Multiple sequence alignment - TraesCS6D01G292900

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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 TraesCS6D01G292900 chr6D 100.000 3050 0 0 1 3050 403652437 403649388 0.000000e+00 5633.0
1 TraesCS6D01G292900 chr6B 92.088 2376 145 23 693 3050 604699264 604696914 0.000000e+00 3306.0
2 TraesCS6D01G292900 chr6B 88.315 445 40 8 164 606 604701889 604701455 9.690000e-145 523.0
3 TraesCS6D01G292900 chr6B 78.281 221 26 15 2186 2392 633551767 633551555 4.130000e-24 122.0
4 TraesCS6D01G292900 chr6A 95.850 1711 55 8 789 2494 549643422 549645121 0.000000e+00 2752.0
5 TraesCS6D01G292900 chr6A 85.612 417 57 3 2635 3050 549720855 549721269 4.670000e-118 435.0
6 TraesCS6D01G292900 chr2D 91.101 1371 101 7 799 2169 296536313 296537662 0.000000e+00 1836.0
7 TraesCS6D01G292900 chr2D 75.155 322 58 15 2167 2475 60187349 60187661 6.860000e-27 132.0
8 TraesCS6D01G292900 chr2D 79.630 162 28 5 5 164 203152793 203152635 8.940000e-21 111.0
9 TraesCS6D01G292900 chr1B 79.791 287 40 11 2199 2475 398382942 398382664 3.100000e-45 193.0
10 TraesCS6D01G292900 chr7B 85.027 187 23 1 164 350 29454908 29455089 5.190000e-43 185.0
11 TraesCS6D01G292900 chr5D 84.536 194 23 2 164 357 509241862 509241676 5.190000e-43 185.0
12 TraesCS6D01G292900 chr5D 81.707 164 25 3 5 164 417663736 417663898 6.860000e-27 132.0
13 TraesCS6D01G292900 chr3D 77.228 303 48 15 2188 2475 590698907 590698611 1.130000e-34 158.0
14 TraesCS6D01G292900 chr3D 77.528 89 18 2 21 109 29708405 29708319 5.000000e-03 52.8
15 TraesCS6D01G292900 chr1D 77.627 295 43 14 2197 2475 363853978 363853691 1.130000e-34 158.0
16 TraesCS6D01G292900 chr2A 77.000 300 51 15 2186 2475 60767382 60767673 4.070000e-34 156.0
17 TraesCS6D01G292900 chr5B 78.088 251 34 12 2232 2471 399177904 399177664 4.100000e-29 139.0
18 TraesCS6D01G292900 chr3B 76.333 300 42 18 2199 2475 778706072 778705779 1.910000e-27 134.0
19 TraesCS6D01G292900 chr2B 79.592 196 30 6 2282 2475 658489797 658489984 6.860000e-27 132.0
20 TraesCS6D01G292900 chr7A 79.394 165 32 2 2 165 51089796 51089959 6.910000e-22 115.0
21 TraesCS6D01G292900 chr7A 78.788 165 33 2 2 165 51258425 51258588 3.220000e-20 110.0
22 TraesCS6D01G292900 chr7A 77.576 165 35 2 2 165 51140653 51140816 6.960000e-17 99.0
23 TraesCS6D01G292900 chr4B 91.667 60 5 0 2305 2364 404603757 404603698 1.950000e-12 84.2
24 TraesCS6D01G292900 chr3A 88.406 69 6 2 2476 2543 424465690 424465757 7.010000e-12 82.4
25 TraesCS6D01G292900 chr3A 82.558 86 13 2 2200 2283 156074542 156074627 1.170000e-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 TraesCS6D01G292900 chr6D 403649388 403652437 3049 True 5633.0 5633 100.0000 1 3050 1 chr6D.!!$R1 3049
1 TraesCS6D01G292900 chr6B 604696914 604701889 4975 True 1914.5 3306 90.2015 164 3050 2 chr6B.!!$R2 2886
2 TraesCS6D01G292900 chr6A 549643422 549645121 1699 False 2752.0 2752 95.8500 789 2494 1 chr6A.!!$F1 1705
3 TraesCS6D01G292900 chr2D 296536313 296537662 1349 False 1836.0 1836 91.1010 799 2169 1 chr2D.!!$F2 1370

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
87 88 0.035739 ACACTCGCGGGGTATTGTTT 59.964 50.0 12.42 0.00 0.00 2.83 F
428 429 0.108089 ATGTTATGTGGGCGTGCGTA 60.108 50.0 0.00 0.00 0.00 4.42 F
454 455 0.503961 GTTGAGCGTGCATGCAAAAC 59.496 50.0 31.36 27.19 37.31 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 3517 0.912486 AGCCATTCTAAGAAGCCGGT 59.088 50.000 1.9 0.0 0.0 5.28 R
1666 3772 1.672356 CCGCCAACAGGAACTCCAG 60.672 63.158 0.0 0.0 34.6 3.86 R
2399 4508 4.232221 GTTCACCTCAACTTGCAATCATG 58.768 43.478 0.0 0.0 0.0 3.07 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
19 20 2.664402 ACATTGGGTTTGCTCAGACT 57.336 45.000 0.00 0.00 0.00 3.24
20 21 2.949447 ACATTGGGTTTGCTCAGACTT 58.051 42.857 0.00 0.00 0.00 3.01
21 22 4.098914 ACATTGGGTTTGCTCAGACTTA 57.901 40.909 0.00 0.00 0.00 2.24
22 23 4.074970 ACATTGGGTTTGCTCAGACTTAG 58.925 43.478 0.00 0.00 0.00 2.18
23 24 2.859165 TGGGTTTGCTCAGACTTAGG 57.141 50.000 0.00 0.00 0.00 2.69
24 25 1.271379 TGGGTTTGCTCAGACTTAGGC 60.271 52.381 0.00 0.00 0.00 3.93
25 26 1.454201 GGTTTGCTCAGACTTAGGCC 58.546 55.000 0.00 0.00 0.00 5.19
26 27 1.271379 GGTTTGCTCAGACTTAGGCCA 60.271 52.381 5.01 0.00 0.00 5.36
27 28 2.079925 GTTTGCTCAGACTTAGGCCAG 58.920 52.381 5.01 0.00 0.00 4.85
28 29 0.615331 TTGCTCAGACTTAGGCCAGG 59.385 55.000 5.01 0.00 0.00 4.45
29 30 1.267574 TGCTCAGACTTAGGCCAGGG 61.268 60.000 5.01 0.00 0.00 4.45
30 31 1.524482 CTCAGACTTAGGCCAGGGC 59.476 63.158 5.01 4.33 41.06 5.19
31 32 2.187946 CAGACTTAGGCCAGGGCG 59.812 66.667 5.01 0.00 43.06 6.13
32 33 2.038975 AGACTTAGGCCAGGGCGA 59.961 61.111 5.01 0.00 43.06 5.54
33 34 1.612442 AGACTTAGGCCAGGGCGAA 60.612 57.895 5.01 7.97 43.06 4.70
34 35 1.198759 AGACTTAGGCCAGGGCGAAA 61.199 55.000 5.01 6.82 43.06 3.46
35 36 0.107165 GACTTAGGCCAGGGCGAAAT 60.107 55.000 5.01 0.00 43.06 2.17
36 37 0.107165 ACTTAGGCCAGGGCGAAATC 60.107 55.000 5.01 0.00 43.06 2.17
37 38 0.819666 CTTAGGCCAGGGCGAAATCC 60.820 60.000 5.01 0.00 43.06 3.01
38 39 2.279037 TTAGGCCAGGGCGAAATCCC 62.279 60.000 5.01 0.00 46.93 3.85
44 45 2.897350 GGGCGAAATCCCTGCTCG 60.897 66.667 0.00 0.00 43.13 5.03
45 46 2.897350 GGCGAAATCCCTGCTCGG 60.897 66.667 0.00 0.00 33.23 4.63
46 47 3.577313 GCGAAATCCCTGCTCGGC 61.577 66.667 0.00 0.00 33.23 5.54
