Multiple sequence alignment - TraesCS2D01G398500

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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 TraesCS2D01G398500 chr2D 100.000 3454 0 0 1 3454 511529850 511526397 0.000000e+00 6379
1 TraesCS2D01G398500 chr2B 93.241 3255 126 34 228 3454 600710054 600706866 0.000000e+00 4706
2 TraesCS2D01G398500 chr2B 98.936 94 0 1 40 132 85695570 85695663 2.130000e-37 167
3 TraesCS2D01G398500 chr2A 89.399 3292 199 75 228 3453 654876605 654873398 0.000000e+00 4008
4 TraesCS2D01G398500 chr2A 97.674 86 2 0 145 230 754446814 754446729 7.720000e-32 148
5 TraesCS2D01G398500 chr1A 86.962 1534 106 51 1477 2955 12181845 12183339 0.000000e+00 1639
6 TraesCS2D01G398500 chr4A 91.276 917 49 18 1477 2381 453299790 453300687 0.000000e+00 1221
7 TraesCS2D01G398500 chr4A 82.026 612 50 28 2378 2955 453307117 453307702 1.880000e-127 466
8 TraesCS2D01G398500 chr5A 96.970 99 2 1 29 126 27637039 27637137 7.670000e-37 165
9 TraesCS2D01G398500 chr5A 96.629 89 3 0 144 232 4131420 4131508 7.720000e-32 148
10 TraesCS2D01G398500 chrUn 95.238 105 1 4 30 132 311997117 311997015 2.760000e-36 163
11 TraesCS2D01G398500 chrUn 94.444 108 2 4 27 132 379298435 379298540 2.760000e-36 163
12 TraesCS2D01G398500 chr7A 96.939 98 2 1 30 126 608875207 608875110 2.760000e-36 163
13 TraesCS2D01G398500 chr7A 92.857 98 7 0 144 241 134734033 134734130 3.590000e-30 143
14 TraesCS2D01G398500 chr1B 95.146 103 3 2 32 132 16522521 16522419 9.920000e-36 161
15 TraesCS2D01G398500 chr1B 95.050 101 4 1 35 134 618002457 618002557 1.280000e-34 158
16 TraesCS2D01G398500 chr1B 94.681 94 5 0 137 230 22433860 22433767 2.780000e-31 147
17 TraesCS2D01G398500 chr6B 94.286 105 2 4 27 130 423189609 423189508 1.280000e-34 158
18 TraesCS2D01G398500 chr3D 89.147 129 10 3 38 165 355714603 355714728 1.280000e-34 158
19 TraesCS2D01G398500 chr3D 98.837 86 1 0 145 230 498280689 498280604 1.660000e-33 154
20 TraesCS2D01G398500 chr3D 95.652 92 3 1 145 236 410422632 410422722 2.780000e-31 147
21 TraesCS2D01G398500 chr3B 90.083 121 8 4 145 264 512513614 512513731 1.660000e-33 154
22 TraesCS2D01G398500 chr7D 96.591 88 3 0 144 231 234804179 234804092 2.780000e-31 147
23 TraesCS2D01G398500 chr4B 93.814 97 4 2 136 231 592079798 592079893 9.990000e-31 145
24 TraesCS2D01G398500 chr4B 85.600 125 18 0 2036 2160 646974747 646974623 7.780000e-27 132
25 TraesCS2D01G398500 chr5D 82.400 125 15 6 1225 1344 412602064 412601942 6.100000e-18 102


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 TraesCS2D01G398500 chr2D 511526397 511529850 3453 True 6379 6379 100.000 1 3454 1 chr2D.!!$R1 3453
1 TraesCS2D01G398500 chr2B 600706866 600710054 3188 True 4706 4706 93.241 228 3454 1 chr2B.!!$R1 3226
2 TraesCS2D01G398500 chr2A 654873398 654876605 3207 True 4008 4008 89.399 228 3453 1 chr2A.!!$R1 3225
3 TraesCS2D01G398500 chr1A 12181845 12183339 1494 False 1639 1639 86.962 1477 2955 1 chr1A.!!$F1 1478
4 TraesCS2D01G398500 chr4A 453299790 453300687 897 False 1221 1221 91.276 1477 2381 1 chr4A.!!$F1 904
5 TraesCS2D01G398500 chr4A 453307117 453307702 585 False 466 466 82.026 2378 2955 1 chr4A.!!$F2 577

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
735 751 0.185175 AAACTTCCCGCCAACTCCTT 59.815 50.0 0.0 0.0 0.0 3.36 F
1770 1805 0.106619 TCTACCTCTTCTCGGGGCTC 60.107 60.0 0.0 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1898 0.247460 TCCAGTTGGTGATGAGCTCG 59.753 55.0 9.64 0.0 36.34 5.03 R
2717 2794 0.938168 GACGTTCGTTCTTCGCCTGT 60.938 55.0 0.00 0.0 39.67 4.00 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
32 33 4.606457 GTCATAAATTGACGCTGCTTCT 57.394 40.909 7.67 0.00 45.00 2.85
33 34 5.718649 GTCATAAATTGACGCTGCTTCTA 57.281 39.130 7.67 0.07 45.00 2.10
34 35 6.106877 GTCATAAATTGACGCTGCTTCTAA 57.893 37.500 7.67 1.37 45.00 2.10
35 36 6.542852 GTCATAAATTGACGCTGCTTCTAAA 58.457 36.000 7.67 0.00 45.00 1.85
36 37 6.684555 GTCATAAATTGACGCTGCTTCTAAAG 59.315 38.462 7.67 0.00 45.00 1.85
37 38 6.371548 TCATAAATTGACGCTGCTTCTAAAGT 59.628 34.615 7.67 0.00 0.00 2.66
38 39 7.547722 TCATAAATTGACGCTGCTTCTAAAGTA 59.452 33.333 7.67 0.00 0.00 2.24
39 40 5.786401 AATTGACGCTGCTTCTAAAGTAG 57.214 39.130 7.67 1.01 43.18 2.57
40 41 3.936372 TGACGCTGCTTCTAAAGTAGT 57.064 42.857 7.67 0.00 42.41 2.73
