Multiple sequence alignment - TraesCS6A01G115200

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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 TraesCS6A01G115200 chr6A 100.000 2588 0 0 1 2588 85024024 85021437 0.000000e+00 4780
1 TraesCS6A01G115200 chr6A 95.233 923 43 1 1666 2588 530606870 530605949 0.000000e+00 1459
2 TraesCS6A01G115200 chr6A 93.493 292 16 3 1 290 33107600 33107890 5.120000e-117 431
3 TraesCS6A01G115200 chr6A 93.197 294 18 2 1 292 45872446 45872153 5.120000e-117 431
4 TraesCS6A01G115200 chr6D 92.136 1386 67 10 312 1666 67518852 67517478 0.000000e+00 1917
5 TraesCS6A01G115200 chr6B 88.724 1419 87 26 289 1666 142503716 142502330 0.000000e+00 1666
6 TraesCS6A01G115200 chr5A 94.788 921 47 1 1668 2588 211459928 211460847 0.000000e+00 1434
7 TraesCS6A01G115200 chr5A 93.836 292 14 4 1 290 645882776 645882487 1.100000e-118 436
8 TraesCS6A01G115200 chr5A 93.537 294 16 3 1 293 17392920 17393211 3.960000e-118 435
9 TraesCS6A01G115200 chr5A 92.808 292 17 4 1 290 452999930 453000219 1.110000e-113 420
10 TraesCS6A01G115200 chr7D 92.416 923 64 5 1666 2587 607103145 607102228 0.000000e+00 1312
11 TraesCS6A01G115200 chr7D 92.736 881 59 4 1666 2545 75982628 75981752 0.000000e+00 1267
12 TraesCS6A01G115200 chr4D 93.182 880 54 5 1666 2545 12186904 12186031 0.000000e+00 1288
13 TraesCS6A01G115200 chr4D 92.702 877 60 3 1669 2545 505821047 505820175 0.000000e+00 1262
14 TraesCS6A01G115200 chr4B 92.980 869 56 4 1672 2539 132856819 132857683 0.000000e+00 1262
15 TraesCS6A01G115200 chr3D 92.711 878 58 3 1668 2545 309656622 309655751 0.000000e+00 1262
16 TraesCS6A01G115200 chr3D 93.066 649 43 1 1891 2539 42998065 42998711 0.000000e+00 948
17 TraesCS6A01G115200 chr2B 92.264 879 64 4 1666 2543 531162812 531161937 0.000000e+00 1243
18 TraesCS6A01G115200 chr2B 89.778 225 16 2 702 919 680769647 680769423 5.450000e-72 281
19 TraesCS6A01G115200 chr1B 90.794 945 63 11 1666 2588 60066342 60065400 0.000000e+00 1242
20 TraesCS6A01G115200 chr3A 89.831 944 71 10 1667 2588 125444041 125444981 0.000000e+00 1188
21 TraesCS6A01G115200 chr2A 94.502 291 14 2 1 290 3255372 3255661 5.080000e-122 448
22 TraesCS6A01G115200 chr2A 94.297 263 13 2 1 261 579968330 579968592 4.010000e-108 401
23 TraesCS6A01G115200 chr2A 90.222 225 15 2 702 919 707750859 707750635 1.170000e-73 287
