Multiple sequence alignment - TraesCS3A01G458400

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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 TraesCS3A01G458400 chr3A 100.000 3260 0 0 1 3260 695530966 695534225 0.000000e+00 6021.0
1 TraesCS3A01G458400 chr3A 94.545 165 8 1 48 212 712544697 712544860 1.500000e-63 254.0
2 TraesCS3A01G458400 chr3D 91.103 2394 128 33 909 3260 559124721 559127071 0.000000e+00 3162.0
3 TraesCS3A01G458400 chr3D 87.829 608 53 13 255 846 559123437 559124039 0.000000e+00 693.0
4 TraesCS3A01G458400 chr3D 84.898 245 21 8 3019 3260 559134115 559134346 1.960000e-57 233.0
5 TraesCS3A01G458400 chr3D 77.143 280 45 12 1678 1955 559158799 559159061 9.430000e-31 145.0
6 TraesCS3A01G458400 chr3B 84.747 1980 160 52 802 2681 742102061 742100124 0.000000e+00 1853.0
7 TraesCS3A01G458400 chr3B 87.309 457 34 11 255 693 742103514 742103064 4.860000e-138 501.0
8 TraesCS3A01G458400 chr3B 79.670 182 24 9 2682 2853 757955830 757955652 5.710000e-23 119.0
9 TraesCS3A01G458400 chr3B 88.571 70 5 2 1889 1955 742157881 742157950 7.500000e-12 82.4
10 TraesCS3A01G458400 chr3B 92.453 53 3 1 213 265 215604565 215604616 1.250000e-09 75.0
11 TraesCS3A01G458400 chr3B 90.196 51 5 0 1905 1955 742148060 742148110 2.100000e-07 67.6
12 TraesCS3A01G458400 chr3B 91.667 48 3 1 203 250 798403335 798403381 7.550000e-07 65.8
13 TraesCS3A01G458400 chr7A 90.816 196 17 1 55 249 715691656 715691461 8.970000e-66 261.0
14 TraesCS3A01G458400 chr7A 94.000 50 2 1 205 254 109838019 109837971 1.250000e-09 75.0
15 TraesCS3A01G458400 chr6B 96.203 158 6 0 55 212 17422261 17422418 3.230000e-65 259.0
16 TraesCS3A01G458400 chr7B 94.545 165 9 0 48 212 513527735 513527571 4.170000e-64 255.0
17 TraesCS3A01G458400 chr2A 93.567 171 11 0 45 215 613472614 613472444 4.170000e-64 255.0
18 TraesCS3A01G458400 chr2A 95.833 48 1 1 205 252 65240252 65240298 3.490000e-10 76.8
19 TraesCS3A01G458400 chr2A 94.000 50 2 1 205 254 692706440 692706488 1.250000e-09 75.0
20 TraesCS3A01G458400 chr1B 95.062 162 8 0 51 212 12757152 12756991 4.170000e-64 255.0
21 TraesCS3A01G458400 chr2D 95.031 161 8 0 52 212 574926924 574927084 1.500000e-63 254.0
22 TraesCS3A01G458400 chr2D 81.768 181 20 4 2684 2859 506399518 506399690 4.390000e-29 139.0
23 TraesCS3A01G458400 chr2D 76.974 152 18 10 707 843 190024096 190023947 1.620000e-08 71.3
24 TraesCS3A01G458400 chr6D 89.604 202 14 2 55 249 454625088 454624887 1.940000e-62 250.0
25 TraesCS3A01G458400 chr6D 85.463 227 23 7 2685 2903 348081799 348081575 9.100000e-56 228.0
26 TraesCS3A01G458400 chr6D 79.532 171 21 9 2728 2886 462636981 462636813 3.440000e-20 110.0
27 TraesCS3A01G458400 chr6D 87.500 64 6 2 2772 2834 157979654 157979592 4.510000e-09 73.1
28 TraesCS3A01G458400 chr6A 94.444 162 9 0 51 212 485754925 485754764 1.940000e-62 250.0
29 TraesCS3A01G458400 chr4D 84.038 213 22 7 2686 2888 327379510 327379720 9.230000e-46 195.0
30 TraesCS3A01G458400 chr4D 79.060 234 32 7 2684 2903 8625055 8624825 9.430000e-31 145.0
31 TraesCS3A01G458400 chr2B 87.059 170 15 3 969 1135 713876403 713876568 5.550000e-43 185.0
32 TraesCS3A01G458400 chr5D 83.099 213 22 7 2684 2888 281011056 281011262 7.190000e-42 182.0
33 TraesCS3A01G458400 chr5D 95.833 48 1 1 205 252 543670761 543670715 3.490000e-10 76.8
34 TraesCS3A01G458400 chr5A 81.553 206 17 7 46 251 71464991 71465175 2.030000e-32 150.0
35 TraesCS3A01G458400 chr5A 100.000 28 0 0 808 835 436100889 436100862 6.000000e-03 52.8
36 TraesCS3A01G458400 chr4A 94.000 50 2 1 205 254 572708460 572708412 1.250000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G458400 chr3A 695530966 695534225 3259 False 6021.0 6021 100.000 1 3260 1 chr3A.!!$F1 3259
1 TraesCS3A01G458400 chr3D 559123437 559127071 3634 False 1927.5 3162 89.466 255 3260 2 chr3D.!!$F3 3005
2 TraesCS3A01G458400 chr3B 742100124 742103514 3390 True 1177.0 1853 86.028 255 2681 2 chr3B.!!$R2 2426

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
131 132 0.035152 TCAAATCCTGGTGCTCGCAT 60.035 50.0 0.00 0.00 0.00 4.73 F
180 181 0.094216 CGATGCGCTTTCAGTGTGAG 59.906 55.0 9.73 0.00 0.00 3.51 F
214 215 0.384669 GACGACAAGGCGCCTACTAT 59.615 55.0 33.07 15.80 33.86 2.12 F
626 642 0.385751 ACATGTAGCATAGCGTCGCT 59.614 50.0 25.08 25.08 43.41 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 3047 0.095935 CGCCATGAAACAGCTTCTCG 59.904 55.000 0.00 0.0 34.86 4.04 R
1922 3509 0.329261 TCATGAGGCCCTTGAACCAG 59.671 55.000 0.00 0.0 0.00 4.00 R
2141 3763 3.865164 CACATTGCTGCTCGTACAATCTA 59.135 43.478 0.00 0.0 31.82 1.98 R
2397 4027 2.635443 CGGCGCCCACCAAAATCTT 61.635 57.895 23.46 0.0 0.00 2.40 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
27 28 2.609920 AAAAAGGGCCGGGGTTCA 59.390 55.556 2.18 0.00 0.00 3.18
28 29 1.835267 AAAAAGGGCCGGGGTTCAC 60.835 57.895 2.18 0.00 0.00 3.18
29 30 2.591193 AAAAAGGGCCGGGGTTCACA 62.591 55.000 2.18 0.00 0.00 3.58
30 31 2.380571 AAAAGGGCCGGGGTTCACAT 62.381 55.000 2.18 0.00 0.00 3.21
31 32 1.502527 AAAGGGCCGGGGTTCACATA 61.503 55.000 2.18 0.00 0.00 2.29
32 33 1.921869 AAGGGCCGGGGTTCACATAG 61.922 60.000 2.18 0.00 0.00 2.23
33 34 2.676265 GGGCCGGGGTTCACATAGT 61.676 63.158 2.18 0.00 0.00 2.12