41 42 5.381174 TTGACGCTGCTTCTAAAGTAGTA 57.619 39.130 7.67 0.00 42.41 1.82
42 43 4.730657 TGACGCTGCTTCTAAAGTAGTAC 58.269 43.478 7.67 0.00 42.41 2.73
43 44 4.458295 TGACGCTGCTTCTAAAGTAGTACT 59.542 41.667 7.67 0.00 42.41 2.73
44 45 4.984205 ACGCTGCTTCTAAAGTAGTACTC 58.016 43.478 2.58 0.00 42.41 2.59
45 46 4.142425 ACGCTGCTTCTAAAGTAGTACTCC 60.142 45.833 2.58 0.00 42.41 3.85
46 47 4.684877 GCTGCTTCTAAAGTAGTACTCCC 58.315 47.826 2.58 0.00 42.41 4.30
47 48 4.403113 GCTGCTTCTAAAGTAGTACTCCCT 59.597 45.833 2.58 0.00 42.41 4.20
48 49 5.450826 GCTGCTTCTAAAGTAGTACTCCCTC 60.451 48.000 2.58 0.00 42.41 4.30
49 50 4.954826 TGCTTCTAAAGTAGTACTCCCTCC 59.045 45.833 2.58 0.00 0.00 4.30
50 51 4.036616 GCTTCTAAAGTAGTACTCCCTCCG 59.963 50.000 2.58 0.00 0.00 4.63
51 52 4.851639 TCTAAAGTAGTACTCCCTCCGT 57.148 45.455 2.58 0.00 0.00 4.69
52 53 5.184892 TCTAAAGTAGTACTCCCTCCGTT 57.815 43.478 2.58 0.00 0.00 4.44
53 54 5.189180 TCTAAAGTAGTACTCCCTCCGTTC 58.811 45.833 2.58 0.00 0.00 3.95
54 55 2.433662 AGTAGTACTCCCTCCGTTCC 57.566 55.000 0.00 0.00 0.00 3.62
55 56 1.637553 AGTAGTACTCCCTCCGTTCCA 59.362 52.381 0.00 0.00 0.00 3.53
56 57 2.042162 AGTAGTACTCCCTCCGTTCCAA 59.958 50.000 0.00 0.00 0.00 3.53
57 58 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
58 59 2.547990 AGTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
59 60 2.910977 AGTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
60 61 4.098894 AGTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
61 62 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
62 63 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
63 64 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
64 65 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
65 66 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
66 67 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
67 68 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
68 69 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
69 70 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
70 71 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
71 72 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
72 73 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
73 74 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
74 75 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
75 76 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
76 77 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
77 78 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
78 79 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
79 80 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
80 81 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
81 82 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
82 83 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
83 84 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
84 85 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
85 86 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
86 87 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
87 88 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
88 89 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
101 102 7.425915 TTCAAATTTGAACTAAAACACGACG 57.574 32.000 26.01 0.00 41.88 5.12
102 103 6.773080 TCAAATTTGAACTAAAACACGACGA 58.227 32.000 18.45 0.00 33.55 4.20
103 104 6.902948 TCAAATTTGAACTAAAACACGACGAG 59.097 34.615 18.45 0.00 33.55 4.18
104 105 5.978934 ATTTGAACTAAAACACGACGAGT 57.021 34.783 0.00 0.00 0.00 4.18
105 106 7.467557 AATTTGAACTAAAACACGACGAGTA 57.532 32.000 0.00 0.00 0.00 2.59
106 107 6.884096 TTTGAACTAAAACACGACGAGTAA 57.116 33.333 0.00 0.00 0.00 2.24
107 108 7.467557 TTTGAACTAAAACACGACGAGTAAT 57.532 32.000 0.00 0.00 0.00 1.89
108 109 7.467557 TTGAACTAAAACACGACGAGTAATT 57.532 32.000 0.00 1.79 0.00 1.40
109 110 7.467557 TGAACTAAAACACGACGAGTAATTT 57.532 32.000 0.00 0.99 0.00 1.82
110 111 7.339207 TGAACTAAAACACGACGAGTAATTTG 58.661 34.615 0.00 3.17 0.00 2.32
111 112 6.219302 ACTAAAACACGACGAGTAATTTGG 57.781 37.500 0.00 3.27 0.00 3.28
112 113 5.984926 ACTAAAACACGACGAGTAATTTGGA 59.015 36.000 0.00 0.00 0.00 3.53
113 114 5.738118 AAAACACGACGAGTAATTTGGAA 57.262 34.783 0.00 0.00 0.00 3.53