24 TraesCS6A01G115200 chr4A 93.898 295 16 2 1 293 583920733 583920439 6.570000e-121 444
25 TraesCS6A01G115200 chr4A 92.784 291 20 1 1 290 566915196 566914906 1.110000e-113 420
26 TraesCS6A01G115200 chr2D 85.185 297 26 8 634 919 568232176 568231887 3.260000e-74 289
27 TraesCS6A01G115200 chrUn 84.390 205 11 8 2404 2587 217882672 217882876 5.690000e-42 182
28 TraesCS6A01G115200 chrUn 84.390 205 11 8 2404 2587 340506975 340507179 5.690000e-42 182
29 TraesCS6A01G115200 chr7B 85.484 186 6 9 2423 2588 565785707 565785891 9.520000e-40 174


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 TraesCS6A01G115200 chr6A 85021437 85024024 2587 True 4780 4780 100.000 1 2588 1 chr6A.!!$R2 2587
1 TraesCS6A01G115200 chr6A 530605949 530606870 921 True 1459 1459 95.233 1666 2588 1 chr6A.!!$R3 922
2 TraesCS6A01G115200 chr6D 67517478 67518852 1374 True 1917 1917 92.136 312 1666 1 chr6D.!!$R1 1354
3 TraesCS6A01G115200 chr6B 142502330 142503716 1386 True 1666 1666 88.724 289 1666 1 chr6B.!!$R1 1377
4 TraesCS6A01G115200 chr5A 211459928 211460847 919 False 1434 1434 94.788 1668 2588 1 chr5A.!!$F2 920
5 TraesCS6A01G115200 chr7D 607102228 607103145 917 True 1312 1312 92.416 1666 2587 1 chr7D.!!$R2 921
6 TraesCS6A01G115200 chr7D 75981752 75982628 876 True 1267 1267 92.736 1666 2545 1 chr7D.!!$R1 879
7 TraesCS6A01G115200 chr4D 12186031 12186904 873 True 1288 1288 93.182 1666 2545 1 chr4D.!!$R1 879
8 TraesCS6A01G115200 chr4D 505820175 505821047 872 True 1262 1262 92.702 1669 2545 1 chr4D.!!$R2 876
9 TraesCS6A01G115200 chr4B 132856819 132857683 864 False 1262 1262 92.980 1672 2539 1 chr4B.!!$F1 867
10 TraesCS6A01G115200 chr3D 309655751 309656622 871 True 1262 1262 92.711 1668 2545 1 chr3D.!!$R1 877
11 TraesCS6A01G115200 chr3D 42998065 42998711 646 False 948 948 93.066 1891 2539 1 chr3D.!!$F1 648
12 TraesCS6A01G115200 chr2B 531161937 531162812 875 True 1243 1243 92.264 1666 2543 1 chr2B.!!$R1 877
13 TraesCS6A01G115200 chr1B 60065400 60066342 942 True 1242 1242 90.794 1666 2588 1 chr1B.!!$R1 922
14 TraesCS6A01G115200 chr3A 125444041 125444981 940 False 1188 1188 89.831 1667 2588 1 chr3A.!!$F1 921

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
997 1018 0.035458 AGAAGCTTGGACGGTGGAAG 59.965 55.0 2.1 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1864 0.704664 CCTAGGACAGGCCCCTTTTT 59.295 55.0 1.05 0.0 37.7 1.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.329588 GACTTCAACCAGTTTTTCCTTTAGA 57.670 36.000 0.00 0.00 0.00 2.10