34 35 1.301954 GGCCGGGGTTCACATAGTT 59.698 57.895 2.18 0.00 0.00 2.24
35 36 0.323087 GGCCGGGGTTCACATAGTTT 60.323 55.000 2.18 0.00 0.00 2.66
36 37 1.541379 GCCGGGGTTCACATAGTTTT 58.459 50.000 2.18 0.00 0.00 2.43
37 38 2.618559 GGCCGGGGTTCACATAGTTTTA 60.619 50.000 2.18 0.00 0.00 1.52
38 39 2.681344 GCCGGGGTTCACATAGTTTTAG 59.319 50.000 2.18 0.00 0.00 1.85
39 40 3.275999 CCGGGGTTCACATAGTTTTAGG 58.724 50.000 0.00 0.00 0.00 2.69
40 41 3.054948 CCGGGGTTCACATAGTTTTAGGA 60.055 47.826 0.00 0.00 0.00 2.94
41 42 4.189231 CGGGGTTCACATAGTTTTAGGAG 58.811 47.826 0.00 0.00 0.00 3.69
42 43 3.945921 GGGGTTCACATAGTTTTAGGAGC 59.054 47.826 0.00 0.00 0.00 4.70
43 44 4.566907 GGGGTTCACATAGTTTTAGGAGCA 60.567 45.833 0.00 0.00 0.00 4.26
44 45 5.007682 GGGTTCACATAGTTTTAGGAGCAA 58.992 41.667 0.00 0.00 0.00 3.91
45 46 5.475564 GGGTTCACATAGTTTTAGGAGCAAA 59.524 40.000 0.00 0.00 0.00 3.68
46 47 6.349363 GGGTTCACATAGTTTTAGGAGCAAAG 60.349 42.308 0.00 0.00 0.00 2.77
47 48 6.430000 GGTTCACATAGTTTTAGGAGCAAAGA 59.570 38.462 0.00 0.00 0.00 2.52
48 49 7.121315 GGTTCACATAGTTTTAGGAGCAAAGAT 59.879 37.037 0.00 0.00 0.00 2.40
49 50 7.615582 TCACATAGTTTTAGGAGCAAAGATG 57.384 36.000 0.00 0.00 0.00 2.90
50 51 6.599244 TCACATAGTTTTAGGAGCAAAGATGG 59.401 38.462 0.00 0.00 0.00 3.51
51 52 5.358160 ACATAGTTTTAGGAGCAAAGATGGC 59.642 40.000 0.00 0.00 0.00 4.40
52 53 2.749621 AGTTTTAGGAGCAAAGATGGCG 59.250 45.455 0.00 0.00 36.08 5.69
53 54 2.488153 GTTTTAGGAGCAAAGATGGCGT 59.512 45.455 0.00 0.00 36.08 5.68
54 55 1.737838 TTAGGAGCAAAGATGGCGTG 58.262 50.000 0.00 0.00 36.08 5.34
55 56 0.901827 TAGGAGCAAAGATGGCGTGA 59.098 50.000 0.00 0.00 36.08 4.35
56 57 0.036732 AGGAGCAAAGATGGCGTGAA 59.963 50.000 0.00 0.00 36.08 3.18
57 58 1.098050 GGAGCAAAGATGGCGTGAAT 58.902 50.000 0.00 0.00 36.08 2.57
58 59 1.064654 GGAGCAAAGATGGCGTGAATC 59.935 52.381 0.00 0.00 36.08 2.52
59 60 1.739466 GAGCAAAGATGGCGTGAATCA 59.261 47.619 0.00 0.00 36.08 2.57
60 61 2.161855 AGCAAAGATGGCGTGAATCAA 58.838 42.857 0.00 0.00 36.08 2.57
61 62 2.095059 AGCAAAGATGGCGTGAATCAAC 60.095 45.455 0.00 0.00 36.08 3.18
62 63 2.867429 CAAAGATGGCGTGAATCAACC 58.133 47.619 0.00 0.00 0.00 3.77
63 64 2.489329 CAAAGATGGCGTGAATCAACCT 59.511 45.455 5.34 0.00 0.00 3.50
64 65 1.742761 AGATGGCGTGAATCAACCTG 58.257 50.000 5.34 0.00 0.00 4.00
65 66 1.003580 AGATGGCGTGAATCAACCTGT 59.996 47.619 5.34 0.00 0.00 4.00
66 67 1.131126 GATGGCGTGAATCAACCTGTG 59.869 52.381 5.34 0.00 0.00 3.66
67 68 0.888736 TGGCGTGAATCAACCTGTGG 60.889 55.000 5.34 0.00 0.00 4.17
68 69 0.889186 GGCGTGAATCAACCTGTGGT 60.889 55.000 0.00 0.00 37.65 4.16
78 79 2.525105 AACCTGTGGTTGAGTTGGTT 57.475 45.000 0.71 0.00 45.07 3.67
79 80 3.655615 AACCTGTGGTTGAGTTGGTTA 57.344 42.857 0.71 0.00 45.07 2.85
80 81 3.208747 ACCTGTGGTTGAGTTGGTTAG 57.791 47.619 0.00 0.00 27.29 2.34
81 82 2.158667 ACCTGTGGTTGAGTTGGTTAGG 60.159 50.000 0.00 0.00 27.29 2.69
82 83 2.158667 CCTGTGGTTGAGTTGGTTAGGT 60.159 50.000 0.00 0.00 0.00 3.08
83 84 2.878406 CTGTGGTTGAGTTGGTTAGGTG 59.122 50.000 0.00 0.00 0.00 4.00
84 85 2.227194 GTGGTTGAGTTGGTTAGGTGG 58.773 52.381 0.00 0.00 0.00 4.61
85 86 2.128535 TGGTTGAGTTGGTTAGGTGGA 58.871 47.619 0.00 0.00 0.00 4.02
86 87 2.714250 TGGTTGAGTTGGTTAGGTGGAT 59.286 45.455 0.00 0.00 0.00 3.41
87 88 3.911260 TGGTTGAGTTGGTTAGGTGGATA 59.089 43.478 0.00 0.00 0.00 2.59
88 89 4.019681 TGGTTGAGTTGGTTAGGTGGATAG 60.020 45.833 0.00 0.00 0.00 2.08
89 90 4.019591 GGTTGAGTTGGTTAGGTGGATAGT 60.020 45.833 0.00 0.00 0.00 2.12
90 91 5.188359 GGTTGAGTTGGTTAGGTGGATAGTA 59.812 44.000 0.00 0.00 0.00 1.82
91 92 6.338937 GTTGAGTTGGTTAGGTGGATAGTAG 58.661 44.000 0.00 0.00 0.00 2.57
92 93 5.586877 TGAGTTGGTTAGGTGGATAGTAGT 58.413 41.667 0.00 0.00 0.00 2.73
93 94 6.734532 TGAGTTGGTTAGGTGGATAGTAGTA 58.265 40.000 0.00 0.00 0.00 1.82
94 95 7.359849 TGAGTTGGTTAGGTGGATAGTAGTAT 58.640 38.462 0.00 0.00 0.00 2.12
95 96 7.504911 TGAGTTGGTTAGGTGGATAGTAGTATC 59.495 40.741 8.83 8.83 35.19 2.24
104 105 3.865571 GGATAGTAGTATCCCCAACCCA 58.134 50.000 21.81 0.00 46.69 4.51
105 106 4.436079 GGATAGTAGTATCCCCAACCCAT 58.564 47.826 21.81 0.00 46.69 4.00
106 107 4.470304 GGATAGTAGTATCCCCAACCCATC 59.530 50.000 21.81 0.00 46.69 3.51
107 108 3.431411 AGTAGTATCCCCAACCCATCA 57.569 47.619 0.00 0.00 0.00 3.07
108 109 3.743132 AGTAGTATCCCCAACCCATCAA 58.257 45.455 0.00 0.00 0.00 2.57
109 110 3.716872 AGTAGTATCCCCAACCCATCAAG 59.283 47.826 0.00 0.00 0.00 3.02
110 111 1.852965 AGTATCCCCAACCCATCAAGG 59.147 52.381 0.00 0.00 37.03 3.61
111 112 1.569072 GTATCCCCAACCCATCAAGGT 59.431 52.381 0.00 0.00 44.00 3.50
120 121 3.833559 ACCCATCAAGGTTCAAATCCT 57.166 42.857 0.00 0.00 36.44 3.24
121 122 3.434309 ACCCATCAAGGTTCAAATCCTG 58.566 45.455 0.00 0.00 36.44 3.86
122 123 2.762327 CCCATCAAGGTTCAAATCCTGG 59.238 50.000 0.00 0.00 35.27 4.45
123 124 3.434309 CCATCAAGGTTCAAATCCTGGT 58.566 45.455 0.00 0.00 35.27 4.00
124 125 3.194116 CCATCAAGGTTCAAATCCTGGTG 59.806 47.826 0.00 0.00 35.27 4.17
125 126 2.238521 TCAAGGTTCAAATCCTGGTGC 58.761 47.619 0.00 0.00 35.27 5.01
126 127 2.158475 TCAAGGTTCAAATCCTGGTGCT 60.158 45.455 0.00 0.00 35.27 4.40
127 128 2.206576 AGGTTCAAATCCTGGTGCTC 57.793 50.000 0.00 0.00 33.62 4.26
128 129 0.804989 GGTTCAAATCCTGGTGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
