAAGGATGA 60.028 50.000 0.00 0.00 0.00 2.92
60 61 2.289444 ACACGGTCAGGTTACAAGGATG 60.289 50.000 0.00 0.00 0.00 3.51
61 62 1.975680 ACACGGTCAGGTTACAAGGAT 59.024 47.619 0.00 0.00 0.00 3.24
62 63 1.416243 ACACGGTCAGGTTACAAGGA 58.584 50.000 0.00 0.00 0.00 3.36
63 64 1.871039 CAACACGGTCAGGTTACAAGG 59.129 52.381 0.00 0.00 0.00 3.61
64 65 2.557317 ACAACACGGTCAGGTTACAAG 58.443 47.619 0.00 0.00 0.00 3.16
65 66 2.695127 ACAACACGGTCAGGTTACAA 57.305 45.000 0.00 0.00 0.00 2.41
66 67 2.695127 AACAACACGGTCAGGTTACA 57.305 45.000 0.00 0.00 0.00 2.41
67 68 3.487879 CCAAAACAACACGGTCAGGTTAC 60.488 47.826 0.00 0.00 0.00 2.50
68 69 2.683867 CCAAAACAACACGGTCAGGTTA 59.316 45.455 0.00 0.00 0.00 2.85
69 70 1.474879 CCAAAACAACACGGTCAGGTT 59.525 47.619 0.00 0.00 0.00 3.50
70 71 1.099689 CCAAAACAACACGGTCAGGT 58.900 50.000 0.00 0.00 0.00 4.00
71 72 0.383949 CCCAAAACAACACGGTCAGG 59.616 55.000 0.00 0.00 0.00 3.86
72 73 0.383949 CCCCAAAACAACACGGTCAG 59.616 55.000 0.00 0.00 0.00 3.51
73 74 1.668101 GCCCCAAAACAACACGGTCA 61.668 55.000 0.00 0.00 0.00 4.02
74 75 1.066752 GCCCCAAAACAACACGGTC 59.933 57.895 0.00 0.00 0.00 4.79
75 76 1.380650 AGCCCCAAAACAACACGGT 60.381 52.632 0.00 0.00 0.00 4.83
76 77 1.067250 CAGCCCCAAAACAACACGG 59.933 57.895 0.00 0.00 0.00 4.94
77 78 0.030638 CTCAGCCCCAAAACAACACG 59.969 55.000 0.00 0.00 0.00 4.49
78 79 0.249447 GCTCAGCCCCAAAACAACAC 60.249 55.000 0.00 0.00 0.00 3.32
79 80 0.685785 TGCTCAGCCCCAAAACAACA 60.686 50.000 0.00 0.00 0.00 3.33
80 81 0.463620 TTGCTCAGCCCCAAAACAAC 59.536 50.000 0.00 0.00 0.00 3.32
81 82 0.463620 GTTGCTCAGCCCCAAAACAA 59.536 50.000 0.00 0.00 0.00 2.83
82 83 1.398958 GGTTGCTCAGCCCCAAAACA 61.399 55.000 0.00 0.00 0.00 2.83
83 84 1.367471 GGTTGCTCAGCCCCAAAAC 59.633 57.895 0.00 0.00 0.00 2.43
84 85 1.836604 GGGTTGCTCAGCCCCAAAA 60.837 57.895 10.32 0.00 45.12 2.44
85 86 2.203625 GGGTTGCTCAGCCCCAAA 60.204 61.111 10.32 0.00 45.12 3.28
90 91 2.828480 GAAGAGGGGGTTGCTCAGCC 62.828 65.000 0.00 0.00 43.15 4.85
91 92 1.377856 GAAGAGGGGGTTGCTCAGC 60.378 63.158 0.00 0.00 0.00 4.26
92 93 0.695347 AAGAAGAGGGGGTTGCTCAG 59.305 55.000 0.00 0.00 0.00 3.35
93 94 0.693049 GAAGAAGAGGGGGTTGCTCA 59.307 55.000 0.00 0.00 0.00 4.26
