Multiple sequence alignment - TraesCS7A01G391300

Loading Multiple Alignment...

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 TraesCS7A01G391300 chr7A 100.000 3468 0 0 2428 5895 567455640 567452173 0.000000e+00 6405.0
1 TraesCS7A01G391300 chr7A 100.000 2288 0 0 1 2288 567458067 567455780 0.000000e+00 4226.0
2 TraesCS7A01G391300 chr7A 92.228 193 12 3 1 192 721781491 721781301 2.710000e-68 270.0
3 TraesCS7A01G391300 chr7A 82.906 117 12 7 5672 5783 18754185 18754298 1.350000e-16 99.0
4 TraesCS7A01G391300 chr7A 97.143 35 1 0 5796 5830 567452215 567452181 6.380000e-05 60.2
5 TraesCS7A01G391300 chr7A 97.143 35 1 0 5853 5887 567452272 567452238 6.380000e-05 60.2
6 TraesCS7A01G391300 chr7D 97.145 3363 58 15 2489 5830 500973080 500969735 0.000000e+00 5644.0
7 TraesCS7A01G391300 chr7D 92.857 2086 100 19 195 2270 500975651 500973605 0.000000e+00 2981.0
8 TraesCS7A01G391300 chr7D 90.104 192 17 2 2 192 309281864 309281674 1.270000e-61 248.0
9 TraesCS7A01G391300 chr7D 100.000 53 0 0 5843 5895 500969779 500969727 1.350000e-16 99.0
10 TraesCS7A01G391300 chr7D 96.078 51 2 0 2441 2491 500973182 500973132 3.790000e-12 84.2
11 TraesCS7A01G391300 chr7B 95.924 2380 73 9 3044 5405 529956300 529953927 0.000000e+00 3836.0
12 TraesCS7A01G391300 chr7B 90.129 2087 127 39 223 2269 529959350 529957303 0.000000e+00 2639.0
13 TraesCS7A01G391300 chr7B 89.009 555 28 16 2521 3047 529956929 529956380 0.000000e+00 656.0
14 TraesCS7A01G391300 chr6D 81.586 391 58 13 3295 3679 138907380 138907762 1.600000e-80 311.0
15 TraesCS7A01G391300 chr6D 82.289 367 36 12 994 1332 138904556 138904921 2.080000e-74 291.0
16 TraesCS7A01G391300 chr6D 87.736 106 13 0 1220 1325 441899548 441899443 2.230000e-24 124.0
17 TraesCS7A01G391300 chr6A 81.330 391 59 13 3295 3679 181567783 181568165 7.420000e-79 305.0
18 TraesCS7A01G391300 chr6A 89.238 223 24 0 1110 1332 181563733 181563955 4.500000e-71 279.0
19 TraesCS7A01G391300 chr6A 87.736 106 13 0 1220 1325 591267554 591267449 2.230000e-24 124.0
20 TraesCS7A01G391300 chr6B 81.074 391 60 13 3295 3679 238170529 238170911 3.450000e-77 300.0
21 TraesCS7A01G391300 chr6B 82.240 366 38 10 994 1332 238167826 238168191 2.080000e-74 291.0
22 TraesCS7A01G391300 chr5A 91.667 192 16 0 1 192 89027805 89027996 3.500000e-67 267.0
23 TraesCS7A01G391300 chr5A 90.000 190 17 2 2 190 48350675 48350863 1.640000e-60 244.0
24 TraesCS7A01G391300 chr3D 91.053 190 15 1 8 195 388334335 388334146 7.580000e-64 255.0
25 TraesCS7A01G391300 chr3D 88.083 193 20 3 2 192 57020411 57020220 5.940000e-55 226.0
26 TraesCS7A01G391300 chr3D 85.600 125 14 4 1193 1315 363871967 363871845 1.720000e-25 128.0
27 TraesCS7A01G391300 chr4B 89.062 192 19 2 2 192 88899998 88899808 2.750000e-58 237.0
28 TraesCS7A01G391300 chr5B 88.144 194 21 1 1 192 417882172 417881979 4.600000e-56 230.0
29 TraesCS7A01G391300 chr5B 88.172 186 17 4 14 196 691428958 691428775 3.580000e-52 217.0
30 TraesCS7A01G391300 chr3A 86.207 116 12 4 1202 1315 485014694 485014581 8.020000e-24 122.0
31 TraesCS7A01G391300 chrUn 83.962 106 9 6 5672 5772 309058955 309058853 1.750000e-15 95.3
32 TraesCS7A01G391300 chrUn 83.962 106 9 6 5672 5772 391832881 391832779 1.750000e-15 95.3
33 TraesCS7A01G391300 chrUn 85.417 96 8 4 5672 5762 436571635 436571729 1.750000e-15 95.3


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 TraesCS7A01G391300 chr7A 567452173 567458067 5894 True 2687.85 6405 98.571500 1 5895 4 chr7A.!!$R2 5894
1 TraesCS7A01G391300 chr7D 500969727 500975651 5924 True 2202.05 5644 96.520000 195 5895 4 chr7D.!!$R2 5700
2 TraesCS7A01G391300 chr7B 529953927 529959350 5423 True 2377.00 3836 91.687333 223 5405 3 chr7B.!!$R1 5182
3 TraesCS7A01G391300 chr6D 138904556 138907762 3206 False 301.00 311 81.937500 994 3679 2 chr6D.!!$F1 2685
4 TraesCS7A01G391300 chr6A 181563733 181568165 4432 False 292.00 305 85.284000 1110 3679 2 chr6A.!!$F1 2569
5 TraesCS7A01G391300 chr6B 238167826 238170911 3085 False 295.50 300 81.657000 994 3679 2 chr6B.!!$F1 2685

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
692 724 0.107459 GATCCACCACTCAAGAGCCC 60.107 60.0 0.00 0.00 0.00 5.19 F
1667 2209 0.970937 TGGTCCGAAGACTAGGCCAG 60.971 60.0 5.01 2.64 43.05 4.85 F
1849 2392 1.560923 ATTCTCGTATCTGTGCACGC 58.439 50.0 13.13 0.00 38.05 5.34 F
2934 6373 0.806102 ACGCGTGGCAGCTACAATAG 60.806 55.0 12.93 0.00 34.40 1.73 F
3936 7467 0.607217 AAAACCGAACCGATGACCCC 60.607 55.0 0.00 0.00 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2032 2985 0.456221 TTTTTCCGCACGGCAAGAAA 59.544 45.000 3.66 0.0 31.65 2.52 R
2693 5328 1.001378 GTTCATTGCTCCACACCACAC 60.001 52.381 0.00 0.0 0.00 3.82 R
3685 7216 3.691609 CCTTTAGGGAATCTTGCTGTCAC 59.308 47.826 0.00 0.0 37.23 3.67 R
3953 7484 1.081892 CAGCAGGTTGACCGATGAAG 58.918 55.000 4.92 0.0 42.08 3.02 R