129 130 0.169009 GTTCAAATCCTGGTGCTCGC 59.831 55.000 0.00 0.00 0.00 5.03
130 131 0.250684 TTCAAATCCTGGTGCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
131 132 0.035152 TCAAATCCTGGTGCTCGCAT 60.035 50.000 0.00 0.00 0.00 4.73
132 133 0.813184 CAAATCCTGGTGCTCGCATT 59.187 50.000 0.00 0.00 0.00 3.56
133 134 2.016318 CAAATCCTGGTGCTCGCATTA 58.984 47.619 0.00 0.00 0.00 1.90
134 135 2.620115 CAAATCCTGGTGCTCGCATTAT 59.380 45.455 0.00 0.00 0.00 1.28
135 136 2.645838 ATCCTGGTGCTCGCATTATT 57.354 45.000 0.00 0.00 0.00 1.40
136 137 1.953559 TCCTGGTGCTCGCATTATTC 58.046 50.000 0.00 0.00 0.00 1.75
137 138 0.947244 CCTGGTGCTCGCATTATTCC 59.053 55.000 0.00 0.00 0.00 3.01
138 139 1.475751 CCTGGTGCTCGCATTATTCCT 60.476 52.381 0.00 0.00 0.00 3.36
139 140 1.600957 CTGGTGCTCGCATTATTCCTG 59.399 52.381 0.00 0.00 0.00 3.86
140 141 0.947244 GGTGCTCGCATTATTCCTGG 59.053 55.000 0.00 0.00 0.00 4.45
141 142 1.475034 GGTGCTCGCATTATTCCTGGA 60.475 52.381 0.00 0.00 0.00 3.86
142 143 2.498167 GTGCTCGCATTATTCCTGGAT 58.502 47.619 0.00 0.00 0.00 3.41
143 144 2.880890 GTGCTCGCATTATTCCTGGATT 59.119 45.455 0.00 0.00 0.00 3.01
144 145 3.316308 GTGCTCGCATTATTCCTGGATTT 59.684 43.478 0.00 0.00 0.00 2.17
145 146 4.515191 GTGCTCGCATTATTCCTGGATTTA 59.485 41.667 0.00 0.00 0.00 1.40
146 147 5.182001 GTGCTCGCATTATTCCTGGATTTAT 59.818 40.000 0.00 0.00 0.00 1.40
147 148 5.769662 TGCTCGCATTATTCCTGGATTTATT 59.230 36.000 0.00 0.00 0.00 1.40
148 149 6.265196 TGCTCGCATTATTCCTGGATTTATTT 59.735 34.615 0.00 0.00 0.00 1.40
149 150 6.803807 GCTCGCATTATTCCTGGATTTATTTC 59.196 38.462 0.00 0.00 0.00 2.17
150 151 7.522073 GCTCGCATTATTCCTGGATTTATTTCA 60.522 37.037 0.00 0.00 0.00 2.69
151 152 7.874940 TCGCATTATTCCTGGATTTATTTCAG 58.125 34.615 0.00 0.00 0.00 3.02
152 153 7.040478 TCGCATTATTCCTGGATTTATTTCAGG 60.040 37.037 0.00 0.00 46.91 3.86
160 161 6.076981 CTGGATTTATTTCAGGATTTCCGG 57.923 41.667 0.00 0.00 42.08 5.14
161 162 4.340950 TGGATTTATTTCAGGATTTCCGGC 59.659 41.667 0.00 0.00 42.08 6.13
162 163 4.537015 GATTTATTTCAGGATTTCCGGCG 58.463 43.478 0.00 0.00 42.08 6.46
163 164 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
164 165 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
165 166 1.378531 TTTCAGGATTTCCGGCGATG 58.621 50.000 9.30 0.00 42.08 3.84
166 167 1.095228 TTCAGGATTTCCGGCGATGC 61.095 55.000 9.30 0.00 42.08 3.91
167 168 2.588877 AGGATTTCCGGCGATGCG 60.589 61.111 9.30 0.00 42.08 4.73
178 179 4.731667 CGATGCGCTTTCAGTGTG 57.268 55.556 9.73 0.00 0.00 3.82
179 180 2.153039 CGATGCGCTTTCAGTGTGA 58.847 52.632 9.73 0.00 0.00 3.58
180 181 0.094216 CGATGCGCTTTCAGTGTGAG 59.906 55.000 9.73 0.00 0.00 3.51
181 182 0.445436 GATGCGCTTTCAGTGTGAGG 59.555 55.000 9.73 0.00 0.00 3.86
182 183 0.957395 ATGCGCTTTCAGTGTGAGGG 60.957 55.000 9.73 7.75 0.00 4.30
183 184 2.328099 GCGCTTTCAGTGTGAGGGG 61.328 63.158 0.00 3.92 0.00 4.79
184 185 1.371183 CGCTTTCAGTGTGAGGGGA 59.629 57.895 0.00 0.00 0.00 4.81
185 186 0.951040 CGCTTTCAGTGTGAGGGGAC 60.951 60.000 0.00 0.00 0.00 4.46
186 187 0.951040 GCTTTCAGTGTGAGGGGACG 60.951 60.000 0.00 0.00 0.00 4.79
187 188 0.393077 CTTTCAGTGTGAGGGGACGT 59.607 55.000 0.00 0.00 0.00 4.34
188 189 0.834612 TTTCAGTGTGAGGGGACGTT 59.165 50.000 0.00 0.00 0.00 3.99
189 190 0.391597 TTCAGTGTGAGGGGACGTTC 59.608 55.000 0.00 0.00 0.00 3.95
190 191 1.004918 CAGTGTGAGGGGACGTTCC 60.005 63.158 3.45 3.45 35.23 3.62
201 202 3.279116 ACGTTCCCGTCGACGACA 61.279 61.111 37.65 21.01 46.28 4.35
202 203 2.051076 CGTTCCCGTCGACGACAA 60.051 61.111 37.65 25.24 41.53 3.18
203 204 2.078914 CGTTCCCGTCGACGACAAG 61.079 63.158 37.65 20.95 41.53 3.16
204 205 1.731969 GTTCCCGTCGACGACAAGG 60.732 63.158 37.65 28.37 43.02 3.61
205 206 3.562779 TTCCCGTCGACGACAAGGC 62.563 63.158 37.65 0.45 43.02 4.35
212 213 2.572284 GACGACAAGGCGCCTACT 59.428 61.111 33.07 18.36 33.86 2.57
213 214 1.805254 GACGACAAGGCGCCTACTA 59.195 57.895 33.07 0.00 33.86 1.82
214 215 0.384669 GACGACAAGGCGCCTACTAT 59.615 55.000 33.07 15.80 33.86 2.12
215 216 1.605710 GACGACAAGGCGCCTACTATA 59.394 52.381 33.07 0.00 33.86 1.31
216 217 2.228343 GACGACAAGGCGCCTACTATAT 59.772 50.000 33.07 14.38 33.86 0.86
217 218 2.030185 ACGACAAGGCGCCTACTATATG 60.030 50.000 33.07 25.20 33.86 1.78
218 219 2.228103 CGACAAGGCGCCTACTATATGA 59.772 50.000 33.07 0.00 0.00 2.15
219 220 3.670895 CGACAAGGCGCCTACTATATGAG 60.671 52.174 33.07 17.57 0.00 2.90
220 221 2.028930 ACAAGGCGCCTACTATATGAGC 60.029 50.000 33.07 0.00 0.00 4.26
224 225 2.638556 CGCCTACTATATGAGCGCTT 57.361 50.000 13.26 0.00 40.35 4.68
225 226 2.254459 CGCCTACTATATGAGCGCTTG 58.746 52.381 13.26 0.50 40.35 4.01
226 227 2.351835 CGCCTACTATATGAGCGCTTGT 60.352 50.000 13.26 5.98 40.35 3.16
227 228 2.989840 GCCTACTATATGAGCGCTTGTG 59.010 50.000 13.26 1.66 0.00 3.33
228 229 3.553096 GCCTACTATATGAGCGCTTGTGT 60.553 47.826 13.26 7.95 0.00 3.72
229 230 4.230657 CCTACTATATGAGCGCTTGTGTC 58.769 47.826 13.26 0.00 0.00 3.67
230 231 4.022762 CCTACTATATGAGCGCTTGTGTCT 60.023 45.833 13.26 0.00 0.00 3.41
231 232 3.711086 ACTATATGAGCGCTTGTGTCTG 58.289 45.455 13.26 2.35 0.00 3.51
232 233 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
233 234 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