114 115 4.720530 AACACGACGAGTAATTTGGAAC 57.279 40.909 0.00 0.00 0.00 3.62
115 116 2.727798 ACACGACGAGTAATTTGGAACG 59.272 45.455 0.00 0.00 0.00 3.95
116 117 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
117 118 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
118 119 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
119 120 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
120 121 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
121 122 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
122 123 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
123 124 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
124 125 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
125 126 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
126 127 0.611714 TTTGGAACGGAGGGAGTAGC 59.388 55.000 0.00 0.00 0.00 3.58
127 128 0.252103 TTGGAACGGAGGGAGTAGCT 60.252 55.000 0.00 0.00 0.00 3.32
128 129 0.252103 TGGAACGGAGGGAGTAGCTT 60.252 55.000 0.00 0.00 0.00 3.74
129 130 0.903236 GGAACGGAGGGAGTAGCTTT 59.097 55.000 0.00 0.00 0.00 3.51
130 131 1.134759 GGAACGGAGGGAGTAGCTTTC 60.135 57.143 0.00 0.00 0.00 2.62
131 132 1.549170 GAACGGAGGGAGTAGCTTTCA 59.451 52.381 0.00 0.00 0.00 2.69
132 133 1.640917 ACGGAGGGAGTAGCTTTCAA 58.359 50.000 0.00 0.00 0.00 2.69
133 134 1.550976 ACGGAGGGAGTAGCTTTCAAG 59.449 52.381 0.00 0.00 0.00 3.02
153 154 2.165282 CGTAACGACGTACTTCCTCC 57.835 55.000 0.00 0.00 44.31 4.30
154 155 1.527793 CGTAACGACGTACTTCCTCCG 60.528 57.143 0.00 0.00 44.31 4.63
155 156 1.464997 GTAACGACGTACTTCCTCCGT 59.535 52.381 0.00 0.00 37.56 4.69
156 157 0.954452 AACGACGTACTTCCTCCGTT 59.046 50.000 0.00 2.08 34.51 4.44
157 158 0.519077 ACGACGTACTTCCTCCGTTC 59.481 55.000 0.00 0.00 34.51 3.95
158 159 0.801251 CGACGTACTTCCTCCGTTCT 59.199 55.000 0.00 0.00 34.51 3.01
159 160 2.002586 CGACGTACTTCCTCCGTTCTA 58.997 52.381 0.00 0.00 34.51 2.10
160 161 2.416547 CGACGTACTTCCTCCGTTCTAA 59.583 50.000 0.00 0.00 34.51 2.10
161 162 3.120199 CGACGTACTTCCTCCGTTCTAAA 60.120 47.826 0.00 0.00 34.51 1.85
162 163 4.613622 CGACGTACTTCCTCCGTTCTAAAA 60.614 45.833 0.00 0.00 34.51 1.52
163 164 5.397142 ACGTACTTCCTCCGTTCTAAAAT 57.603 39.130 0.00 0.00 0.00 1.82
164 165 6.515272 ACGTACTTCCTCCGTTCTAAAATA 57.485 37.500 0.00 0.00 0.00 1.40
165 166 6.558909 ACGTACTTCCTCCGTTCTAAAATAG 58.441 40.000 0.00 0.00 0.00 1.73
166 167 6.375455 ACGTACTTCCTCCGTTCTAAAATAGA 59.625 38.462 0.00 0.00 0.00 1.98
167 168 7.067981 ACGTACTTCCTCCGTTCTAAAATAGAT 59.932 37.037 0.00 0.00 34.22 1.98
168 169 7.378995 CGTACTTCCTCCGTTCTAAAATAGATG 59.621 40.741 0.00 0.00 34.22 2.90
169 170 7.419711 ACTTCCTCCGTTCTAAAATAGATGA 57.580 36.000 0.00 0.00 34.22 2.92
170 171 7.266400 ACTTCCTCCGTTCTAAAATAGATGAC 58.734 38.462 0.00 0.00 34.22 3.06
171 172 7.124448 ACTTCCTCCGTTCTAAAATAGATGACT 59.876 37.037 0.00 0.00 34.22 3.41
172 173 7.040473 TCCTCCGTTCTAAAATAGATGACTC 57.960 40.000 0.00 0.00 34.22 3.36
173 174 6.605995 TCCTCCGTTCTAAAATAGATGACTCA 59.394 38.462 0.00 0.00 34.22 3.41
174 175 7.123697 TCCTCCGTTCTAAAATAGATGACTCAA 59.876 37.037 0.00 0.00 34.22 3.02
175 176 7.222999 CCTCCGTTCTAAAATAGATGACTCAAC 59.777 40.741 0.00 0.00 34.22 3.18
176 177 7.837863 TCCGTTCTAAAATAGATGACTCAACT 58.162 34.615 0.00 0.00 34.22 3.16
177 178 8.311836 TCCGTTCTAAAATAGATGACTCAACTT 58.688 33.333 0.00 0.00 34.22 2.66
178 179 8.936864 CCGTTCTAAAATAGATGACTCAACTTT 58.063 33.333 0.00 0.00 34.22 2.66
179 180 9.746711 CGTTCTAAAATAGATGACTCAACTTTG 57.253 33.333 0.00 0.00 34.22 2.77
206 207 8.571461 ACTAAAGTTAGTACAAAGTTGAGTCG 57.429 34.615 1.81 0.00 41.92 4.18
207 208 8.193438 ACTAAAGTTAGTACAAAGTTGAGTCGT 58.807 33.333 1.81 0.00 41.92 4.34
208 209 7.460751 AAAGTTAGTACAAAGTTGAGTCGTC 57.539 36.000 0.00 0.00 0.00 4.20
209 210 6.388435 AGTTAGTACAAAGTTGAGTCGTCT 57.612 37.500 0.00 0.00 0.00 4.18
210 211 7.502120 AGTTAGTACAAAGTTGAGTCGTCTA 57.498 36.000 0.00 0.00 0.00 2.59
211 212 8.108551 AGTTAGTACAAAGTTGAGTCGTCTAT 57.891 34.615 0.00 0.00 0.00 1.98
212 213 8.574737 AGTTAGTACAAAGTTGAGTCGTCTATT 58.425 33.333 0.00 0.00 0.00 1.73
213 214 9.189723 GTTAGTACAAAGTTGAGTCGTCTATTT 57.810 33.333 0.00 0.00 0.00 1.40
214 215 9.754382 TTAGTACAAAGTTGAGTCGTCTATTTT 57.246 29.630 0.00 0.00 0.00 1.82
215 216 8.073355 AGTACAAAGTTGAGTCGTCTATTTTG 57.927 34.615 0.00 4.77 39.42 2.44