94 95 0.988063 AGAAGAAGAGGGGGTTGCTC 59.012 55.000 0.00 0.00 0.00 4.26
95 96 0.695347 CAGAAGAAGAGGGGGTTGCT 59.305 55.000 0.00 0.00 0.00 3.91
96 97 0.962855 GCAGAAGAAGAGGGGGTTGC 60.963 60.000 0.00 0.00 0.00 4.17
97 98 0.695347 AGCAGAAGAAGAGGGGGTTG 59.305 55.000 0.00 0.00 0.00 3.77
98 99 0.988063 GAGCAGAAGAAGAGGGGGTT 59.012 55.000 0.00 0.00 0.00 4.11
99 100 0.912006 GGAGCAGAAGAAGAGGGGGT 60.912 60.000 0.00 0.00 0.00 4.95
100 101 0.620121 AGGAGCAGAAGAAGAGGGGG 60.620 60.000 0.00 0.00 0.00 5.40
101 102 1.284313 AAGGAGCAGAAGAAGAGGGG 58.716 55.000 0.00 0.00 0.00 4.79
102 103 2.039613 ACAAAGGAGCAGAAGAAGAGGG 59.960 50.000 0.00 0.00 0.00 4.30
103 104 3.415457 ACAAAGGAGCAGAAGAAGAGG 57.585 47.619 0.00 0.00 0.00 3.69
104 105 3.932089 GCTACAAAGGAGCAGAAGAAGAG 59.068 47.826 0.00 0.00 39.84 2.85
105 106 3.580458 AGCTACAAAGGAGCAGAAGAAGA 59.420 43.478 3.78 0.00 42.69 2.87
106 107 3.936564 AGCTACAAAGGAGCAGAAGAAG 58.063 45.455 3.78 0.00 42.69 2.85
107 108 4.319177 GAAGCTACAAAGGAGCAGAAGAA 58.681 43.478 3.78 0.00 42.69 2.52
108 109 3.615110 CGAAGCTACAAAGGAGCAGAAGA 60.615 47.826 3.78 0.00 42.69 2.87
109 110 2.670414 CGAAGCTACAAAGGAGCAGAAG 59.330 50.000 3.78 0.00 42.69 2.85
110 111 2.037251 ACGAAGCTACAAAGGAGCAGAA 59.963 45.455 3.78 0.00 42.69 3.02
111 112 1.618837 ACGAAGCTACAAAGGAGCAGA 59.381 47.619 3.78 0.00 42.69 4.26
112 113 1.996191 GACGAAGCTACAAAGGAGCAG 59.004 52.381 3.78 0.00 42.69 4.24
113 114 1.343142 TGACGAAGCTACAAAGGAGCA 59.657 47.619 3.78 0.00 42.69 4.26
114 115 2.080286 TGACGAAGCTACAAAGGAGC 57.920 50.000 0.00 0.00 40.42 4.70
115 116 2.408704 CGTTGACGAAGCTACAAAGGAG 59.591 50.000 0.00 0.00 43.02 3.69
116 117 2.400399 CGTTGACGAAGCTACAAAGGA 58.600 47.619 0.00 0.00 43.02 3.36
117 118 1.136336 GCGTTGACGAAGCTACAAAGG 60.136 52.381 7.85 0.00 43.02 3.11
118 119 1.136336 GGCGTTGACGAAGCTACAAAG 60.136 52.381 7.85 0.00 43.02 2.77
119 120 0.863144 GGCGTTGACGAAGCTACAAA 59.137 50.000 7.85 0.00 43.02 2.83
120 121 0.032952 AGGCGTTGACGAAGCTACAA 59.967 50.000 7.85 0.00 43.02 2.41
121 122 0.666274 CAGGCGTTGACGAAGCTACA 60.666 55.000 7.85 0.00 43.02 2.74
122 123 1.956620 GCAGGCGTTGACGAAGCTAC 61.957 60.000 7.85 0.00 43.02 3.58
