Multiple sequence alignment - TraesCS6D01G239100

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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 TraesCS6D01G239100 chr6D 100.000 3494 0 0 1 3494 339694102 339690609 0.000000e+00 6453.0
1 TraesCS6D01G239100 chr6D 90.588 170 16 0 632 801 392897136 392896967 3.510000e-55 226.0
2 TraesCS6D01G239100 chr6A 96.559 2674 68 9 844 3494 479891857 479889185 0.000000e+00 4407.0
3 TraesCS6D01G239100 chr6A 87.597 258 29 3 378 633 479892674 479892418 2.640000e-76 296.0
4 TraesCS6D01G239100 chr6A 90.230 174 17 0 629 802 222571244 222571417 9.760000e-56 228.0
5 TraesCS6D01G239100 chr6A 86.404 228 8 5 166 375 479892929 479892707 9.760000e-56 228.0
6 TraesCS6D01G239100 chr6A 94.915 59 3 0 792 850 479892422 479892364 3.710000e-15 93.5
7 TraesCS6D01G239100 chr6B 95.079 2093 55 10 844 2929 481040753 481042804 0.000000e+00 3251.0
8 TraesCS6D01G239100 chr6B 95.172 580 13 7 2925 3494 481043024 481043598 0.000000e+00 902.0
9 TraesCS6D01G239100 chr6B 79.845 258 30 11 376 633 480853333 480853568 6.000000e-38 169.0
10 TraesCS6D01G239100 chr2D 90.751 173 14 2 629 799 24312193 24312365 2.710000e-56 230.0
11 TraesCS6D01G239100 chr5D 90.588 170 16 0 624 793 181626107 181626276 3.510000e-55 226.0
12 TraesCS6D01G239100 chr5D 90.698 43 2 1 250 292 450543355 450543315 4.870000e-04 56.5
13 TraesCS6D01G239100 chr3B 88.587 184 21 0 614 797 571752704 571752521 1.260000e-54 224.0
14 TraesCS6D01G239100 chr3B 84.118 170 11 6 6 173 2905097 2905252 2.170000e-32 150.0
15 TraesCS6D01G239100 chr5B 89.655 174 17 1 628 800 275369966 275370139 1.630000e-53 220.0
16 TraesCS6D01G239100 chr2B 89.326 178 16 3 628 803 651353994 651354170 1.630000e-53 220.0
17 TraesCS6D01G239100 chr2B 88.108 185 19 3 620 802 546426317 546426134 2.110000e-52 217.0
18 TraesCS6D01G239100 chr7A 87.978 183 20 2 632 813 115807684 115807503 7.600000e-52 215.0
19 TraesCS6D01G239100 chr7A 86.992 123 11 2 44 166 25025563 25025680 2.190000e-27 134.0
20 TraesCS6D01G239100 chr7A 91.667 48 4 0 574 621 67620553 67620506 2.250000e-07 67.6
21 TraesCS6D01G239100 chr7A 100.000 28 0 0 262 289 256179622 256179595 6.000000e-03 52.8
22 TraesCS6D01G239100 chr2A 84.337 166 12 4 2 166 23493069 23493221 2.170000e-32 150.0
23 TraesCS6D01G239100 chr1B 87.603 121 8 3 43 162 665073233 665073347 2.190000e-27 134.0
24 TraesCS6D01G239100 chr1B 87.629 97 5 4 70 165 665094225 665094315 4.770000e-19 106.0


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 TraesCS6D01G239100 chr6D 339690609 339694102 3493 True 6453.000 6453 100.00000 1 3494 1 chr6D.!!$R1 3493
1 TraesCS6D01G239100 chr6A 479889185 479892929 3744 True 1256.125 4407 91.36875 166 3494 4 chr6A.!!$R1 3328
2 TraesCS6D01G239100 chr6B 481040753 481043598 2845 False 2076.500 3251 95.12550 844 3494 2 chr6B.!!$F2 2650

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
36 37 0.032952 TGGTCGTTTAGCTGAGCGTT 59.967 50.0 14.08 0.0 35.43 4.84 F
92 93 0.036388 CGCGGGCTGTAATGGGATAT 60.036 55.0 0.00 0.0 0.00 1.63 F
153 154 0.102844 CTGTGTGGTGTGCCCTTTTG 59.897 55.0 0.00 0.0 0.00 2.44 F
976 1553 0.108089 TCCTCTCTCTCCGTCTCACG 60.108 60.0 0.00 0.0 42.11 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 2518 0.240945 GCGCATTGTAAGTTGCCACT 59.759 50.000 0.3 0.0 35.41 4.00 R
2340 2917 2.406559 CCTCTCTCCACCATCTCCATT 58.593 52.381 0.0 0.0 0.00 3.16 R
2391 2968 4.278170 GTCAACATCAACCCATTCAGAACA 59.722 41.667 0.0 0.0 0.00 3.18 R
3017 3818 3.134574 TCTTGTTGCGAGTATTTGGGT 57.865 42.857 0.0 0.0 0.00 4.51 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
22 23 0.818296 CCTGTTAGGGAGAGTGGTCG 59.182 60.000 0.00 0.00 0.00 4.79
23 24 1.546961 CTGTTAGGGAGAGTGGTCGT 58.453 55.000 0.00 0.00 0.00 4.34
24 25 1.893801 CTGTTAGGGAGAGTGGTCGTT 59.106 52.381 0.00 0.00 0.00 3.85
25 26 2.299297 CTGTTAGGGAGAGTGGTCGTTT 59.701 50.000 0.00 0.00 0.00 3.60
26 27 3.499338 TGTTAGGGAGAGTGGTCGTTTA 58.501 45.455 0.00 0.00 0.00 2.01
27 28 3.508793 TGTTAGGGAGAGTGGTCGTTTAG 59.491 47.826 0.00 0.00 0.00 1.85
28 29 0.896226 AGGGAGAGTGGTCGTTTAGC 59.104 55.000 0.00 0.00 0.00 3.09
29 30 0.896226 GGGAGAGTGGTCGTTTAGCT 59.104 55.000 0.00 0.00 0.00 3.32
30 31 1.404315 GGGAGAGTGGTCGTTTAGCTG 60.404 57.143 0.00 0.00 0.00 4.24
31 32 1.544691 GGAGAGTGGTCGTTTAGCTGA 59.455 52.381 0.00 0.00 0.00 4.26
32 33 2.416162 GGAGAGTGGTCGTTTAGCTGAG 60.416 54.545 0.00 0.00 0.00 3.35
33 34 1.067495 AGAGTGGTCGTTTAGCTGAGC 60.067 52.381 0.00 0.00 0.00 4.26
34 35 0.388649 AGTGGTCGTTTAGCTGAGCG 60.389 55.000 8.47 8.47 35.43 5.03
35 36 0.666577 GTGGTCGTTTAGCTGAGCGT 60.667 55.000 14.08 0.00 35.43 5.07
36 37 0.032952 TGGTCGTTTAGCTGAGCGTT 59.967 50.000 14.08 0.00 35.43 4.84
37 38 1.145803 GGTCGTTTAGCTGAGCGTTT 58.854 50.000 14.08 0.00 0.00 3.60