216 217 6.300354 ACAAAGTTGAGTCGTCTATTTTGG 57.700 37.500 0.00 0.00 38.53 3.28
217 218 6.053005 ACAAAGTTGAGTCGTCTATTTTGGA 58.947 36.000 0.00 0.00 38.53 3.53
218 219 6.540914 ACAAAGTTGAGTCGTCTATTTTGGAA 59.459 34.615 0.00 0.00 38.53 3.53
219 220 6.541111 AAGTTGAGTCGTCTATTTTGGAAC 57.459 37.500 0.00 0.00 0.00 3.62
220 221 4.684703 AGTTGAGTCGTCTATTTTGGAACG 59.315 41.667 0.00 0.00 0.00 3.95
221 222 3.581755 TGAGTCGTCTATTTTGGAACGG 58.418 45.455 0.00 0.00 0.00 4.44
222 223 3.256383 TGAGTCGTCTATTTTGGAACGGA 59.744 43.478 0.00 0.00 0.00 4.69
223 224 3.846360 AGTCGTCTATTTTGGAACGGAG 58.154 45.455 0.00 0.00 0.00 4.63
224 225 2.928116 GTCGTCTATTTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
225 226 2.093869 TCGTCTATTTTGGAACGGAGGG 60.094 50.000 0.00 0.00 0.00 4.30
226 227 2.093869 CGTCTATTTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
287 288 2.318908 AGCATGGCCAGAAACTTTTCA 58.681 42.857 13.05 0.00 39.61 2.69
288 289 2.036346 AGCATGGCCAGAAACTTTTCAC 59.964 45.455 13.05 0.00 39.61 3.18
326 327 0.380378 TTGAGACCAACAAGCGCAAC 59.620 50.000 11.47 0.00 0.00 4.17
330 331 1.408702 AGACCAACAAGCGCAACAAAT 59.591 42.857 11.47 0.00 0.00 2.32
337 339 5.164100 CCAACAAGCGCAACAAATTGTATAC 60.164 40.000 11.47 0.00 38.17 1.47
386 390 3.190327 TGAAACATCCTGTGCCAAATACG 59.810 43.478 0.00 0.00 0.00 3.06
444 449 7.949434 ACTCCTACAAAAATACTATCCTACCG 58.051 38.462 0.00 0.00 0.00 4.02
455 460 1.722034 ATCCTACCGTGCATCTGGAT 58.278 50.000 9.30 6.71 0.00 3.41
456 461 2.375014 TCCTACCGTGCATCTGGATA 57.625 50.000 9.30 0.00 0.00 2.59
457 462 2.673258 TCCTACCGTGCATCTGGATAA 58.327 47.619 9.30 0.00 0.00 1.75
458 463 3.239449 TCCTACCGTGCATCTGGATAAT 58.761 45.455 9.30 0.00 0.00 1.28
459 464 4.412843 TCCTACCGTGCATCTGGATAATA 58.587 43.478 9.30 0.00 0.00 0.98
460 465 4.219944 TCCTACCGTGCATCTGGATAATAC 59.780 45.833 9.30 0.00 0.00 1.89
461 466 4.220821 CCTACCGTGCATCTGGATAATACT 59.779 45.833 9.30 0.00 0.00 2.12
462 467 4.258702 ACCGTGCATCTGGATAATACTC 57.741 45.455 9.30 0.00 0.00 2.59
526 533 5.300792 TCCAGTTGGTTGGTTGATTCTAAAC 59.699 40.000 0.00 0.00 39.35 2.01
535 542 6.494893 TGGTTGATTCTAAACAAAGGATCG 57.505 37.500 0.00 0.00 34.62 3.69
665 677 2.289195 ACGGGTCAACTTCTAATTGCGA 60.289 45.455 0.00 0.00 0.00 5.10
735 751 0.185175 AAACTTCCCGCCAACTCCTT 59.815 50.000 0.00 0.00 0.00 3.36
738 754 2.474112 ACTTCCCGCCAACTCCTTATA 58.526 47.619 0.00 0.00 0.00 0.98
789 805 1.412343 GGCGGCCAATATTTGTCCATT 59.588 47.619 15.62 0.00 0.00 3.16
792 808 3.938334 GCGGCCAATATTTGTCCATTTTT 59.062 39.130 2.24 0.00 0.00 1.94
862 878 1.404843 GGGTTAAAGCCACCACAACA 58.595 50.000 0.00 0.00 35.80 3.33
871 887 1.654220 CACCACAACAAAGGCTCCG 59.346 57.895 0.00 0.00 0.00 4.63
905 921 1.370587 CTCCAGTCGTCGTCTCCTCC 61.371 65.000 0.00 0.00 0.00 4.30
932 948 2.384382 CAACCAGCAAACGATTGTGTC 58.616 47.619 7.29 0.00 38.85 3.67
948 964 4.680237 TCTGCACCGAACAGGCCG 62.680 66.667 0.00 0.00 46.52 6.13
1615 1648 0.804544 TTCGGATTCTGTAAGCGCCG 60.805 55.000 2.29 0.00 40.98 6.46
1681 1716 3.240203 GTGCGCACGCTGTTTCTA 58.760 55.556 26.77 0.00 42.51 2.10
1692 1727 5.005299 GCACGCTGTTTCTATTTGTTTTGTT 59.995 36.000 0.00 0.00 0.00 2.83
1770 1805 0.106619 TCTACCTCTTCTCGGGGCTC 60.107 60.000 0.00 0.00 0.00 4.70
1863 1898 4.864334 CTCGGGGCCATGCTGTCC 62.864 72.222 4.39 0.00 0.00 4.02
1935 1970 2.215196 CCCTCGTCTCTGCTACTACTC 58.785 57.143 0.00 0.00 0.00 2.59
1943 1979 5.527951 CGTCTCTGCTACTACTCCTATTTGA 59.472 44.000 0.00 0.00 0.00 2.69
1947 1983 8.001875 TCTCTGCTACTACTCCTATTTGATTCT 58.998 37.037 0.00 0.00 0.00 2.40
1949 1985 6.516718 TGCTACTACTCCTATTTGATTCTGC 58.483 40.000 0.00 0.00 0.00 4.26
1966 2002 1.462283 CTGCTCATGTCGAACACCTTG 59.538 52.381 0.00 0.00 0.00 3.61
1967 2003 1.069978 TGCTCATGTCGAACACCTTGA 59.930 47.619 0.00 0.00 0.00 3.02
1968 2004 1.461127 GCTCATGTCGAACACCTTGAC 59.539 52.381 0.00 0.00 0.00 3.18
1969 2005 1.721389 CTCATGTCGAACACCTTGACG 59.279 52.381 0.00 0.00 35.40 4.35
1970 2006 1.067974 TCATGTCGAACACCTTGACGT 59.932 47.619 0.00 0.00 35.40 4.34
1971 2007 1.864711 CATGTCGAACACCTTGACGTT 59.135 47.619 0.00 0.00 35.40 3.99
1972 2008 1.282817 TGTCGAACACCTTGACGTTG 58.717 50.000 0.00 0.00 35.40 4.10
1973 2009 0.042448 GTCGAACACCTTGACGTTGC 60.042 55.000 0.00 0.00 0.00 4.17