234 235 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
235 236 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
236 237 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
237 238 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
238 239 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
239 240 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
240 241 1.391485 CGCTTGTGTCTGTACTGATGC 59.609 52.381 5.69 3.20 0.00 3.91
241 242 2.693069 GCTTGTGTCTGTACTGATGCT 58.307 47.619 5.69 0.00 0.00 3.79
242 243 3.673323 CGCTTGTGTCTGTACTGATGCTA 60.673 47.826 5.69 0.00 0.00 3.49
243 244 4.245660 GCTTGTGTCTGTACTGATGCTAA 58.754 43.478 5.69 0.07 0.00 3.09
244 245 4.690748 GCTTGTGTCTGTACTGATGCTAAA 59.309 41.667 5.69 0.00 0.00 1.85
245 246 5.179368 GCTTGTGTCTGTACTGATGCTAAAA 59.821 40.000 5.69 0.00 0.00 1.52
246 247 6.293407 GCTTGTGTCTGTACTGATGCTAAAAA 60.293 38.462 5.69 0.00 0.00 1.94
335 339 1.739067 CTTTGCTTAGCTAGGGCGTT 58.261 50.000 5.60 0.00 44.37 4.84
394 398 5.627172 TCTTCGCCTCATTTTGTTTATTCG 58.373 37.500 0.00 0.00 0.00 3.34
441 445 1.161843 CTACGCAATTGAACCCGGTT 58.838 50.000 10.34 1.22 0.00 4.44
449 453 1.090625 TTGAACCCGGTTGACACACG 61.091 55.000 7.78 0.00 0.00 4.49
624 640 0.504384 GCACATGTAGCATAGCGTCG 59.496 55.000 13.27 0.00 0.00 5.12
626 642 0.385751 ACATGTAGCATAGCGTCGCT 59.614 50.000 25.08 25.08 43.41 4.93
727 1669 5.297029 TCGAGTCTCAGTCGAATGACATAAT 59.703 40.000 12.21 0.00 45.87 1.28
805 1747 2.755103 TCATGGATATAGCATCGCGACT 59.245 45.455 12.93 7.89 0.00 4.18
816 1759 0.817654 ATCGCGACTGGTCTCAATCA 59.182 50.000 12.93 0.00 0.00 2.57
835 1778 4.258702 TCAACTGAGACTTAGCAAGACC 57.741 45.455 0.00 0.00 0.00 3.85
846 1789 7.034397 AGACTTAGCAAGACCGAATAAGTTAC 58.966 38.462 3.37 0.00 36.94 2.50
847 1790 6.104665 ACTTAGCAAGACCGAATAAGTTACC 58.895 40.000 3.37 0.00 33.96 2.85
853 2402 5.904362 AGACCGAATAAGTTACCTAACGT 57.096 39.130 0.00 0.00 40.96 3.99
868 2417 9.573133 GTTACCTAACGTCTACAGCTAATTAAA 57.427 33.333 0.00 0.00 0.00 1.52
873 2422 6.461110 ACGTCTACAGCTAATTAAAGGCTA 57.539 37.500 0.00 0.00 34.71 3.93
874 2423 6.870769 ACGTCTACAGCTAATTAAAGGCTAA 58.129 36.000 0.00 0.00 34.71 3.09
902 2451 4.858850 TGTTTGGTGAGCCTTGATATCAT 58.141 39.130 6.17 0.00 35.27 2.45
903 2452 4.641541 TGTTTGGTGAGCCTTGATATCATG 59.358 41.667 6.17 8.92 35.27 3.07
904 2453 2.854963 TGGTGAGCCTTGATATCATGC 58.145 47.619 16.17 16.17 35.27 4.06
949 2516 2.571653 TCGACCATTGACCAAATCTCCT 59.428 45.455 0.00 0.00 0.00 3.69
959 2526 2.290260 ACCAAATCTCCTGTGCGATTCA 60.290 45.455 0.00 0.00 0.00 2.57
963 2530 0.532573 TCTCCTGTGCGATTCACCTC 59.467 55.000 0.00 0.00 45.03 3.85
964 2531 0.803768 CTCCTGTGCGATTCACCTCG 60.804 60.000 0.00 0.00 45.03 4.63
981 2556 2.469516 CGACTACAAATGCCCCGGC 61.470 63.158 0.00 0.00 42.35 6.13
1001 2576 1.440893 CGCTCCCATCTCACTCCAG 59.559 63.158 0.00 0.00 0.00 3.86
1031 2609 1.350684 TCTGTTCCTGCTACAATGGCA 59.649 47.619 0.00 0.00 38.10 4.92
1070 2648 1.313129 GCTCCTCCTCTCCCTCCTT 59.687 63.158 0.00 0.00 0.00 3.36
1142 2720 0.900647 CCAACTCCGTCCTCCTCACT 60.901 60.000 0.00 0.00 0.00 3.41
1217 2795 4.308458 CCGGCAGTCACGGTGGAA 62.308 66.667 8.50 0.00 46.03 3.53
1357 2935 3.138798 CGTCCATCCCTCCGTCGT 61.139 66.667 0.00 0.00 0.00 4.34
1401 2979 2.646175 CGCGGGGAAGACCAAGAGA 61.646 63.158 0.00 0.00 42.91 3.10
1493 3080 1.045911 ATGGCGAGGAGGAGGAAGAC 61.046 60.000 0.00 0.00 0.00 3.01
1499 3086 2.185608 GAGGAGGAAGACGCAGCC 59.814 66.667 0.00 0.00 0.00 4.85
1504 3091 2.747855 GGAAGACGCAGCCAAGGG 60.748 66.667 0.00 0.00 0.00 3.95
1521 3108 0.914417 GGGGTGGAAGGTGGAGATGA 60.914 60.000 0.00 0.00 0.00 2.92
1523 3110 1.141858 GGGTGGAAGGTGGAGATGATC 59.858 57.143 0.00 0.00 0.00 2.92
1559 3146 3.319198 ATCCGCTTCCACCACCGT 61.319 61.111 0.00 0.00 0.00 4.83
1584 3171 4.308458 TTCGCCACCACCACGAGG 62.308 66.667 0.00 0.00 37.11 4.63
1679 3266 2.047274 CACCGCCACCATCTTCGT 60.047 61.111 0.00 0.00 0.00 3.85
1685 3272 0.392998 GCCACCATCTTCGTCACCAT 60.393 55.000 0.00 0.00 0.00 3.55
1691 3278 1.920574 CATCTTCGTCACCATCACGAC 59.079 52.381 0.00 0.00 45.65 4.34
1733 3320 1.136329 ACCACCAGCAGGACAAGGAT 61.136 55.000 0.35 0.00 38.69 3.24
1828 3415 1.208293 GGTGGAAGAACTGGCTAGGAG 59.792 57.143 0.85 0.00 0.00 3.69
1856 3443 1.000731 GAGGCGATCATGAGAAGGAGG 59.999 57.143 0.09 0.00 0.00 4.30
1898 3485 2.520458 CACCACCACCACCACCAT 59.480 61.111 0.00 0.00 0.00 3.55
1901 3488 2.839609 CCACCACCACCACCATGGA 61.840 63.158 21.47 0.00 43.02 3.41
1922 3509 2.046217 GAGGGCGGGGTGAAGAAC 60.046 66.667 0.00 0.00 0.00 3.01
1992 3593 3.365969 GGCTGGTTGATTTGGTCGTTTAG 60.366 47.826 0.00 0.00 0.00 1.85
2056 3657 1.276421 AGTGCTCTGCCATTTCGTACT 59.724 47.619 0.00 0.00 0.00 2.73
2057 3658 2.496070 AGTGCTCTGCCATTTCGTACTA 59.504 45.455 0.00 0.00 0.00 1.82
2058 3659 2.603560 GTGCTCTGCCATTTCGTACTAC 59.396 50.000 0.00 0.00 0.00 2.73
2059 3660 2.202566 GCTCTGCCATTTCGTACTACC 58.797 52.381 0.00 0.00 0.00 3.18
2060 3661 2.159085 GCTCTGCCATTTCGTACTACCT 60.159 50.000 0.00 0.00 0.00 3.08
2061 3662 3.679083 GCTCTGCCATTTCGTACTACCTT 60.679 47.826 0.00 0.00 0.00 3.50
2062 3663 4.504858 CTCTGCCATTTCGTACTACCTTT 58.495 43.478 0.00 0.00 0.00 3.11
2063 3664 4.901868 TCTGCCATTTCGTACTACCTTTT 58.098 39.130 0.00 0.00 0.00 2.27