25 26 7.898014 ACTTCAACCAGTTTTTCCTTTAGAT 57.102 32.000 0.00 0.00 0.00 1.98
26 27 8.306313 ACTTCAACCAGTTTTTCCTTTAGATT 57.694 30.769 0.00 0.00 0.00 2.40
27 28 9.416284 ACTTCAACCAGTTTTTCCTTTAGATTA 57.584 29.630 0.00 0.00 0.00 1.75
28 29 9.899226 CTTCAACCAGTTTTTCCTTTAGATTAG 57.101 33.333 0.00 0.00 0.00 1.73
29 30 8.990163 TCAACCAGTTTTTCCTTTAGATTAGT 57.010 30.769 0.00 0.00 0.00 2.24
30 31 9.416284 TCAACCAGTTTTTCCTTTAGATTAGTT 57.584 29.630 0.00 0.00 0.00 2.24
60 61 9.973246 GTATATGTGCTATGTAATGAAAATCCG 57.027 33.333 0.00 0.00 0.00 4.18
61 62 6.942532 ATGTGCTATGTAATGAAAATCCGT 57.057 33.333 0.00 0.00 0.00 4.69
62 63 6.117911 TGTGCTATGTAATGAAAATCCGTG 57.882 37.500 0.00 0.00 0.00 4.94
63 64 5.877564 TGTGCTATGTAATGAAAATCCGTGA 59.122 36.000 0.00 0.00 0.00 4.35
64 65 6.372937 TGTGCTATGTAATGAAAATCCGTGAA 59.627 34.615 0.00 0.00 0.00 3.18
65 66 6.687105 GTGCTATGTAATGAAAATCCGTGAAC 59.313 38.462 0.00 0.00 0.00 3.18
66 67 6.597672 TGCTATGTAATGAAAATCCGTGAACT 59.402 34.615 0.00 0.00 0.00 3.01
67 68 7.120579 TGCTATGTAATGAAAATCCGTGAACTT 59.879 33.333 0.00 0.00 0.00 2.66
68 69 7.640240 GCTATGTAATGAAAATCCGTGAACTTC 59.360 37.037 0.00 0.00 0.00 3.01
69 70 5.922546 TGTAATGAAAATCCGTGAACTTCG 58.077 37.500 0.00 0.00 0.00 3.79
70 71 2.961522 TGAAAATCCGTGAACTTCGC 57.038 45.000 0.00 0.00 0.00 4.70
71 72 1.533731 TGAAAATCCGTGAACTTCGCC 59.466 47.619 0.00 0.00 0.00 5.54
72 73 0.515564 AAAATCCGTGAACTTCGCCG 59.484 50.000 0.00 0.00 0.00 6.46
73 74 0.320073 AAATCCGTGAACTTCGCCGA 60.320 50.000 0.00 0.00 0.00 5.54
74 75 0.320073 AATCCGTGAACTTCGCCGAA 60.320 50.000 0.00 0.00 0.00 4.30
75 76 0.320073 ATCCGTGAACTTCGCCGAAA 60.320 50.000 0.00 0.00 0.00 3.46
76 77 0.320073 TCCGTGAACTTCGCCGAAAT 60.320 50.000 0.00 0.00 0.00 2.17
77 78 0.179225 CCGTGAACTTCGCCGAAATG 60.179 55.000 0.00 0.00 0.00 2.32
78 79 0.511221 CGTGAACTTCGCCGAAATGT 59.489 50.000 0.00 0.00 0.00 2.71
79 80 1.721489 CGTGAACTTCGCCGAAATGTG 60.721 52.381 0.00 0.00 0.00 3.21
80 81 0.237235 TGAACTTCGCCGAAATGTGC 59.763 50.000 0.00 0.00 0.00 4.57
81 82 0.454452 GAACTTCGCCGAAATGTGCC 60.454 55.000 0.00 0.00 0.00 5.01
82 83 2.098298 CTTCGCCGAAATGTGCCG 59.902 61.111 0.00 0.00 0.00 5.69
83 84 2.357638 TTCGCCGAAATGTGCCGA 60.358 55.556 0.00 0.00 0.00 5.54
84 85 1.906994 CTTCGCCGAAATGTGCCGAA 61.907 55.000 0.00 0.00 0.00 4.30