1974 2010 0.179094 TCGAACACCTTGACGTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
2026 2067 1.754234 GGCCATGGCGAACCTGATT 60.754 57.895 29.90 0.00 43.06 2.57
2280 2321 8.636843 GTTACAAGATACAGTACAAACTCTTCG 58.363 37.037 0.00 0.00 31.97 3.79
2500 2562 2.821366 CGTGCTGCCCATCCAGAC 60.821 66.667 0.00 0.00 34.77 3.51
2512 2574 2.159282 CCATCCAGACAATTGCTTCAGC 60.159 50.000 5.05 0.00 42.50 4.26
2518 2580 0.319405 ACAATTGCTTCAGCTTGGCC 59.681 50.000 5.05 0.00 42.66 5.36
2640 2717 6.727824 TTAAAGCTCTGTAAATCACTCTGC 57.272 37.500 0.00 0.00 0.00 4.26
2651 2728 2.849880 TCACTCTGCTTTGTTTGTGC 57.150 45.000 0.00 0.00 0.00 4.57
2694 2771 1.596464 GGTTCTACATAGTCGGTCGCG 60.596 57.143 0.00 0.00 0.00 5.87
2717 2794 6.635239 GCGTTTGCAATGTTAGAGACTAAAAA 59.365 34.615 0.00 0.00 42.15 1.94
2789 2873 1.411977 AGTATGCACTAGCCTGCTCTG 59.588 52.381 6.85 0.00 41.13 3.35
2847 2943 3.389329 ACAGTGTCAGGACTTGAGTCATT 59.611 43.478 12.76 0.00 46.47 2.57
2852 2948 5.529060 GTGTCAGGACTTGAGTCATTTTTCT 59.471 40.000 12.76 0.00 46.47 2.52
2942 3044 6.209391 CCATACACTTTTCACAAGGGAGAATT 59.791 38.462 0.00 0.00 0.00 2.17
3022 3126 5.462398 ACAGAACACGTAGAAAGAATCACAC 59.538 40.000 0.00 0.00 0.00 3.82
3097 3207 6.699575 AATAAAGCTATTTCCGCATCAACT 57.300 33.333 0.00 0.00 0.00 3.16
3159 3269 6.887002 AGACTCAAAATCAGGGGAATCTAAAC 59.113 38.462 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.371548 ACTTTAGAAGCAGCGTCAATTTATGA 59.628 34.615 11.18 0.00 35.05 2.15
13 14 6.546395 ACTTTAGAAGCAGCGTCAATTTATG 58.454 36.000 11.18 0.00 0.00 1.90
14 15 6.743575 ACTTTAGAAGCAGCGTCAATTTAT 57.256 33.333 11.18 0.00 0.00 1.40
15 16 6.872020 ACTACTTTAGAAGCAGCGTCAATTTA 59.128 34.615 11.18 0.00 0.00 1.40
16 17 5.701290 ACTACTTTAGAAGCAGCGTCAATTT 59.299 36.000 11.18 0.00 0.00 1.82
17 18 5.238583 ACTACTTTAGAAGCAGCGTCAATT 58.761 37.500 11.18 0.00 0.00 2.32
18 19 4.822026 ACTACTTTAGAAGCAGCGTCAAT 58.178 39.130 11.18 0.00 0.00 2.57
19 20 4.252971 ACTACTTTAGAAGCAGCGTCAA 57.747 40.909 11.18 0.66 0.00 3.18
20 21 3.936372 ACTACTTTAGAAGCAGCGTCA 57.064 42.857 11.18 0.00 0.00 4.35
21 22 4.984205 AGTACTACTTTAGAAGCAGCGTC 58.016 43.478 0.00 0.00 0.00 5.19
22 23 4.142425 GGAGTACTACTTTAGAAGCAGCGT 60.142 45.833 0.00 0.00 0.00 5.07
23 24 4.352887 GGAGTACTACTTTAGAAGCAGCG 58.647 47.826 0.00 0.00 0.00 5.18
24 25 4.403113 AGGGAGTACTACTTTAGAAGCAGC 59.597 45.833 4.77 0.00 0.00 5.25
25 26 5.068067 GGAGGGAGTACTACTTTAGAAGCAG 59.932 48.000 4.77 0.00 0.00 4.24
26 27 4.954826 GGAGGGAGTACTACTTTAGAAGCA 59.045 45.833 4.77 0.00 0.00 3.91
27 28 4.036616 CGGAGGGAGTACTACTTTAGAAGC 59.963 50.000 4.77 0.00 0.00 3.86
28 29 5.192176 ACGGAGGGAGTACTACTTTAGAAG 58.808 45.833 4.77 0.00 0.00 2.85
29 30 5.184892 ACGGAGGGAGTACTACTTTAGAA 57.815 43.478 4.77 0.00 0.00 2.10
30 31 4.851639 ACGGAGGGAGTACTACTTTAGA 57.148 45.455 4.77 0.00 0.00 2.10
31 32 4.337836 GGAACGGAGGGAGTACTACTTTAG 59.662 50.000 4.77 0.00 0.00 1.85
32 33 4.263905 TGGAACGGAGGGAGTACTACTTTA 60.264 45.833 4.77 0.00 0.00 1.85
33 34 3.095332 GGAACGGAGGGAGTACTACTTT 58.905 50.000 4.77 0.00 0.00 2.66
34 35 2.042162 TGGAACGGAGGGAGTACTACTT 59.958 50.000 4.77 0.00 0.00 2.24
35 36 1.637553 TGGAACGGAGGGAGTACTACT 59.362 52.381 4.77 1.85 0.00 2.57
36 37 2.134789 TGGAACGGAGGGAGTACTAC 57.865 55.000 0.00 0.00 0.00 2.73
37 38 2.905415 TTGGAACGGAGGGAGTACTA 57.095 50.000 0.00 0.00 0.00 1.82
38 39 2.019807 TTTGGAACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
39 40 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
40 41 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
41 42 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
42 43 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
43 44 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
44 45 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
45 46 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
46 47 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
47 48 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
48 49 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
49 50 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
50 51 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
51 52 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
52 53 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