123 124 1.736645 GCAGGCGTTGACGAAGCTA 60.737 57.895 7.85 0.00 43.02 3.32
124 125 2.154798 TAGCAGGCGTTGACGAAGCT 62.155 55.000 17.15 17.15 43.02 3.74
125 126 1.687494 CTAGCAGGCGTTGACGAAGC 61.687 60.000 7.85 7.36 43.02 3.86
126 127 0.388649 ACTAGCAGGCGTTGACGAAG 60.389 55.000 7.85 0.00 43.02 3.79
127 128 0.666274 CACTAGCAGGCGTTGACGAA 60.666 55.000 7.85 0.00 43.02 3.85
128 129 1.080772 CACTAGCAGGCGTTGACGA 60.081 57.895 7.85 0.00 43.02 4.20
129 130 0.109458 TACACTAGCAGGCGTTGACG 60.109 55.000 0.00 0.00 43.27 4.35
130 131 2.295253 ATACACTAGCAGGCGTTGAC 57.705 50.000 0.00 0.00 0.00 3.18
131 132 3.243737 CCATATACACTAGCAGGCGTTGA 60.244 47.826 0.00 0.00 0.00 3.18
132 133 3.059884 CCATATACACTAGCAGGCGTTG 58.940 50.000 0.00 0.00 0.00 4.10
133 134 2.963101 TCCATATACACTAGCAGGCGTT 59.037 45.455 0.00 0.00 0.00 4.84
134 135 2.594131 TCCATATACACTAGCAGGCGT 58.406 47.619 0.00 0.00 0.00 5.68
135 136 3.876274 ATCCATATACACTAGCAGGCG 57.124 47.619 0.00 0.00 0.00 5.52
136 137 5.152623 TCAATCCATATACACTAGCAGGC 57.847 43.478 0.00 0.00 0.00 4.85
137 138 5.247110 ACCTCAATCCATATACACTAGCAGG 59.753 44.000 0.00 0.00 0.00 4.85
138 139 6.352016 ACCTCAATCCATATACACTAGCAG 57.648 41.667 0.00 0.00 0.00 4.24
139 140 6.524734 CAACCTCAATCCATATACACTAGCA 58.475 40.000 0.00 0.00 0.00 3.49
140 141 5.409826 GCAACCTCAATCCATATACACTAGC 59.590 44.000 0.00 0.00 0.00 3.42
141 142 6.524734 TGCAACCTCAATCCATATACACTAG 58.475 40.000 0.00 0.00 0.00 2.57
142 143 6.493189 TGCAACCTCAATCCATATACACTA 57.507 37.500 0.00 0.00 0.00 2.74
143 144 5.372343 TGCAACCTCAATCCATATACACT 57.628 39.130 0.00 0.00 0.00 3.55
144 145 5.221048 GGTTGCAACCTCAATCCATATACAC 60.221 44.000 36.26 7.95 45.75 2.90
145 146 4.887071 GGTTGCAACCTCAATCCATATACA 59.113 41.667 36.26 0.00 45.75 2.29
146 147 5.438761 GGTTGCAACCTCAATCCATATAC 57.561 43.478 36.26 8.95 45.75 1.47
147 148 4.167892 AGGGTTGCAACCTCAATCCATATA 59.832 41.667 39.80 0.00 47.00 0.86
148 149 3.052642 AGGGTTGCAACCTCAATCCATAT 60.053 43.478 39.80 14.63 47.00 1.78
149 150 2.311542 AGGGTTGCAACCTCAATCCATA 59.688 45.455 39.80 0.00 47.00 2.74
150 151 1.077663 AGGGTTGCAACCTCAATCCAT 59.922 47.619 39.80 14.38 47.00 3.41
151 152 0.482446 AGGGTTGCAACCTCAATCCA 59.518 50.000 39.80 0.00 47.00 3.41