47 48 2.187946 CGAAATCCCTGCTCGGCT 59.812 61.111 0.00 0.00 0.00 5.52
48 49 1.450312 CGAAATCCCTGCTCGGCTT 60.450 57.895 0.00 0.00 0.00 4.35
49 50 0.179084 CGAAATCCCTGCTCGGCTTA 60.179 55.000 0.00 0.00 0.00 3.09
50 51 1.300481 GAAATCCCTGCTCGGCTTAC 58.700 55.000 0.00 0.00 0.00 2.34
51 52 0.107165 AAATCCCTGCTCGGCTTACC 60.107 55.000 0.00 0.00 0.00 2.85
62 63 2.906047 GGCTTACCGATGCTAGCAG 58.094 57.895 23.89 12.17 35.36 4.24
63 64 1.224722 GGCTTACCGATGCTAGCAGC 61.225 60.000 22.92 22.92 42.82 5.25
70 71 3.352447 GATGCTAGCAGCGAAGACA 57.648 52.632 23.89 0.00 46.26 3.41
71 72 0.926846 GATGCTAGCAGCGAAGACAC 59.073 55.000 23.89 2.35 46.26 3.67
72 73 0.534412 ATGCTAGCAGCGAAGACACT 59.466 50.000 23.89 0.00 46.26 3.55
73 74 0.109086 TGCTAGCAGCGAAGACACTC 60.109 55.000 14.93 0.00 46.26 3.51
74 75 1.136872 GCTAGCAGCGAAGACACTCG 61.137 60.000 10.63 0.00 41.84 4.18
80 81 4.052229 CGAAGACACTCGCGGGGT 62.052 66.667 12.42 6.55 31.04 4.95
81 82 2.693762 CGAAGACACTCGCGGGGTA 61.694 63.158 12.42 0.00 31.04 3.69
82 83 1.814527 GAAGACACTCGCGGGGTAT 59.185 57.895 12.42 0.15 0.00 2.73
83 84 0.175073 GAAGACACTCGCGGGGTATT 59.825 55.000 12.42 10.42 35.25 1.89
84 85 0.108329 AAGACACTCGCGGGGTATTG 60.108 55.000 12.42 0.76 30.89 1.90
85 86 1.217244 GACACTCGCGGGGTATTGT 59.783 57.895 12.42 5.01 0.00 2.71
86 87 0.390735 GACACTCGCGGGGTATTGTT 60.391 55.000 12.42 0.00 0.00 2.83
87 88 0.035739 ACACTCGCGGGGTATTGTTT 59.964 50.000 12.42 0.00 0.00 2.83
88 89 0.725117 CACTCGCGGGGTATTGTTTC 59.275 55.000 12.42 0.00 0.00 2.78
89 90 0.392060 ACTCGCGGGGTATTGTTTCC 60.392 55.000 12.42 0.00 0.00 3.13
90 91 1.078285 TCGCGGGGTATTGTTTCCC 60.078 57.895 6.13 0.00 42.73 3.97
91 92 1.078001 CGCGGGGTATTGTTTCCCT 60.078 57.895 0.00 0.00 43.00 4.20
92 93 0.678684 CGCGGGGTATTGTTTCCCTT 60.679 55.000 0.00 0.00 43.00 3.95
93 94 1.100510 GCGGGGTATTGTTTCCCTTC 58.899 55.000 0.00 0.00 43.00 3.46
94 95 1.340697 GCGGGGTATTGTTTCCCTTCT 60.341 52.381 0.00 0.00 43.00 2.85
95 96 2.882643 GCGGGGTATTGTTTCCCTTCTT 60.883 50.000 0.00 0.00 43.00 2.52
96 97 2.752903 CGGGGTATTGTTTCCCTTCTTG 59.247 50.000 0.00 0.00 43.00 3.02
97 98 3.096852 GGGGTATTGTTTCCCTTCTTGG 58.903 50.000 0.00 0.00 43.00 3.61
98 99 3.245479 GGGGTATTGTTTCCCTTCTTGGA 60.245 47.826 0.00 0.00 43.00 3.53
99 100 4.572007 GGGGTATTGTTTCCCTTCTTGGAT 60.572 45.833 0.00 0.00 43.00 3.41
100 101 5.023452 GGGTATTGTTTCCCTTCTTGGATT 58.977 41.667 0.00 0.00 40.48 3.01
101 102 5.127194 GGGTATTGTTTCCCTTCTTGGATTC 59.873 44.000 0.00 0.00 40.48 2.52
102 103 5.163652 GGTATTGTTTCCCTTCTTGGATTCG 60.164 44.000 0.00 0.00 38.35 3.34
103 104 2.159382 TGTTTCCCTTCTTGGATTCGC 58.841 47.619 0.00 0.00 38.35 4.70
104 105 2.224769 TGTTTCCCTTCTTGGATTCGCT 60.225 45.455 0.00 0.00 38.35 4.93
105 106 2.113860 TTCCCTTCTTGGATTCGCTG 57.886 50.000 0.00 0.00 38.35 5.18
106 107 0.392998 TCCCTTCTTGGATTCGCTGC 60.393 55.000 0.00 0.00 38.35 5.25
107 108 1.379642 CCCTTCTTGGATTCGCTGCC 61.380 60.000 0.00 0.00 38.35 4.85
108 109 0.677731 CCTTCTTGGATTCGCTGCCA 60.678 55.000 0.00 0.00 38.35 4.92
109 110 1.386533 CTTCTTGGATTCGCTGCCAT 58.613 50.000 0.00 0.00 33.46 4.40
110 111 1.065102 CTTCTTGGATTCGCTGCCATG 59.935 52.381 0.00 0.00 33.46 3.66
111 112 0.252761 TCTTGGATTCGCTGCCATGA 59.747 50.000 0.00 0.00 36.39 3.07
112 113 0.379669 CTTGGATTCGCTGCCATGAC 59.620 55.000 0.00 0.00 33.46 3.06
113 114 1.031571 TTGGATTCGCTGCCATGACC 61.032 55.000 0.00 0.00 33.46 4.02
114 115 1.153086 GGATTCGCTGCCATGACCT 60.153 57.895 0.00 0.00 0.00 3.85
115 116 0.749454 GGATTCGCTGCCATGACCTT 60.749 55.000 0.00 0.00 0.00 3.50
116 117 1.475034 GGATTCGCTGCCATGACCTTA 60.475 52.381 0.00 0.00 0.00 2.69
117 118 2.498167 GATTCGCTGCCATGACCTTAT 58.502 47.619 0.00 0.00 0.00 1.73
118 119 2.418368 TTCGCTGCCATGACCTTATT 57.582 45.000 0.00 0.00 0.00 1.40
119 120 2.418368 TCGCTGCCATGACCTTATTT 57.582 45.000 0.00 0.00 0.00 1.40
120 121 2.016318 TCGCTGCCATGACCTTATTTG 58.984 47.619 0.00 0.00 0.00 2.32
121 122 1.745087 CGCTGCCATGACCTTATTTGT 59.255 47.619 0.00 0.00 0.00 2.83
122 123 2.478370 CGCTGCCATGACCTTATTTGTG 60.478 50.000 0.00 0.00 0.00 3.33
123 124 2.736400 GCTGCCATGACCTTATTTGTGC 60.736 50.000 0.00 0.00 0.00 4.57
124 125 1.824230 TGCCATGACCTTATTTGTGCC 59.176 47.619 0.00 0.00 0.00 5.01
125 126 1.136891 GCCATGACCTTATTTGTGCCC 59.863 52.381 0.00 0.00 0.00 5.36
126 127 1.756538 CCATGACCTTATTTGTGCCCC 59.243 52.381 0.00 0.00 0.00 5.80
127 128 2.624029 CCATGACCTTATTTGTGCCCCT 60.624 50.000 0.00 0.00 0.00 4.79
128 129 2.990740 TGACCTTATTTGTGCCCCTT 57.009 45.000 0.00 0.00 0.00 3.95
129 130 3.252554 TGACCTTATTTGTGCCCCTTT 57.747 42.857 0.00 0.00 0.00 3.11
130 131 3.582164 TGACCTTATTTGTGCCCCTTTT 58.418 40.909 0.00 0.00 0.00 2.27
131 132 3.970640 TGACCTTATTTGTGCCCCTTTTT 59.029 39.130 0.00 0.00 0.00 1.94
132 133 4.202305 TGACCTTATTTGTGCCCCTTTTTG 60.202 41.667 0.00 0.00 0.00 2.44
133 134 3.970640 ACCTTATTTGTGCCCCTTTTTGA 59.029 39.130 0.00 0.00 0.00 2.69
134 135 4.040339 ACCTTATTTGTGCCCCTTTTTGAG 59.960 41.667 0.00 0.00 0.00 3.02
135 136 2.549064 ATTTGTGCCCCTTTTTGAGC 57.451 45.000 0.00 0.00 0.00 4.26
136 137 1.198713 TTTGTGCCCCTTTTTGAGCA 58.801 45.000 0.00 0.00 0.00 4.26
138 139 3.869481 TGCCCCTTTTTGAGCACC 58.131 55.556 0.00 0.00 0.00 5.01
139 140 1.836604 TGCCCCTTTTTGAGCACCC 60.837 57.895 0.00 0.00 0.00 4.61
140 141 1.836604 GCCCCTTTTTGAGCACCCA 60.837 57.895 0.00 0.00 0.00 4.51
141 142 1.820010 GCCCCTTTTTGAGCACCCAG 61.820 60.000 0.00 0.00 0.00 4.45