38 39 1.529865 GGTCGTTTAGCTGAGCGTTTT 59.470 47.619 14.08 0.00 0.00 2.43
39 40 2.032290 GGTCGTTTAGCTGAGCGTTTTT 60.032 45.455 14.08 0.00 0.00 1.94
64 65 3.420606 CTGAGGCAGCGTGCTGTG 61.421 66.667 21.76 0.19 44.28 3.66
71 72 4.923942 AGCGTGCTGTGCTGTGCT 62.924 61.111 0.00 0.00 42.14 4.40
72 73 4.380628 GCGTGCTGTGCTGTGCTC 62.381 66.667 0.00 0.00 0.00 4.26
73 74 3.720193 CGTGCTGTGCTGTGCTCC 61.720 66.667 0.00 0.00 0.00 4.70
74 75 3.720193 GTGCTGTGCTGTGCTCCG 61.720 66.667 0.00 0.00 0.00 4.63
84 85 4.752879 GTGCTCCGCGGGCTGTAA 62.753 66.667 30.01 14.00 0.00 2.41
85 86 3.781307 TGCTCCGCGGGCTGTAAT 61.781 61.111 30.01 0.00 0.00 1.89
86 87 3.272334 GCTCCGCGGGCTGTAATG 61.272 66.667 27.83 6.63 0.00 1.90
87 88 2.588877 CTCCGCGGGCTGTAATGG 60.589 66.667 27.83 0.00 0.00 3.16
88 89 4.169696 TCCGCGGGCTGTAATGGG 62.170 66.667 27.83 0.00 0.00 4.00
89 90 4.169696 CCGCGGGCTGTAATGGGA 62.170 66.667 20.10 0.00 0.00 4.37
90 91 2.111043 CGCGGGCTGTAATGGGAT 59.889 61.111 0.00 0.00 0.00 3.85
91 92 1.369692 CGCGGGCTGTAATGGGATA 59.630 57.895 0.00 0.00 0.00 2.59
92 93 0.036388 CGCGGGCTGTAATGGGATAT 60.036 55.000 0.00 0.00 0.00 1.63
93 94 1.453155 GCGGGCTGTAATGGGATATG 58.547 55.000 0.00 0.00 0.00 1.78
94 95 1.453155 CGGGCTGTAATGGGATATGC 58.547 55.000 0.00 0.00 0.00 3.14
95 96 1.003580 CGGGCTGTAATGGGATATGCT 59.996 52.381 0.00 0.00 0.00 3.79
96 97 2.553028 CGGGCTGTAATGGGATATGCTT 60.553 50.000 0.00 0.00 0.00 3.91
97 98 2.821969 GGGCTGTAATGGGATATGCTTG 59.178 50.000 0.00 0.00 0.00 4.01
98 99 3.490348 GGCTGTAATGGGATATGCTTGT 58.510 45.455 0.00 0.00 0.00 3.16
99 100 3.503748 GGCTGTAATGGGATATGCTTGTC 59.496 47.826 0.00 0.00 0.00 3.18
100 101 4.136796 GCTGTAATGGGATATGCTTGTCA 58.863 43.478 0.00 0.00 0.00 3.58
101 102 4.023707 GCTGTAATGGGATATGCTTGTCAC 60.024 45.833 0.00 0.00 0.00 3.67
102 103 5.109500 TGTAATGGGATATGCTTGTCACA 57.891 39.130 3.75 3.75 30.30 3.58
103 104 4.881273 TGTAATGGGATATGCTTGTCACAC 59.119 41.667 3.33 0.00 28.21 3.82
104 105 3.939740 ATGGGATATGCTTGTCACACT 57.060 42.857 3.33 0.00 28.21 3.55
105 106 2.989909 TGGGATATGCTTGTCACACTG 58.010 47.619 0.00 0.00 0.00 3.66
106 107 2.292267 GGGATATGCTTGTCACACTGG 58.708 52.381 0.00 0.00 0.00 4.00
107 108 2.356125 GGGATATGCTTGTCACACTGGT 60.356 50.000 0.00 0.00 0.00 4.00
108 109 3.347216 GGATATGCTTGTCACACTGGTT 58.653 45.455 0.00 0.00 0.00 3.67
109 110 3.758554 GGATATGCTTGTCACACTGGTTT 59.241 43.478 0.00 0.00 0.00 3.27
110 111 4.142600 GGATATGCTTGTCACACTGGTTTC 60.143 45.833 0.00 0.00 0.00 2.78
111 112 1.013596 TGCTTGTCACACTGGTTTCG 58.986 50.000 0.00 0.00 0.00 3.46
112 113 1.014352 GCTTGTCACACTGGTTTCGT 58.986 50.000 0.00 0.00 0.00 3.85
113 114 1.400494 GCTTGTCACACTGGTTTCGTT 59.600 47.619 0.00 0.00 0.00 3.85
114 115 2.791158 GCTTGTCACACTGGTTTCGTTG 60.791 50.000 0.00 0.00 0.00 4.10
115 116 2.102070 TGTCACACTGGTTTCGTTGT 57.898 45.000 0.00 0.00 0.00 3.32
116 117 2.428491 TGTCACACTGGTTTCGTTGTT 58.572 42.857 0.00 0.00 0.00 2.83
117 118 2.814919 TGTCACACTGGTTTCGTTGTTT 59.185 40.909 0.00 0.00 0.00 2.83
118 119 3.168193 GTCACACTGGTTTCGTTGTTTG 58.832 45.455 0.00 0.00 0.00 2.93
119 120 1.917303 CACACTGGTTTCGTTGTTTGC 59.083 47.619 0.00 0.00 0.00 3.68
120 121 1.542030 ACACTGGTTTCGTTGTTTGCA 59.458 42.857 0.00 0.00 0.00 4.08
121 122 2.029828 ACACTGGTTTCGTTGTTTGCAA 60.030 40.909 0.00 0.00 0.00 4.08
122 123 2.989840 CACTGGTTTCGTTGTTTGCAAA 59.010 40.909 8.05 8.05 36.22 3.68
123 124 3.616379 CACTGGTTTCGTTGTTTGCAAAT 59.384 39.130 16.21 0.00 36.22 2.32
124 125 3.616379 ACTGGTTTCGTTGTTTGCAAATG 59.384 39.130 16.21 6.27 36.22 2.32
125 126 2.932614 TGGTTTCGTTGTTTGCAAATGG 59.067 40.909 16.21 5.37 36.22 3.16
126 127 3.190874 GGTTTCGTTGTTTGCAAATGGA 58.809 40.909 16.21 7.64 36.22 3.41
127 128 3.619038 GGTTTCGTTGTTTGCAAATGGAA 59.381 39.130 16.21 12.89 36.22 3.53
128 129 4.493382 GGTTTCGTTGTTTGCAAATGGAAC 60.493 41.667 16.21 16.14 36.22 3.62
129 130 2.815478 TCGTTGTTTGCAAATGGAACC 58.185 42.857 16.21 1.50 36.22 3.62
130 131 1.520590 CGTTGTTTGCAAATGGAACCG 59.479 47.619 16.21 8.42 36.22 4.44
131 132 1.864082 GTTGTTTGCAAATGGAACCGG 59.136 47.619 16.21 0.00 36.22 5.28
132 133 0.390860 TGTTTGCAAATGGAACCGGG 59.609 50.000 16.21 0.00 0.00 5.73
133 134 0.676736 GTTTGCAAATGGAACCGGGA 59.323 50.000 16.21 0.00 0.00 5.14
134 135 0.676736 TTTGCAAATGGAACCGGGAC 59.323 50.000 8.05 0.00 0.00 4.46
135 136 0.178975 TTGCAAATGGAACCGGGACT 60.179 50.000 6.32 0.00 0.00 3.85
136 137 0.893270 TGCAAATGGAACCGGGACTG 60.893 55.000 6.32 0.00 0.00 3.51
137 138 0.893727 GCAAATGGAACCGGGACTGT 60.894 55.000 6.32 0.00 0.00 3.55
138 139 0.881118 CAAATGGAACCGGGACTGTG 59.119 55.000 6.32 0.00 0.00 3.66
139 140 0.476771 AAATGGAACCGGGACTGTGT 59.523 50.000 6.32 0.00 0.00 3.72