160 161 6.866770 GGTAGAAGAAAATAAAGGGTTGCAAC 59.133 38.462 21.59 21.59 0.00 4.17
161 162 6.780522 AGGTAGAAGAAAATAAAGGGTTGCAA 59.219 34.615 0.00 0.00 0.00 4.08
162 163 6.311735 AGGTAGAAGAAAATAAAGGGTTGCA 58.688 36.000 0.00 0.00 0.00 4.08
163 164 6.835819 AGGTAGAAGAAAATAAAGGGTTGC 57.164 37.500 0.00 0.00 0.00 4.17
164 165 9.681062 TGATAGGTAGAAGAAAATAAAGGGTTG 57.319 33.333 0.00 0.00 0.00 3.77
177 178 8.577296 CGTATCTTTCCATTGATAGGTAGAAGA 58.423 37.037 0.00 0.00 0.00 2.87
178 179 7.329717 GCGTATCTTTCCATTGATAGGTAGAAG 59.670 40.741 0.00 0.00 35.05 2.85
179 180 7.015292 AGCGTATCTTTCCATTGATAGGTAGAA 59.985 37.037 0.00 0.00 35.05 2.10
180 181 6.493802 AGCGTATCTTTCCATTGATAGGTAGA 59.506 38.462 0.00 0.00 35.05 2.59
181 182 6.692486 AGCGTATCTTTCCATTGATAGGTAG 58.308 40.000 0.00 0.00 35.05 3.18
182 183 6.493802 AGAGCGTATCTTTCCATTGATAGGTA 59.506 38.462 0.00 0.00 32.99 3.08
183 184 5.305644 AGAGCGTATCTTTCCATTGATAGGT 59.694 40.000 0.00 0.00 32.99 3.08
184 185 5.788450 AGAGCGTATCTTTCCATTGATAGG 58.212 41.667 0.00 0.00 32.99 2.57
185 186 8.818141 TTTAGAGCGTATCTTTCCATTGATAG 57.182 34.615 0.00 0.00 39.64 2.08
186 187 7.385205 GCTTTAGAGCGTATCTTTCCATTGATA 59.615 37.037 0.00 0.00 39.48 2.15
187 188 6.203723 GCTTTAGAGCGTATCTTTCCATTGAT 59.796 38.462 0.00 0.00 39.48 2.57
188 189 5.523916 GCTTTAGAGCGTATCTTTCCATTGA 59.476 40.000 0.00 0.00 39.48 2.57
189 190 5.742446 GCTTTAGAGCGTATCTTTCCATTG 58.258 41.667 0.00 0.00 39.48 2.82
190 191 5.993106 GCTTTAGAGCGTATCTTTCCATT 57.007 39.130 0.00 0.00 39.48 3.16
269 270 9.825972 CTCAATAAAATAGTGATGTGAACGTTT 57.174 29.630 0.46 0.00 31.85 3.60
270 271 8.450964 CCTCAATAAAATAGTGATGTGAACGTT 58.549 33.333 0.00 0.00 31.85 3.99
271 272 7.065803 CCCTCAATAAAATAGTGATGTGAACGT 59.934 37.037 0.00 0.00 31.85 3.99
272 273 7.279981 TCCCTCAATAAAATAGTGATGTGAACG 59.720 37.037 0.00 0.00 31.85 3.95
273 274 8.506168 TCCCTCAATAAAATAGTGATGTGAAC 57.494 34.615 0.00 0.00 31.85 3.18
274 275 8.328758 ACTCCCTCAATAAAATAGTGATGTGAA 58.671 33.333 0.00 0.00 31.85 3.18
275 276 7.861629 ACTCCCTCAATAAAATAGTGATGTGA 58.138 34.615 0.00 0.00 31.85 3.58
276 277 9.046296 GTACTCCCTCAATAAAATAGTGATGTG 57.954 37.037 0.00 0.00 31.85 3.21