142 143 1.187567 CCCCTTTTTGAGCACCCAGG 61.188 60.000 0.00 0.00 0.00 4.45
143 144 0.178964 CCCTTTTTGAGCACCCAGGA 60.179 55.000 0.00 0.00 0.00 3.86
144 145 1.703411 CCTTTTTGAGCACCCAGGAA 58.297 50.000 0.00 0.00 0.00 3.36
145 146 2.038659 CCTTTTTGAGCACCCAGGAAA 58.961 47.619 0.00 0.00 0.00 3.13
146 147 2.433970 CCTTTTTGAGCACCCAGGAAAA 59.566 45.455 0.00 0.00 0.00 2.29
147 148 3.457234 CTTTTTGAGCACCCAGGAAAAC 58.543 45.455 0.00 0.00 0.00 2.43
148 149 1.408969 TTTGAGCACCCAGGAAAACC 58.591 50.000 0.00 0.00 0.00 3.27
149 150 0.469144 TTGAGCACCCAGGAAAACCC 60.469 55.000 0.00 0.00 0.00 4.11
150 151 1.606601 GAGCACCCAGGAAAACCCC 60.607 63.158 0.00 0.00 34.66 4.95
151 152 2.200092 GCACCCAGGAAAACCCCA 59.800 61.111 0.00 0.00 34.66 4.96
152 153 1.229177 GCACCCAGGAAAACCCCAT 60.229 57.895 0.00 0.00 34.66 4.00
153 154 1.543944 GCACCCAGGAAAACCCCATG 61.544 60.000 0.00 0.00 34.66 3.66
154 155 1.229177 ACCCAGGAAAACCCCATGC 60.229 57.895 0.00 0.00 34.66 4.06
155 156 1.989508 CCCAGGAAAACCCCATGCC 60.990 63.158 0.00 0.00 34.66 4.40
156 157 1.989508 CCAGGAAAACCCCATGCCC 60.990 63.158 0.00 0.00 34.66 5.36
157 158 2.037208 AGGAAAACCCCATGCCCG 59.963 61.111 0.00 0.00 34.66 6.13
158 159 3.074369 GGAAAACCCCATGCCCGG 61.074 66.667 0.00 0.00 0.00 5.73
159 160 2.283604 GAAAACCCCATGCCCGGT 60.284 61.111 0.00 0.00 0.00 5.28
160 161 1.911269 GAAAACCCCATGCCCGGTT 60.911 57.895 0.00 4.69 44.35 4.44
161 162 1.884075 GAAAACCCCATGCCCGGTTC 61.884 60.000 0.00 0.00 41.58 3.62
162 163 2.380571 AAAACCCCATGCCCGGTTCT 62.381 55.000 0.00 0.00 41.58 3.01
179 180 1.048601 TCTTTTGCTCGAGGTGTCCT 58.951 50.000 15.58 0.00 36.03 3.85
180 181 1.000955 TCTTTTGCTCGAGGTGTCCTC 59.999 52.381 15.58 5.79 46.44 3.71
197 198 4.036262 TGTCCTCGATGTTTGGTTTTTGAG 59.964 41.667 0.00 0.00 0.00 3.02
202 203 6.142818 TCGATGTTTGGTTTTTGAGATGTT 57.857 33.333 0.00 0.00 0.00 2.71
258 259 0.321653 AGGCTTCGTGGGTTTAGCAG 60.322 55.000 0.00 0.00 35.36 4.24
259 260 0.605589 GGCTTCGTGGGTTTAGCAGT 60.606 55.000 0.00 0.00 35.36 4.40
260 261 0.517316 GCTTCGTGGGTTTAGCAGTG 59.483 55.000 0.00 0.00 33.88 3.66
261 262 1.878953 CTTCGTGGGTTTAGCAGTGT 58.121 50.000 0.00 0.00 0.00 3.55
262 263 2.218603 CTTCGTGGGTTTAGCAGTGTT 58.781 47.619 0.00 0.00 0.00 3.32
263 264 2.335316 TCGTGGGTTTAGCAGTGTTT 57.665 45.000 0.00 0.00 0.00 2.83
285 286 2.358322 TTTTTCCCTCTGTTTCGGCT 57.642 45.000 0.00 0.00 0.00 5.52
294 295 0.392193 CTGTTTCGGCTGAGCATCCT 60.392 55.000 6.82 0.00 0.00 3.24
300 301 1.903294 GGCTGAGCATCCTCTGTCA 59.097 57.895 6.82 0.00 40.25 3.58
306 307 0.982704 AGCATCCTCTGTCACTGCTT 59.017 50.000 0.00 0.00 40.08 3.91
309 310 2.619147 CATCCTCTGTCACTGCTTCTG 58.381 52.381 0.00 0.00 0.00 3.02
310 311 0.972134 TCCTCTGTCACTGCTTCTGG 59.028 55.000 0.00 0.00 0.00 3.86
315 316 1.069823 CTGTCACTGCTTCTGGTGTCT 59.930 52.381 0.00 0.00 35.26 3.41
320 321 1.155042 CTGCTTCTGGTGTCTTGCTC 58.845 55.000 0.00 0.00 0.00 4.26
322 323 1.072806 TGCTTCTGGTGTCTTGCTCAT 59.927 47.619 0.00 0.00 0.00 2.90
324 325 1.467734 CTTCTGGTGTCTTGCTCATGC 59.532 52.381 0.00 0.00 40.20 4.06
328 329 0.807496 GGTGTCTTGCTCATGCCTTC 59.193 55.000 0.00 0.00 38.71 3.46
331 332 2.102438 TCTTGCTCATGCCTTCGCG 61.102 57.895 0.00 0.00 38.08 5.87
334 335 1.911293 TTGCTCATGCCTTCGCGTTC 61.911 55.000 5.77 0.00 38.08 3.95
344 345 1.333115 CTTCGCGTTCGTGTCATGTA 58.667 50.000 5.77 0.00 36.96 2.29
350 351 3.242016 CGCGTTCGTGTCATGTATTGTAT 59.758 43.478 0.00 0.00 0.00 2.29
353 354 5.671140 GCGTTCGTGTCATGTATTGTATTTC 59.329 40.000 0.00 0.00 0.00 2.17
358 359 8.407457 TCGTGTCATGTATTGTATTTCTTCTC 57.593 34.615 0.00 0.00 0.00 2.87
376 377 8.620116 TTCTTCTCAATGAAATGATACACACA 57.380 30.769 0.00 0.00 33.79 3.72
385 386 6.747125 TGAAATGATACACACACTTTGCATT 58.253 32.000 0.00 0.00 0.00 3.56
386 387 6.862608 TGAAATGATACACACACTTTGCATTC 59.137 34.615 0.00 0.00 0.00 2.67
387 388 4.403015 TGATACACACACTTTGCATTCG 57.597 40.909 0.00 0.00 0.00 3.34
388 389 3.812609 TGATACACACACTTTGCATTCGT 59.187 39.130 0.00 0.00 0.00 3.85
390 391 2.013400 ACACACACTTTGCATTCGTGA 58.987 42.857 14.89 0.00 33.13 4.35
391 392 2.421775 ACACACACTTTGCATTCGTGAA 59.578 40.909 14.89 0.00 33.13 3.18
392 393 3.119673 ACACACACTTTGCATTCGTGAAA 60.120 39.130 14.89 0.00 33.13 2.69
428 429 0.108089 ATGTTATGTGGGCGTGCGTA 60.108 50.000 0.00 0.00 0.00 4.42
454 455 0.503961 GTTGAGCGTGCATGCAAAAC 59.496 50.000 31.36 27.19 37.31 2.43
489 490 0.514691 GAAAGTGCAGAAGCTGACGG 59.485 55.000 0.00 0.00 42.74 4.79
527 528 0.743097 GCCTGAATGGGTGAATCTGC 59.257 55.000 0.00 0.00 36.00 4.26
558 559 1.028130 TGCGTGGCATGAAAAGTCAA 58.972 45.000 11.71 0.00 37.30 3.18
567 568 5.811613 TGGCATGAAAAGTCAAAACTGAAAG 59.188 36.000 0.00 0.00 37.30 2.62
610 611 1.675552 AAAAGTTCCACACGACCCTG 58.324 50.000 0.00 0.00 0.00 4.45
611 612 0.818040 AAAGTTCCACACGACCCTGC 60.818 55.000 0.00 0.00 0.00 4.85
612 613 2.989055 AAGTTCCACACGACCCTGCG 62.989 60.000 0.00 0.00 37.29 5.18
613 614 3.542676 TTCCACACGACCCTGCGT 61.543 61.111 0.00 0.00 46.88 5.24
614 615 2.201708 TTCCACACGACCCTGCGTA 61.202 57.895 0.00 0.00 43.59 4.42
615 616 1.746322 TTCCACACGACCCTGCGTAA 61.746 55.000 0.00 0.00 43.59 3.18
616 617 1.301087 CCACACGACCCTGCGTAAA 60.301 57.895 0.00 0.00 43.59 2.01
617 618 0.881159 CCACACGACCCTGCGTAAAA 60.881 55.000 0.00 0.00 43.59 1.52
618 619 1.153353 CACACGACCCTGCGTAAAAT 58.847 50.000 0.00 0.00 43.59 1.82