4992 8539 1.544246 GTGCATAACCCTCACCCAAAC 59.456 52.381 0.00 0.0 0.00 2.93 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
24 25 7.576861 GAACCTAGTAGCAGACTTAGATCTT 57.423 40.000 0.00 0.00 39.81 2.40
25 26 7.964666 AACCTAGTAGCAGACTTAGATCTTT 57.035 36.000 0.00 0.00 39.81 2.52
26 27 7.341445 ACCTAGTAGCAGACTTAGATCTTTG 57.659 40.000 0.00 0.00 39.81 2.77
27 28 6.322712 ACCTAGTAGCAGACTTAGATCTTTGG 59.677 42.308 0.00 0.00 39.81 3.28
28 29 6.322712 CCTAGTAGCAGACTTAGATCTTTGGT 59.677 42.308 0.00 0.00 39.81 3.67
29 30 6.215495 AGTAGCAGACTTAGATCTTTGGTC 57.785 41.667 0.00 7.37 33.13 4.02
30 31 5.717178 AGTAGCAGACTTAGATCTTTGGTCA 59.283 40.000 18.11 2.59 33.13 4.02
31 32 4.826556 AGCAGACTTAGATCTTTGGTCAC 58.173 43.478 18.11 12.39 0.00 3.67
32 33 4.284490 AGCAGACTTAGATCTTTGGTCACA 59.716 41.667 18.11 0.00 0.00 3.58
33 34 5.046014 AGCAGACTTAGATCTTTGGTCACAT 60.046 40.000 18.11 6.43 0.00 3.21
34 35 5.293079 GCAGACTTAGATCTTTGGTCACATC 59.707 44.000 18.11 6.44 0.00 3.06
35 36 5.518128 CAGACTTAGATCTTTGGTCACATCG 59.482 44.000 18.11 0.00 0.00 3.84
36 37 5.186021 AGACTTAGATCTTTGGTCACATCGT 59.814 40.000 18.11 1.84 0.00 3.73
37 38 5.411781 ACTTAGATCTTTGGTCACATCGTC 58.588 41.667 0.00 0.00 0.00 4.20
38 39 5.186021 ACTTAGATCTTTGGTCACATCGTCT 59.814 40.000 0.00 0.00 0.00 4.18
39 40 4.543590 AGATCTTTGGTCACATCGTCTT 57.456 40.909 0.00 0.00 0.00 3.01
40 41 4.248859 AGATCTTTGGTCACATCGTCTTG 58.751 43.478 0.00 0.00 0.00 3.02
41 42 3.469008 TCTTTGGTCACATCGTCTTGT 57.531 42.857 0.00 0.00 0.00 3.16
42 43 3.804036 TCTTTGGTCACATCGTCTTGTT 58.196 40.909 0.00 0.00 0.00 2.83
43 44 3.559655 TCTTTGGTCACATCGTCTTGTTG 59.440 43.478 0.00 0.00 0.00 3.33
44 45 2.900716 TGGTCACATCGTCTTGTTGA 57.099 45.000 0.00 0.00 0.00 3.18
45 46 3.401033 TGGTCACATCGTCTTGTTGAT 57.599 42.857 0.00 0.00 0.00 2.57
46 47 4.529109 TGGTCACATCGTCTTGTTGATA 57.471 40.909 0.00 0.00 0.00 2.15
47 48 4.242475 TGGTCACATCGTCTTGTTGATAC 58.758 43.478 0.00 0.00 0.00 2.24
48 49 3.303495 GGTCACATCGTCTTGTTGATACG 59.697 47.826 0.00 0.00 37.96 3.06
49 50 3.303495 GTCACATCGTCTTGTTGATACGG 59.697 47.826 0.00 0.00 37.24 4.02
50 51 2.603110 CACATCGTCTTGTTGATACGGG 59.397 50.000 0.00 0.00 37.24 5.28
51 52 2.232941 ACATCGTCTTGTTGATACGGGT 59.767 45.455 0.00 0.00 37.24 5.28
52 53 2.357327 TCGTCTTGTTGATACGGGTG 57.643 50.000 0.00 0.00 37.24 4.61
53 54 1.887854 TCGTCTTGTTGATACGGGTGA 59.112 47.619 0.00 0.00 37.24 4.02
54 55 1.990563 CGTCTTGTTGATACGGGTGAC 59.009 52.381 0.00 0.00 33.13 3.67
55 56 2.608506 CGTCTTGTTGATACGGGTGACA 60.609 50.000 0.00 0.00 33.13 3.58
56 57 3.395639 GTCTTGTTGATACGGGTGACAA 58.604 45.455 0.00 0.00 0.00 3.18
57 58 3.432252 GTCTTGTTGATACGGGTGACAAG 59.568 47.826 7.93 7.93 45.17 3.16
58 59 2.465860 TGTTGATACGGGTGACAAGG 57.534 50.000 0.00 0.00 0.00 3.61
59 60 1.972075 TGTTGATACGGGTGACAAGGA 59.028 47.619 0.00 0.00 0.00 3.36
60 61 2.028476 TGTTGATACGGGTGACAAGGAG 60.028 50.000 0.00 0.00 0.00 3.69
61 62 1.191535 TGATACGGGTGACAAGGAGG 58.808 55.000 0.00 0.00 0.00 4.30
62 63 1.272816 TGATACGGGTGACAAGGAGGA 60.273 52.381 0.00 0.00 0.00 3.71
63 64 1.136500 GATACGGGTGACAAGGAGGAC 59.864 57.143 0.00 0.00 0.00 3.85
64 65 1.246056 TACGGGTGACAAGGAGGACG 61.246 60.000 0.00 0.00 0.00 4.79
65 66 2.571216 CGGGTGACAAGGAGGACGT 61.571 63.158 0.00 0.00 0.00 4.34
66 67 1.292541 GGGTGACAAGGAGGACGTC 59.707 63.158 7.13 7.13 0.00 4.34
67 68 1.186267 GGGTGACAAGGAGGACGTCT 61.186 60.000 16.46 0.90 0.00 4.18
68 69 0.244178 GGTGACAAGGAGGACGTCTC 59.756 60.000 16.46 10.65 41.71 3.36
76 77 3.063084 AGGACGTCTCCTCGTGGC 61.063 66.667 16.46 0.00 44.59 5.01
77 78 4.477975 GGACGTCTCCTCGTGGCG 62.478 72.222 16.46 0.00 44.21 5.69
78 79 3.735029 GACGTCTCCTCGTGGCGT 61.735 66.667 8.70 7.27 44.21 5.68
79 80 2.359107 ACGTCTCCTCGTGGCGTA 60.359 61.111 5.97 0.00 42.56 4.42
80 81 2.099831 CGTCTCCTCGTGGCGTAC 59.900 66.667 0.00 0.00 0.00 3.67
81 82 2.488820 GTCTCCTCGTGGCGTACC 59.511 66.667 0.00 0.00 0.00 3.34
82 83 2.045131 GTCTCCTCGTGGCGTACCT 61.045 63.158 0.00 0.00 36.63 3.08
83 84 0.745845 GTCTCCTCGTGGCGTACCTA 60.746 60.000 0.00 0.00 36.63 3.08
84 85 0.745845 TCTCCTCGTGGCGTACCTAC 60.746 60.000 0.00 0.00 36.63 3.18
85 86 1.722636 CTCCTCGTGGCGTACCTACC 61.723 65.000 0.00 0.00 36.63 3.18
86 87 1.751927 CCTCGTGGCGTACCTACCT 60.752 63.158 0.00 0.00 36.63 3.08
87 88 1.722636 CCTCGTGGCGTACCTACCTC 61.723 65.000 0.00 0.00 36.63 3.85
88 89 0.747283 CTCGTGGCGTACCTACCTCT 60.747 60.000 0.00 0.00 36.63 3.69
89 90 0.745845 TCGTGGCGTACCTACCTCTC 60.746 60.000 0.00 0.00 36.63 3.20
90 91 0.747283 CGTGGCGTACCTACCTCTCT 60.747 60.000 0.00 0.00 36.63 3.10
91 92 0.739561 GTGGCGTACCTACCTCTCTG 59.260 60.000 0.00 0.00 36.63 3.35
92 93 1.035932 TGGCGTACCTACCTCTCTGC 61.036 60.000 0.00 0.00 36.63 4.26
93 94 1.035932 GGCGTACCTACCTCTCTGCA 61.036 60.000 0.00 0.00 0.00 4.41
94 95 1.033574 GCGTACCTACCTCTCTGCAT 58.966 55.000 0.00 0.00 0.00 3.96