2163 3785 2.674852 AGATTGTACGAGCAGCAATGTG 59.325 45.455 0.34 0.00 33.56 3.21
2192 3820 9.787532 TTTCTGCAGATTAACTAATACATTTGC 57.212 29.630 19.04 0.00 0.00 3.68
2210 3838 8.413309 ACATTTGCCTTGTTATATATGCATCT 57.587 30.769 0.19 0.00 0.00 2.90
2211 3839 9.519191 ACATTTGCCTTGTTATATATGCATCTA 57.481 29.630 0.19 0.00 0.00 1.98
2297 3926 1.344065 TCTCTGTTTTACCCCTCGCA 58.656 50.000 0.00 0.00 0.00 5.10
2310 3939 2.223572 CCCCTCGCATTTGCATAGTTTC 60.224 50.000 3.13 0.00 42.21 2.78
2312 3941 2.539547 CCTCGCATTTGCATAGTTTCCG 60.540 50.000 3.13 0.00 42.21 4.30
2440 4074 9.739786 CGAAATATTTGTAAGTTTGCAATTTCC 57.260 29.630 5.17 0.00 31.53 3.13
2566 4208 7.888021 TGATGAGGTCCAAATTGTTATGTTACT 59.112 33.333 0.00 0.00 0.00 2.24
2618 4261 5.948992 ACTCAAACTCTTGATACTTTGGC 57.051 39.130 0.00 0.00 40.78 4.52
2619 4262 5.376625 ACTCAAACTCTTGATACTTTGGCA 58.623 37.500 0.00 0.00 40.78 4.92
2670 4314 4.021544 ACGATTTGCCCTTTCATTTTAGCA 60.022 37.500 0.00 0.00 0.00 3.49
2671 4315 5.111293 CGATTTGCCCTTTCATTTTAGCAT 58.889 37.500 0.00 0.00 0.00 3.79
2735 4379 7.122501 TCCACACGCCTATACGGATATTAAATA 59.877 37.037 0.00 0.00 37.37 1.40
2789 4436 3.593442 TGAGGATGTCAAACTGGGTTT 57.407 42.857 0.00 0.00 36.05 3.27
2790 4437 3.486383 TGAGGATGTCAAACTGGGTTTC 58.514 45.455 0.00 0.00 33.10 2.78
2802 4449 2.576648 ACTGGGTTTCCAATCTACTCCC 59.423 50.000 0.00 0.00 43.51 4.30
2815 4462 2.030540 TCTACTCCCGTGTGAAGTTTCG 60.031 50.000 0.00 0.00 0.00 3.46
2859 4511 0.529992 GCGAGGGAAATACTGTCCGG 60.530 60.000 0.00 0.00 35.86 5.14
2861 4513 1.202382 CGAGGGAAATACTGTCCGGAC 60.202 57.143 28.17 28.17 35.86 4.79
2868 4520 5.526479 GGGAAATACTGTCCGGACTAAAATC 59.474 44.000 33.39 22.42 35.86 2.17
2878 4530 3.380320 CCGGACTAAAATCCATCCAAACC 59.620 47.826 0.00 0.00 38.87 3.27
2880 4532 3.380320 GGACTAAAATCCATCCAAACCGG 59.620 47.826 0.00 0.00 38.77 5.28
2951 4603 7.365831 CCAAATTTGATATCCCAAAATCCCAGT 60.366 37.037 19.86 0.00 39.20 4.00
3017 4669 1.052124 TATAGGGGGTTGGAGCACCG 61.052 60.000 0.00 0.00 45.69 4.94
3021 4673 3.637273 GGGTTGGAGCACCGAGGT 61.637 66.667 0.00 0.00 37.76 3.85
3042 4694 6.326970 AGGTGCTACATATCCTCTTCCTTAT 58.673 40.000 0.00 0.00 0.00 1.73
3047 4699 9.326489 TGCTACATATCCTCTTCCTTATACAAT 57.674 33.333 0.00 0.00 0.00 2.71
3158 4810 2.623889 ACATATGGGTCGTGTCTAGCTC 59.376 50.000 7.80 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.835267 GTGAACCCCGGCCCTTTTT 60.835 57.895 0.00 0.00 0.00 1.94
11 12 2.203582 GTGAACCCCGGCCCTTTT 60.204 61.111 0.00 0.00 0.00 2.27
12 13 1.502527 TATGTGAACCCCGGCCCTTT 61.503 55.000 0.00 0.00 0.00 3.11
13 14 1.921869 CTATGTGAACCCCGGCCCTT 61.922 60.000 0.00 0.00 0.00 3.95
14 15 2.285818 TATGTGAACCCCGGCCCT 60.286 61.111 0.00 0.00 0.00 5.19
15 16 2.192175 CTATGTGAACCCCGGCCC 59.808 66.667 0.00 0.00 0.00 5.80
16 17 0.323087 AAACTATGTGAACCCCGGCC 60.323 55.000 0.00 0.00 0.00 6.13
17 18 1.541379 AAAACTATGTGAACCCCGGC 58.459 50.000 0.00 0.00 0.00 6.13
18 19 3.054948 TCCTAAAACTATGTGAACCCCGG 60.055 47.826 0.00 0.00 0.00 5.73
19 20 4.189231 CTCCTAAAACTATGTGAACCCCG 58.811 47.826 0.00 0.00 0.00 5.73
20 21 3.945921 GCTCCTAAAACTATGTGAACCCC 59.054 47.826 0.00 0.00 0.00 4.95
21 22 4.585879 TGCTCCTAAAACTATGTGAACCC 58.414 43.478 0.00 0.00 0.00 4.11
22 23 6.430000 TCTTTGCTCCTAAAACTATGTGAACC 59.570 38.462 0.00 0.00 0.00 3.62
23 24 7.435068 TCTTTGCTCCTAAAACTATGTGAAC 57.565 36.000 0.00 0.00 0.00 3.18
24 25 7.121168 CCATCTTTGCTCCTAAAACTATGTGAA 59.879 37.037 0.00 0.00 0.00 3.18
25 26 6.599244 CCATCTTTGCTCCTAAAACTATGTGA 59.401 38.462 0.00 0.00 0.00 3.58
26 27 6.678900 GCCATCTTTGCTCCTAAAACTATGTG 60.679 42.308 0.00 0.00 0.00 3.21
27 28 5.358160 GCCATCTTTGCTCCTAAAACTATGT 59.642 40.000 0.00 0.00 0.00 2.29
28 29 5.504665 CGCCATCTTTGCTCCTAAAACTATG 60.505 44.000 0.00 0.00 0.00 2.23
29 30 4.576463 CGCCATCTTTGCTCCTAAAACTAT 59.424 41.667 0.00 0.00 0.00 2.12
30 31 3.938963 CGCCATCTTTGCTCCTAAAACTA 59.061 43.478 0.00 0.00 0.00 2.24
31 32 2.749621 CGCCATCTTTGCTCCTAAAACT 59.250 45.455 0.00 0.00 0.00 2.66
32 33 2.488153 ACGCCATCTTTGCTCCTAAAAC 59.512 45.455 0.00 0.00 0.00 2.43
33 34 2.487762 CACGCCATCTTTGCTCCTAAAA 59.512 45.455 0.00 0.00 0.00 1.52
34 35 2.083774 CACGCCATCTTTGCTCCTAAA 58.916 47.619 0.00 0.00 0.00 1.85
35 36 1.277842 TCACGCCATCTTTGCTCCTAA 59.722 47.619 0.00 0.00 0.00 2.69
36 37 0.901827 TCACGCCATCTTTGCTCCTA 59.098 50.000 0.00 0.00 0.00 2.94
37 38 0.036732 TTCACGCCATCTTTGCTCCT 59.963 50.000 0.00 0.00 0.00 3.69
38 39 1.064654 GATTCACGCCATCTTTGCTCC 59.935 52.381 0.00 0.00 0.00 4.70
39 40 1.739466 TGATTCACGCCATCTTTGCTC 59.261 47.619 0.00 0.00 0.00 4.26
40 41 1.825090 TGATTCACGCCATCTTTGCT 58.175 45.000 0.00 0.00 0.00 3.91
41 42 2.253603 GTTGATTCACGCCATCTTTGC 58.746 47.619 0.00 0.00 0.00 3.68
42 43 2.489329 AGGTTGATTCACGCCATCTTTG 59.511 45.455 8.60 0.00 0.00 2.77
43 44 2.489329 CAGGTTGATTCACGCCATCTTT 59.511 45.455 8.60 0.00 0.00 2.52
44 45 2.086869 CAGGTTGATTCACGCCATCTT 58.913 47.619 8.60 0.00 0.00 2.40
45 46 1.003580 ACAGGTTGATTCACGCCATCT 59.996 47.619 8.60 0.00 0.00 2.90
46 47 1.131126 CACAGGTTGATTCACGCCATC 59.869 52.381 8.60 0.00 0.00 3.51
47 48 1.167851 CACAGGTTGATTCACGCCAT 58.832 50.000 8.60 0.00 0.00 4.40