277 278 8.993424 AGTACTCCCTCAATAAAATAGTGATGT 58.007 33.333 0.00 0.00 31.85 3.06
278 279 9.482627 GAGTACTCCCTCAATAAAATAGTGATG 57.517 37.037 12.13 0.00 31.85 3.07
279 280 8.361139 CGAGTACTCCCTCAATAAAATAGTGAT 58.639 37.037 17.23 0.00 31.85 3.06
280 281 7.683704 GCGAGTACTCCCTCAATAAAATAGTGA 60.684 40.741 17.23 0.00 0.00 3.41
281 282 6.421202 GCGAGTACTCCCTCAATAAAATAGTG 59.579 42.308 17.23 0.00 0.00 2.74
282 283 6.324254 AGCGAGTACTCCCTCAATAAAATAGT 59.676 38.462 17.23 0.00 0.00 2.12
283 284 6.750148 AGCGAGTACTCCCTCAATAAAATAG 58.250 40.000 17.23 0.00 0.00 1.73
284 285 6.726490 AGCGAGTACTCCCTCAATAAAATA 57.274 37.500 17.23 0.00 0.00 1.40
285 286 5.602628 GAGCGAGTACTCCCTCAATAAAAT 58.397 41.667 25.89 0.00 35.26 1.82
286 287 5.007385 GAGCGAGTACTCCCTCAATAAAA 57.993 43.478 25.89 0.00 35.26 1.52
287 288 4.650754 GAGCGAGTACTCCCTCAATAAA 57.349 45.455 25.89 0.00 35.26 1.40
380 381 3.443681 CCTCCGTGGCAAACATATCTTTT 59.556 43.478 0.00 0.00 0.00 2.27
420 423 8.924511 TTGTTTCTCCTCTGATAAGAACAATT 57.075 30.769 0.00 0.00 0.00 2.32
421 424 8.924511 TTTGTTTCTCCTCTGATAAGAACAAT 57.075 30.769 0.00 0.00 0.00 2.71
442 462 8.149647 TCCATGCATAAACTTTTCTGATTTTGT 58.850 29.630 0.00 0.00 0.00 2.83
459 479 5.072055 CCCAATTGACTACATCCATGCATA 58.928 41.667 7.12 0.00 0.00 3.14
480 500 2.122783 TCCCAACGATTGATTGTCCC 57.877 50.000 0.00 0.00 0.00 4.46
493 521 5.897377 ACAAAGTAATAGTGCATCCCAAC 57.103 39.130 0.00 0.00 0.00 3.77
623 668 2.026990 CTTGTCGTTTGCGTTTTCTCG 58.973 47.619 0.00 0.00 39.49 4.04
627 672 1.544686 CAGCTTGTCGTTTGCGTTTT 58.455 45.000 0.00 0.00 39.49 2.43
628 673 0.248458 CCAGCTTGTCGTTTGCGTTT 60.248 50.000 0.00 0.00 39.49 3.60
660 705 1.021390 AGCTCGCCGGAATTCTGTTG 61.021 55.000 5.05 5.24 0.00 3.33
679 732 4.388499 GAGAAACTCCGCCGGCCA 62.388 66.667 23.46 6.73 0.00 5.36
737 790 7.615365 TGATTTTGATAACATTTCCAGCCTAGT 59.385 33.333 0.00 0.00 0.00 2.57
761 814 7.685481 TGTCTGAGTTGGGTTCTATATTTTGA 58.315 34.615 0.00 0.00 0.00 2.69
808 861 0.257039 GGTTCAGGAGGCCATGATGT 59.743 55.000 5.01 0.00 0.00 3.06
818 871 1.374758 GGCACGACAGGTTCAGGAG 60.375 63.158 0.00 0.00 0.00 3.69
822 875 2.391724 GAAGGGGCACGACAGGTTCA 62.392 60.000 0.00 0.00 0.00 3.18