619 620 1.127951 CACACGACCCTGCGTAAAATC 59.872 52.381 0.00 0.00 43.59 2.17
620 621 1.270412 ACACGACCCTGCGTAAAATCA 60.270 47.619 0.00 0.00 43.59 2.57
621 622 1.801771 CACGACCCTGCGTAAAATCAA 59.198 47.619 0.00 0.00 43.59 2.57
622 623 2.418628 CACGACCCTGCGTAAAATCAAT 59.581 45.455 0.00 0.00 43.59 2.57
623 624 3.078837 ACGACCCTGCGTAAAATCAATT 58.921 40.909 0.00 0.00 43.61 2.32
624 625 4.093703 CACGACCCTGCGTAAAATCAATTA 59.906 41.667 0.00 0.00 43.59 1.40
625 626 4.879545 ACGACCCTGCGTAAAATCAATTAT 59.120 37.500 0.00 0.00 43.61 1.28
626 627 5.355910 ACGACCCTGCGTAAAATCAATTATT 59.644 36.000 0.00 0.00 43.61 1.40
629 630 6.329496 ACCCTGCGTAAAATCAATTATTGTG 58.671 36.000 4.77 0.00 0.00 3.33
632 633 6.405286 CCTGCGTAAAATCAATTATTGTGGGA 60.405 38.462 4.77 0.00 0.00 4.37
633 634 6.559810 TGCGTAAAATCAATTATTGTGGGAG 58.440 36.000 4.77 0.00 0.00 4.30
634 635 6.151985 TGCGTAAAATCAATTATTGTGGGAGT 59.848 34.615 4.77 0.00 0.00 3.85
636 637 8.185505 GCGTAAAATCAATTATTGTGGGAGTTA 58.814 33.333 4.77 0.00 0.00 2.24
637 638 9.716507 CGTAAAATCAATTATTGTGGGAGTTAG 57.283 33.333 4.77 0.00 0.00 2.34
643 2088 8.677148 TCAATTATTGTGGGAGTTAGATTAGC 57.323 34.615 4.77 0.00 0.00 3.09
644 2089 8.271458 TCAATTATTGTGGGAGTTAGATTAGCA 58.729 33.333 4.77 0.00 0.00 3.49
645 2090 8.902806 CAATTATTGTGGGAGTTAGATTAGCAA 58.097 33.333 0.00 0.00 0.00 3.91
647 2092 9.646522 ATTATTGTGGGAGTTAGATTAGCAAAT 57.353 29.630 0.00 0.00 0.00 2.32
648 2093 7.573968 ATTGTGGGAGTTAGATTAGCAAATC 57.426 36.000 0.00 0.00 41.65 2.17
649 2094 5.437060 TGTGGGAGTTAGATTAGCAAATCC 58.563 41.667 0.00 0.00 42.20 3.01
658 2103 8.739972 AGTTAGATTAGCAAATCCGACATTTTT 58.260 29.630 0.00 0.00 42.20 1.94
660 2105 6.564328 AGATTAGCAAATCCGACATTTTTCC 58.436 36.000 0.00 0.00 42.20 3.13
661 2106 5.975693 TTAGCAAATCCGACATTTTTCCT 57.024 34.783 0.00 0.00 0.00 3.36
663 2108 4.809673 AGCAAATCCGACATTTTTCCTTC 58.190 39.130 0.00 0.00 0.00 3.46
665 2110 5.011023 AGCAAATCCGACATTTTTCCTTCTT 59.989 36.000 0.00 0.00 0.00 2.52
669 2114 6.901081 ATCCGACATTTTTCCTTCTTTCTT 57.099 33.333 0.00 0.00 0.00 2.52
670 2115 7.996098 ATCCGACATTTTTCCTTCTTTCTTA 57.004 32.000 0.00 0.00 0.00 2.10
672 2117 6.072673 TCCGACATTTTTCCTTCTTTCTTAGC 60.073 38.462 0.00 0.00 0.00 3.09
673 2118 6.293955 CCGACATTTTTCCTTCTTTCTTAGCA 60.294 38.462 0.00 0.00 0.00 3.49
678 2123 9.965824 CATTTTTCCTTCTTTCTTAGCAGTAAA 57.034 29.630 0.00 0.00 0.00 2.01
681 2126 8.974060 TTTCCTTCTTTCTTAGCAGTAAAGAA 57.026 30.769 12.63 12.63 43.40 2.52
682 2127 9.574516 TTTCCTTCTTTCTTAGCAGTAAAGAAT 57.425 29.630 13.27 0.00 44.11 2.40
683 2128 8.553459 TCCTTCTTTCTTAGCAGTAAAGAATG 57.447 34.615 13.27 11.57 44.11 2.67
684 2129 8.375506 TCCTTCTTTCTTAGCAGTAAAGAATGA 58.624 33.333 13.27 13.01 44.11 2.57
685 2130 9.003658 CCTTCTTTCTTAGCAGTAAAGAATGAA 57.996 33.333 18.15 18.15 45.31 2.57
732 2837 6.631636 GCAAGTAACTTTTTCTTTGAGGTACG 59.368 38.462 0.00 0.00 38.34 3.67
763 2868 1.539827 CCCTTGGAGCACTTAAAACGG 59.460 52.381 0.00 0.00 0.00 4.44
767 2872 3.478857 TGGAGCACTTAAAACGGAGAA 57.521 42.857 0.00 0.00 0.00 2.87
961 3066 2.346099 AATATTTTGCACAACGCGCT 57.654 40.000 5.73 0.00 46.97 5.92
989 3095 1.739049 GGAGCCTCGGACATCAGAG 59.261 63.158 2.38 2.38 37.81 3.35
1504 3610 2.515057 ACTTTGGCCGCGTGTTCA 60.515 55.556 4.92 0.00 0.00 3.18
1676 3782 3.394836 GGAGGCGCTGGAGTTCCT 61.395 66.667 7.64 0.00 36.82 3.36
2023 4129 3.354645 TCGTCGACAGCTGCGTCT 61.355 61.111 23.32 2.52 33.54 4.18
2480 4589 0.652592 ACATGTTGAGATAAGCGCGC 59.347 50.000 26.66 26.66 0.00 6.86
2486 4595 1.872234 GAGATAAGCGCGCGTGACA 60.872 57.895 32.35 14.63 0.00 3.58
2502 4611 3.951775 TGACAAACACAGCAACCTTTT 57.048 38.095 0.00 0.00 0.00 2.27
2510 4619 2.140138 AGCAACCTTTTGGGGGCAC 61.140 57.895 0.00 0.00 46.08 5.01
2516 4625 2.281208 TTTTGGGGGCACGAGACG 60.281 61.111 0.00 0.00 0.00 4.18
2567 4676 3.645975 CCGCACGTGTTGGACCAC 61.646 66.667 20.26 0.00 0.00 4.16
2569 4678 2.250939 CGCACGTGTTGGACCACAT 61.251 57.895 18.38 0.00 34.98 3.21
2571 4680 0.796312 GCACGTGTTGGACCACATAG 59.204 55.000 18.38 0.00 34.98 2.23
2578 4687 0.322456 TTGGACCACATAGCACTGCC 60.322 55.000 0.00 0.00 0.00 4.85
2609 4718 0.820074 TAGGAGGCTCGCTCTGTAGC 60.820 60.000 8.69 0.00 45.86 3.58
2671 4796 3.080641 CACTGGCATCCACCCTCA 58.919 61.111 0.00 0.00 0.00 3.86
2672 4797 1.377725 CACTGGCATCCACCCTCAC 60.378 63.158 0.00 0.00 0.00 3.51
2673 4798 1.539869 ACTGGCATCCACCCTCACT 60.540 57.895 0.00 0.00 0.00 3.41
2711 4836 2.361357 CCCCGACGACCACTCTCT 60.361 66.667 0.00 0.00 0.00 3.10
2722 4847 3.426615 GACCACTCTCTCTTCTCCTTCA 58.573 50.000 0.00 0.00 0.00 3.02
2724 4849 3.161067 CCACTCTCTCTTCTCCTTCACA 58.839 50.000 0.00 0.00 0.00 3.58
2725 4850 3.056891 CCACTCTCTCTTCTCCTTCACAC 60.057 52.174 0.00 0.00 0.00 3.82
2729 4854 1.613925 TCTCTTCTCCTTCACACGGTG 59.386 52.381 6.58 6.58 34.45 4.94
2733 4858 0.888619 TCTCCTTCACACGGTGCTAG 59.111 55.000 8.30 3.08 32.98 3.42
2748 4873 2.124736 TAGCGGTGAAGCATGGGC 60.125 61.111 0.00 0.00 40.15 5.36
2766 4891 1.580815 GCTCTAGCCTGCAGTCATTC 58.419 55.000 13.81 0.00 34.31 2.67
2775 4900 0.596082 TGCAGTCATTCTCGTCGTCA 59.404 50.000 0.00 0.00 0.00 4.35
2781 4906 1.200483 CATTCTCGTCGTCATTCCGG 58.800 55.000 0.00 0.00 0.00 5.14
2831 4956 2.751837 CGGGCTTTTGGGGAGCTC 60.752 66.667 4.71 4.71 40.01 4.09
2832 4957 2.751837 GGGCTTTTGGGGAGCTCG 60.752 66.667 7.83 0.00 40.01 5.03