53 54 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
54 55 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
55 56 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
56 57 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
57 58 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
58 59 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
59 60 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
60 61 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
61 62 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
62 63 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
63 64 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
64 65 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
77 78 7.242079 TCGTCGTGTTTTAGTTCAAATTTGAA 58.758 30.769 26.01 26.01 44.31 2.69
78 79 6.773080 TCGTCGTGTTTTAGTTCAAATTTGA 58.227 32.000 16.91 16.91 34.92 2.69
79 80 6.685403 ACTCGTCGTGTTTTAGTTCAAATTTG 59.315 34.615 12.15 12.15 0.00 2.32
80 81 6.778108 ACTCGTCGTGTTTTAGTTCAAATTT 58.222 32.000 0.00 0.00 0.00 1.82
81 82 6.354039 ACTCGTCGTGTTTTAGTTCAAATT 57.646 33.333 0.00 0.00 0.00 1.82
82 83 5.978934 ACTCGTCGTGTTTTAGTTCAAAT 57.021 34.783 0.00 0.00 0.00 2.32
83 84 6.884096 TTACTCGTCGTGTTTTAGTTCAAA 57.116 33.333 5.14 0.00 0.00 2.69
84 85 7.467557 AATTACTCGTCGTGTTTTAGTTCAA 57.532 32.000 5.14 0.00 0.00 2.69
85 86 7.339207 CAAATTACTCGTCGTGTTTTAGTTCA 58.661 34.615 5.14 0.00 0.00 3.18
86 87 6.788930 CCAAATTACTCGTCGTGTTTTAGTTC 59.211 38.462 5.14 0.00 0.00 3.01
87 88 6.479660 TCCAAATTACTCGTCGTGTTTTAGTT 59.520 34.615 5.14 0.00 0.00 2.24
88 89 5.984926 TCCAAATTACTCGTCGTGTTTTAGT 59.015 36.000 5.14 0.00 0.00 2.24
89 90 6.456447 TCCAAATTACTCGTCGTGTTTTAG 57.544 37.500 5.14 0.00 0.00 1.85
90 91 6.561902 CGTTCCAAATTACTCGTCGTGTTTTA 60.562 38.462 5.14 0.00 0.00 1.52
91 92 5.504392 GTTCCAAATTACTCGTCGTGTTTT 58.496 37.500 5.14 0.00 0.00 2.43
92 93 4.318263 CGTTCCAAATTACTCGTCGTGTTT 60.318 41.667 5.14 0.00 0.00 2.83
93 94 3.182972 CGTTCCAAATTACTCGTCGTGTT 59.817 43.478 5.14 0.00 0.00 3.32
94 95 2.727798 CGTTCCAAATTACTCGTCGTGT 59.272 45.455 5.19 5.19 0.00 4.49
95 96 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
96 97 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
97 98 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
98 99 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
99 100 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
100 101 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
101 102 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
102 103 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
103 104 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
104 105 3.118519 GCTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
105 106 2.355818 GCTACTCCCTCCGTTCCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
106 107 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
107 108 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
108 109 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
109 110 0.252103 AAGCTACTCCCTCCGTTCCA 60.252 55.000 0.00 0.00 0.00 3.53
110 111 0.903236 AAAGCTACTCCCTCCGTTCC 59.097 55.000 0.00 0.00 0.00 3.62
111 112 1.549170 TGAAAGCTACTCCCTCCGTTC 59.451 52.381 0.00 0.00 0.00 3.95
112 113 1.640917 TGAAAGCTACTCCCTCCGTT 58.359 50.000 0.00 0.00 0.00 4.44
113 114 1.550976 CTTGAAAGCTACTCCCTCCGT 59.449 52.381 0.00 0.00 0.00 4.69
114 115 2.301577 CTTGAAAGCTACTCCCTCCG 57.698 55.000 0.00 0.00 0.00 4.63
135 136 1.464997 ACGGAGGAAGTACGTCGTTAC 59.535 52.381 1.78 0.00 35.77 2.50
136 137 1.808411 ACGGAGGAAGTACGTCGTTA 58.192 50.000 1.78 0.00 35.77 3.18
137 138 0.954452 AACGGAGGAAGTACGTCGTT 59.046 50.000 1.78 0.00 40.31 3.85
138 139 0.519077 GAACGGAGGAAGTACGTCGT 59.481 55.000 2.21 2.21 40.31 4.34
139 140 0.801251 AGAACGGAGGAAGTACGTCG 59.199 55.000 0.00 0.00 40.31 5.12
140 141 4.425577 TTTAGAACGGAGGAAGTACGTC 57.574 45.455 0.00 0.00 40.31 4.34
141 142 4.853924 TTTTAGAACGGAGGAAGTACGT 57.146 40.909 0.00 0.00 43.43 3.57
142 143 6.789262 TCTATTTTAGAACGGAGGAAGTACG 58.211 40.000 0.00 0.00 0.00 3.67
143 144 8.411683 TCATCTATTTTAGAACGGAGGAAGTAC 58.588 37.037 0.00 0.00 38.50 2.73
144 145 8.411683 GTCATCTATTTTAGAACGGAGGAAGTA 58.588 37.037 0.00 0.00 38.50 2.24