95 96 1.269309 GCGTACCTACCTCTCTGCATG 60.269 57.143 0.00 0.00 0.00 4.06
96 97 2.298610 CGTACCTACCTCTCTGCATGA 58.701 52.381 0.00 0.00 0.00 3.07
97 98 2.887783 CGTACCTACCTCTCTGCATGAT 59.112 50.000 0.00 0.00 0.00 2.45
98 99 3.304996 CGTACCTACCTCTCTGCATGATG 60.305 52.174 0.00 0.00 0.00 3.07
99 100 1.415659 ACCTACCTCTCTGCATGATGC 59.584 52.381 11.12 11.12 45.29 3.91
108 109 3.136123 GCATGATGCACCGTGCCT 61.136 61.111 14.89 11.20 44.23 4.75
109 110 2.703798 GCATGATGCACCGTGCCTT 61.704 57.895 14.89 8.36 44.23 4.35
110 111 1.885157 CATGATGCACCGTGCCTTT 59.115 52.632 20.67 5.76 44.23 3.11
111 112 0.457166 CATGATGCACCGTGCCTTTG 60.457 55.000 20.67 9.30 44.23 2.77
112 113 0.895100 ATGATGCACCGTGCCTTTGT 60.895 50.000 20.67 1.92 44.23 2.83
113 114 0.250510 TGATGCACCGTGCCTTTGTA 60.251 50.000 20.67 1.02 44.23 2.41
114 115 0.878416 GATGCACCGTGCCTTTGTAA 59.122 50.000 20.67 0.25 44.23 2.41
115 116 1.268352 GATGCACCGTGCCTTTGTAAA 59.732 47.619 20.67 0.00 44.23 2.01
116 117 1.323412 TGCACCGTGCCTTTGTAAAT 58.677 45.000 20.67 0.00 44.23 1.40
117 118 1.683917 TGCACCGTGCCTTTGTAAATT 59.316 42.857 20.67 0.00 44.23 1.82
118 119 2.058057 GCACCGTGCCTTTGTAAATTG 58.942 47.619 12.80 0.00 37.42 2.32
119 120 2.544903 GCACCGTGCCTTTGTAAATTGT 60.545 45.455 12.80 0.00 37.42 2.71
120 121 3.712187 CACCGTGCCTTTGTAAATTGTT 58.288 40.909 0.00 0.00 0.00 2.83
121 122 4.116238 CACCGTGCCTTTGTAAATTGTTT 58.884 39.130 0.00 0.00 0.00 2.83
122 123 4.208253 CACCGTGCCTTTGTAAATTGTTTC 59.792 41.667 0.00 0.00 0.00 2.78
123 124 4.098807 ACCGTGCCTTTGTAAATTGTTTCT 59.901 37.500 0.00 0.00 0.00 2.52
124 125 4.444056 CCGTGCCTTTGTAAATTGTTTCTG 59.556 41.667 0.00 0.00 0.00 3.02
125 126 4.085107 CGTGCCTTTGTAAATTGTTTCTGC 60.085 41.667 0.00 0.00 0.00 4.26
126 127 5.049828 GTGCCTTTGTAAATTGTTTCTGCT 58.950 37.500 0.00 0.00 0.00 4.24
127 128 5.049167 TGCCTTTGTAAATTGTTTCTGCTG 58.951 37.500 0.00 0.00 0.00 4.41
128 129 4.084380 GCCTTTGTAAATTGTTTCTGCTGC 60.084 41.667 0.00 0.00 0.00 5.25
129 130 5.291971 CCTTTGTAAATTGTTTCTGCTGCT 58.708 37.500 0.00 0.00 0.00 4.24
130 131 5.403466 CCTTTGTAAATTGTTTCTGCTGCTC 59.597 40.000 0.00 0.00 0.00 4.26
131 132 5.772825 TTGTAAATTGTTTCTGCTGCTCT 57.227 34.783 0.00 0.00 0.00 4.09
132 133 5.112220 TGTAAATTGTTTCTGCTGCTCTG 57.888 39.130 0.00 0.00 0.00 3.35
133 134 3.655276 AAATTGTTTCTGCTGCTCTGG 57.345 42.857 0.00 0.00 0.00 3.86
134 135 0.886563 ATTGTTTCTGCTGCTCTGGC 59.113 50.000 0.00 0.00 39.26 4.85
143 144 4.876701 TGCTCTGGCAGTCGTTTT 57.123 50.000 15.27 0.00 44.28 2.43
144 145 2.320215 TGCTCTGGCAGTCGTTTTG 58.680 52.632 15.27 0.00 44.28 2.44
145 146 0.179059 TGCTCTGGCAGTCGTTTTGA 60.179 50.000 15.27 0.00 44.28 2.69
146 147 0.514691 GCTCTGGCAGTCGTTTTGAG 59.485 55.000 15.27 3.01 38.54 3.02
147 148 0.514691 CTCTGGCAGTCGTTTTGAGC 59.485 55.000 15.27 0.00 0.00 4.26
148 149 0.179059 TCTGGCAGTCGTTTTGAGCA 60.179 50.000 15.27 0.00 0.00 4.26
149 150 0.662619 CTGGCAGTCGTTTTGAGCAA 59.337 50.000 6.28 0.00 0.00 3.91
150 151 1.267806 CTGGCAGTCGTTTTGAGCAAT 59.732 47.619 6.28 0.00 0.00 3.56
151 152 2.483877 CTGGCAGTCGTTTTGAGCAATA 59.516 45.455 6.28 0.00 0.00 1.90
152 153 3.081061 TGGCAGTCGTTTTGAGCAATAT 58.919 40.909 0.00 0.00 0.00 1.28
153 154 4.257731 TGGCAGTCGTTTTGAGCAATATA 58.742 39.130 0.00 0.00 0.00 0.86
154 155 4.881273 TGGCAGTCGTTTTGAGCAATATAT 59.119 37.500 0.00 0.00 0.00 0.86
155 156 5.356751 TGGCAGTCGTTTTGAGCAATATATT 59.643 36.000 0.00 0.00 0.00 1.28
156 157 5.909610 GGCAGTCGTTTTGAGCAATATATTC 59.090 40.000 0.00 0.00 0.00 1.75
157 158 6.458206 GGCAGTCGTTTTGAGCAATATATTCA 60.458 38.462 0.00 0.00 0.00 2.57
158 159 6.630443 GCAGTCGTTTTGAGCAATATATTCAG 59.370 38.462 0.00 0.00 0.00 3.02
159 160 7.128331 CAGTCGTTTTGAGCAATATATTCAGG 58.872 38.462 0.00 0.00 0.00 3.86
160 161 6.823689 AGTCGTTTTGAGCAATATATTCAGGT 59.176 34.615 0.00 0.00 0.00 4.00
161 162 6.907212 GTCGTTTTGAGCAATATATTCAGGTG 59.093 38.462 0.00 0.00 0.00 4.00
162 163 6.038161 TCGTTTTGAGCAATATATTCAGGTGG 59.962 38.462 0.00 0.00 0.00 4.61
163 164 6.507023 GTTTTGAGCAATATATTCAGGTGGG 58.493 40.000 0.00 0.00 0.00 4.61
164 165 4.371624 TGAGCAATATATTCAGGTGGGG 57.628 45.455 0.00 0.00 0.00 4.96
165 166 3.980022 TGAGCAATATATTCAGGTGGGGA 59.020 43.478 0.00 0.00 0.00 4.81
166 167 4.042062 TGAGCAATATATTCAGGTGGGGAG 59.958 45.833 0.00 0.00 0.00 4.30
167 168 3.084786 GCAATATATTCAGGTGGGGAGC 58.915 50.000 0.00 0.00 0.00 4.70
168 169 3.245052 GCAATATATTCAGGTGGGGAGCT 60.245 47.826 0.00 0.00 0.00 4.09
169 170 4.583871 CAATATATTCAGGTGGGGAGCTC 58.416 47.826 4.71 4.71 0.00 4.09
170 171 1.439543 ATATTCAGGTGGGGAGCTCC 58.560 55.000 25.59 25.59 0.00 4.70
188 189 3.662290 CCCCCGGTGATTCTCAAAA 57.338 52.632 0.00 0.00 0.00 2.44
189 190 1.917872 CCCCCGGTGATTCTCAAAAA 58.082 50.000 0.00 0.00 0.00 1.94
239 240 2.027192 ACACATACTTGAATCGCCACCT 60.027 45.455 0.00 0.00 0.00 4.00