140 141 0.250727 AATGGAACCGGGACTGTGTG 60.251 55.000 6.32 0.00 0.00 3.82
141 142 2.032071 GGAACCGGGACTGTGTGG 59.968 66.667 6.32 0.00 0.00 4.17
142 143 2.814835 GGAACCGGGACTGTGTGGT 61.815 63.158 6.32 0.00 35.90 4.16
143 144 1.597027 GAACCGGGACTGTGTGGTG 60.597 63.158 6.32 0.00 34.26 4.17
144 145 2.319890 GAACCGGGACTGTGTGGTGT 62.320 60.000 6.32 0.00 34.26 4.16
145 146 2.280797 CCGGGACTGTGTGGTGTG 60.281 66.667 0.00 0.00 0.00 3.82
146 147 2.972505 CGGGACTGTGTGGTGTGC 60.973 66.667 0.00 0.00 0.00 4.57
147 148 2.594592 GGGACTGTGTGGTGTGCC 60.595 66.667 0.00 0.00 37.50 5.01
148 149 2.594592 GGACTGTGTGGTGTGCCC 60.595 66.667 0.00 0.00 0.00 5.36
149 150 2.510906 GACTGTGTGGTGTGCCCT 59.489 61.111 0.00 0.00 0.00 5.19
150 151 1.152963 GACTGTGTGGTGTGCCCTT 60.153 57.895 0.00 0.00 0.00 3.95
151 152 0.751643 GACTGTGTGGTGTGCCCTTT 60.752 55.000 0.00 0.00 0.00 3.11
152 153 0.324275 ACTGTGTGGTGTGCCCTTTT 60.324 50.000 0.00 0.00 0.00 2.27
153 154 0.102844 CTGTGTGGTGTGCCCTTTTG 59.897 55.000 0.00 0.00 0.00 2.44
154 155 1.227234 GTGTGGTGTGCCCTTTTGC 60.227 57.895 0.00 0.00 0.00 3.68
155 156 1.381056 TGTGGTGTGCCCTTTTGCT 60.381 52.632 0.00 0.00 0.00 3.91
156 157 1.363807 GTGGTGTGCCCTTTTGCTC 59.636 57.895 0.00 0.00 0.00 4.26
157 158 1.076412 TGGTGTGCCCTTTTGCTCA 60.076 52.632 0.00 0.00 32.78 4.26
158 159 0.685785 TGGTGTGCCCTTTTGCTCAA 60.686 50.000 0.00 0.00 36.60 3.02
159 160 0.463620 GGTGTGCCCTTTTGCTCAAA 59.536 50.000 0.00 0.00 36.60 2.69
160 161 1.134551 GGTGTGCCCTTTTGCTCAAAA 60.135 47.619 7.46 7.46 36.60 2.44
161 162 2.626840 GTGTGCCCTTTTGCTCAAAAA 58.373 42.857 8.83 0.00 39.49 1.94
215 216 5.353956 CGGTGATCTTCAAACACATCCATTA 59.646 40.000 0.00 0.00 36.42 1.90
221 222 8.585471 ATCTTCAAACACATCCATTATTGAGT 57.415 30.769 0.00 0.00 0.00 3.41
222 223 9.685276 ATCTTCAAACACATCCATTATTGAGTA 57.315 29.630 0.00 0.00 0.00 2.59
223 224 9.685276 TCTTCAAACACATCCATTATTGAGTAT 57.315 29.630 0.00 0.00 0.00 2.12
248 249 7.216973 AGACAGTAACTGAACTTAGGTACAG 57.783 40.000 0.00 0.00 42.11 2.74
251 252 7.603651 ACAGTAACTGAACTTAGGTACAGATG 58.396 38.462 0.00 0.00 42.11 2.90
260 261 2.233305 AGGTACAGATGAACCCGTCT 57.767 50.000 0.00 0.00 39.15 4.18
261 262 2.537143 AGGTACAGATGAACCCGTCTT 58.463 47.619 0.00 0.00 36.55 3.01
335 354 4.308526 TGTAGAATATGTGTGGGGCAAA 57.691 40.909 0.00 0.00 0.00 3.68
392 441 3.626977 TGCACGTTTCATGACACATTTC 58.373 40.909 12.28 0.00 0.00 2.17
395 444 4.739716 GCACGTTTCATGACACATTTCTTT 59.260 37.500 12.28 0.00 0.00 2.52
396 445 5.231991 GCACGTTTCATGACACATTTCTTTT 59.768 36.000 12.28 0.00 0.00 2.27
423 473 4.879104 TTTTGTGCATGCCAAAAGAAAG 57.121 36.364 28.24 0.00 36.99 2.62
426 476 3.196463 TGTGCATGCCAAAAGAAAGTTG 58.804 40.909 16.68 0.00 0.00 3.16
427 477 2.032636 GTGCATGCCAAAAGAAAGTTGC 60.033 45.455 16.68 0.00 0.00 4.17
436 486 3.518634 AAAGAAAGTTGCTTTTCGGCA 57.481 38.095 2.70 0.00 40.99 5.69
459 509 4.410492 AACTTTTTGAGCGCACATAGAG 57.590 40.909 11.47 12.11 0.00 2.43
470 520 2.480932 CGCACATAGAGCACAGAGATGT 60.481 50.000 0.00 0.00 0.00 3.06
568 619 7.280876 GCGTTCATACATATATGTTCCATCCAT 59.719 37.037 22.90 6.46 41.97 3.41
609 660 6.147821 TGTTGCTCATTTGTTAGCTAGAGTTC 59.852 38.462 0.00 1.07 39.53 3.01
614 665 7.306283 GCTCATTTGTTAGCTAGAGTTCGTATG 60.306 40.741 0.00 0.00 35.80 2.39
621 672 8.680001 TGTTAGCTAGAGTTCGTATGTATTCAA 58.320 33.333 0.00 0.00 0.00 2.69
623 674 7.336161 AGCTAGAGTTCGTATGTATTCAAGT 57.664 36.000 0.00 0.00 0.00 3.16
626 677 8.533153 GCTAGAGTTCGTATGTATTCAAGTTTC 58.467 37.037 0.00 0.00 0.00 2.78
628 679 7.612677 AGAGTTCGTATGTATTCAAGTTTCCT 58.387 34.615 0.00 0.00 0.00 3.36
629 680 8.746530 AGAGTTCGTATGTATTCAAGTTTCCTA 58.253 33.333 0.00 0.00 0.00 2.94
630 681 9.530633 GAGTTCGTATGTATTCAAGTTTCCTAT 57.469 33.333 0.00 0.00 0.00 2.57
631 682 9.886132 AGTTCGTATGTATTCAAGTTTCCTATT 57.114 29.630 0.00 0.00 0.00 1.73
633 684 8.882415 TCGTATGTATTCAAGTTTCCTATTCC 57.118 34.615 0.00 0.00 0.00 3.01
634 685 7.929785 TCGTATGTATTCAAGTTTCCTATTCCC 59.070 37.037 0.00 0.00 0.00 3.97
635 686 7.931948 CGTATGTATTCAAGTTTCCTATTCCCT 59.068 37.037 0.00 0.00 0.00 4.20
636 687 9.274206 GTATGTATTCAAGTTTCCTATTCCCTC 57.726 37.037 0.00 0.00 0.00 4.30
637 688 7.510675 TGTATTCAAGTTTCCTATTCCCTCT 57.489 36.000 0.00 0.00 0.00 3.69
638 689 7.338710 TGTATTCAAGTTTCCTATTCCCTCTG 58.661 38.462 0.00 0.00 0.00 3.35
639 690 5.843019 TTCAAGTTTCCTATTCCCTCTGT 57.157 39.130 0.00 0.00 0.00 3.41
640 691 5.843019 TCAAGTTTCCTATTCCCTCTGTT 57.157 39.130 0.00 0.00 0.00 3.16
641 692 5.805728 TCAAGTTTCCTATTCCCTCTGTTC 58.194 41.667 0.00 0.00 0.00 3.18
642 693 4.846168 AGTTTCCTATTCCCTCTGTTCC 57.154 45.455 0.00 0.00 0.00 3.62
643 694 4.439860 AGTTTCCTATTCCCTCTGTTCCT 58.560 43.478 0.00 0.00 0.00 3.36
644 695 5.600749 AGTTTCCTATTCCCTCTGTTCCTA 58.399 41.667 0.00 0.00 0.00 2.94