85 86 1.507974 TTCGCCGAAATGTGCCGAAA 61.508 50.000 0.00 0.00 0.00 3.46
86 87 1.136565 CGCCGAAATGTGCCGAAAT 59.863 52.632 0.00 0.00 0.00 2.17
87 88 0.455972 CGCCGAAATGTGCCGAAATT 60.456 50.000 0.00 0.00 0.00 1.82
88 89 1.708822 GCCGAAATGTGCCGAAATTT 58.291 45.000 0.00 0.00 0.00 1.82
89 90 2.729467 CGCCGAAATGTGCCGAAATTTA 60.729 45.455 0.00 0.00 0.00 1.40
90 91 3.443976 GCCGAAATGTGCCGAAATTTAT 58.556 40.909 0.00 0.00 0.00 1.40
91 92 3.485743 GCCGAAATGTGCCGAAATTTATC 59.514 43.478 0.00 0.00 0.00 1.75
92 93 3.723764 CCGAAATGTGCCGAAATTTATCG 59.276 43.478 0.00 0.00 42.37 2.92
93 94 4.339429 CGAAATGTGCCGAAATTTATCGT 58.661 39.130 0.00 0.00 41.16 3.73
94 95 4.202158 CGAAATGTGCCGAAATTTATCGTG 59.798 41.667 0.00 0.00 41.16 4.35
95 96 4.695217 AATGTGCCGAAATTTATCGTGT 57.305 36.364 0.00 0.00 41.16 4.49
96 97 4.695217 ATGTGCCGAAATTTATCGTGTT 57.305 36.364 0.00 0.00 41.16 3.32
97 98 4.491234 TGTGCCGAAATTTATCGTGTTT 57.509 36.364 0.00 0.00 41.16 2.83
98 99 4.222886 TGTGCCGAAATTTATCGTGTTTG 58.777 39.130 0.00 0.00 41.16 2.93
99 100 3.606346 GTGCCGAAATTTATCGTGTTTGG 59.394 43.478 0.00 0.00 41.16 3.28
100 101 2.596862 GCCGAAATTTATCGTGTTTGGC 59.403 45.455 0.00 0.00 41.16 4.52
101 102 3.175929 CCGAAATTTATCGTGTTTGGCC 58.824 45.455 0.00 0.00 41.16 5.36
102 103 2.843643 CGAAATTTATCGTGTTTGGCCG 59.156 45.455 0.00 0.00 38.01 6.13
103 104 3.425094 CGAAATTTATCGTGTTTGGCCGA 60.425 43.478 0.00 0.00 38.01 5.54
104 105 4.477780 GAAATTTATCGTGTTTGGCCGAA 58.522 39.130 0.00 0.00 36.57 4.30
105 106 4.506886 AATTTATCGTGTTTGGCCGAAA 57.493 36.364 7.10 1.29 36.57 3.46
106 107 4.712122 ATTTATCGTGTTTGGCCGAAAT 57.288 36.364 7.10 0.00 36.57 2.17
107 108 4.506886 TTTATCGTGTTTGGCCGAAATT 57.493 36.364 7.10 0.00 36.57 1.82
108 109 4.506886 TTATCGTGTTTGGCCGAAATTT 57.493 36.364 7.10 0.00 36.57 1.82
109 110 5.624344 TTATCGTGTTTGGCCGAAATTTA 57.376 34.783 7.10 0.00 36.57 1.40
110 111 4.712122 ATCGTGTTTGGCCGAAATTTAT 57.288 36.364 7.10 0.00 36.57 1.40
111 112 4.506886 TCGTGTTTGGCCGAAATTTATT 57.493 36.364 7.10 0.00 0.00 1.40
112 113 4.230657 TCGTGTTTGGCCGAAATTTATTG 58.769 39.130 7.10 0.00 0.00 1.90
113 114 3.984633 CGTGTTTGGCCGAAATTTATTGT 59.015 39.130 7.10 0.00 0.00 2.71
114 115 4.143431 CGTGTTTGGCCGAAATTTATTGTG 60.143 41.667 7.10 0.00 0.00 3.33
115 116 4.747605 GTGTTTGGCCGAAATTTATTGTGT 59.252 37.500 7.10 0.00 0.00 3.72
116 117 5.235401 GTGTTTGGCCGAAATTTATTGTGTT 59.765 36.000 7.10 0.00 0.00 3.32