277 278 9.410556 ACAATGCATTAGAAACTCAATTACAAC 57.589 29.630 12.53 0.00 0.00 3.32
286 287 6.369065 AGAAACTCAATTACAACGATGAGACC 59.631 38.462 8.48 0.00 41.38 3.85
312 313 5.485662 GCTTAGCCATTTAAACATCGACT 57.514 39.130 0.00 0.00 0.00 4.18
333 334 5.068636 ACTAGAGACGTACTCCAAACTTGA 58.931 41.667 0.00 0.00 45.96 3.02
381 382 5.710099 GGAACACAAAACCTCATGGAATCTA 59.290 40.000 0.00 0.00 37.04 1.98
388 389 4.762289 ACCTCATGGAATCTAGACAACC 57.238 45.455 0.00 0.00 37.04 3.77
435 436 1.529438 GCTCCACATCGACGTTGAAAA 59.471 47.619 10.11 0.00 0.00 2.29
456 457 1.053424 AGACGCCTACCTTTTCACCA 58.947 50.000 0.00 0.00 0.00 4.17
476 477 1.738432 CATGCTGCCGCTCTCTAGA 59.262 57.895 0.70 0.00 36.97 2.43
479 480 0.174389 TGCTGCCGCTCTCTAGAAAG 59.826 55.000 0.70 0.00 36.97 2.62
483 484 3.186119 CTGCCGCTCTCTAGAAAGAAAG 58.814 50.000 0.00 0.00 0.00 2.62
484 485 1.930503 GCCGCTCTCTAGAAAGAAAGC 59.069 52.381 0.00 0.00 41.62 3.51
536 538 3.195661 CGAGAGGGAAAAATAAGGTCCG 58.804 50.000 0.00 0.00 31.73 4.79
575 577 2.833582 GTGATCGGAGGCGAGGGA 60.834 66.667 0.00 0.00 0.00 4.20
635 637 5.524284 CATGGTGACCAAATTTTCGTTACA 58.476 37.500 9.06 0.00 36.95 2.41
636 638 4.922719 TGGTGACCAAATTTTCGTTACAC 58.077 39.130 0.00 0.00 0.00 2.90
692 724 0.107459 GATCCACCACTCAAGAGCCC 60.107 60.000 0.00 0.00 0.00 5.19
730 762 6.538945 TTTTCCAAAGCCCTAATGATAACC 57.461 37.500 0.00 0.00 0.00 2.85
762 795 3.071602 GCTGGGATCATTAGCCACTCTAA 59.928 47.826 0.00 0.00 41.17 2.10
763 796 4.636249 CTGGGATCATTAGCCACTCTAAC 58.364 47.826 0.00 0.00 39.86 2.34
764 797 3.391296 TGGGATCATTAGCCACTCTAACC 59.609 47.826 0.00 0.00 39.86 2.85
1351 1412 5.263968 ACGTCTCCCATCTGTTAGTAATG 57.736 43.478 0.00 0.00 0.00 1.90
1357 1418 4.873827 TCCCATCTGTTAGTAATGTTTCGC 59.126 41.667 0.00 0.00 0.00 4.70
1378 1439 3.184581 GCTATGAATTACGGTGCTGCTAC 59.815 47.826 0.00 0.00 0.00 3.58
1382 1443 2.295253 ATTACGGTGCTGCTACTGTC 57.705 50.000 16.27 0.00 40.48 3.51
1397 1585 3.238108 ACTGTCAGGTTGCTCGATTAG 57.762 47.619 4.53 0.00 0.00 1.73
1399 1587 3.762288 ACTGTCAGGTTGCTCGATTAGTA 59.238 43.478 4.53 0.00 0.00 1.82
1461 1766 2.008242 TTTGCTTGTTGGGGTATGCT 57.992 45.000 0.00 0.00 0.00 3.79
1464 1769 2.722094 TGCTTGTTGGGGTATGCTTAG 58.278 47.619 0.00 0.00 0.00 2.18
1483 1788 1.362355 GAACGTTTGGGCCCTGTTG 59.638 57.895 25.70 13.20 0.00 3.33
1494 1799 1.001048 GGCCCTGTTGTTCCGTAAAAC 60.001 52.381 0.00 0.00 0.00 2.43
1508 1814 3.181537 CCGTAAAACGTCGATGGAAGTTC 60.182 47.826 9.90 0.00 42.77 3.01
1530 1836 2.664851 TTCAAGGTCGTGCTGGCG 60.665 61.111 0.00 0.00 0.00 5.69
1625 2167 1.106285 GAACCCATGGGAATGTCTGC 58.894 55.000 38.07 8.62 38.96 4.26
1667 2209 0.970937 TGGTCCGAAGACTAGGCCAG 60.971 60.000 5.01 2.64 43.05 4.85
1849 2392 1.560923 ATTCTCGTATCTGTGCACGC 58.439 50.000 13.13 0.00 38.05 5.34
1897 2440 7.025963 GTGTTGAATTGTGAATCTTCTGATCC 58.974 38.462 0.00 0.00 31.51 3.36
1956 2499 4.379394 CCATTGTGTCGGAATGTAGTTTGG 60.379 45.833 0.00 0.00 0.00 3.28
2015 2968 8.095792 TCATTGGCACATTCATATGTTCTTTTT 58.904 29.630 1.90 0.00 42.29 1.94
2141 3209 7.887381 AGGGATCTTATACTGTTAACGATGAG 58.113 38.462 0.26 1.48 0.00 2.90
2144 3212 7.808856 GGATCTTATACTGTTAACGATGAGGAC 59.191 40.741 0.26 0.50 0.00 3.85
2145 3213 7.634671 TCTTATACTGTTAACGATGAGGACA 57.365 36.000 0.26 0.00 0.00 4.02
2149 3217 2.233922 CTGTTAACGATGAGGACAGGGT 59.766 50.000 0.26 0.00 35.32 4.34
2159 3230 5.106673 CGATGAGGACAGGGTTTTTACTTTC 60.107 44.000 0.00 0.00 0.00 2.62
2164 3235 7.179516 TGAGGACAGGGTTTTTACTTTCTTTTT 59.820 33.333 0.00 0.00 0.00 1.94
2242 3313 4.163268 ACCTGCAAAATTGGTTAGGTTTGT 59.837 37.500 0.00 0.00 35.09 2.83
2278 3349 9.871238 TTAGCTATAGATTTGTTTCGTTCTTCT 57.129 29.630 3.21 0.00 0.00 2.85
2279 3350 8.190888 AGCTATAGATTTGTTTCGTTCTTCTG 57.809 34.615 3.21 0.00 0.00 3.02
2280 3351 7.819900 AGCTATAGATTTGTTTCGTTCTTCTGT 59.180 33.333 3.21 0.00 0.00 3.41
2286 3357 9.450807 AGATTTGTTTCGTTCTTCTGTTTAATG 57.549 29.630 0.00 0.00 0.00 1.90
2287 3358 7.979115 TTTGTTTCGTTCTTCTGTTTAATGG 57.021 32.000 0.00 0.00 0.00 3.16
2629 5172 9.494271 GTTTATAATTGATAGACTGCCAGATGA 57.506 33.333 0.00 0.00 0.00 2.92
2693 5328 3.016736 AGGCATACCCAGTTTCAAATCG 58.983 45.455 0.00 0.00 36.11 3.34
2754 5389 5.178797 TCCAGCTTATCTTGTTTGAGTAGC 58.821 41.667 0.00 0.00 0.00 3.58
2875 6314 6.793505 TCCAAAGGGTCTATCTCTAGTTTC 57.206 41.667 0.00 0.00 34.93 2.78
2934 6373 0.806102 ACGCGTGGCAGCTACAATAG 60.806 55.000 12.93 0.00 34.40 1.73
2937 6376 1.571919 CGTGGCAGCTACAATAGGTC 58.428 55.000 9.87 0.00 33.57 3.85
2956 6395 4.834496 AGGTCATGCAAATTTCAAGGAGAA 59.166 37.500 0.00 0.00 0.00 2.87
3640 7171 6.625362 TGTTTGCAGAACATTGACAAAGTTA 58.375 32.000 8.67 0.00 31.39 2.24
3795 7326 8.971073 CCTATGAAAAGGAAATCAATAGTTGGT 58.029 33.333 0.00 0.00 39.15 3.67
3936 7467 0.607217 AAAACCGAACCGATGACCCC 60.607 55.000 0.00 0.00 0.00 4.95