2876 5001 3.818787 GTTAGCGGAGGCGGACGA 61.819 66.667 0.00 0.00 46.35 4.20
2908 5033 1.598701 AAAGGCGCCCTTCATTCAGC 61.599 55.000 26.15 0.00 43.92 4.26
2909 5034 3.521796 GGCGCCCTTCATTCAGCC 61.522 66.667 18.11 0.00 37.61 4.85
2924 5049 3.717294 GCCGAGGCCTTCCAGGAA 61.717 66.667 6.77 0.71 37.67 3.36
2932 5057 0.617935 GCCTTCCAGGAAAGAGCTCT 59.382 55.000 11.45 11.45 37.67 4.09
2938 5063 1.274712 CAGGAAAGAGCTCTGGAGGT 58.725 55.000 19.06 0.00 42.58 3.85
2940 5065 0.251634 GGAAAGAGCTCTGGAGGTGG 59.748 60.000 19.06 0.00 39.57 4.61
2942 5067 2.177594 AAAGAGCTCTGGAGGTGGCG 62.178 60.000 19.06 0.00 39.57 5.69
2948 5073 4.415150 CTGGAGGTGGCGCCATGT 62.415 66.667 35.23 23.32 40.61 3.21
2951 5076 3.127533 GAGGTGGCGCCATGTGAC 61.128 66.667 35.23 19.50 40.61 3.67
2957 5082 3.053291 GCGCCATGTGACGGGAAA 61.053 61.111 0.00 0.00 0.00 3.13
2960 5085 0.744414 CGCCATGTGACGGGAAATCT 60.744 55.000 0.00 0.00 0.00 2.40
2971 5096 0.729690 GGGAAATCTTGACTCGCAGC 59.270 55.000 0.00 0.00 0.00 5.25
3004 5129 4.612412 TTGCGCGTCGGGAGGTTT 62.612 61.111 14.18 0.00 0.00 3.27
3020 5145 0.179084 GTTTCGCCGGAGATGGATGA 60.179 55.000 9.30 0.00 0.00 2.92
3029 5154 2.559440 GGAGATGGATGACAAGTGCTC 58.441 52.381 0.00 0.00 0.00 4.26
3030 5155 2.559440 GAGATGGATGACAAGTGCTCC 58.441 52.381 0.00 0.00 0.00 4.70
3031 5156 1.211457 AGATGGATGACAAGTGCTCCC 59.789 52.381 0.00 0.00 0.00 4.30
3032 5157 0.994247 ATGGATGACAAGTGCTCCCA 59.006 50.000 0.00 0.00 0.00 4.37
3033 5158 0.770499 TGGATGACAAGTGCTCCCAA 59.230 50.000 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.664402 AGTCTGAGCAAACCCAATGT 57.336 45.000 0.00 0.00 0.00 2.71
1 2 3.441572 CCTAAGTCTGAGCAAACCCAATG 59.558 47.826 0.00 0.00 0.00 2.82
2 3 3.690460 CCTAAGTCTGAGCAAACCCAAT 58.310 45.455 0.00 0.00 0.00 3.16
3 4 2.814097 GCCTAAGTCTGAGCAAACCCAA 60.814 50.000 0.00 0.00 0.00 4.12
4 5 1.271379 GCCTAAGTCTGAGCAAACCCA 60.271 52.381 0.00 0.00 0.00 4.51
5 6 1.454201 GCCTAAGTCTGAGCAAACCC 58.546 55.000 0.00 0.00 0.00 4.11
6 7 1.271379 TGGCCTAAGTCTGAGCAAACC 60.271 52.381 3.32 0.00 0.00 3.27
7 8 2.079925 CTGGCCTAAGTCTGAGCAAAC 58.920 52.381 3.32 0.00 0.00 2.93
8 9 1.003580 CCTGGCCTAAGTCTGAGCAAA 59.996 52.381 3.32 0.00 0.00 3.68
9 10 0.615331 CCTGGCCTAAGTCTGAGCAA 59.385 55.000 3.32 0.00 0.00 3.91
10 11 1.267574 CCCTGGCCTAAGTCTGAGCA 61.268 60.000 3.32 0.00 0.00 4.26
11 12 1.524482 CCCTGGCCTAAGTCTGAGC 59.476 63.158 3.32 0.00 0.00 4.26
12 13 1.524482 GCCCTGGCCTAAGTCTGAG 59.476 63.158 3.32 0.00 34.56 3.35
13 14 2.359169 CGCCCTGGCCTAAGTCTGA 61.359 63.158 3.32 0.00 37.98 3.27
14 15 1.899437 TTCGCCCTGGCCTAAGTCTG 61.899 60.000 3.32 0.00 37.98 3.51
15 16 1.198759 TTTCGCCCTGGCCTAAGTCT 61.199 55.000 3.32 0.00 37.98 3.24
16 17 0.107165 ATTTCGCCCTGGCCTAAGTC 60.107 55.000 3.32 0.00 37.98 3.01
17 18 0.107165 GATTTCGCCCTGGCCTAAGT 60.107 55.000 3.32 0.00 37.98 2.24
18 19 0.819666 GGATTTCGCCCTGGCCTAAG 60.820 60.000 3.32 0.00 37.98 2.18
19 20 1.226262 GGATTTCGCCCTGGCCTAA 59.774 57.895 3.32 0.00 37.98 2.69
20 21 2.752807 GGGATTTCGCCCTGGCCTA 61.753 63.158 3.32 0.00 45.12 3.93
21 22 4.129148 GGGATTTCGCCCTGGCCT 62.129 66.667 3.32 0.00 45.12 5.19
28 29 2.897350 CCGAGCAGGGATTTCGCC 60.897 66.667 0.00 0.00 35.97 5.54
29 30 3.577313 GCCGAGCAGGGATTTCGC 61.577 66.667 0.00 0.00 41.48 4.70
30 31 0.179084 TAAGCCGAGCAGGGATTTCG 60.179 55.000 1.79 0.00 41.48 3.46
31 32 1.300481 GTAAGCCGAGCAGGGATTTC 58.700 55.000 1.79 0.00 41.48 2.17
32 33 0.107165 GGTAAGCCGAGCAGGGATTT 60.107 55.000 1.79 0.00 41.48 2.17
33 34 1.527370 GGTAAGCCGAGCAGGGATT 59.473 57.895 2.11 2.11 41.48 3.01
34 35 3.231298 GGTAAGCCGAGCAGGGAT 58.769 61.111 0.00 0.00 41.48 3.85
44 45 1.224722 GCTGCTAGCATCGGTAAGCC 61.225 60.000 19.72 0.00 41.89 4.35
45 46 1.552348 CGCTGCTAGCATCGGTAAGC 61.552 60.000 28.52 20.02 42.58 3.09
46 47 0.030773 TCGCTGCTAGCATCGGTAAG 59.969 55.000 33.15 15.80 42.58 2.34
47 48 0.458260 TTCGCTGCTAGCATCGGTAA 59.542 50.000 33.15 21.72 42.58 2.85
48 49 0.030773 CTTCGCTGCTAGCATCGGTA 59.969 55.000 33.15 22.61 42.58 4.02
49 50 1.227089 CTTCGCTGCTAGCATCGGT 60.227 57.895 33.15 0.00 42.58 4.69
50 51 1.066422 TCTTCGCTGCTAGCATCGG 59.934 57.895 33.15 21.58 42.58 4.18
51 52 0.526310 TGTCTTCGCTGCTAGCATCG 60.526 55.000 29.85 29.85 42.58 3.84
52 53 0.926846 GTGTCTTCGCTGCTAGCATC 59.073 55.000 19.72 13.77 42.58 3.91
53 54 0.534412 AGTGTCTTCGCTGCTAGCAT 59.466 50.000 19.72 0.00 42.58 3.79
54 55 0.109086 GAGTGTCTTCGCTGCTAGCA 60.109 55.000 18.22 18.22 42.58 3.49
55 56 1.136872 CGAGTGTCTTCGCTGCTAGC 61.137 60.000 8.10 8.10 38.02 3.42
56 57 2.937026 CGAGTGTCTTCGCTGCTAG 58.063 57.895 0.00 0.00 34.29 3.42
63 64 2.001361 ATACCCCGCGAGTGTCTTCG 62.001 60.000 8.23 0.00 43.23 3.79
64 65 0.175073 AATACCCCGCGAGTGTCTTC 59.825 55.000 8.23 0.00 0.00 2.87
65 66 0.108329 CAATACCCCGCGAGTGTCTT 60.108 55.000 8.23 0.00 0.00 3.01
66 67 1.255667 ACAATACCCCGCGAGTGTCT 61.256 55.000 8.23 0.00 0.00 3.41
67 68 0.390735 AACAATACCCCGCGAGTGTC 60.391 55.000 8.23 0.00 0.00 3.67
68 69 0.035739 AAACAATACCCCGCGAGTGT 59.964 50.000 8.23 0.00 0.00 3.55
69 70 0.725117 GAAACAATACCCCGCGAGTG 59.275 55.000 8.23 0.00 0.00 3.51
70 71 0.392060 GGAAACAATACCCCGCGAGT 60.392 55.000 8.23 7.43 0.00 4.18
71 72 1.093496 GGGAAACAATACCCCGCGAG 61.093 60.000 8.23 0.00 40.19 5.03
72 73 1.078285 GGGAAACAATACCCCGCGA 60.078 57.895 8.23 0.00 40.19 5.87
73 74 0.678684 AAGGGAAACAATACCCCGCG 60.679 55.000 0.00 0.00 46.64 6.46