48 49 0.888736 CCACAGGTTGATTCACGCCA 60.889 55.000 8.60 0.00 0.00 5.69
49 50 0.889186 ACCACAGGTTGATTCACGCC 60.889 55.000 0.00 0.00 27.29 5.68
50 51 0.951558 AACCACAGGTTGATTCACGC 59.048 50.000 0.00 0.00 45.07 5.34
60 61 2.158667 CCTAACCAACTCAACCACAGGT 60.159 50.000 0.00 0.00 37.65 4.00
61 62 2.158667 ACCTAACCAACTCAACCACAGG 60.159 50.000 0.00 0.00 0.00 4.00
62 63 2.878406 CACCTAACCAACTCAACCACAG 59.122 50.000 0.00 0.00 0.00 3.66
63 64 2.422235 CCACCTAACCAACTCAACCACA 60.422 50.000 0.00 0.00 0.00 4.17
64 65 2.158726 TCCACCTAACCAACTCAACCAC 60.159 50.000 0.00 0.00 0.00 4.16
65 66 2.128535 TCCACCTAACCAACTCAACCA 58.871 47.619 0.00 0.00 0.00 3.67
66 67 2.943036 TCCACCTAACCAACTCAACC 57.057 50.000 0.00 0.00 0.00 3.77
67 68 5.161943 ACTATCCACCTAACCAACTCAAC 57.838 43.478 0.00 0.00 0.00 3.18
68 69 6.021030 ACTACTATCCACCTAACCAACTCAA 58.979 40.000 0.00 0.00 0.00 3.02
69 70 5.586877 ACTACTATCCACCTAACCAACTCA 58.413 41.667 0.00 0.00 0.00 3.41
70 71 7.039853 GGATACTACTATCCACCTAACCAACTC 60.040 44.444 4.11 0.00 45.82 3.01
71 72 6.781507 GGATACTACTATCCACCTAACCAACT 59.218 42.308 4.11 0.00 45.82 3.16
72 73 6.990798 GGATACTACTATCCACCTAACCAAC 58.009 44.000 4.11 0.00 45.82 3.77
83 84 3.865571 TGGGTTGGGGATACTACTATCC 58.134 50.000 0.88 0.88 45.81 2.59
84 85 5.091552 TGATGGGTTGGGGATACTACTATC 58.908 45.833 0.00 0.00 0.00 2.08
85 86 5.101254 TGATGGGTTGGGGATACTACTAT 57.899 43.478 0.00 0.00 0.00 2.12
86 87 4.562934 TGATGGGTTGGGGATACTACTA 57.437 45.455 0.00 0.00 0.00 1.82
87 88 3.431411 TGATGGGTTGGGGATACTACT 57.569 47.619 0.00 0.00 0.00 2.57
88 89 3.181443 CCTTGATGGGTTGGGGATACTAC 60.181 52.174 0.00 0.00 0.00 2.73
89 90 3.053077 CCTTGATGGGTTGGGGATACTA 58.947 50.000 0.00 0.00 0.00 1.82
90 91 1.852965 CCTTGATGGGTTGGGGATACT 59.147 52.381 0.00 0.00 0.00 2.12
91 92 1.569072 ACCTTGATGGGTTGGGGATAC 59.431 52.381 0.00 0.00 41.11 2.24
92 93 1.994399 ACCTTGATGGGTTGGGGATA 58.006 50.000 0.00 0.00 41.11 2.59
93 94 1.092549 AACCTTGATGGGTTGGGGAT 58.907 50.000 0.00 0.00 46.51 3.85
94 95 2.575290 AACCTTGATGGGTTGGGGA 58.425 52.632 0.00 0.00 46.51 4.81
100 101 3.434309 CAGGATTTGAACCTTGATGGGT 58.566 45.455 0.00 0.00 42.05 4.51
101 102 2.762327 CCAGGATTTGAACCTTGATGGG 59.238 50.000 0.00 0.00 41.11 4.00
102 103 3.194116 CACCAGGATTTGAACCTTGATGG 59.806 47.826 0.00 0.00 42.93 3.51
103 104 3.367703 GCACCAGGATTTGAACCTTGATG 60.368 47.826 0.00 0.00 35.35 3.07
104 105 2.827921 GCACCAGGATTTGAACCTTGAT 59.172 45.455 0.00 0.00 35.35 2.57
105 106 2.158475 AGCACCAGGATTTGAACCTTGA 60.158 45.455 0.00 0.00 35.35 3.02
106 107 2.229784 GAGCACCAGGATTTGAACCTTG 59.770 50.000 0.00 0.00 35.35 3.61
107 108 2.519013 GAGCACCAGGATTTGAACCTT 58.481 47.619 0.00 0.00 35.35 3.50
108 109 1.611673 CGAGCACCAGGATTTGAACCT 60.612 52.381 0.00 0.00 38.40 3.50
109 110 0.804989 CGAGCACCAGGATTTGAACC 59.195 55.000 0.00 0.00 0.00 3.62
110 111 0.169009 GCGAGCACCAGGATTTGAAC 59.831 55.000 0.00 0.00 0.00 3.18
111 112 0.250684 TGCGAGCACCAGGATTTGAA 60.251 50.000 0.00 0.00 0.00 2.69
112 113 0.035152 ATGCGAGCACCAGGATTTGA 60.035 50.000 0.00 0.00 0.00 2.69
113 114 0.813184 AATGCGAGCACCAGGATTTG 59.187 50.000 0.00 0.00 0.00 2.32
114 115 2.418368 TAATGCGAGCACCAGGATTT 57.582 45.000 0.00 0.00 31.11 2.17
115 116 2.645838 ATAATGCGAGCACCAGGATT 57.354 45.000 0.00 0.00 33.17 3.01
116 117 2.498167 GAATAATGCGAGCACCAGGAT 58.502 47.619 0.00 0.00 0.00 3.24
117 118 1.475034 GGAATAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
118 119 0.947244 GGAATAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
119 120 1.600957 CAGGAATAATGCGAGCACCAG 59.399 52.381 0.00 0.00 0.00 4.00
120 121 1.667236 CAGGAATAATGCGAGCACCA 58.333 50.000 0.00 0.00 0.00 4.17
121 122 0.947244 CCAGGAATAATGCGAGCACC 59.053 55.000 0.00 0.00 0.00 5.01
122 123 1.953559 TCCAGGAATAATGCGAGCAC 58.046 50.000 0.00 0.00 0.00 4.40
123 124 2.936919 ATCCAGGAATAATGCGAGCA 57.063 45.000 0.00 0.00 0.00 4.26
124 125 5.886960 ATAAATCCAGGAATAATGCGAGC 57.113 39.130 0.00 0.00 0.00 5.03
125 126 7.874940 TGAAATAAATCCAGGAATAATGCGAG 58.125 34.615 0.00 0.00 0.00 5.03
126 127 7.815840 TGAAATAAATCCAGGAATAATGCGA 57.184 32.000 0.00 0.00 0.00 5.10
136 137 5.010012 CCGGAAATCCTGAAATAAATCCAGG 59.990 44.000 0.00 0.00 46.64 4.45
137 138 5.507985 GCCGGAAATCCTGAAATAAATCCAG 60.508 44.000 5.05 0.00 0.00 3.86
138 139 4.340950 GCCGGAAATCCTGAAATAAATCCA 59.659 41.667 5.05 0.00 0.00 3.41
139 140 4.556699 CGCCGGAAATCCTGAAATAAATCC 60.557 45.833 5.05 0.00 0.00 3.01
140 141 4.274950 TCGCCGGAAATCCTGAAATAAATC 59.725 41.667 5.05 0.00 0.00 2.17
141 142 4.204012 TCGCCGGAAATCCTGAAATAAAT 58.796 39.130 5.05 0.00 0.00 1.40
142 143 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
143 144 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
144 145 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
145 146 1.949525 CATCGCCGGAAATCCTGAAAT 59.050 47.619 5.05 0.00 0.00 2.17
146 147 1.378531 CATCGCCGGAAATCCTGAAA 58.621 50.000 5.05 0.00 0.00 2.69
147 148 1.095228 GCATCGCCGGAAATCCTGAA 61.095 55.000 5.05 0.00 0.00 3.02
148 149 1.523711 GCATCGCCGGAAATCCTGA 60.524 57.895 5.05 0.00 0.00 3.86
149 150 2.885676 CGCATCGCCGGAAATCCTG 61.886 63.158 5.05 0.00 0.00 3.86
150 151 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