823 876 1.671379 GAAGGGGCACGACAGGTTC 60.671 63.158 0.00 0.00 0.00 3.62
848 901 1.269723 GGGAAAGAAAAGTCAAGCCCG 59.730 52.381 0.00 0.00 0.00 6.13
863 916 1.284408 GCGTTTCATGCACGGGAAA 59.716 52.632 16.18 6.06 38.13 3.13
864 917 1.851021 CTGCGTTTCATGCACGGGAA 61.851 55.000 16.18 0.00 34.76 3.97
865 918 2.281139 TGCGTTTCATGCACGGGA 60.281 55.556 16.18 0.00 34.76 5.14
866 919 2.176546 CTGCGTTTCATGCACGGG 59.823 61.111 16.18 0.00 34.76 5.28
867 920 2.502510 GCTGCGTTTCATGCACGG 60.503 61.111 16.18 4.85 34.76 4.94
892 945 1.081641 ACGACCTTCTACGTGCGTG 60.082 57.895 7.55 0.00 41.17 5.34
916 972 1.425412 CGGTTTTATATCGCCCTCCG 58.575 55.000 0.00 0.00 38.61 4.63
957 1013 3.385384 TGGAGCTGTGGAGGCGAG 61.385 66.667 0.00 0.00 34.52 5.03
961 1017 1.294780 GTCAGTGGAGCTGTGGAGG 59.705 63.158 0.00 0.00 45.23 4.30
968 1024 1.920835 GGGAAGGGTCAGTGGAGCT 60.921 63.158 0.00 0.00 41.29 4.09
970 1026 1.557269 CCAGGGAAGGGTCAGTGGAG 61.557 65.000 0.00 0.00 32.26 3.86
974 1030 1.920835 GCTCCAGGGAAGGGTCAGT 60.921 63.158 0.00 0.00 0.00 3.41
975 1031 1.614824 AGCTCCAGGGAAGGGTCAG 60.615 63.158 0.00 0.00 0.00 3.51
976 1032 1.613630 GAGCTCCAGGGAAGGGTCA 60.614 63.158 0.87 0.00 0.00 4.02
977 1033 2.726351 CGAGCTCCAGGGAAGGGTC 61.726 68.421 8.47 0.00 0.00 4.46
978 1034 2.685380 CGAGCTCCAGGGAAGGGT 60.685 66.667 8.47 0.00 0.00 4.34
979 1035 2.364317 TCGAGCTCCAGGGAAGGG 60.364 66.667 8.47 0.00 0.00 3.95
1002 1058 2.182030 GGAGCAGAGGAACCGTCG 59.818 66.667 0.00 0.00 0.00 5.12
1015 1071 0.525311 GAAAGCAGCAAAGAGGGAGC 59.475 55.000 0.00 0.00 0.00 4.70
1200 1270 4.862823 GGACGAGGAGGGGGAGGG 62.863 77.778 0.00 0.00 0.00 4.30
1236 1306 2.027625 CCTTGGCGACGTCCTTGAC 61.028 63.158 10.58 0.00 0.00 3.18
1237 1307 2.154798 CTCCTTGGCGACGTCCTTGA 62.155 60.000 10.58 0.00 0.00 3.02
1238 1308 1.738099 CTCCTTGGCGACGTCCTTG 60.738 63.158 10.58 0.00 0.00 3.61
1239 1309 2.657237 CTCCTTGGCGACGTCCTT 59.343 61.111 10.58 0.00 0.00 3.36
1240 1310 4.070552 GCTCCTTGGCGACGTCCT 62.071 66.667 10.58 0.00 0.00 3.85
1272 1342 4.353437 GACGACGTCGCCCTTGGT 62.353 66.667 35.92 16.33 44.43 3.67
1345 1415 2.521958 ATCCTTCTTGACCGCCACCG 62.522 60.000 0.00 0.00 0.00 4.94
1351 1421 1.726853 GGTGACATCCTTCTTGACCG 58.273 55.000 0.00 0.00 0.00 4.79