4001 7548 1.071699 GTCCAACAGCCAGTTCACCTA 59.928 52.381 0.00 0.00 38.74 3.08
4212 7759 2.238521 TGGTGTTTTGGGAAGAGATGC 58.761 47.619 0.00 0.00 0.00 3.91
4585 8132 0.818296 ATCACAGGCGGAGTACAGAC 59.182 55.000 0.00 0.00 0.00 3.51
4806 8353 4.707105 TGTCTTCTTGACTCTTGCAATGA 58.293 39.130 0.00 0.00 45.54 2.57
4986 8533 6.153000 TGTTTTTAGTTTTGCTGTGGAAGGTA 59.847 34.615 0.00 0.00 0.00 3.08
4992 8539 5.418840 AGTTTTGCTGTGGAAGGTATATTGG 59.581 40.000 0.00 0.00 0.00 3.16
5166 8715 6.706055 AGTTGTTGTATCATTACACTGTCG 57.294 37.500 0.00 0.00 38.05 4.35
5289 8841 5.353400 TGATTGCTTTGTCATAGAGCTTGAG 59.647 40.000 0.00 0.00 37.32 3.02
5792 9348 7.979444 AAAGTTCGACTTAAGGATCATTGAA 57.021 32.000 7.53 0.00 37.47 2.69
5793 9349 7.979444 AAGTTCGACTTAAGGATCATTGAAA 57.021 32.000 7.53 0.00 36.52 2.69
5794 9350 8.567285 AAGTTCGACTTAAGGATCATTGAAAT 57.433 30.769 7.53 0.00 36.52 2.17
5795 9351 8.567285 AGTTCGACTTAAGGATCATTGAAATT 57.433 30.769 7.53 0.00 0.00 1.82
5796 9352 9.014297 AGTTCGACTTAAGGATCATTGAAATTT 57.986 29.630 7.53 0.00 0.00 1.82
5797 9353 9.065871 GTTCGACTTAAGGATCATTGAAATTTG 57.934 33.333 7.53 0.00 0.00 2.32
5798 9354 8.335532 TCGACTTAAGGATCATTGAAATTTGT 57.664 30.769 7.53 0.00 0.00 2.83
5799 9355 9.443323 TCGACTTAAGGATCATTGAAATTTGTA 57.557 29.630 7.53 0.00 0.00 2.41
5833 9389 9.829507 TGAAATTATGAACAAGAAATTTGGTGT 57.170 25.926 0.00 0.00 33.03 4.16
5836 9392 9.612066 AATTATGAACAAGAAATTTGGTGTTGT 57.388 25.926 16.81 9.00 34.44 3.32
5838 9394 9.743057 TTATGAACAAGAAATTTGGTGTTGTAG 57.257 29.630 16.81 0.00 34.44 2.74
5839 9395 7.397892 TGAACAAGAAATTTGGTGTTGTAGA 57.602 32.000 16.81 2.07 34.44 2.59
5840 9396 8.006298 TGAACAAGAAATTTGGTGTTGTAGAT 57.994 30.769 16.81 0.14 34.44 1.98
5841 9397 7.920151 TGAACAAGAAATTTGGTGTTGTAGATG 59.080 33.333 16.81 0.00 34.44 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.576861 AAGATCTAAGTCTGCTACTAGGTTC 57.423 40.000 0.00 0.00 37.50 3.62
1 2 7.147811 CCAAAGATCTAAGTCTGCTACTAGGTT 60.148 40.741 0.00 0.00 37.50 3.50
3 4 6.322712 ACCAAAGATCTAAGTCTGCTACTAGG 59.677 42.308 0.00 0.00 37.50 3.02
5 6 6.890268 TGACCAAAGATCTAAGTCTGCTACTA 59.110 38.462 16.35 0.00 37.50 1.82
6 7 5.717178 TGACCAAAGATCTAAGTCTGCTACT 59.283 40.000 16.35 0.00 41.49 2.57
7 8 5.808030 GTGACCAAAGATCTAAGTCTGCTAC 59.192 44.000 16.35 6.67 0.00 3.58
8 9 5.480422 TGTGACCAAAGATCTAAGTCTGCTA 59.520 40.000 16.35 0.00 0.00 3.49
9 10 4.284490 TGTGACCAAAGATCTAAGTCTGCT 59.716 41.667 16.35 0.00 0.00 4.24
10 11 4.569943 TGTGACCAAAGATCTAAGTCTGC 58.430 43.478 16.35 11.49 0.00 4.26
11 12 5.518128 CGATGTGACCAAAGATCTAAGTCTG 59.482 44.000 16.35 2.81 0.00 3.51
12 13 5.186021 ACGATGTGACCAAAGATCTAAGTCT 59.814 40.000 16.35 2.13 0.00 3.24
13 14 5.411781 ACGATGTGACCAAAGATCTAAGTC 58.588 41.667 0.00 4.23 0.00 3.01
14 15 5.186021 AGACGATGTGACCAAAGATCTAAGT 59.814 40.000 0.00 0.00 0.00 2.24
15 16 5.655488 AGACGATGTGACCAAAGATCTAAG 58.345 41.667 0.00 0.00 0.00 2.18
16 17 5.661056 AGACGATGTGACCAAAGATCTAA 57.339 39.130 0.00 0.00 0.00 2.10
17 18 5.047306 ACAAGACGATGTGACCAAAGATCTA 60.047 40.000 0.00 0.00 30.82 1.98
18 19 4.248859 CAAGACGATGTGACCAAAGATCT 58.751 43.478 0.00 0.00 0.00 2.75
19 20 3.997021 ACAAGACGATGTGACCAAAGATC 59.003 43.478 0.00 0.00 30.82 2.75
20 21 4.008074 ACAAGACGATGTGACCAAAGAT 57.992 40.909 0.00 0.00 30.82 2.40
21 22 3.469008 ACAAGACGATGTGACCAAAGA 57.531 42.857 0.00 0.00 30.82 2.52
22 23 3.559655 TCAACAAGACGATGTGACCAAAG 59.440 43.478 0.00 0.00 32.81 2.77
23 24 3.536570 TCAACAAGACGATGTGACCAAA 58.463 40.909 0.00 0.00 32.81 3.28
24 25 3.186702 TCAACAAGACGATGTGACCAA 57.813 42.857 0.00 0.00 32.81 3.67
25 26 2.900716 TCAACAAGACGATGTGACCA 57.099 45.000 0.00 0.00 32.81 4.02
26 27 3.303495 CGTATCAACAAGACGATGTGACC 59.697 47.826 0.00 0.00 38.88 4.02
27 28 3.303495 CCGTATCAACAAGACGATGTGAC 59.697 47.826 0.00 0.00 38.88 3.67
28 29 3.507786 CCGTATCAACAAGACGATGTGA 58.492 45.455 0.00 0.00 38.88 3.58
29 30 2.603110 CCCGTATCAACAAGACGATGTG 59.397 50.000 0.00 0.00 38.88 3.21
30 31 2.232941 ACCCGTATCAACAAGACGATGT 59.767 45.455 0.00 0.00 38.88 3.06
31 32 2.603110 CACCCGTATCAACAAGACGATG 59.397 50.000 0.00 0.00 38.88 3.84
32 33 2.494471 TCACCCGTATCAACAAGACGAT 59.506 45.455 0.00 0.00 38.88 3.73
33 34 1.887854 TCACCCGTATCAACAAGACGA 59.112 47.619 0.00 0.00 38.88 4.20
34 35 1.990563 GTCACCCGTATCAACAAGACG 59.009 52.381 0.00 0.00 36.36 4.18
35 36 3.034721 TGTCACCCGTATCAACAAGAC 57.965 47.619 0.00 0.00 0.00 3.01
36 37 3.556213 CCTTGTCACCCGTATCAACAAGA 60.556 47.826 13.51 0.00 46.09 3.02
37 38 2.742053 CCTTGTCACCCGTATCAACAAG 59.258 50.000 6.58 6.58 43.98 3.16
38 39 2.369203 TCCTTGTCACCCGTATCAACAA 59.631 45.455 0.00 0.00 0.00 2.83
39 40 1.972075 TCCTTGTCACCCGTATCAACA 59.028 47.619 0.00 0.00 0.00 3.33
40 41 2.618053 CTCCTTGTCACCCGTATCAAC 58.382 52.381 0.00 0.00 0.00 3.18
41 42 1.553248 CCTCCTTGTCACCCGTATCAA 59.447 52.381 0.00 0.00 0.00 2.57