645 696 5.425862 AGTTTCCTATTCCCTCTGTTCCTAC 59.574 44.000 0.00 0.00 0.00 3.18
646 697 4.620086 TCCTATTCCCTCTGTTCCTACA 57.380 45.455 0.00 0.00 0.00 2.74
647 698 5.157770 TCCTATTCCCTCTGTTCCTACAT 57.842 43.478 0.00 0.00 32.86 2.29
648 699 6.289482 TCCTATTCCCTCTGTTCCTACATA 57.711 41.667 0.00 0.00 32.86 2.29
649 700 6.875469 TCCTATTCCCTCTGTTCCTACATAT 58.125 40.000 0.00 0.00 32.86 1.78
650 701 7.313731 TCCTATTCCCTCTGTTCCTACATATT 58.686 38.462 0.00 0.00 32.86 1.28
651 702 7.794683 TCCTATTCCCTCTGTTCCTACATATTT 59.205 37.037 0.00 0.00 32.86 1.40
652 703 7.880195 CCTATTCCCTCTGTTCCTACATATTTG 59.120 40.741 0.00 0.00 32.86 2.32
653 704 6.636454 TTCCCTCTGTTCCTACATATTTGT 57.364 37.500 0.00 0.00 39.98 2.83
654 705 6.235231 TCCCTCTGTTCCTACATATTTGTC 57.765 41.667 0.00 0.00 37.28 3.18
655 706 5.964477 TCCCTCTGTTCCTACATATTTGTCT 59.036 40.000 0.00 0.00 37.28 3.41
656 707 6.443849 TCCCTCTGTTCCTACATATTTGTCTT 59.556 38.462 0.00 0.00 37.28 3.01
657 708 7.037586 TCCCTCTGTTCCTACATATTTGTCTTT 60.038 37.037 0.00 0.00 37.28 2.52
658 709 7.611855 CCCTCTGTTCCTACATATTTGTCTTTT 59.388 37.037 0.00 0.00 37.28 2.27
659 710 9.014297 CCTCTGTTCCTACATATTTGTCTTTTT 57.986 33.333 0.00 0.00 37.28 1.94
676 727 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
677 728 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
692 743 1.411246 TGGACTACCACATACGGATGC 59.589 52.381 7.78 0.00 41.77 3.91
693 744 1.411246 GGACTACCACATACGGATGCA 59.589 52.381 7.78 0.00 36.43 3.96
694 745 2.037251 GGACTACCACATACGGATGCAT 59.963 50.000 7.78 0.00 36.43 3.96
695 746 3.257375 GGACTACCACATACGGATGCATA 59.743 47.826 7.78 0.00 36.43 3.14
696 747 4.262292 GGACTACCACATACGGATGCATAA 60.262 45.833 7.78 0.00 36.43 1.90
697 748 5.284861 ACTACCACATACGGATGCATAAA 57.715 39.130 7.78 0.00 36.43 1.40
698 749 5.297547 ACTACCACATACGGATGCATAAAG 58.702 41.667 7.78 1.85 36.43 1.85
699 750 4.415881 ACCACATACGGATGCATAAAGA 57.584 40.909 7.78 0.00 36.43 2.52
700 751 4.127171 ACCACATACGGATGCATAAAGAC 58.873 43.478 7.78 0.00 36.43 3.01
701 752 4.126437 CCACATACGGATGCATAAAGACA 58.874 43.478 7.78 0.00 36.43 3.41
702 753 4.024893 CCACATACGGATGCATAAAGACAC 60.025 45.833 7.78 0.00 36.43 3.67
703 754 4.570369 CACATACGGATGCATAAAGACACA 59.430 41.667 7.78 0.00 36.43 3.72
704 755 4.811024 ACATACGGATGCATAAAGACACAG 59.189 41.667 7.78 0.00 36.43 3.66
705 756 3.334583 ACGGATGCATAAAGACACAGT 57.665 42.857 0.00 0.00 0.00 3.55
706 757 3.674997 ACGGATGCATAAAGACACAGTT 58.325 40.909 0.00 0.00 0.00 3.16
707 758 4.072131 ACGGATGCATAAAGACACAGTTT 58.928 39.130 0.00 0.00 0.00 2.66
708 759 5.242434 ACGGATGCATAAAGACACAGTTTA 58.758 37.500 0.00 0.00 0.00 2.01
709 760 5.351465 ACGGATGCATAAAGACACAGTTTAG 59.649 40.000 0.00 0.00 0.00 1.85
710 761 5.580691 CGGATGCATAAAGACACAGTTTAGA 59.419 40.000 0.00 0.00 0.00 2.10
711 762 6.092122 CGGATGCATAAAGACACAGTTTAGAA 59.908 38.462 0.00 0.00 0.00 2.10
712 763 7.201644 CGGATGCATAAAGACACAGTTTAGAAT 60.202 37.037 0.00 0.00 0.00 2.40
713 764 7.912250 GGATGCATAAAGACACAGTTTAGAATG 59.088 37.037 0.00 0.00 0.00 2.67
714 765 7.744087 TGCATAAAGACACAGTTTAGAATGT 57.256 32.000 0.00 0.00 0.00 2.71
715 766 8.165239 TGCATAAAGACACAGTTTAGAATGTT 57.835 30.769 0.00 0.00 0.00 2.71
716 767 8.075574 TGCATAAAGACACAGTTTAGAATGTTG 58.924 33.333 0.00 0.00 0.00 3.33
717 768 8.289618 GCATAAAGACACAGTTTAGAATGTTGA 58.710 33.333 0.00 0.00 0.00 3.18
721 772 8.450578 AAGACACAGTTTAGAATGTTGATTCA 57.549 30.769 0.00 0.00 40.59 2.57
722 773 7.865707 AGACACAGTTTAGAATGTTGATTCAC 58.134 34.615 0.00 0.00 40.59 3.18
723 774 7.716998 AGACACAGTTTAGAATGTTGATTCACT 59.283 33.333 0.00 0.00 40.59 3.41
724 775 7.865707 ACACAGTTTAGAATGTTGATTCACTC 58.134 34.615 0.00 0.00 40.59 3.51
725 776 7.498900 ACACAGTTTAGAATGTTGATTCACTCA 59.501 33.333 0.00 0.00 40.59 3.41
726 777 8.509690 CACAGTTTAGAATGTTGATTCACTCAT 58.490 33.333 0.00 0.00 40.59 2.90
727 778 9.071276 ACAGTTTAGAATGTTGATTCACTCATT 57.929 29.630 12.91 12.91 40.59 2.57
728 779 9.903682 CAGTTTAGAATGTTGATTCACTCATTT 57.096 29.630 13.76 8.95 40.59 2.32
734 785 9.603921 AGAATGTTGATTCACTCATTTTGTTTT 57.396 25.926 13.76 0.00 40.59 2.43
735 786 9.853921 GAATGTTGATTCACTCATTTTGTTTTC 57.146 29.630 13.76 2.40 38.33 2.29
736 787 9.603921 AATGTTGATTCACTCATTTTGTTTTCT 57.396 25.926 9.21 0.00 32.72 2.52
764 815 9.996554 TGTAATCACTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 37.92 2.10
767 818 9.784531 AATCACTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 37.92 2.52
768 819 9.956640 ATCACTTGTTGAAATCTCTAGAAAGAT 57.043 29.630 0.00 0.00 37.92 2.40
790 841 9.780186 AAGATAAATATTTAGGAACGGAAGGAG 57.220 33.333 13.15 0.00 0.00 3.69
828 879 0.174845 TGCATACGGGAAACTCTCGG 59.825 55.000 0.45 0.00 46.41 4.63