161 162 0.094216 CTCACACTGAAAGCGCATCG 59.906 55.000 11.47 6.82 37.60 3.84
162 163 0.445436 CCTCACACTGAAAGCGCATC 59.555 55.000 11.47 8.39 37.60 3.91
163 164 0.957395 CCCTCACACTGAAAGCGCAT 60.957 55.000 11.47 0.00 37.60 4.73
164 165 1.597854 CCCTCACACTGAAAGCGCA 60.598 57.895 11.47 0.00 37.60 6.09
165 166 2.328099 CCCCTCACACTGAAAGCGC 61.328 63.158 0.00 0.00 37.60 5.92
166 167 0.951040 GTCCCCTCACACTGAAAGCG 60.951 60.000 0.00 0.00 37.60 4.68
167 168 0.951040 CGTCCCCTCACACTGAAAGC 60.951 60.000 0.00 0.00 37.60 3.51
168 169 0.393077 ACGTCCCCTCACACTGAAAG 59.607 55.000 0.00 0.00 42.29 2.62
169 170 0.834612 AACGTCCCCTCACACTGAAA 59.165 50.000 0.00 0.00 0.00 2.69
170 171 0.391597 GAACGTCCCCTCACACTGAA 59.608 55.000 0.00 0.00 0.00 3.02
171 172 1.469335 GGAACGTCCCCTCACACTGA 61.469 60.000 0.00 0.00 0.00 3.41
172 173 1.004918 GGAACGTCCCCTCACACTG 60.005 63.158 0.00 0.00 0.00 3.66
173 174 3.468063 GGAACGTCCCCTCACACT 58.532 61.111 0.00 0.00 0.00 3.55
186 187 1.731969 CCTTGTCGTCGACGGGAAC 60.732 63.158 35.05 26.09 40.29 3.62
187 188 2.646719 CCTTGTCGTCGACGGGAA 59.353 61.111 35.05 25.26 40.29 3.97
188 189 4.047059 GCCTTGTCGTCGACGGGA 62.047 66.667 35.05 20.33 40.29 5.14
192 193 3.332493 TAGGCGCCTTGTCGTCGAC 62.332 63.158 37.74 18.51 39.34 4.20
193 194 3.057548 TAGGCGCCTTGTCGTCGA 61.058 61.111 37.74 11.48 39.34 4.20
194 195 1.985447 TAGTAGGCGCCTTGTCGTCG 61.985 60.000 37.74 0.00 39.34 5.12
195 196 0.384669 ATAGTAGGCGCCTTGTCGTC 59.615 55.000 37.74 17.37 0.00 4.20
196 197 1.683943 TATAGTAGGCGCCTTGTCGT 58.316 50.000 37.74 19.21 0.00 4.34
197 198 2.228103 TCATATAGTAGGCGCCTTGTCG 59.772 50.000 37.74 16.69 0.00 4.35
198 199 3.839293 CTCATATAGTAGGCGCCTTGTC 58.161 50.000 37.74 24.18 0.00 3.18
199 200 2.028930 GCTCATATAGTAGGCGCCTTGT 60.029 50.000 37.74 24.32 0.00 3.16
200 201 2.611518 GCTCATATAGTAGGCGCCTTG 58.388 52.381 37.74 25.47 0.00 3.61
201 202 1.202582 CGCTCATATAGTAGGCGCCTT 59.797 52.381 37.74 21.30 39.42 4.35
202 203 0.811915 CGCTCATATAGTAGGCGCCT 59.188 55.000 34.85 34.85 39.42 5.52
203 204 3.330766 CGCTCATATAGTAGGCGCC 57.669 57.895 21.89 21.89 39.42 6.53
206 207 2.989840 CACAAGCGCTCATATAGTAGGC 59.010 50.000 12.06 0.00 0.00 3.93
207 208 4.022762 AGACACAAGCGCTCATATAGTAGG 60.023 45.833 12.06 0.00 0.00 3.18
208 209 4.914504 CAGACACAAGCGCTCATATAGTAG 59.085 45.833 12.06 0.00 0.00 2.57
209 210 4.338400 ACAGACACAAGCGCTCATATAGTA 59.662 41.667 12.06 0.00 0.00 1.82
210 211 3.131223 ACAGACACAAGCGCTCATATAGT 59.869 43.478 12.06 3.77 0.00 2.12
211 212 3.711086 ACAGACACAAGCGCTCATATAG 58.289 45.455 12.06 0.74 0.00 1.31
212 213 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
213 214 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
214 215 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
215 216 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
216 217 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
217 218 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
218 219 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
219 220 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
220 221 1.391485 GCATCAGTACAGACACAAGCG 59.609 52.381 0.00 0.00 0.00 4.68
221 222 2.693069 AGCATCAGTACAGACACAAGC 58.307 47.619 0.00 0.00 0.00 4.01
222 223 6.785488 TTTTAGCATCAGTACAGACACAAG 57.215 37.500 0.00 0.00 0.00 3.16
247 248 3.638160 TGTGCCATCTTTGCTCTCTTTTT 59.362 39.130 0.00 0.00 0.00 1.94
248 249 3.005155 GTGTGCCATCTTTGCTCTCTTTT 59.995 43.478 0.00 0.00 0.00 2.27
249 250 2.555757 GTGTGCCATCTTTGCTCTCTTT 59.444 45.455 0.00 0.00 0.00 2.52
250 251 2.157738 GTGTGCCATCTTTGCTCTCTT 58.842 47.619 0.00 0.00 0.00 2.85
251 252 1.818642 GTGTGCCATCTTTGCTCTCT 58.181 50.000 0.00 0.00 0.00 3.10
252 253 0.445436 CGTGTGCCATCTTTGCTCTC 59.555 55.000 0.00 0.00 0.00 3.20
253 254 1.580845 GCGTGTGCCATCTTTGCTCT 61.581 55.000 0.00 0.00 33.98 4.09
330 334 2.411748 GGCAAAAAGATTTAGCAACGCC 59.588 45.455 0.00 0.00 0.00 5.68
335 339 3.069300 TGTGCTGGCAAAAAGATTTAGCA 59.931 39.130 0.00 0.00 36.03 3.49
394 398 4.047822 GACGTCAATCATCTCACCATCTC 58.952 47.826 11.55 0.00 0.00 2.75
441 445 1.590525 GACGAACCAGCGTGTGTCA 60.591 57.895 0.00 0.00 45.72 3.58
648 664 5.198207 TCCATCATATATACCGGATGACGT 58.802 41.667 9.46 0.00 39.52 4.34
700 718 2.416893 TCATTCGACTGAGACTCGACAG 59.583 50.000 0.65 0.00 39.82 3.51
701 719 2.159824 GTCATTCGACTGAGACTCGACA 59.840 50.000 5.61 0.00 39.82 4.35
783 1725 2.854777 GTCGCGATGCTATATCCATGAC 59.145 50.000 14.06 0.00 0.00 3.06
788 1730 1.202582 ACCAGTCGCGATGCTATATCC 59.797 52.381 14.06 0.00 0.00 2.59
816 1759 2.891580 TCGGTCTTGCTAAGTCTCAGTT 59.108 45.455 0.00 0.00 0.00 3.16
846 1789 6.200475 GCCTTTAATTAGCTGTAGACGTTAGG 59.800 42.308 0.00 0.00 0.00 2.69
847 1790 6.979238 AGCCTTTAATTAGCTGTAGACGTTAG 59.021 38.462 0.00 0.00 34.99 2.34
853 2402 8.326529 AGGTTTTAGCCTTTAATTAGCTGTAGA 58.673 33.333 7.72 0.00 37.45 2.59
868 2417 3.636764 CTCACCAAACAAGGTTTTAGCCT 59.363 43.478 0.00 0.00 40.77 4.58
873 2422 2.466846 AGGCTCACCAAACAAGGTTTT 58.533 42.857 0.00 0.00 40.77 2.43
874 2423 2.159179 AGGCTCACCAAACAAGGTTT 57.841 45.000 0.00 0.00 40.77 3.27
884 2433 2.487805 GGCATGATATCAAGGCTCACCA 60.488 50.000 22.89 0.00 37.20 4.17
928 2493 2.571653 AGGAGATTTGGTCAATGGTCGA 59.428 45.455 0.00 0.00 0.00 4.20