74 75 1.100510 GAAGGGAAACAATACCCCGC 58.899 55.000 0.00 0.00 46.64 6.13
75 76 2.752903 CAAGAAGGGAAACAATACCCCG 59.247 50.000 0.00 0.00 46.64 5.73
76 77 3.096852 CCAAGAAGGGAAACAATACCCC 58.903 50.000 0.00 0.00 46.64 4.95
77 78 4.042271 TCCAAGAAGGGAAACAATACCC 57.958 45.455 0.00 0.00 45.88 3.69
78 79 5.163652 CGAATCCAAGAAGGGAAACAATACC 60.164 44.000 0.00 0.00 41.12 2.73
79 80 5.676331 GCGAATCCAAGAAGGGAAACAATAC 60.676 44.000 0.00 0.00 41.12 1.89
80 81 4.398044 GCGAATCCAAGAAGGGAAACAATA 59.602 41.667 0.00 0.00 41.12 1.90
81 82 3.193479 GCGAATCCAAGAAGGGAAACAAT 59.807 43.478 0.00 0.00 41.12 2.71
82 83 2.556622 GCGAATCCAAGAAGGGAAACAA 59.443 45.455 0.00 0.00 41.12 2.83
83 84 2.159382 GCGAATCCAAGAAGGGAAACA 58.841 47.619 0.00 0.00 41.12 2.83
84 85 2.162408 CAGCGAATCCAAGAAGGGAAAC 59.838 50.000 0.00 0.00 41.12 2.78
85 86 2.436417 CAGCGAATCCAAGAAGGGAAA 58.564 47.619 0.00 0.00 41.12 3.13
86 87 1.950484 GCAGCGAATCCAAGAAGGGAA 60.950 52.381 0.00 0.00 41.12 3.97
87 88 0.392998 GCAGCGAATCCAAGAAGGGA 60.393 55.000 0.00 0.00 42.21 4.20
88 89 1.379642 GGCAGCGAATCCAAGAAGGG 61.380 60.000 0.00 0.00 38.24 3.95
89 90 0.677731 TGGCAGCGAATCCAAGAAGG 60.678 55.000 0.00 0.00 39.47 3.46
90 91 1.065102 CATGGCAGCGAATCCAAGAAG 59.935 52.381 0.00 0.00 35.75 2.85
91 92 1.097232 CATGGCAGCGAATCCAAGAA 58.903 50.000 0.00 0.00 35.75 2.52
92 93 0.252761 TCATGGCAGCGAATCCAAGA 59.747 50.000 0.00 0.00 35.75 3.02
93 94 0.379669 GTCATGGCAGCGAATCCAAG 59.620 55.000 0.00 0.00 35.75 3.61
94 95 1.031571 GGTCATGGCAGCGAATCCAA 61.032 55.000 0.00 0.00 35.75 3.53
95 96 1.451927 GGTCATGGCAGCGAATCCA 60.452 57.895 0.00 0.00 36.70 3.41
96 97 0.749454 AAGGTCATGGCAGCGAATCC 60.749 55.000 0.00 0.00 0.00 3.01
97 98 1.953559 TAAGGTCATGGCAGCGAATC 58.046 50.000 0.00 0.00 0.00 2.52
98 99 2.645838 ATAAGGTCATGGCAGCGAAT 57.354 45.000 0.00 0.00 0.00 3.34
99 100 2.418368 AATAAGGTCATGGCAGCGAA 57.582 45.000 0.00 0.00 0.00 4.70
100 101 2.016318 CAAATAAGGTCATGGCAGCGA 58.984 47.619 0.00 0.00 0.00 4.93
101 102 1.745087 ACAAATAAGGTCATGGCAGCG 59.255 47.619 0.00 0.00 0.00 5.18
102 103 2.736400 GCACAAATAAGGTCATGGCAGC 60.736 50.000 0.00 0.00 0.00 5.25
103 104 2.159198 GGCACAAATAAGGTCATGGCAG 60.159 50.000 0.00 0.00 33.20 4.85
104 105 1.824230 GGCACAAATAAGGTCATGGCA 59.176 47.619 0.00 0.00 33.20 4.92
105 106 1.136891 GGGCACAAATAAGGTCATGGC 59.863 52.381 0.00 0.00 0.00 4.40
106 107 1.756538 GGGGCACAAATAAGGTCATGG 59.243 52.381 0.00 0.00 0.00 3.66
107 108 2.738743 AGGGGCACAAATAAGGTCATG 58.261 47.619 0.00 0.00 0.00 3.07
108 109 3.473113 AAGGGGCACAAATAAGGTCAT 57.527 42.857 0.00 0.00 0.00 3.06
109 110 2.990740 AAGGGGCACAAATAAGGTCA 57.009 45.000 0.00 0.00 0.00 4.02
110 111 4.039852 TCAAAAAGGGGCACAAATAAGGTC 59.960 41.667 0.00 0.00 0.00 3.85
111 112 3.970640 TCAAAAAGGGGCACAAATAAGGT 59.029 39.130 0.00 0.00 0.00 3.50
112 113 4.568956 CTCAAAAAGGGGCACAAATAAGG 58.431 43.478 0.00 0.00 0.00 2.69
113 114 3.996363 GCTCAAAAAGGGGCACAAATAAG 59.004 43.478 0.00 0.00 0.00 1.73
114 115 3.389329 TGCTCAAAAAGGGGCACAAATAA 59.611 39.130 0.00 0.00 0.00 1.40
115 116 2.968574 TGCTCAAAAAGGGGCACAAATA 59.031 40.909 0.00 0.00 0.00 1.40
116 117 1.767681 TGCTCAAAAAGGGGCACAAAT 59.232 42.857 0.00 0.00 0.00 2.32
117 118 1.198713 TGCTCAAAAAGGGGCACAAA 58.801 45.000 0.00 0.00 0.00 2.83
118 119 2.907703 TGCTCAAAAAGGGGCACAA 58.092 47.368 0.00 0.00 0.00 3.33
119 120 4.695014 TGCTCAAAAAGGGGCACA 57.305 50.000 0.00 0.00 0.00 4.57
121 122 1.836604 GGGTGCTCAAAAAGGGGCA 60.837 57.895 0.00 0.00 0.00 5.36
122 123 1.820010 CTGGGTGCTCAAAAAGGGGC 61.820 60.000 0.00 0.00 0.00 5.80
123 124 1.187567 CCTGGGTGCTCAAAAAGGGG 61.188 60.000 0.00 0.00 0.00 4.79
124 125 0.178964 TCCTGGGTGCTCAAAAAGGG 60.179 55.000 0.00 0.00 0.00 3.95
125 126 1.703411 TTCCTGGGTGCTCAAAAAGG 58.297 50.000 0.00 0.00 0.00 3.11
126 127 3.457234 GTTTTCCTGGGTGCTCAAAAAG 58.543 45.455 0.00 0.00 0.00 2.27
127 128 2.169561 GGTTTTCCTGGGTGCTCAAAAA 59.830 45.455 0.00 0.00 36.94 1.94
128 129 1.760029 GGTTTTCCTGGGTGCTCAAAA 59.240 47.619 0.00 0.00 36.94 2.44
129 130 1.408969 GGTTTTCCTGGGTGCTCAAA 58.591 50.000 0.00 0.00 36.94 2.69
130 131 0.469144 GGGTTTTCCTGGGTGCTCAA 60.469 55.000 0.00 0.00 40.46 3.02
131 132 1.152830 GGGTTTTCCTGGGTGCTCA 59.847 57.895 0.00 0.00 40.46 4.26
132 133 1.606601 GGGGTTTTCCTGGGTGCTC 60.607 63.158 0.00 0.00 40.46 4.26
133 134 1.739608 ATGGGGTTTTCCTGGGTGCT 61.740 55.000 0.00 0.00 40.46 4.40
134 135 1.229177 ATGGGGTTTTCCTGGGTGC 60.229 57.895 0.00 0.00 40.46 5.01
135 136 1.543944 GCATGGGGTTTTCCTGGGTG 61.544 60.000 0.00 0.00 40.46 4.61
136 137 1.229177 GCATGGGGTTTTCCTGGGT 60.229 57.895 0.00 0.00 40.46 4.51
137 138 1.989508 GGCATGGGGTTTTCCTGGG 60.990 63.158 0.00 0.00 40.46 4.45
138 139 1.989508 GGGCATGGGGTTTTCCTGG 60.990 63.158 0.00 0.00 40.46 4.45
139 140 2.350458 CGGGCATGGGGTTTTCCTG 61.350 63.158 0.00 0.00 40.46 3.86
140 141 2.037208 CGGGCATGGGGTTTTCCT 59.963 61.111 0.00 0.00 40.46 3.36
141 142 3.074369 CCGGGCATGGGGTTTTCC 61.074 66.667 0.00 0.00 39.75 3.13
142 143 1.884075 GAACCGGGCATGGGGTTTTC 61.884 60.000 6.32 0.00 46.16 2.29
143 144 1.911269 GAACCGGGCATGGGGTTTT 60.911 57.895 6.32 0.00 46.16 2.43
144 145 2.283604 GAACCGGGCATGGGGTTT 60.284 61.111 6.32 0.00 46.16 3.27
146 147 2.380571 AAAAGAACCGGGCATGGGGT 62.381 55.000 6.32 0.00 38.44 4.95
147 148 1.609210 AAAAGAACCGGGCATGGGG 60.609 57.895 6.32 0.00 0.00 4.96