830 881 1.801765 GCATACGGGAAACTCTCGGTC 60.802 57.143 0.45 0.00 46.41 4.79
970 1547 2.818751 AACTGATCCTCTCTCTCCGT 57.181 50.000 0.00 0.00 0.00 4.69
976 1553 0.108089 TCCTCTCTCTCCGTCTCACG 60.108 60.000 0.00 0.00 42.11 4.35
1043 1620 1.899054 CCTCGCTCTCGCCATCCTA 60.899 63.158 0.00 0.00 35.26 2.94
1054 1631 2.505982 CATCCTACCCCACGCCTG 59.494 66.667 0.00 0.00 0.00 4.85
1072 1649 2.051518 GCAACCGCATCATCCCCAA 61.052 57.895 0.00 0.00 38.36 4.12
1105 1682 2.264794 CCGCCCTCGTGCTTAACT 59.735 61.111 0.00 0.00 0.00 2.24
1311 1888 3.647649 CTGCACCATCGACCTCGCA 62.648 63.158 0.00 0.00 39.60 5.10
1941 2518 2.933878 AAGAAGGTTGCACGCCGTCA 62.934 55.000 19.32 0.00 37.05 4.35
2040 2617 2.642139 TGGTTCGACAGGATTACGTC 57.358 50.000 0.00 0.00 0.00 4.34
2367 2944 3.205507 AGATGGTGGAGAGAGGCTACTTA 59.794 47.826 0.00 0.00 0.00 2.24
2391 2968 1.072331 AGAAGGTTCATGCTCAACCGT 59.928 47.619 8.67 6.14 46.98 4.83
2749 3326 8.371770 AGTTTTGTTTTGAGCTTGTGTTTTAA 57.628 26.923 0.00 0.00 0.00 1.52
2862 3439 8.577048 TGTGGTATATAGTTACTAGGATCTGC 57.423 38.462 0.00 0.00 0.00 4.26
2871 3448 6.902408 AGTTACTAGGATCTGCAGTAGTAGT 58.098 40.000 14.67 16.98 31.34 2.73
3016 3817 5.843969 TGCATGGAGGGAGACTGTATTAATA 59.156 40.000 0.00 0.00 0.00 0.98
3017 3818 6.328934 TGCATGGAGGGAGACTGTATTAATAA 59.671 38.462 0.00 0.00 0.00 1.40
3049 3850 3.625764 TCGCAACAAGAAACAAAGCTAGT 59.374 39.130 0.00 0.00 0.00 2.57
3155 3956 3.738982 TGTGTGGAATCTGTACTGTTGG 58.261 45.455 0.00 0.00 0.00 3.77
3214 4025 8.652463 GGCGCAAACACAAATAATAAGTATTTT 58.348 29.630 10.83 0.00 39.88 1.82
3279 4090 6.633500 AGCAAAGCAGTGTTGTCTTTATTA 57.367 33.333 0.00 0.00 32.88 0.98
3377 4188 9.626045 CTTATTTTGGTGTTTTCTCCATAGTTC 57.374 33.333 0.00 0.00 42.09 3.01
3446 4257 5.006358 GTCGCGAGCAATAAATTCCTTTCTA 59.994 40.000 10.24 0.00 0.00 2.10
3447 4258 5.234329 TCGCGAGCAATAAATTCCTTTCTAG 59.766 40.000 3.71 0.00 0.00 2.43
3449 4260 6.563010 CGCGAGCAATAAATTCCTTTCTAGAG 60.563 42.308 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.818296 CGACCACTCTCCCTAACAGG 59.182 60.000 0.00 0.00 34.30 4.00
4 5 1.546961 ACGACCACTCTCCCTAACAG 58.453 55.000 0.00 0.00 0.00 3.16
5 6 2.005370 AACGACCACTCTCCCTAACA 57.995 50.000 0.00 0.00 0.00 2.41
6 7 3.675502 GCTAAACGACCACTCTCCCTAAC 60.676 52.174 0.00 0.00 0.00 2.34
7 8 2.494870 GCTAAACGACCACTCTCCCTAA 59.505 50.000 0.00 0.00 0.00 2.69
8 9 2.097825 GCTAAACGACCACTCTCCCTA 58.902 52.381 0.00 0.00 0.00 3.53
9 10 0.896226 GCTAAACGACCACTCTCCCT 59.104 55.000 0.00 0.00 0.00 4.20
10 11 0.896226 AGCTAAACGACCACTCTCCC 59.104 55.000 0.00 0.00 0.00 4.30
11 12 1.544691 TCAGCTAAACGACCACTCTCC 59.455 52.381 0.00 0.00 0.00 3.71
12 13 2.869897 CTCAGCTAAACGACCACTCTC 58.130 52.381 0.00 0.00 0.00 3.20
13 14 1.067495 GCTCAGCTAAACGACCACTCT 60.067 52.381 0.00 0.00 0.00 3.24
14 15 1.351153 GCTCAGCTAAACGACCACTC 58.649 55.000 0.00 0.00 0.00 3.51
15 16 0.388649 CGCTCAGCTAAACGACCACT 60.389 55.000 0.00 0.00 0.00 4.00
16 17 0.666577 ACGCTCAGCTAAACGACCAC 60.667 55.000 8.25 0.00 0.00 4.16
17 18 0.032952 AACGCTCAGCTAAACGACCA 59.967 50.000 8.25 0.00 0.00 4.02
18 19 1.145803 AAACGCTCAGCTAAACGACC 58.854 50.000 8.25 0.00 0.00 4.79
19 20 2.943843 AAAACGCTCAGCTAAACGAC 57.056 45.000 8.25 0.00 0.00 4.34
47 48 3.420606 CACAGCACGCTGCCTCAG 61.421 66.667 18.72 0.87 46.52 3.35
54 55 4.923942 AGCACAGCACAGCACGCT 62.924 61.111 0.00 0.00 41.47 5.07
55 56 4.380628 GAGCACAGCACAGCACGC 62.381 66.667 0.00 0.00 0.00 5.34
56 57 3.720193 GGAGCACAGCACAGCACG 61.720 66.667 0.00 0.00 0.00 5.34
57 58 3.720193 CGGAGCACAGCACAGCAC 61.720 66.667 0.00 0.00 0.00 4.40
70 71 2.588877 CCATTACAGCCCGCGGAG 60.589 66.667 30.73 18.40 0.00 4.63
71 72 4.169696 CCCATTACAGCCCGCGGA 62.170 66.667 30.73 5.29 0.00 5.54
72 73 2.107041 TATCCCATTACAGCCCGCGG 62.107 60.000 21.04 21.04 0.00 6.46
73 74 0.036388 ATATCCCATTACAGCCCGCG 60.036 55.000 0.00 0.00 0.00 6.46
74 75 1.453155 CATATCCCATTACAGCCCGC 58.547 55.000 0.00 0.00 0.00 6.13
75 76 1.003580 AGCATATCCCATTACAGCCCG 59.996 52.381 0.00 0.00 0.00 6.13
76 77 2.821969 CAAGCATATCCCATTACAGCCC 59.178 50.000 0.00 0.00 0.00 5.19
77 78 3.490348 ACAAGCATATCCCATTACAGCC 58.510 45.455 0.00 0.00 0.00 4.85
78 79 4.023707 GTGACAAGCATATCCCATTACAGC 60.024 45.833 0.00 0.00 0.00 4.40
79 80 5.008019 GTGTGACAAGCATATCCCATTACAG 59.992 44.000 0.00 0.00 0.00 2.74
80 81 4.881273 GTGTGACAAGCATATCCCATTACA 59.119 41.667 0.00 0.00 0.00 2.41
81 82 5.008019 CAGTGTGACAAGCATATCCCATTAC 59.992 44.000 0.00 0.00 0.00 1.89
82 83 5.125356 CAGTGTGACAAGCATATCCCATTA 58.875 41.667 0.00 0.00 0.00 1.90
83 84 3.949754 CAGTGTGACAAGCATATCCCATT 59.050 43.478 0.00 0.00 0.00 3.16
84 85 3.548770 CAGTGTGACAAGCATATCCCAT 58.451 45.455 0.00 0.00 0.00 4.00
85 86 2.356022 CCAGTGTGACAAGCATATCCCA 60.356 50.000 0.00 0.00 0.00 4.37