959 2526 0.252197 GGGGCATTTGTAGTCGAGGT 59.748 55.000 0.00 0.00 0.00 3.85
963 2530 2.469516 GCCGGGGCATTTGTAGTCG 61.470 63.158 2.18 0.00 41.49 4.18
964 2531 2.119029 GGCCGGGGCATTTGTAGTC 61.119 63.158 16.76 0.00 44.11 2.59
981 2556 2.801631 GGAGTGAGATGGGAGCGGG 61.802 68.421 0.00 0.00 0.00 6.13
994 2569 1.067000 CAGAAGGTCTCAGCTGGAGTG 60.067 57.143 15.13 2.30 44.40 3.51
1001 2576 1.943507 GCAGGAACAGAAGGTCTCAGC 60.944 57.143 0.00 0.00 0.00 4.26
1142 2720 1.541889 GCATCCGCCTGATCATCTTGA 60.542 52.381 0.00 0.00 0.00 3.02
1340 2918 3.122250 GACGACGGAGGGATGGACG 62.122 68.421 0.00 0.00 0.00 4.79
1394 2972 1.515020 CTCCAGCTCGGTCTCTTGG 59.485 63.158 2.68 0.00 35.57 3.61
1460 3047 0.095935 CGCCATGAAACAGCTTCTCG 59.904 55.000 0.00 0.00 34.86 4.04
1493 3080 4.659172 TTCCACCCCTTGGCTGCG 62.659 66.667 0.00 0.00 46.47 5.18
1499 3086 1.133809 TCTCCACCTTCCACCCCTTG 61.134 60.000 0.00 0.00 0.00 3.61
1504 3091 1.839994 TGATCATCTCCACCTTCCACC 59.160 52.381 0.00 0.00 0.00 4.61
1521 3108 2.990479 GTGGCGGAACCTCCTGAT 59.010 61.111 1.55 0.00 40.22 2.90
1559 3146 1.003839 GTGGTGGCGAAGATGGTGA 60.004 57.895 0.00 0.00 0.00 4.02
1584 3171 3.462678 GTGCTCCTCCCCGTCCTC 61.463 72.222 0.00 0.00 0.00 3.71
1679 3266 1.873270 CGTCCTGGTCGTGATGGTGA 61.873 60.000 5.15 0.00 0.00 4.02
1691 3278 2.037367 TCCTCCTCCACGTCCTGG 59.963 66.667 0.00 0.00 42.29 4.45
1733 3320 0.392998 GCTTCATCTTCGGGCCTTCA 60.393 55.000 0.84 0.00 0.00 3.02
1784 3371 1.007734 GACCTCGTTGTCGCTGTCA 60.008 57.895 0.00 0.00 37.31 3.58
1828 3415 3.512223 ATGATCGCCTCGCTCAGCC 62.512 63.158 0.00 0.00 35.55 4.85
1879 3466 4.204028 GGTGGTGGTGGTGGTGCT 62.204 66.667 0.00 0.00 0.00 4.40
1880 3467 3.808218 ATGGTGGTGGTGGTGGTGC 62.808 63.158 0.00 0.00 0.00 5.01
1881 3468 1.902918 CATGGTGGTGGTGGTGGTG 60.903 63.158 0.00 0.00 0.00 4.17
1922 3509 0.329261 TCATGAGGCCCTTGAACCAG 59.671 55.000 0.00 0.00 0.00 4.00
1992 3593 6.077838 CAGCGAACAGATTAACCAAAGTAAC 58.922 40.000 0.00 0.00 0.00 2.50
2106 3707 5.116680 CGAGTAAACTAACACAGCAGTACAC 59.883 44.000 0.00 0.00 0.00 2.90
2141 3763 3.865164 CACATTGCTGCTCGTACAATCTA 59.135 43.478 0.00 0.00 31.82 1.98
2297 3926 4.949856 AGGAACATCGGAAACTATGCAAAT 59.050 37.500 0.00 0.00 37.03 2.32
2310 3939 6.737254 AACTTGTAACATAAGGAACATCGG 57.263 37.500 0.00 0.00 0.00 4.18
2389 4019 4.379499 CGCCCACCAAAATCTTAGAAGTTC 60.379 45.833 0.00 0.00 0.00 3.01
2397 4027 2.635443 CGGCGCCCACCAAAATCTT 61.635 57.895 23.46 0.00 0.00 2.40
2493 4133 5.337009 GCATTTTGATCCATCAGTTTCACCT 60.337 40.000 0.00 0.00 38.19 4.00
2501 4141 7.843490 AAAAATCTGCATTTTGATCCATCAG 57.157 32.000 0.00 0.00 40.68 2.90
2527 4168 5.953548 TGGACCTCATCATCATTTCATGTTT 59.046 36.000 0.00 0.00 0.00 2.83
2528 4169 5.512298 TGGACCTCATCATCATTTCATGTT 58.488 37.500 0.00 0.00 0.00 2.71
2531 4172 7.125204 ACAATTTGGACCTCATCATCATTTCAT 59.875 33.333 0.78 0.00 0.00 2.57
2566 4208 5.356751 AGCAGCAACGATGGTTAATATTTCA 59.643 36.000 0.00 0.00 34.35 2.69
2618 4261 5.163963 GCGCAAAAGGAAAATAAGACCAATG 60.164 40.000 0.30 0.00 0.00 2.82
2619 4262 4.929211 GCGCAAAAGGAAAATAAGACCAAT 59.071 37.500 0.30 0.00 0.00 3.16
2671 4315 9.923143 CTCCGGTGTATTTTCTGAATGTATATA 57.077 33.333 0.00 0.00 0.00 0.86
2689 4333 4.640690 ACCCAGGAGCTCCGGTGT 62.641 66.667 29.68 23.79 42.08 4.16
2708 4352 0.959553 ATCCGTATAGGCGTGTGGAG 59.040 55.000 0.00 0.00 40.77 3.86
2761 4408 6.239402 CCCAGTTTGACATCCTCAATTTTCTT 60.239 38.462 0.00 0.00 38.74 2.52
2762 4409 5.244626 CCCAGTTTGACATCCTCAATTTTCT 59.755 40.000 0.00 0.00 38.74 2.52
2767 4414 3.814504 ACCCAGTTTGACATCCTCAAT 57.185 42.857 0.00 0.00 38.74 2.57
2776 4423 5.070685 AGTAGATTGGAAACCCAGTTTGAC 58.929 41.667 0.00 0.00 35.77 3.18
2789 4436 2.225382 TCACACGGGAGTAGATTGGA 57.775 50.000 0.00 0.00 44.67 3.53
2790 4437 2.233922 ACTTCACACGGGAGTAGATTGG 59.766 50.000 0.00 0.00 44.67 3.16
2802 4449 7.267600 GGTATTTTATTCACGAAACTTCACACG 59.732 37.037 0.00 0.00 0.00 4.49
2815 4462 8.082242 GCCACATATTCCTGGTATTTTATTCAC 58.918 37.037 0.00 0.00 0.00 3.18
2859 4511 4.014406 ACCGGTTTGGATGGATTTTAGTC 58.986 43.478 0.00 0.00 42.00 2.59
2861 4513 5.400066 AAACCGGTTTGGATGGATTTTAG 57.600 39.130 31.17 0.00 42.00 1.85
2908 4560 4.360951 TTTGGGTGTCCGATCTACTTTT 57.639 40.909 0.00 0.00 35.24 2.27
2961 4613 9.458374 GTTCAAGAAAATACCGAGAAAATTTGA 57.542 29.630 0.00 0.00 0.00 2.69
2962 4614 9.463443 AGTTCAAGAAAATACCGAGAAAATTTG 57.537 29.630 0.00 0.00 0.00 2.32
3000 4652 3.006728 CGGTGCTCCAACCCCCTA 61.007 66.667 5.52 0.00 36.84 3.53
3003 4655 4.410400 CCTCGGTGCTCCAACCCC 62.410 72.222 5.52 0.00 36.84 4.95
3017 4669 4.156477 AGGAAGAGGATATGTAGCACCTC 58.844 47.826 0.00 0.00 46.28 3.85
3021 4673 8.721133 TTGTATAAGGAAGAGGATATGTAGCA 57.279 34.615 0.00 0.00 0.00 3.49
3042 4694 5.009210 CGGTGAAGAGGTTGGAAAAATTGTA 59.991 40.000 0.00 0.00 0.00 2.41
3047 4699 2.303175 CCGGTGAAGAGGTTGGAAAAA 58.697 47.619 0.00 0.00 0.00 1.94
3148 4800 4.399004 AAGATGATGGTGAGCTAGACAC 57.601 45.455 10.64 10.64 37.51 3.67
3151 4803 5.668471 CAGAAAAGATGATGGTGAGCTAGA 58.332 41.667 0.00 0.00 0.00 2.43
3158 4810 4.328983 GCAATTGCAGAAAAGATGATGGTG 59.671 41.667 25.36 0.00 41.59 4.17


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

AutoCloner maintained by Alex Coulton.