42 43 1.191535 CCTCCTTGTCACCCGTATCA 58.808 55.000 0.00 0.00 0.00 2.15
43 44 1.136500 GTCCTCCTTGTCACCCGTATC 59.864 57.143 0.00 0.00 0.00 2.24
44 45 1.192428 GTCCTCCTTGTCACCCGTAT 58.808 55.000 0.00 0.00 0.00 3.06
45 46 1.246056 CGTCCTCCTTGTCACCCGTA 61.246 60.000 0.00 0.00 0.00 4.02
46 47 2.571216 CGTCCTCCTTGTCACCCGT 61.571 63.158 0.00 0.00 0.00 5.28
47 48 2.261671 CGTCCTCCTTGTCACCCG 59.738 66.667 0.00 0.00 0.00 5.28
48 49 1.186267 AGACGTCCTCCTTGTCACCC 61.186 60.000 13.01 0.00 35.09 4.61
49 50 0.244178 GAGACGTCCTCCTTGTCACC 59.756 60.000 13.01 0.00 35.87 4.02
50 51 3.796667 GAGACGTCCTCCTTGTCAC 57.203 57.895 13.01 0.00 35.87 3.67
60 61 4.477975 CGCCACGAGGAGACGTCC 62.478 72.222 13.01 3.55 44.76 4.79
61 62 2.393768 TACGCCACGAGGAGACGTC 61.394 63.158 9.97 7.70 44.76 4.34
63 64 2.099831 GTACGCCACGAGGAGACG 59.900 66.667 9.97 2.66 38.21 4.18
64 65 0.745845 TAGGTACGCCACGAGGAGAC 60.746 60.000 9.97 3.47 38.21 3.36
65 66 0.745845 GTAGGTACGCCACGAGGAGA 60.746 60.000 9.97 0.00 38.21 3.71
66 67 1.722636 GGTAGGTACGCCACGAGGAG 61.723 65.000 1.86 0.98 41.02 3.69
67 68 1.750399 GGTAGGTACGCCACGAGGA 60.750 63.158 1.86 0.00 36.89 3.71
68 69 1.722636 GAGGTAGGTACGCCACGAGG 61.723 65.000 0.00 0.00 37.19 4.63
69 70 0.747283 AGAGGTAGGTACGCCACGAG 60.747 60.000 0.00 0.00 37.19 4.18
70 71 0.745845 GAGAGGTAGGTACGCCACGA 60.746 60.000 0.00 0.00 37.19 4.35
71 72 0.747283 AGAGAGGTAGGTACGCCACG 60.747 60.000 3.21 0.00 37.19 4.94
72 73 0.739561 CAGAGAGGTAGGTACGCCAC 59.260 60.000 3.21 0.00 37.19 5.01
73 74 1.035932 GCAGAGAGGTAGGTACGCCA 61.036 60.000 3.21 0.00 37.19 5.69
74 75 1.035932 TGCAGAGAGGTAGGTACGCC 61.036 60.000 0.00 0.00 0.00 5.68
75 76 1.033574 ATGCAGAGAGGTAGGTACGC 58.966 55.000 0.00 0.00 0.00 4.42
76 77 2.298610 TCATGCAGAGAGGTAGGTACG 58.701 52.381 0.00 0.00 0.00 3.67
77 78 3.553922 GCATCATGCAGAGAGGTAGGTAC 60.554 52.174 4.20 0.00 44.26 3.34
78 79 2.630098 GCATCATGCAGAGAGGTAGGTA 59.370 50.000 4.20 0.00 44.26 3.08
79 80 1.415659 GCATCATGCAGAGAGGTAGGT 59.584 52.381 4.20 0.00 44.26 3.08
80 81 2.166821 GCATCATGCAGAGAGGTAGG 57.833 55.000 4.20 0.00 44.26 3.18
98 99 2.058057 CAATTTACAAAGGCACGGTGC 58.942 47.619 24.43 24.43 44.08 5.01
99 100 3.363341 ACAATTTACAAAGGCACGGTG 57.637 42.857 3.15 3.15 0.00 4.94
100 101 4.098807 AGAAACAATTTACAAAGGCACGGT 59.901 37.500 0.00 0.00 0.00 4.83
101 102 4.444056 CAGAAACAATTTACAAAGGCACGG 59.556 41.667 0.00 0.00 0.00 4.94
102 103 4.085107 GCAGAAACAATTTACAAAGGCACG 60.085 41.667 0.00 0.00 0.00 5.34
103 104 5.049828 AGCAGAAACAATTTACAAAGGCAC 58.950 37.500 0.00 0.00 0.00 5.01
104 105 5.049167 CAGCAGAAACAATTTACAAAGGCA 58.951 37.500 0.00 0.00 0.00 4.75
105 106 4.084380 GCAGCAGAAACAATTTACAAAGGC 60.084 41.667 0.00 0.00 0.00 4.35
106 107 5.291971 AGCAGCAGAAACAATTTACAAAGG 58.708 37.500 0.00 0.00 0.00 3.11
107 108 6.143438 CAGAGCAGCAGAAACAATTTACAAAG 59.857 38.462 0.00 0.00 0.00 2.77
108 109 5.978919 CAGAGCAGCAGAAACAATTTACAAA 59.021 36.000 0.00 0.00 0.00 2.83
109 110 5.507817 CCAGAGCAGCAGAAACAATTTACAA 60.508 40.000 0.00 0.00 0.00 2.41
110 111 4.022935 CCAGAGCAGCAGAAACAATTTACA 60.023 41.667 0.00 0.00 0.00 2.41
111 112 4.479619 CCAGAGCAGCAGAAACAATTTAC 58.520 43.478 0.00 0.00 0.00 2.01
112 113 3.057315 GCCAGAGCAGCAGAAACAATTTA 60.057 43.478 0.00 0.00 39.53 1.40
113 114 2.288640 GCCAGAGCAGCAGAAACAATTT 60.289 45.455 0.00 0.00 39.53 1.82
114 115 1.271656 GCCAGAGCAGCAGAAACAATT 59.728 47.619 0.00 0.00 39.53 2.32
115 116 0.886563 GCCAGAGCAGCAGAAACAAT 59.113 50.000 0.00 0.00 39.53 2.71
116 117 0.466007 TGCCAGAGCAGCAGAAACAA 60.466 50.000 0.00 0.00 46.52 2.83
117 118 1.148949 TGCCAGAGCAGCAGAAACA 59.851 52.632 0.00 0.00 46.52 2.83
118 119 4.069869 TGCCAGAGCAGCAGAAAC 57.930 55.556 0.00 0.00 46.52 2.78
127 128 0.514691 CTCAAAACGACTGCCAGAGC 59.485 55.000 0.00 0.00 40.48 4.09
128 129 0.514691 GCTCAAAACGACTGCCAGAG 59.485 55.000 0.00 0.00 0.00 3.35
129 130 0.179059 TGCTCAAAACGACTGCCAGA 60.179 50.000 0.00 0.00 0.00 3.86
130 131 0.662619 TTGCTCAAAACGACTGCCAG 59.337 50.000 0.00 0.00 0.00 4.85
131 132 1.317613 ATTGCTCAAAACGACTGCCA 58.682 45.000 0.00 0.00 0.00 4.92
132 133 3.764885 ATATTGCTCAAAACGACTGCC 57.235 42.857 0.00 0.00 0.00 4.85
133 134 6.486248 TGAATATATTGCTCAAAACGACTGC 58.514 36.000 1.78 0.00 0.00 4.40
134 135 7.128331 CCTGAATATATTGCTCAAAACGACTG 58.872 38.462 1.78 0.00 0.00 3.51
135 136 6.823689 ACCTGAATATATTGCTCAAAACGACT 59.176 34.615 1.78 0.00 0.00 4.18
136 137 6.907212 CACCTGAATATATTGCTCAAAACGAC 59.093 38.462 1.78 0.00 0.00 4.34
137 138 6.038161 CCACCTGAATATATTGCTCAAAACGA 59.962 38.462 1.78 0.00 0.00 3.85
138 139 6.201517 CCACCTGAATATATTGCTCAAAACG 58.798 40.000 1.78 0.00 0.00 3.60
139 140 6.461509 CCCCACCTGAATATATTGCTCAAAAC 60.462 42.308 1.78 0.00 0.00 2.43
140 141 5.598005 CCCCACCTGAATATATTGCTCAAAA 59.402 40.000 1.78 0.00 0.00 2.44