145 146 7.124448 AGTCATCTATTTTAGAACGGAGGAAGT 59.876 37.037 0.00 0.00 38.50 3.01
146 147 7.493367 AGTCATCTATTTTAGAACGGAGGAAG 58.507 38.462 0.00 0.00 38.50 3.46
147 148 7.123697 TGAGTCATCTATTTTAGAACGGAGGAA 59.876 37.037 0.00 0.00 38.50 3.36
148 149 6.605995 TGAGTCATCTATTTTAGAACGGAGGA 59.394 38.462 0.00 0.00 38.50 3.71
149 150 6.806751 TGAGTCATCTATTTTAGAACGGAGG 58.193 40.000 0.00 0.00 38.50 4.30
150 151 7.976734 AGTTGAGTCATCTATTTTAGAACGGAG 59.023 37.037 1.70 0.00 38.50 4.63
151 152 7.837863 AGTTGAGTCATCTATTTTAGAACGGA 58.162 34.615 1.70 0.00 38.50 4.69
152 153 8.480643 AAGTTGAGTCATCTATTTTAGAACGG 57.519 34.615 4.14 0.00 38.50 4.44
153 154 9.746711 CAAAGTTGAGTCATCTATTTTAGAACG 57.253 33.333 4.14 0.00 38.50 3.95
180 181 9.669353 CGACTCAACTTTGTACTAACTTTAGTA 57.331 33.333 4.98 4.98 43.36 1.82
181 182 8.193438 ACGACTCAACTTTGTACTAACTTTAGT 58.807 33.333 6.85 6.85 45.39 2.24
182 183 8.571461 ACGACTCAACTTTGTACTAACTTTAG 57.429 34.615 0.00 0.00 36.82 1.85
183 184 8.408601 AGACGACTCAACTTTGTACTAACTTTA 58.591 33.333 0.00 0.00 0.00 1.85
184 185 7.263496 AGACGACTCAACTTTGTACTAACTTT 58.737 34.615 0.00 0.00 0.00 2.66
185 186 6.803642 AGACGACTCAACTTTGTACTAACTT 58.196 36.000 0.00 0.00 0.00 2.66
186 187 6.388435 AGACGACTCAACTTTGTACTAACT 57.612 37.500 0.00 0.00 0.00 2.24
187 188 8.739649 AATAGACGACTCAACTTTGTACTAAC 57.260 34.615 0.00 0.00 0.00 2.34
188 189 9.754382 AAAATAGACGACTCAACTTTGTACTAA 57.246 29.630 0.00 0.00 0.00 2.24
189 190 9.188588 CAAAATAGACGACTCAACTTTGTACTA 57.811 33.333 0.00 0.00 0.00 1.82
190 191 7.170998 CCAAAATAGACGACTCAACTTTGTACT 59.829 37.037 0.00 0.00 0.00 2.73
191 192 7.170320 TCCAAAATAGACGACTCAACTTTGTAC 59.830 37.037 0.00 0.00 0.00 2.90
192 193 7.211573 TCCAAAATAGACGACTCAACTTTGTA 58.788 34.615 0.00 0.00 0.00 2.41
193 194 6.053005 TCCAAAATAGACGACTCAACTTTGT 58.947 36.000 0.00 0.00 0.00 2.83
194 195 6.539649 TCCAAAATAGACGACTCAACTTTG 57.460 37.500 0.00 0.00 0.00 2.77
195 196 6.292703 CGTTCCAAAATAGACGACTCAACTTT 60.293 38.462 0.00 0.00 37.69 2.66
196 197 5.176958 CGTTCCAAAATAGACGACTCAACTT 59.823 40.000 0.00 0.00 37.69 2.66
197 198 4.684703 CGTTCCAAAATAGACGACTCAACT 59.315 41.667 0.00 0.00 37.69 3.16
198 199 4.143179 CCGTTCCAAAATAGACGACTCAAC 60.143 45.833 0.00 0.00 37.69 3.18
199 200 3.991773 CCGTTCCAAAATAGACGACTCAA 59.008 43.478 0.00 0.00 37.69 3.02
200 201 3.256383 TCCGTTCCAAAATAGACGACTCA 59.744 43.478 0.00 0.00 37.69 3.41
201 202 3.841643 TCCGTTCCAAAATAGACGACTC 58.158 45.455 0.00 0.00 37.69 3.36
202 203 3.368116 CCTCCGTTCCAAAATAGACGACT 60.368 47.826 0.00 0.00 37.69 4.18
203 204 2.928116 CCTCCGTTCCAAAATAGACGAC 59.072 50.000 0.00 0.00 37.69 4.34
204 205 2.093869 CCCTCCGTTCCAAAATAGACGA 60.094 50.000 0.00 0.00 37.69 4.20
205 206 2.093869 TCCCTCCGTTCCAAAATAGACG 60.094 50.000 0.00 0.00 35.44 4.18
206 207 3.055312 ACTCCCTCCGTTCCAAAATAGAC 60.055 47.826 0.00 0.00 0.00 2.59
207 208 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
208 209 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
209 210 5.221884 TGTTTACTCCCTCCGTTCCAAAATA 60.222 40.000 0.00 0.00 0.00 1.40
210 211 4.077108 GTTTACTCCCTCCGTTCCAAAAT 58.923 43.478 0.00 0.00 0.00 1.82
211 212 3.117963 TGTTTACTCCCTCCGTTCCAAAA 60.118 43.478 0.00 0.00 0.00 2.44
212 213 2.438763 TGTTTACTCCCTCCGTTCCAAA 59.561 45.455 0.00 0.00 0.00 3.28
213 214 2.048601 TGTTTACTCCCTCCGTTCCAA 58.951 47.619 0.00 0.00 0.00 3.53
214 215 1.719529 TGTTTACTCCCTCCGTTCCA 58.280 50.000 0.00 0.00 0.00 3.53
215 216 2.224354 TGTTGTTTACTCCCTCCGTTCC 60.224 50.000 0.00 0.00 0.00 3.62
216 217 3.064931 CTGTTGTTTACTCCCTCCGTTC 58.935 50.000 0.00 0.00 0.00 3.95
217 218 2.809299 GCTGTTGTTTACTCCCTCCGTT 60.809 50.000 0.00 0.00 0.00 4.44
218 219 1.270678 GCTGTTGTTTACTCCCTCCGT 60.271 52.381 0.00 0.00 0.00 4.69
219 220 1.439679 GCTGTTGTTTACTCCCTCCG 58.560 55.000 0.00 0.00 0.00 4.63
220 221 1.439679 CGCTGTTGTTTACTCCCTCC 58.560 55.000 0.00 0.00 0.00 4.30
221 222 0.796927 GCGCTGTTGTTTACTCCCTC 59.203 55.000 0.00 0.00 0.00 4.30
222 223 0.107831 TGCGCTGTTGTTTACTCCCT 59.892 50.000 9.73 0.00 0.00 4.20
223 224 0.948678 TTGCGCTGTTGTTTACTCCC 59.051 50.000 9.73 0.00 0.00 4.30
224 225 2.414161 GGATTGCGCTGTTGTTTACTCC 60.414 50.000 9.73 0.00 0.00 3.85
225 226 2.484264 AGGATTGCGCTGTTGTTTACTC 59.516 45.455 9.73 0.00 0.00 2.59
226 227 2.504367 AGGATTGCGCTGTTGTTTACT 58.496 42.857 9.73 0.00 0.00 2.24