86 87 2.292267 CCAGTGTGACAAGCATATCCC 58.708 52.381 0.00 0.00 0.00 3.85
87 88 2.991250 ACCAGTGTGACAAGCATATCC 58.009 47.619 0.00 0.00 0.00 2.59
88 89 4.436050 CGAAACCAGTGTGACAAGCATATC 60.436 45.833 0.00 0.00 0.00 1.63
89 90 3.436704 CGAAACCAGTGTGACAAGCATAT 59.563 43.478 0.00 0.00 0.00 1.78
90 91 2.805671 CGAAACCAGTGTGACAAGCATA 59.194 45.455 0.00 0.00 0.00 3.14
91 92 1.603802 CGAAACCAGTGTGACAAGCAT 59.396 47.619 0.00 0.00 0.00 3.79
92 93 1.013596 CGAAACCAGTGTGACAAGCA 58.986 50.000 0.00 0.00 0.00 3.91
93 94 1.014352 ACGAAACCAGTGTGACAAGC 58.986 50.000 0.00 0.00 0.00 4.01
94 95 2.418628 ACAACGAAACCAGTGTGACAAG 59.581 45.455 0.00 0.00 0.00 3.16
95 96 2.428491 ACAACGAAACCAGTGTGACAA 58.572 42.857 0.00 0.00 0.00 3.18
96 97 2.102070 ACAACGAAACCAGTGTGACA 57.898 45.000 0.00 0.00 0.00 3.58
97 98 3.168193 CAAACAACGAAACCAGTGTGAC 58.832 45.455 0.00 0.00 0.00 3.67
98 99 2.414824 GCAAACAACGAAACCAGTGTGA 60.415 45.455 0.00 0.00 0.00 3.58
99 100 1.917303 GCAAACAACGAAACCAGTGTG 59.083 47.619 0.00 0.00 0.00 3.82
100 101 1.542030 TGCAAACAACGAAACCAGTGT 59.458 42.857 0.00 0.00 0.00 3.55
101 102 2.270275 TGCAAACAACGAAACCAGTG 57.730 45.000 0.00 0.00 0.00 3.66
102 103 3.305398 TTTGCAAACAACGAAACCAGT 57.695 38.095 8.05 0.00 34.87 4.00
103 104 3.001127 CCATTTGCAAACAACGAAACCAG 59.999 43.478 15.41 0.00 34.87 4.00
104 105 2.932614 CCATTTGCAAACAACGAAACCA 59.067 40.909 15.41 0.00 34.87 3.67
105 106 3.190874 TCCATTTGCAAACAACGAAACC 58.809 40.909 15.41 0.00 34.87 3.27
106 107 4.493382 GGTTCCATTTGCAAACAACGAAAC 60.493 41.667 15.41 11.99 34.87 2.78
107 108 3.619038 GGTTCCATTTGCAAACAACGAAA 59.381 39.130 15.41 0.88 34.87 3.46
108 109 3.190874 GGTTCCATTTGCAAACAACGAA 58.809 40.909 15.41 10.49 34.87 3.85
109 110 2.796383 CGGTTCCATTTGCAAACAACGA 60.796 45.455 15.41 4.69 34.87 3.85
110 111 1.520590 CGGTTCCATTTGCAAACAACG 59.479 47.619 15.41 9.59 34.87 4.10
111 112 1.864082 CCGGTTCCATTTGCAAACAAC 59.136 47.619 15.41 16.26 34.87 3.32
112 113 1.202580 CCCGGTTCCATTTGCAAACAA 60.203 47.619 15.41 4.99 0.00 2.83
113 114 0.390860 CCCGGTTCCATTTGCAAACA 59.609 50.000 15.41 0.00 0.00 2.83
114 115 0.676736 TCCCGGTTCCATTTGCAAAC 59.323 50.000 15.41 1.27 0.00 2.93
115 116 0.676736 GTCCCGGTTCCATTTGCAAA 59.323 50.000 15.44 15.44 0.00 3.68
116 117 0.178975 AGTCCCGGTTCCATTTGCAA 60.179 50.000 0.00 0.00 0.00 4.08
117 118 0.893270 CAGTCCCGGTTCCATTTGCA 60.893 55.000 0.00 0.00 0.00 4.08
118 119 0.893727 ACAGTCCCGGTTCCATTTGC 60.894 55.000 0.00 0.00 0.00 3.68
119 120 0.881118 CACAGTCCCGGTTCCATTTG 59.119 55.000 0.00 0.00 0.00 2.32
120 121 0.476771 ACACAGTCCCGGTTCCATTT 59.523 50.000 0.00 0.00 0.00 2.32
121 122 0.250727 CACACAGTCCCGGTTCCATT 60.251 55.000 0.00 0.00 0.00 3.16
122 123 1.374947 CACACAGTCCCGGTTCCAT 59.625 57.895 0.00 0.00 0.00 3.41
123 124 2.813726 CCACACAGTCCCGGTTCCA 61.814 63.158 0.00 0.00 0.00 3.53
124 125 2.032071 CCACACAGTCCCGGTTCC 59.968 66.667 0.00 0.00 0.00 3.62
125 126 1.597027 CACCACACAGTCCCGGTTC 60.597 63.158 0.00 0.00 0.00 3.62
126 127 2.372074 ACACCACACAGTCCCGGTT 61.372 57.895 0.00 0.00 0.00 4.44
127 128 2.766651 ACACCACACAGTCCCGGT 60.767 61.111 0.00 0.00 0.00 5.28
128 129 2.280797 CACACCACACAGTCCCGG 60.281 66.667 0.00 0.00 0.00 5.73
129 130 2.972505 GCACACCACACAGTCCCG 60.973 66.667 0.00 0.00 0.00 5.14
130 131 2.594592 GGCACACCACACAGTCCC 60.595 66.667 0.00 0.00 35.26 4.46
131 132 2.594592 GGGCACACCACACAGTCC 60.595 66.667 0.00 0.00 39.85 3.85
132 133 0.751643 AAAGGGCACACCACACAGTC 60.752 55.000 0.00 0.00 43.89 3.51
133 134 0.324275 AAAAGGGCACACCACACAGT 60.324 50.000 0.00 0.00 43.89 3.55
134 135 0.102844 CAAAAGGGCACACCACACAG 59.897 55.000 0.00 0.00 43.89 3.66
135 136 1.954362 GCAAAAGGGCACACCACACA 61.954 55.000 0.00 0.00 43.89 3.72
136 137 1.227234 GCAAAAGGGCACACCACAC 60.227 57.895 0.00 0.00 43.89 3.82
137 138 1.381056 AGCAAAAGGGCACACCACA 60.381 52.632 0.00 0.00 43.89 4.17
138 139 1.363807 GAGCAAAAGGGCACACCAC 59.636 57.895 0.00 0.00 43.89 4.16
139 140 0.685785 TTGAGCAAAAGGGCACACCA 60.686 50.000 0.00 0.00 43.89 4.17
140 141 0.463620 TTTGAGCAAAAGGGCACACC 59.536 50.000 0.00 0.00 34.11 4.16
141 142 2.307934 TTTTGAGCAAAAGGGCACAC 57.692 45.000 4.39 0.00 35.57 3.82
221 222 9.964354 TGTACCTAAGTTCAGTTACTGTCTATA 57.036 33.333 12.41 2.19 32.61 1.31
222 223 8.874744 TGTACCTAAGTTCAGTTACTGTCTAT 57.125 34.615 12.41 1.14 32.61 1.98
223 224 8.159447 TCTGTACCTAAGTTCAGTTACTGTCTA 58.841 37.037 12.41 0.00 41.00 2.59
226 227 7.450634 TCATCTGTACCTAAGTTCAGTTACTGT 59.549 37.037 12.41 0.00 41.00 3.55
375 394 8.955061 AGATAAAAGAAATGTGTCATGAAACG 57.045 30.769 11.43 0.00 0.00 3.60
407 457 2.158928 AGCAACTTTCTTTTGGCATGCA 60.159 40.909 21.36 2.54 35.11 3.96
408 458 2.486918 AGCAACTTTCTTTTGGCATGC 58.513 42.857 9.90 9.90 0.00 4.06