1354 1424 1.001974 CACCGGTGACATCCTTCTTGA 59.998 52.381 31.31 0.00 0.00 3.02
1371 1441 0.586802 GTGGCAGAAACTTCGTCACC 59.413 55.000 0.00 0.00 33.48 4.02
1373 1443 0.878523 CCGTGGCAGAAACTTCGTCA 60.879 55.000 0.00 0.00 0.00 4.35
1380 1450 2.604174 CGTCCACCGTGGCAGAAAC 61.604 63.158 13.19 4.54 37.47 2.78
1432 1502 0.179129 CATGTTGGATTTCGGCAGCC 60.179 55.000 0.00 0.00 0.00 4.85
1487 1557 1.150567 CTGCTTCCTTCGCCTCATCG 61.151 60.000 0.00 0.00 0.00 3.84
1534 1604 1.305046 TCCTTGGTCTCCTCGGGTC 60.305 63.158 0.00 0.00 0.00 4.46
1583 1653 0.670239 TAGTGCGAGACGTACCACGA 60.670 55.000 5.61 0.00 46.05 4.35
1622 2116 8.964150 GTTAACTTTGCTTAAATCACGATTTGT 58.036 29.630 13.95 0.63 40.83 2.83
1623 2117 8.147172 CGTTAACTTTGCTTAAATCACGATTTG 58.853 33.333 13.95 1.33 40.83 2.32
1624 2118 8.071368 TCGTTAACTTTGCTTAAATCACGATTT 58.929 29.630 9.77 9.77 42.95 2.17
1680 2174 7.188157 AGTGTCGTTAACTTATTTCGCAAAAA 58.812 30.769 3.71 0.00 0.00 1.94
1681 2175 6.717413 AGTGTCGTTAACTTATTTCGCAAAA 58.283 32.000 3.71 0.00 0.00 2.44
1682 2176 6.289745 AGTGTCGTTAACTTATTTCGCAAA 57.710 33.333 3.71 0.00 0.00 3.68
1683 2177 5.910637 AGTGTCGTTAACTTATTTCGCAA 57.089 34.783 3.71 0.00 0.00 4.85
1684 2178 5.234757 ACAAGTGTCGTTAACTTATTTCGCA 59.765 36.000 3.71 0.00 35.70 5.10
1685 2179 5.558888 CACAAGTGTCGTTAACTTATTTCGC 59.441 40.000 3.71 0.00 35.70 4.70
1686 2180 5.558888 GCACAAGTGTCGTTAACTTATTTCG 59.441 40.000 3.71 0.00 35.70 3.46
1687 2181 6.423862 TGCACAAGTGTCGTTAACTTATTTC 58.576 36.000 3.71 0.00 35.70 2.17
1688 2182 6.366315 TGCACAAGTGTCGTTAACTTATTT 57.634 33.333 3.71 0.00 35.70 1.40
1689 2183 5.994887 TGCACAAGTGTCGTTAACTTATT 57.005 34.783 3.71 0.00 35.70 1.40
1690 2184 5.294799 TGTTGCACAAGTGTCGTTAACTTAT 59.705 36.000 3.71 0.00 35.70 1.73
1691 2185 4.630505 TGTTGCACAAGTGTCGTTAACTTA 59.369 37.500 3.71 0.00 35.70 2.24
1692 2186 3.437395 TGTTGCACAAGTGTCGTTAACTT 59.563 39.130 3.71 0.00 38.40 2.66
1791 2286 5.163561 TGGTTGTTTGAGGCTTTCTAAAGTG 60.164 40.000 4.50 0.00 38.28 3.16
1927 2428 7.517614 TTGAGTAATGCAAGTTTATTCACCA 57.482 32.000 3.92 0.00 28.69 4.17
2665 3172 1.473257 GCCGCTGAATGATGTAGGACA 60.473 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.