287 288 9.696917 GTCTCAACTTATTTTGGAAATCATTGT 57.303 29.630 0.00 0.00 0.00 2.71
288 289 9.143631 GGTCTCAACTTATTTTGGAAATCATTG 57.856 33.333 0.00 0.00 0.00 2.82
307 308 0.380378 GTTGCGCTTGTTGGTCTCAA 59.620 50.000 9.73 0.00 0.00 3.02
386 390 4.965119 ATAAGGAAATGGACTTTCGTGC 57.035 40.909 0.00 0.00 43.57 5.34
444 449 7.880195 ACAATTAGGAGTATTATCCAGATGCAC 59.120 37.037 0.00 0.00 42.26 4.57
535 542 1.378531 TTTACACGCATGGATCAGCC 58.621 50.000 0.00 0.00 37.10 4.85
610 622 5.240844 TGATGCTACGCTCTAGCTGTATTTA 59.759 40.000 0.00 0.00 40.95 1.40
665 677 5.688814 TCAAGGAGTTGAGATGATGATGT 57.311 39.130 0.00 0.00 37.79 3.06
735 751 3.112263 CTGGTTGTTGGAGGGGAGTATA 58.888 50.000 0.00 0.00 0.00 1.47
738 754 0.401395 TCTGGTTGTTGGAGGGGAGT 60.401 55.000 0.00 0.00 0.00 3.85
862 878 1.029681 GGTGTTTGTTCGGAGCCTTT 58.970 50.000 0.00 0.00 0.00 3.11
871 887 2.222027 CTGGAGACCTGGTGTTTGTTC 58.778 52.381 2.82 0.00 0.00 3.18
905 921 1.007387 GTTTGCTGGTTGGCTTCCG 60.007 57.895 0.00 0.00 0.00 4.30
948 964 3.741476 CACCGCTTCTTGGCTGCC 61.741 66.667 12.87 12.87 0.00 4.85
986 1002 0.730834 CGACATGGCCTCGATCGATC 60.731 60.000 19.78 15.68 34.77 3.69
1586 1619 0.459237 AGAATCCGAACTGCTGCTCG 60.459 55.000 9.18 9.18 34.83 5.03
1615 1648 3.808656 GAGTCGTCGGTCGGGTCC 61.809 72.222 0.00 0.00 40.32 4.46
1679 1714 9.753669 GGTCAGAAAACAAAACAAAACAAATAG 57.246 29.630 0.00 0.00 0.00 1.73
1680 1715 8.436200 CGGTCAGAAAACAAAACAAAACAAATA 58.564 29.630 0.00 0.00 0.00 1.40
1681 1716 7.294473 CGGTCAGAAAACAAAACAAAACAAAT 58.706 30.769 0.00 0.00 0.00 2.32
1692 1727 2.097791 CGAAACCCGGTCAGAAAACAAA 59.902 45.455 0.00 0.00 33.91 2.83
1699 1734 4.367023 CGGCGAAACCCGGTCAGA 62.367 66.667 0.00 0.00 44.46 3.27
1718 1753 3.030308 CTGCACGACGCGACAAGT 61.030 61.111 15.93 3.64 46.97 3.16
1863 1898 0.247460 TCCAGTTGGTGATGAGCTCG 59.753 55.000 9.64 0.00 36.34 5.03
1935 1970 5.052481 TCGACATGAGCAGAATCAAATAGG 58.948 41.667 0.00 0.00 31.76 2.57
1943 1979 2.027745 AGGTGTTCGACATGAGCAGAAT 60.028 45.455 0.00 0.00 38.59 2.40
1947 1983 1.069978 TCAAGGTGTTCGACATGAGCA 59.930 47.619 0.00 0.00 35.21 4.26
1949 1985 1.721389 CGTCAAGGTGTTCGACATGAG 59.279 52.381 0.00 0.00 0.00 2.90
1966 2002 1.795768 TTCCATGTCAGAGCAACGTC 58.204 50.000 0.00 0.00 0.00 4.34
1967 2003 2.079158 CATTCCATGTCAGAGCAACGT 58.921 47.619 0.00 0.00 0.00 3.99
1968 2004 2.094894 GTCATTCCATGTCAGAGCAACG 59.905 50.000 0.00 0.00 0.00 4.10
1969 2005 3.076621 TGTCATTCCATGTCAGAGCAAC 58.923 45.455 0.00 0.00 0.00 4.17
1970 2006 3.076621 GTGTCATTCCATGTCAGAGCAA 58.923 45.455 0.00 0.00 0.00 3.91
1971 2007 2.616256 GGTGTCATTCCATGTCAGAGCA 60.616 50.000 0.00 0.00 0.00 4.26
1972 2008 2.012673 GGTGTCATTCCATGTCAGAGC 58.987 52.381 0.00 0.00 0.00 4.09
1973 2009 3.339253 TGGTGTCATTCCATGTCAGAG 57.661 47.619 0.00 0.00 0.00 3.35
1974 2010 4.305539 AATGGTGTCATTCCATGTCAGA 57.694 40.909 0.00 0.00 43.85 3.27
1989 2025 1.566563 GCGAGCTGCGATAATGGTG 59.433 57.895 9.32 0.00 44.57 4.17
2026 2067 0.602638 GGTTGATGGCGGCGATGATA 60.603 55.000 12.98 0.00 0.00 2.15
2280 2321 3.125316 CAGGAAGCGTGTAGAATTTGGAC 59.875 47.826 0.00 0.00 0.00 4.02
2456 2518 1.490490 TCCACAGCTGTTGTCCTCTTT 59.510 47.619 18.94 0.00 38.16 2.52
2500 2562 0.606604 AGGCCAAGCTGAAGCAATTG 59.393 50.000 5.01 0.00 45.16 2.32
2512 2574 5.572896 CAGCGAAAAAGTATAAAAGGCCAAG 59.427 40.000 5.01 0.00 0.00 3.61
2575 2652 1.927174 CTAATCAACGCCTCTTGGACG 59.073 52.381 0.00 0.00 38.30 4.79
2640 2717 3.078594 ACGCTTTAGGCACAAACAAAG 57.921 42.857 0.00 0.00 41.91 2.77
2651 2728 5.402270 CCAAAGAATGAACAAACGCTTTAGG 59.598 40.000 0.00 0.00 0.00 2.69
2694 2771 8.850454 TGTTTTTAGTCTCTAACATTGCAAAC 57.150 30.769 1.71 0.00 0.00 2.93
2717 2794 0.938168 GACGTTCGTTCTTCGCCTGT 60.938 55.000 0.00 0.00 39.67 4.00
2789 2873 2.734492 GCCATTTCATGACTCTGCAAGC 60.734 50.000 0.00 0.00 0.00 4.01
2813 2897 2.620115 CTGACACTGTTTCATGCCAACT 59.380 45.455 0.00 0.00 0.00 3.16
2852 2948 9.713713 TGCAATATAAACCATTCTATTAGCGTA 57.286 29.630 0.00 0.00 0.00 4.42
2907 3006 7.032580 TGTGAAAAGTGTATGGTTTGTTCAAG 58.967 34.615 0.00 0.00 0.00 3.02
3022 3126 5.470047 AAGAGTTAGTTACTGAGGTGTGG 57.530 43.478 0.00 0.00 37.17 4.17
3097 3207 4.907269 TGGAGGGATTAGCACTGATATCAA 59.093 41.667 6.90 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.