141 142 5.103728 TCCCCACCTGAATATATTGCTCAAA 60.104 40.000 1.78 0.00 0.00 2.69
142 143 4.415179 TCCCCACCTGAATATATTGCTCAA 59.585 41.667 1.78 0.00 0.00 3.02
143 144 3.980022 TCCCCACCTGAATATATTGCTCA 59.020 43.478 1.78 0.00 0.00 4.26
144 145 4.583871 CTCCCCACCTGAATATATTGCTC 58.416 47.826 1.78 0.00 0.00 4.26
145 146 3.245052 GCTCCCCACCTGAATATATTGCT 60.245 47.826 1.78 0.00 0.00 3.91
146 147 3.084786 GCTCCCCACCTGAATATATTGC 58.915 50.000 1.78 0.00 0.00 3.56
147 148 4.566488 GGAGCTCCCCACCTGAATATATTG 60.566 50.000 23.19 0.00 0.00 1.90
148 149 3.589288 GGAGCTCCCCACCTGAATATATT 59.411 47.826 23.19 0.00 0.00 1.28
149 150 3.185455 GGAGCTCCCCACCTGAATATAT 58.815 50.000 23.19 0.00 0.00 0.86
150 151 2.621070 GGAGCTCCCCACCTGAATATA 58.379 52.381 23.19 0.00 0.00 0.86
151 152 1.439543 GGAGCTCCCCACCTGAATAT 58.560 55.000 23.19 0.00 0.00 1.28
152 153 2.930935 GGAGCTCCCCACCTGAATA 58.069 57.895 23.19 0.00 0.00 1.75
153 154 3.746957 GGAGCTCCCCACCTGAAT 58.253 61.111 23.19 0.00 0.00 2.57
213 214 4.868171 TGGCGATTCAAGTATGTGTAGTTC 59.132 41.667 0.00 0.00 0.00 3.01
239 240 8.972458 TTCTAATGCATTGTGTAAAGCCTATA 57.028 30.769 22.27 0.00 29.78 1.31
277 278 1.576356 GCTAAGCCTTGGTCTCATCG 58.424 55.000 0.00 0.00 0.00 3.84
312 313 4.823442 TGTCAAGTTTGGAGTACGTCTCTA 59.177 41.667 12.62 6.12 42.40 2.43
333 334 6.097554 CCTACTCTATCTTCAACCATGTCTGT 59.902 42.308 0.00 0.00 0.00 3.41
381 382 0.907704 TATGGCGGGTCTGGTTGTCT 60.908 55.000 0.00 0.00 0.00 3.41
409 410 1.591703 GTCGATGTGGAGCCAGTGA 59.408 57.895 0.00 0.00 0.00 3.41
412 413 1.079819 AACGTCGATGTGGAGCCAG 60.080 57.895 11.82 0.00 0.00 4.85
435 436 2.158726 TGGTGAAAAGGTAGGCGTCTTT 60.159 45.455 0.00 0.00 35.01 2.52
476 477 4.086199 TGTGTTTTTCGTCGCTTTCTTT 57.914 36.364 0.00 0.00 0.00 2.52
479 480 3.676540 TCTTGTGTTTTTCGTCGCTTTC 58.323 40.909 0.00 0.00 0.00 2.62
483 484 3.604627 TGTTTTCTTGTGTTTTTCGTCGC 59.395 39.130 0.00 0.00 0.00 5.19
484 485 5.732849 TTGTTTTCTTGTGTTTTTCGTCG 57.267 34.783 0.00 0.00 0.00 5.12
521 523 0.099968 GGCGCGGACCTTATTTTTCC 59.900 55.000 8.83 0.00 0.00 3.13
523 525 0.524414 GTGGCGCGGACCTTATTTTT 59.476 50.000 8.83 0.00 0.00 1.94
555 557 3.209812 CTCGCCTCCGATCACCGA 61.210 66.667 0.00 0.00 43.47 4.69
575 577 2.126071 CCGGTGAGTCGACGCATT 60.126 61.111 24.73 0.00 0.00 3.56
594 596 0.037697 TGCGATGTAGCCAAGACGTT 60.038 50.000 0.00 0.00 36.02 3.99
635 637 2.943036 TTTGGAAGAGTTTAGGGCGT 57.057 45.000 0.00 0.00 0.00 5.68
636 638 4.201920 GCTAATTTGGAAGAGTTTAGGGCG 60.202 45.833 0.00 0.00 0.00 6.13
730 762 0.841961 TGATCCCAGCCAGATCAAGG 59.158 55.000 8.11 0.00 45.42 3.61
762 795 4.608774 TCCCGGTCGAGTGGTGGT 62.609 66.667 0.00 0.00 0.00 4.16
763 796 3.760035 CTCCCGGTCGAGTGGTGG 61.760 72.222 0.00 0.00 0.00 4.61
764 797 3.760035 CCTCCCGGTCGAGTGGTG 61.760 72.222 0.00 0.00 0.00 4.17
1325 1386 0.172803 AACAGATGGGAGACGTACGC 59.827 55.000 16.72 8.42 0.00 4.42
1351 1412 3.308866 AGCACCGTAATTCATAGCGAAAC 59.691 43.478 0.00 0.00 37.12 2.78
1357 1418 4.445718 CAGTAGCAGCACCGTAATTCATAG 59.554 45.833 0.00 0.00 0.00 2.23
1367 1428 1.446792 CCTGACAGTAGCAGCACCG 60.447 63.158 0.93 0.00 32.06 4.94
1378 1439 3.238108 ACTAATCGAGCAACCTGACAG 57.762 47.619 0.00 0.00 0.00 3.51
1382 1443 2.431057 ACCCTACTAATCGAGCAACCTG 59.569 50.000 0.00 0.00 0.00 4.00
1397 1585 3.953542 ATCCAATTCCTTCCACCCTAC 57.046 47.619 0.00 0.00 0.00 3.18
1399 1587 3.852858 AAATCCAATTCCTTCCACCCT 57.147 42.857 0.00 0.00 0.00 4.34
1461 1766 0.250989 CAGGGCCCAAACGTTCCTAA 60.251 55.000 27.56 0.00 0.00 2.69
1464 1769 1.830847 AACAGGGCCCAAACGTTCC 60.831 57.895 27.56 0.00 0.00 3.62
1494 1799 3.926527 TGAAGATTGAACTTCCATCGACG 59.073 43.478 0.00 0.00 43.67 5.12
1508 1814 1.466167 CCAGCACGACCTTGAAGATTG 59.534 52.381 0.00 0.00 0.00 2.67
1530 1836 1.285641 CGTGGATGCACAACCAACC 59.714 57.895 18.05 0.37 37.94 3.77
1625 2167 3.700961 CCGATAACAACGGCCTCG 58.299 61.111 0.00 0.41 43.74 4.63
1667 2209 7.601856 TCAAATCAACCAATTATTGACCAGAC 58.398 34.615 6.50 0.00 38.84 3.51
1849 2392 9.480053 ACACTAGAATCCAAATGTTTCATTTTG 57.520 29.630 0.00 3.23 33.58 2.44
1956 2499 4.260194 GCCAAAAATGGCGACCAC 57.740 55.556 3.80 0.00 45.79 4.16
2016 2969 9.398538 ACGGCAAGAAACTTAATATTGGTAATA 57.601 29.630 0.00 0.00 0.00 0.98
2017 2970 8.188139 CACGGCAAGAAACTTAATATTGGTAAT 58.812 33.333 0.00 0.00 0.00 1.89
2018 2971 7.531716 CACGGCAAGAAACTTAATATTGGTAA 58.468 34.615 0.00 0.00 0.00 2.85
2019 2972 6.403855 GCACGGCAAGAAACTTAATATTGGTA 60.404 38.462 0.00 0.00 0.00 3.25
2032 2985 0.456221 TTTTTCCGCACGGCAAGAAA 59.544 45.000 3.66 0.00 31.65 2.52
2059 3127 5.184711 ACAACAATGATGCAAACCTTTTGT 58.815 33.333 0.00 0.00 0.00 2.83
2060 3128 5.738118 ACAACAATGATGCAAACCTTTTG 57.262 34.783 0.00 0.00 0.00 2.44
2135 3203 3.939066 AGTAAAAACCCTGTCCTCATCG 58.061 45.455 0.00 0.00 0.00 3.84
2141 3209 8.472413 AGTAAAAAGAAAGTAAAAACCCTGTCC 58.528 33.333 0.00 0.00 0.00 4.02