426 476 4.577639 CTCAAAAAGTTTTGCCGAAAAGC 58.422 39.130 10.94 0.00 45.35 3.51
427 477 4.577639 GCTCAAAAAGTTTTGCCGAAAAG 58.422 39.130 10.94 4.53 45.35 2.27
436 486 5.181690 TCTATGTGCGCTCAAAAAGTTTT 57.818 34.783 16.95 0.00 0.00 2.43
443 493 1.078709 GTGCTCTATGTGCGCTCAAA 58.921 50.000 16.95 4.47 37.87 2.69
450 500 3.176552 ACATCTCTGTGCTCTATGTGC 57.823 47.619 0.00 0.00 33.22 4.57
459 509 0.302890 GCATGCGTACATCTCTGTGC 59.697 55.000 0.00 0.00 36.79 4.57
499 550 5.387279 TCGGAAAACGCATTTCTAAATGTC 58.613 37.500 14.98 8.02 45.77 3.06
501 552 5.220024 GCTTCGGAAAACGCATTTCTAAATG 60.220 40.000 10.43 10.43 45.57 2.32
529 580 2.049802 AACGCGGGTACACGTGAG 60.050 61.111 35.56 20.87 46.47 3.51
534 585 1.930567 ATGTATGAACGCGGGTACAC 58.069 50.000 12.47 3.05 30.67 2.90
536 587 5.404946 ACATATATGTATGAACGCGGGTAC 58.595 41.667 16.85 8.21 40.12 3.34
568 619 9.491675 AATGAGCAACAATATTCAAATGACAAA 57.508 25.926 0.00 0.00 0.00 2.83
609 660 7.931948 AGGGAATAGGAAACTTGAATACATACG 59.068 37.037 0.00 0.00 43.67 3.06
614 665 7.339482 ACAGAGGGAATAGGAAACTTGAATAC 58.661 38.462 0.00 0.00 43.67 1.89
618 669 5.280521 GGAACAGAGGGAATAGGAAACTTGA 60.281 44.000 0.00 0.00 43.67 3.02
621 672 8.251823 ATGTAGGAACAGAGGGAATAGGAAACT 61.252 40.741 0.00 0.00 41.49 2.66
623 674 5.347124 TGTAGGAACAGAGGGAATAGGAAA 58.653 41.667 0.00 0.00 0.00 3.13
626 677 7.560796 AATATGTAGGAACAGAGGGAATAGG 57.439 40.000 0.00 0.00 39.49 2.57
628 679 8.331931 ACAAATATGTAGGAACAGAGGGAATA 57.668 34.615 0.00 0.00 39.49 1.75
629 680 7.127955 AGACAAATATGTAGGAACAGAGGGAAT 59.872 37.037 0.00 0.00 40.74 3.01
630 681 6.443849 AGACAAATATGTAGGAACAGAGGGAA 59.556 38.462 0.00 0.00 40.74 3.97
631 682 5.964477 AGACAAATATGTAGGAACAGAGGGA 59.036 40.000 0.00 0.00 40.74 4.20
632 683 6.240549 AGACAAATATGTAGGAACAGAGGG 57.759 41.667 0.00 0.00 40.74 4.30
633 684 8.567285 AAAAGACAAATATGTAGGAACAGAGG 57.433 34.615 0.00 0.00 40.74 3.69
650 701 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
651 702 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
655 706 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
656 707 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
657 708 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
658 709 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
659 710 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
660 711 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
661 712 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
662 713 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
663 714 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
664 715 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
665 716 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
666 717 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
667 718 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
668 719 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
669 720 4.703897 CATCCGTATGTGGTAGTCCATTT 58.296 43.478 0.00 0.00 46.20 2.32
670 721 3.494398 GCATCCGTATGTGGTAGTCCATT 60.494 47.826 0.00 0.00 46.20 3.16
671 722 2.037251 GCATCCGTATGTGGTAGTCCAT 59.963 50.000 0.00 0.00 46.20 3.41
672 723 1.411246 GCATCCGTATGTGGTAGTCCA 59.589 52.381 0.00 0.00 36.08 4.02
673 724 1.411246 TGCATCCGTATGTGGTAGTCC 59.589 52.381 0.00 0.00 35.38 3.85
674 725 2.882927 TGCATCCGTATGTGGTAGTC 57.117 50.000 0.00 0.00 35.38 2.59
675 726 4.948341 TTATGCATCCGTATGTGGTAGT 57.052 40.909 0.19 0.00 35.38 2.73
676 727 5.405571 GTCTTTATGCATCCGTATGTGGTAG 59.594 44.000 0.19 0.00 35.38 3.18
677 728 5.163395 TGTCTTTATGCATCCGTATGTGGTA 60.163 40.000 0.19 0.00 35.38 3.25
678 729 4.127171 GTCTTTATGCATCCGTATGTGGT 58.873 43.478 0.19 0.00 35.38 4.16
679 730 4.024893 GTGTCTTTATGCATCCGTATGTGG 60.025 45.833 0.19 0.00 35.38 4.17
680 731 4.570369 TGTGTCTTTATGCATCCGTATGTG 59.430 41.667 0.19 0.00 35.38 3.21
681 732 4.765273 TGTGTCTTTATGCATCCGTATGT 58.235 39.130 0.19 0.00 35.38 2.29
682 733 4.811024 ACTGTGTCTTTATGCATCCGTATG 59.189 41.667 0.19 0.00 36.09 2.39
683 734 5.023533 ACTGTGTCTTTATGCATCCGTAT 57.976 39.130 0.19 0.00 0.00 3.06
684 735 4.465632 ACTGTGTCTTTATGCATCCGTA 57.534 40.909 0.19 0.00 0.00 4.02
685 736 3.334583 ACTGTGTCTTTATGCATCCGT 57.665 42.857 0.19 0.00 0.00 4.69
686 737 4.685169 AAACTGTGTCTTTATGCATCCG 57.315 40.909 0.19 0.00 0.00 4.18
687 738 6.985188 TCTAAACTGTGTCTTTATGCATCC 57.015 37.500 0.19 0.00 0.00 3.51
688 739 8.454106 ACATTCTAAACTGTGTCTTTATGCATC 58.546 33.333 0.19 0.00 0.00 3.91
689 740 8.340618 ACATTCTAAACTGTGTCTTTATGCAT 57.659 30.769 3.79 3.79 0.00 3.96
690 741 7.744087 ACATTCTAAACTGTGTCTTTATGCA 57.256 32.000 0.00 0.00 0.00 3.96
691 742 8.289618 TCAACATTCTAAACTGTGTCTTTATGC 58.710 33.333 0.00 0.00 0.00 3.14