148 149 1.591183 CAAAAGAACCGGGCATGGG 59.409 57.895 6.32 0.00 0.00 4.00
149 150 1.079888 GCAAAAGAACCGGGCATGG 60.080 57.895 6.32 0.00 0.00 3.66
150 151 0.109132 GAGCAAAAGAACCGGGCATG 60.109 55.000 6.32 0.00 0.00 4.06
151 152 1.586154 CGAGCAAAAGAACCGGGCAT 61.586 55.000 6.32 0.00 0.00 4.40
152 153 2.258013 CGAGCAAAAGAACCGGGCA 61.258 57.895 6.32 0.00 0.00 5.36
153 154 1.912371 CTCGAGCAAAAGAACCGGGC 61.912 60.000 6.32 0.00 0.00 6.13
154 155 1.298859 CCTCGAGCAAAAGAACCGGG 61.299 60.000 6.99 0.00 0.00 5.73
155 156 0.602905 ACCTCGAGCAAAAGAACCGG 60.603 55.000 6.99 0.00 0.00 5.28
156 157 0.512952 CACCTCGAGCAAAAGAACCG 59.487 55.000 6.99 0.00 0.00 4.44
157 158 1.531578 GACACCTCGAGCAAAAGAACC 59.468 52.381 6.99 0.00 0.00 3.62
158 159 1.531578 GGACACCTCGAGCAAAAGAAC 59.468 52.381 6.99 0.00 0.00 3.01
159 160 1.416401 AGGACACCTCGAGCAAAAGAA 59.584 47.619 6.99 0.00 0.00 2.52
160 161 1.000955 GAGGACACCTCGAGCAAAAGA 59.999 52.381 6.99 0.00 41.08 2.52
161 162 1.433534 GAGGACACCTCGAGCAAAAG 58.566 55.000 6.99 0.00 41.08 2.27
162 163 3.606886 GAGGACACCTCGAGCAAAA 57.393 52.632 6.99 0.00 41.08 2.44
179 180 5.766150 ACATCTCAAAAACCAAACATCGA 57.234 34.783 0.00 0.00 0.00 3.59
180 181 5.175491 CCAACATCTCAAAAACCAAACATCG 59.825 40.000 0.00 0.00 0.00 3.84
197 198 2.860735 GACTAGTGCGACATCCAACATC 59.139 50.000 0.00 0.00 0.00 3.06
202 203 0.817654 CTGGACTAGTGCGACATCCA 59.182 55.000 10.02 3.60 37.11 3.41
268 269 0.762418 TCAGCCGAAACAGAGGGAAA 59.238 50.000 0.00 0.00 0.00 3.13
271 272 1.743252 GCTCAGCCGAAACAGAGGG 60.743 63.158 0.00 0.00 0.00 4.30
277 278 0.107945 AGAGGATGCTCAGCCGAAAC 60.108 55.000 17.24 0.00 42.82 2.78
281 282 1.227205 GACAGAGGATGCTCAGCCG 60.227 63.158 17.24 4.39 42.82 5.52
282 283 0.461693 GTGACAGAGGATGCTCAGCC 60.462 60.000 17.24 1.06 37.08 4.85
285 286 0.248565 GCAGTGACAGAGGATGCTCA 59.751 55.000 17.24 0.00 34.10 4.26
294 295 1.069204 GACACCAGAAGCAGTGACAGA 59.931 52.381 0.00 0.00 37.43 3.41
300 301 0.471617 AGCAAGACACCAGAAGCAGT 59.528 50.000 0.00 0.00 0.00 4.40
306 307 0.321919 GGCATGAGCAAGACACCAGA 60.322 55.000 0.00 0.00 44.61 3.86
309 310 0.807496 GAAGGCATGAGCAAGACACC 59.193 55.000 0.00 0.00 44.61 4.16
310 311 0.445436 CGAAGGCATGAGCAAGACAC 59.555 55.000 0.00 0.00 44.61 3.67
315 316 1.911293 GAACGCGAAGGCATGAGCAA 61.911 55.000 15.93 0.00 44.61 3.91
320 321 2.096406 CACGAACGCGAAGGCATG 59.904 61.111 15.93 0.00 41.64 4.06
322 323 3.033764 GACACGAACGCGAAGGCA 61.034 61.111 15.93 0.00 41.64 4.75
324 325 1.282248 ACATGACACGAACGCGAAGG 61.282 55.000 15.93 2.86 41.64 3.46
328 329 1.388768 ACAATACATGACACGAACGCG 59.611 47.619 3.53 3.53 44.79 6.01
331 332 8.656849 AGAAGAAATACAATACATGACACGAAC 58.343 33.333 0.00 0.00 0.00 3.95
334 335 8.185003 TGAGAAGAAATACAATACATGACACG 57.815 34.615 0.00 0.00 0.00 4.49
350 351 9.065798 TGTGTGTATCATTTCATTGAGAAGAAA 57.934 29.630 0.00 0.00 37.57 2.52
353 354 8.037382 AGTGTGTGTATCATTTCATTGAGAAG 57.963 34.615 0.00 0.00 37.57 2.85
358 359 6.641723 TGCAAAGTGTGTGTATCATTTCATTG 59.358 34.615 0.00 0.00 0.00 2.82
367 368 4.084066 TCACGAATGCAAAGTGTGTGTATC 60.084 41.667 15.79 0.00 37.20 2.24
372 373 3.773860 TTTCACGAATGCAAAGTGTGT 57.226 38.095 15.79 0.00 37.20 3.72
397 398 5.540911 CCCACATAACATCTTGCAAACTTT 58.459 37.500 0.00 0.00 0.00 2.66
409 410 0.108089 TACGCACGCCCACATAACAT 60.108 50.000 0.00 0.00 0.00 2.71
479 480 0.166814 GTTGCACATCCGTCAGCTTC 59.833 55.000 0.00 0.00 0.00 3.86
510 511 3.087031 ACTTGCAGATTCACCCATTCAG 58.913 45.455 0.00 0.00 0.00 3.02
527 528 0.443869 GCCACGCATGACTACACTTG 59.556 55.000 0.00 0.00 0.00 3.16
596 597 1.746322 TTACGCAGGGTCGTGTGGAA 61.746 55.000 8.69 3.90 43.21 3.53
606 607 5.748152 CCACAATAATTGATTTTACGCAGGG 59.252 40.000 0.00 0.00 0.00 4.45
607 608 5.748152 CCCACAATAATTGATTTTACGCAGG 59.252 40.000 0.00 0.00 0.00 4.85
610 611 6.560711 ACTCCCACAATAATTGATTTTACGC 58.439 36.000 0.00 0.00 0.00 4.42
611 612 9.716507 CTAACTCCCACAATAATTGATTTTACG 57.283 33.333 0.00 0.00 0.00 3.18
617 618 9.289782 GCTAATCTAACTCCCACAATAATTGAT 57.710 33.333 0.00 0.00 0.00 2.57
618 619 8.271458 TGCTAATCTAACTCCCACAATAATTGA 58.729 33.333 0.00 0.00 0.00 2.57
619 620 8.450578 TGCTAATCTAACTCCCACAATAATTG 57.549 34.615 0.00 0.00 0.00 2.32
620 621 9.474313 TTTGCTAATCTAACTCCCACAATAATT 57.526 29.630 0.00 0.00 0.00 1.40
621 622 9.646522 ATTTGCTAATCTAACTCCCACAATAAT 57.353 29.630 0.00 0.00 0.00 1.28
622 623 9.120538 GATTTGCTAATCTAACTCCCACAATAA 57.879 33.333 12.83 0.00 37.70 1.40
623 624 7.719633 GGATTTGCTAATCTAACTCCCACAATA 59.280 37.037 18.26 0.00 40.07 1.90
624 625 6.547510 GGATTTGCTAATCTAACTCCCACAAT 59.452 38.462 18.26 0.00 40.07 2.71
625 626 5.885912 GGATTTGCTAATCTAACTCCCACAA 59.114 40.000 18.26 0.00 40.07 3.33
626 627 5.437060 GGATTTGCTAATCTAACTCCCACA 58.563 41.667 18.26 0.00 40.07 4.17
629 630 4.750598 GTCGGATTTGCTAATCTAACTCCC 59.249 45.833 18.26 2.39 40.07 4.30
632 633 7.865706 AAATGTCGGATTTGCTAATCTAACT 57.134 32.000 18.26 6.59 40.07 2.24
633 634 8.911247 AAAAATGTCGGATTTGCTAATCTAAC 57.089 30.769 18.26 16.01 40.07 2.34
634 635 8.188139 GGAAAAATGTCGGATTTGCTAATCTAA 58.812 33.333 18.26 6.31 40.07 2.10
636 637 6.378280 AGGAAAAATGTCGGATTTGCTAATCT 59.622 34.615 18.26 0.00 40.07 2.40
637 638 6.564328 AGGAAAAATGTCGGATTTGCTAATC 58.436 36.000 11.84 11.84 39.57 1.75
642 2087 4.809673 AGAAGGAAAAATGTCGGATTTGC 58.190 39.130 0.00 0.00 0.00 3.68
643 2088 7.147976 AGAAAGAAGGAAAAATGTCGGATTTG 58.852 34.615 0.00 0.00 0.00 2.32