2144 3212 9.863845 TGAAGTAAAAAGAAAGTAAAAACCCTG 57.136 29.630 0.00 0.00 0.00 4.45
2145 3213 9.865321 GTGAAGTAAAAAGAAAGTAAAAACCCT 57.135 29.630 0.00 0.00 0.00 4.34
2242 3313 9.959721 AACAAATCTATAGCTAAAACTTCTGGA 57.040 29.630 0.00 0.00 0.00 3.86
2437 3508 9.527157 TGGGAATTCATTACTTTATCAAGAACA 57.473 29.630 7.93 0.00 33.72 3.18
2438 3509 9.788960 GTGGGAATTCATTACTTTATCAAGAAC 57.211 33.333 7.93 0.00 33.72 3.01
2439 3510 9.753674 AGTGGGAATTCATTACTTTATCAAGAA 57.246 29.630 7.93 0.00 33.72 2.52
2505 3882 5.509670 GCTACCAACAAAAGCTCCTTCATTT 60.510 40.000 0.00 0.00 33.40 2.32
2508 3885 2.884639 GCTACCAACAAAAGCTCCTTCA 59.115 45.455 0.00 0.00 33.40 3.02
2629 5172 9.167311 CTCAATTAATCTAACCAGTAAACAGCT 57.833 33.333 0.00 0.00 0.00 4.24
2693 5328 1.001378 GTTCATTGCTCCACACCACAC 60.001 52.381 0.00 0.00 0.00 3.82
2719 5354 4.759693 AGATAAGCTGGAGACACGATAGAG 59.240 45.833 0.00 0.00 41.38 2.43
2934 6373 4.789012 TCTCCTTGAAATTTGCATGACC 57.211 40.909 0.00 0.00 0.00 4.02
2937 6376 7.900782 AAGAATTCTCCTTGAAATTTGCATG 57.099 32.000 8.78 0.00 38.29 4.06
2979 6418 8.629158 TCATAAACACAAACACAGAGCTTAAAT 58.371 29.630 0.00 0.00 0.00 1.40
3685 7216 3.691609 CCTTTAGGGAATCTTGCTGTCAC 59.308 47.826 0.00 0.00 37.23 3.67
3953 7484 1.081892 CAGCAGGTTGACCGATGAAG 58.918 55.000 4.92 0.00 42.08 3.02
4001 7548 5.934402 ACTTATAAGACCGGTGAGTGAAT 57.066 39.130 14.63 0.00 0.00 2.57
4585 8132 1.375523 CCTTGGTTTCTCCCGTCGG 60.376 63.158 3.60 3.60 34.77 4.79
4806 8353 2.624838 CCTCCAAAGCTGTCACACAATT 59.375 45.455 0.00 0.00 0.00 2.32
4954 8501 5.584251 ACAGCAAAACTAAAAACACCCAATG 59.416 36.000 0.00 0.00 0.00 2.82
4986 8533 3.845109 AACCCTCACCCAAACCAATAT 57.155 42.857 0.00 0.00 0.00 1.28
4992 8539 1.544246 GTGCATAACCCTCACCCAAAC 59.456 52.381 0.00 0.00 0.00 2.93
5257 8809 5.717078 ATGACAAAGCAATCAAGTGACAT 57.283 34.783 0.00 0.00 0.00 3.06
5289 8841 3.436704 TGATCCAGTGATTCGTTTCAAGC 59.563 43.478 0.00 0.00 0.00 4.01
5297 8849 5.746307 ACATTGAATGATCCAGTGATTCG 57.254 39.130 12.80 0.00 0.00 3.34
5565 9117 7.668052 AGAGTAATAACCAGCCACAACAATTAA 59.332 33.333 0.00 0.00 0.00 1.40
5807 9363 9.829507 ACACCAAATTTCTTGTTCATAATTTCA 57.170 25.926 0.00 0.00 30.17 2.69
5810 9366 9.612066 ACAACACCAAATTTCTTGTTCATAATT 57.388 25.926 9.90 0.00 29.65 1.40
5812 9368 9.743057 CTACAACACCAAATTTCTTGTTCATAA 57.257 29.630 9.90 0.00 29.65 1.90
5813 9369 9.126151 TCTACAACACCAAATTTCTTGTTCATA 57.874 29.630 9.90 6.45 29.65 2.15
5814 9370 8.006298 TCTACAACACCAAATTTCTTGTTCAT 57.994 30.769 9.90 5.83 29.65 2.57
5815 9371 7.397892 TCTACAACACCAAATTTCTTGTTCA 57.602 32.000 9.90 3.11 29.65 3.18
5816 9372 7.920682 ACATCTACAACACCAAATTTCTTGTTC 59.079 33.333 9.90 0.00 29.65 3.18
5817 9373 7.781056 ACATCTACAACACCAAATTTCTTGTT 58.219 30.769 7.75 7.75 32.34 2.83
5818 9374 7.346751 ACATCTACAACACCAAATTTCTTGT 57.653 32.000 0.00 0.00 0.00 3.16
5819 9375 7.706179 ACAACATCTACAACACCAAATTTCTTG 59.294 33.333 0.00 0.00 0.00 3.02
5820 9376 7.781056 ACAACATCTACAACACCAAATTTCTT 58.219 30.769 0.00 0.00 0.00 2.52
5821 9377 7.346751 ACAACATCTACAACACCAAATTTCT 57.653 32.000 0.00 0.00 0.00 2.52
5822 9378 8.564574 TCTACAACATCTACAACACCAAATTTC 58.435 33.333 0.00 0.00 0.00 2.17
5823 9379 8.349983 GTCTACAACATCTACAACACCAAATTT 58.650 33.333 0.00 0.00 0.00 1.82
5824 9380 7.500892 TGTCTACAACATCTACAACACCAAATT 59.499 33.333 0.00 0.00 31.20 1.82
5825 9381 6.995686 TGTCTACAACATCTACAACACCAAAT 59.004 34.615 0.00 0.00 31.20 2.32
5826 9382 6.350103 TGTCTACAACATCTACAACACCAAA 58.650 36.000 0.00 0.00 31.20 3.28
5827 9383 5.919755 TGTCTACAACATCTACAACACCAA 58.080 37.500 0.00 0.00 31.20 3.67
5828 9384 5.538849 TGTCTACAACATCTACAACACCA 57.461 39.130 0.00 0.00 31.20 4.17
5829 9385 7.298122 CAATTGTCTACAACATCTACAACACC 58.702 38.462 0.00 0.00 38.86 4.16
5830 9386 6.797033 GCAATTGTCTACAACATCTACAACAC 59.203 38.462 7.40 0.00 38.86 3.32
5831 9387 6.484977 TGCAATTGTCTACAACATCTACAACA 59.515 34.615 7.40 0.00 38.86 3.33
5832 9388 6.898041 TGCAATTGTCTACAACATCTACAAC 58.102 36.000 7.40 0.00 38.86 3.32
5833 9389 7.503521 TTGCAATTGTCTACAACATCTACAA 57.496 32.000 7.40 0.00 38.86 2.41
5834 9390 7.503521 TTTGCAATTGTCTACAACATCTACA 57.496 32.000 7.40 0.00 38.86 2.74
5835 9391 8.853345 CATTTTGCAATTGTCTACAACATCTAC 58.147 33.333 7.40 0.00 38.86 2.59
5836 9392 8.791675 TCATTTTGCAATTGTCTACAACATCTA 58.208 29.630 7.40 0.00 38.86 1.98
5837 9393 7.660112 TCATTTTGCAATTGTCTACAACATCT 58.340 30.769 7.40 0.00 38.86 2.90
5838 9394 7.872163 TCATTTTGCAATTGTCTACAACATC 57.128 32.000 7.40 0.00 38.86 3.06
5839 9395 8.714179 CAATCATTTTGCAATTGTCTACAACAT 58.286 29.630 7.40 0.00 38.86 2.71
5840 9396 7.924947 TCAATCATTTTGCAATTGTCTACAACA 59.075 29.630 7.40 0.00 38.86 3.33
5841 9397 8.296799 TCAATCATTTTGCAATTGTCTACAAC 57.703 30.769 7.40 0.00 38.86 3.32


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

AutoCloner maintained by Alex Coulton.