695 746 8.902806 TGAATCAACATTCTAAACTGTGTCTTT 58.097 29.630 0.00 0.00 39.49 2.52
696 747 8.345565 GTGAATCAACATTCTAAACTGTGTCTT 58.654 33.333 0.00 0.00 39.49 3.01
697 748 7.716998 AGTGAATCAACATTCTAAACTGTGTCT 59.283 33.333 0.00 0.00 39.49 3.41
698 749 7.865707 AGTGAATCAACATTCTAAACTGTGTC 58.134 34.615 0.00 0.00 39.49 3.67
699 750 7.498900 TGAGTGAATCAACATTCTAAACTGTGT 59.501 33.333 0.00 0.00 39.49 3.72
700 751 7.864686 TGAGTGAATCAACATTCTAAACTGTG 58.135 34.615 0.00 0.00 39.49 3.66
701 752 8.627208 ATGAGTGAATCAACATTCTAAACTGT 57.373 30.769 0.00 0.00 42.53 3.55
702 753 9.903682 AAATGAGTGAATCAACATTCTAAACTG 57.096 29.630 14.00 0.00 42.53 3.16
708 759 9.603921 AAAACAAAATGAGTGAATCAACATTCT 57.396 25.926 14.00 2.31 42.53 2.40
709 760 9.853921 GAAAACAAAATGAGTGAATCAACATTC 57.146 29.630 14.00 0.00 42.53 2.67
710 761 9.603921 AGAAAACAAAATGAGTGAATCAACATT 57.396 25.926 9.82 9.82 42.53 2.71
738 789 9.996554 TTCTAGAGATTTCAACAAGTGATTACA 57.003 29.630 0.00 0.00 35.70 2.41
741 792 9.784531 TCTTTCTAGAGATTTCAACAAGTGATT 57.215 29.630 0.00 0.00 35.70 2.57
742 793 9.956640 ATCTTTCTAGAGATTTCAACAAGTGAT 57.043 29.630 0.00 0.00 32.54 3.06
764 815 9.780186 CTCCTTCCGTTCCTAAATATTTATCTT 57.220 33.333 8.34 0.00 0.00 2.40
765 816 8.935741 ACTCCTTCCGTTCCTAAATATTTATCT 58.064 33.333 8.34 0.00 0.00 1.98
773 824 9.916360 AAAATAATACTCCTTCCGTTCCTAAAT 57.084 29.630 0.00 0.00 0.00 1.40
774 825 9.169592 CAAAATAATACTCCTTCCGTTCCTAAA 57.830 33.333 0.00 0.00 0.00 1.85
775 826 8.323567 ACAAAATAATACTCCTTCCGTTCCTAA 58.676 33.333 0.00 0.00 0.00 2.69
776 827 7.854337 ACAAAATAATACTCCTTCCGTTCCTA 58.146 34.615 0.00 0.00 0.00 2.94
777 828 6.718294 ACAAAATAATACTCCTTCCGTTCCT 58.282 36.000 0.00 0.00 0.00 3.36
778 829 6.037940 GGACAAAATAATACTCCTTCCGTTCC 59.962 42.308 0.00 0.00 0.00 3.62
779 830 6.822170 AGGACAAAATAATACTCCTTCCGTTC 59.178 38.462 0.00 0.00 0.00 3.95
780 831 6.598064 CAGGACAAAATAATACTCCTTCCGTT 59.402 38.462 0.00 0.00 0.00 4.44
781 832 6.113411 CAGGACAAAATAATACTCCTTCCGT 58.887 40.000 0.00 0.00 0.00 4.69
782 833 5.527582 CCAGGACAAAATAATACTCCTTCCG 59.472 44.000 0.00 0.00 0.00 4.30
783 834 6.659824 TCCAGGACAAAATAATACTCCTTCC 58.340 40.000 0.00 0.00 0.00 3.46
784 835 8.624776 CAATCCAGGACAAAATAATACTCCTTC 58.375 37.037 0.00 0.00 0.00 3.46
785 836 7.068716 GCAATCCAGGACAAAATAATACTCCTT 59.931 37.037 0.00 0.00 0.00 3.36
786 837 6.547510 GCAATCCAGGACAAAATAATACTCCT 59.452 38.462 0.00 0.00 0.00 3.69
787 838 6.321181 TGCAATCCAGGACAAAATAATACTCC 59.679 38.462 0.00 0.00 0.00 3.85
788 839 7.333528 TGCAATCCAGGACAAAATAATACTC 57.666 36.000 0.00 0.00 0.00 2.59
789 840 7.902920 ATGCAATCCAGGACAAAATAATACT 57.097 32.000 0.00 0.00 0.00 2.12
790 841 7.803189 CGTATGCAATCCAGGACAAAATAATAC 59.197 37.037 0.00 0.00 0.00 1.89
795 846 3.381272 CCGTATGCAATCCAGGACAAAAT 59.619 43.478 0.00 0.00 0.00 1.82
828 879 7.411157 GCTTTATTGATTGCTCAACAACATGAC 60.411 37.037 0.00 0.00 43.92 3.06
830 881 6.588756 AGCTTTATTGATTGCTCAACAACATG 59.411 34.615 0.00 0.00 43.92 3.21
932 1509 4.209288 CAGTTACACAAAGACGAAGGAGTG 59.791 45.833 0.00 0.00 0.00 3.51
1054 1631 2.051518 TTGGGGATGATGCGGTTGC 61.052 57.895 0.00 0.00 43.20 4.17
1105 1682 1.228521 TGAGGTTGGACGACGGGTA 60.229 57.895 0.00 0.00 0.00 3.69
1840 2417 7.323420 CCATGAATGATGGTAGTGTACGATAT 58.677 38.462 0.00 0.00 46.20 1.63
1941 2518 0.240945 GCGCATTGTAAGTTGCCACT 59.759 50.000 0.30 0.00 35.41 4.00
2340 2917 2.406559 CCTCTCTCCACCATCTCCATT 58.593 52.381 0.00 0.00 0.00 3.16
2391 2968 4.278170 GTCAACATCAACCCATTCAGAACA 59.722 41.667 0.00 0.00 0.00 3.18
2725 3302 8.279800 AGTTAAAACACAAGCTCAAAACAAAAC 58.720 29.630 0.00 0.00 0.00 2.43
2749 3326 6.699575 AGAACATGCAGTTAACAAAAGAGT 57.300 33.333 8.61 0.00 41.51 3.24
2862 3439 4.748892 ACACTTGCAGCATACTACTACTG 58.251 43.478 0.00 0.00 0.00 2.74
2871 3448 5.405935 TCTAGAGAAACACTTGCAGCATA 57.594 39.130 0.00 0.00 0.00 3.14
3016 3817 3.482436 TCTTGTTGCGAGTATTTGGGTT 58.518 40.909 0.00 0.00 0.00 4.11
3017 3818 3.134574 TCTTGTTGCGAGTATTTGGGT 57.865 42.857 0.00 0.00 0.00 4.51
3028 3829 3.725740 CACTAGCTTTGTTTCTTGTTGCG 59.274 43.478 0.00 0.00 0.00 4.85
3049 3850 6.824196 TGACACAATACAACTAAAAGTCACCA 59.176 34.615 0.00 0.00 0.00 4.17
3155 3956 8.664211 TTCAACCCATAACATTTACCAAAAAC 57.336 30.769 0.00 0.00 0.00 2.43
3279 4090 0.464036 TTCGCTCACACAGTCAGGTT 59.536 50.000 0.00 0.00 0.00 3.50
3377 4188 2.386661 ATGTGAAAGCCCGACACTAG 57.613 50.000 0.00 0.00 35.83 2.57
3446 4257 4.285863 AGACTAGCCATCAAACTAGCTCT 58.714 43.478 0.00 0.00 39.63 4.09
3447 4258 4.098654 TGAGACTAGCCATCAAACTAGCTC 59.901 45.833 0.00 0.00 39.63 4.09
3449 4260 4.392921 TGAGACTAGCCATCAAACTAGC 57.607 45.455 0.00 0.00 39.63 3.42


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

AutoCloner maintained by Alex Coulton.