644 2089 7.290110 AGAAAGAAGGAAAAATGTCGGATTT 57.710 32.000 0.00 0.00 0.00 2.17
645 2090 6.901081 AGAAAGAAGGAAAAATGTCGGATT 57.099 33.333 0.00 0.00 0.00 3.01
647 2092 6.072673 GCTAAGAAAGAAGGAAAAATGTCGGA 60.073 38.462 0.00 0.00 0.00 4.55
648 2093 6.086871 GCTAAGAAAGAAGGAAAAATGTCGG 58.913 40.000 0.00 0.00 0.00 4.79
649 2094 6.668323 TGCTAAGAAAGAAGGAAAAATGTCG 58.332 36.000 0.00 0.00 0.00 4.35
658 2103 8.553459 CATTCTTTACTGCTAAGAAAGAAGGA 57.447 34.615 13.00 0.00 46.30 3.36
687 2132 8.919777 ACTTGCTTTACCACTTAATAAACTCT 57.080 30.769 0.00 0.00 0.00 3.24
708 2813 7.912383 TCGTACCTCAAAGAAAAAGTTACTTG 58.088 34.615 0.00 0.00 0.00 3.16
732 2837 4.829492 AGTGCTCCAAGGGCAAATATATTC 59.171 41.667 0.00 0.00 41.54 1.75
737 2842 2.603075 AAGTGCTCCAAGGGCAAATA 57.397 45.000 0.00 0.00 41.54 1.40
738 2843 2.603075 TAAGTGCTCCAAGGGCAAAT 57.397 45.000 0.00 0.00 41.54 2.32
739 2844 2.373335 TTAAGTGCTCCAAGGGCAAA 57.627 45.000 0.00 0.00 41.54 3.68
740 2845 2.364002 GTTTTAAGTGCTCCAAGGGCAA 59.636 45.455 0.00 0.00 41.54 4.52
741 2846 1.960689 GTTTTAAGTGCTCCAAGGGCA 59.039 47.619 0.00 0.00 37.36 5.36
742 2847 1.068541 CGTTTTAAGTGCTCCAAGGGC 60.069 52.381 0.00 0.00 0.00 5.19
763 2868 3.792421 GCGTCCTTTCTACGAATCTTCTC 59.208 47.826 0.00 0.00 42.90 2.87
767 2872 2.753452 TGAGCGTCCTTTCTACGAATCT 59.247 45.455 0.00 0.00 42.90 2.40
961 3066 2.970639 GAGGCTCCGTGCACACTA 59.029 61.111 18.64 0.00 45.15 2.74
1411 3517 0.912486 AGCCATTCTAAGAAGCCGGT 59.088 50.000 1.90 0.00 0.00 5.28
1666 3772 1.672356 CCGCCAACAGGAACTCCAG 60.672 63.158 0.00 0.00 34.60 3.86
2170 4277 5.654603 TCAACACGACTGGTATCATTAGT 57.345 39.130 0.00 0.00 0.00 2.24
2171 4278 6.019559 CACATCAACACGACTGGTATCATTAG 60.020 42.308 0.00 0.00 0.00 1.73
2172 4279 5.810074 CACATCAACACGACTGGTATCATTA 59.190 40.000 0.00 0.00 0.00 1.90
2399 4508 4.232221 GTTCACCTCAACTTGCAATCATG 58.768 43.478 0.00 0.00 0.00 3.07
2462 4571 0.382272 CGCGCGCTTATCTCAACATG 60.382 55.000 30.48 4.24 0.00 3.21
2486 4595 1.209261 CCCCAAAAGGTTGCTGTGTTT 59.791 47.619 0.00 0.00 33.01 2.83
2510 4619 2.022129 GGCACAAGACCACGTCTCG 61.022 63.158 0.00 0.00 42.59 4.04
2516 4625 2.591715 AGTGCGGCACAAGACCAC 60.592 61.111 32.29 5.37 36.74 4.16
2554 4663 0.394938 TGCTATGTGGTCCAACACGT 59.605 50.000 0.00 0.00 44.21 4.49
2567 4676 2.149578 GCTATGGAAGGCAGTGCTATG 58.850 52.381 16.11 0.00 0.00 2.23
2650 4775 4.408821 GGTGGATGCCAGTGCCGA 62.409 66.667 0.00 0.00 32.34 5.54
2655 4780 1.539869 AGTGAGGGTGGATGCCAGT 60.540 57.895 0.00 0.00 32.34 4.00
2657 4782 2.300967 GGAGTGAGGGTGGATGCCA 61.301 63.158 0.00 0.00 0.00 4.92
2661 4786 2.450243 ACGGGAGTGAGGGTGGAT 59.550 61.111 0.00 0.00 44.82 3.41
2695 4820 0.961358 AAGAGAGAGTGGTCGTCGGG 60.961 60.000 0.00 0.00 0.00 5.14
2702 4827 3.161866 GTGAAGGAGAAGAGAGAGTGGT 58.838 50.000 0.00 0.00 0.00 4.16
2707 4832 2.163509 CCGTGTGAAGGAGAAGAGAGA 58.836 52.381 0.00 0.00 0.00 3.10
2709 4834 1.613925 CACCGTGTGAAGGAGAAGAGA 59.386 52.381 0.00 0.00 35.23 3.10
2711 4836 0.033504 GCACCGTGTGAAGGAGAAGA 59.966 55.000 8.04 0.00 35.23 2.87
2722 4847 2.765250 CTTCACCGCTAGCACCGTGT 62.765 60.000 16.45 0.23 0.00 4.49
2724 4849 2.261671 CTTCACCGCTAGCACCGT 59.738 61.111 16.45 4.31 0.00 4.83
2725 4850 3.188786 GCTTCACCGCTAGCACCG 61.189 66.667 16.45 3.62 37.35 4.94
2729 4854 2.182842 CCCATGCTTCACCGCTAGC 61.183 63.158 4.06 4.06 37.89 3.42
2748 4873 2.543445 CGAGAATGACTGCAGGCTAGAG 60.543 54.545 22.80 3.50 0.00 2.43
2751 4876 1.135139 GACGAGAATGACTGCAGGCTA 59.865 52.381 22.80 7.72 0.00 3.93
2754 4879 0.109086 ACGACGAGAATGACTGCAGG 60.109 55.000 19.93 0.00 0.00 4.85
2756 4881 0.596082 TGACGACGAGAATGACTGCA 59.404 50.000 0.00 0.00 0.00 4.41
2764 4889 0.450583 CTCCGGAATGACGACGAGAA 59.549 55.000 5.23 0.00 35.47 2.87
2766 4891 1.064296 CCTCCGGAATGACGACGAG 59.936 63.158 5.23 0.00 35.47 4.18
2775 4900 0.827368 GCTCTGAACTCCTCCGGAAT 59.173 55.000 5.23 0.00 0.00 3.01
2781 4906 0.172352 CCGTCTGCTCTGAACTCCTC 59.828 60.000 0.00 0.00 0.00 3.71
2859 4984 3.818787 TCGTCCGCCTCCGCTAAC 61.819 66.667 0.00 0.00 0.00 2.34
2860 4985 3.818787 GTCGTCCGCCTCCGCTAA 61.819 66.667 0.00 0.00 0.00 3.09
2902 5027 2.262774 CTGGAAGGCCTCGGCTGAAT 62.263 60.000 5.23 0.00 38.81 2.57
2924 5049 2.654079 CGCCACCTCCAGAGCTCTT 61.654 63.158 15.27 0.00 0.00 2.85
2932 5057 4.720902 CACATGGCGCCACCTCCA 62.721 66.667 35.50 8.13 40.22 3.86
2940 5065 2.322999 GATTTCCCGTCACATGGCGC 62.323 60.000 0.00 0.00 42.59 6.53
2942 5067 1.133025 CAAGATTTCCCGTCACATGGC 59.867 52.381 0.00 0.00 0.00 4.40
2948 5073 1.671850 GCGAGTCAAGATTTCCCGTCA 60.672 52.381 0.00 0.00 0.00 4.35
2951 5076 1.002366 CTGCGAGTCAAGATTTCCCG 58.998 55.000 0.00 0.00 0.00 5.14
2954 5079 0.371645 CGGCTGCGAGTCAAGATTTC 59.628 55.000 0.00 0.00 0.00 2.17
2957 5082 2.185350 CCGGCTGCGAGTCAAGAT 59.815 61.111 0.00 0.00 0.00 2.40
2971 5096 3.721706 AAGCTCTTGAGCCCCCGG 61.722 66.667 17.78 0.00 34.90 5.73
2987 5112 4.612412 AAACCTCCCGACGCGCAA 62.612 61.111 5.73 0.00 0.00 4.85
3004 5129 1.326951 TTGTCATCCATCTCCGGCGA 61.327 55.000 9.30 0.00 0.00 5.54
3005 5130 0.877649 CTTGTCATCCATCTCCGGCG 60.878 60.000 0.00 0.00 0.00 6.46
3020 5145 0.610232 GAGGCATTGGGAGCACTTGT 60.610 55.000 0.00 0.00 0.00 3.16
3029 5154 2.816746 CCATCCTTGAGGCATTGGG 58.183 57.895 0.00 0.00 34.44 4.12


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

AutoCloner maintained by Alex Coulton.