117 118 5.817816 TGTTTGGCCGAAATTTATTGTGTTT 59.182 32.000 7.10 0.00 0.00 2.83
118 119 5.914085 TTGGCCGAAATTTATTGTGTTTG 57.086 34.783 0.00 0.00 0.00 2.93
119 120 4.310769 TGGCCGAAATTTATTGTGTTTGG 58.689 39.130 0.00 0.00 0.00 3.28
120 121 3.124466 GGCCGAAATTTATTGTGTTTGGC 59.876 43.478 5.14 5.14 38.03 4.52
121 122 3.124466 GCCGAAATTTATTGTGTTTGGCC 59.876 43.478 0.00 0.00 32.75 5.36
122 123 3.366422 CCGAAATTTATTGTGTTTGGCCG 59.634 43.478 0.00 0.00 0.00 6.13
123 124 4.230657 CGAAATTTATTGTGTTTGGCCGA 58.769 39.130 0.00 0.00 0.00 5.54
124 125 4.681942 CGAAATTTATTGTGTTTGGCCGAA 59.318 37.500 0.00 0.00 0.00 4.30
125 126 5.347364 CGAAATTTATTGTGTTTGGCCGAAT 59.653 36.000 9.15 0.00 0.00 3.34
126 127 6.128688 CGAAATTTATTGTGTTTGGCCGAATT 60.129 34.615 9.15 0.00 0.00 2.17
127 128 7.503521 AAATTTATTGTGTTTGGCCGAATTT 57.496 28.000 9.15 0.00 0.00 1.82
128 129 7.503521 AATTTATTGTGTTTGGCCGAATTTT 57.496 28.000 9.15 0.00 0.00 1.82
129 130 8.608844 AATTTATTGTGTTTGGCCGAATTTTA 57.391 26.923 9.15 0.00 0.00 1.52
130 131 8.785329 ATTTATTGTGTTTGGCCGAATTTTAT 57.215 26.923 9.15 3.92 0.00 1.40
131 132 7.820044 TTATTGTGTTTGGCCGAATTTTATC 57.180 32.000 9.15 0.00 0.00 1.75
132 133 3.827625 TGTGTTTGGCCGAATTTTATCG 58.172 40.909 9.15 0.00 42.37 2.92
133 134 3.253677 TGTGTTTGGCCGAATTTTATCGT 59.746 39.130 9.15 0.00 41.16 3.73
134 135 3.606346 GTGTTTGGCCGAATTTTATCGTG 59.394 43.478 9.15 0.00 41.16 4.35
135 136 3.253677 TGTTTGGCCGAATTTTATCGTGT 59.746 39.130 9.15 0.00 41.16 4.49
136 137 4.231439 GTTTGGCCGAATTTTATCGTGTT 58.769 39.130 9.15 0.00 41.16 3.32
137 138 4.506886 TTGGCCGAATTTTATCGTGTTT 57.493 36.364 0.00 0.00 41.16 2.83
138 139 5.624344 TTGGCCGAATTTTATCGTGTTTA 57.376 34.783 0.00 0.00 41.16 2.01
139 140 5.624344 TGGCCGAATTTTATCGTGTTTAA 57.376 34.783 0.00 0.00 41.16 1.52
140 141 5.632959 TGGCCGAATTTTATCGTGTTTAAG 58.367 37.500 0.00 0.00 41.16 1.85
141 142 4.497966 GGCCGAATTTTATCGTGTTTAAGC 59.502 41.667 0.00 0.00 41.16 3.09
142 143 4.497966 GCCGAATTTTATCGTGTTTAAGCC 59.502 41.667 0.00 0.00 41.16 4.35
143 144 4.726704 CCGAATTTTATCGTGTTTAAGCCG 59.273 41.667 0.00 0.00 41.16 5.52
144 145 5.446206 CCGAATTTTATCGTGTTTAAGCCGA 60.446 40.000 5.63 5.63 41.16 5.54
145 146 6.016718 CGAATTTTATCGTGTTTAAGCCGAA 58.983 36.000 6.90 0.00 38.01 4.30
146 147 6.022794 CGAATTTTATCGTGTTTAAGCCGAAC 60.023 38.462 6.90 0.00 38.01 3.95
147 148 5.927954 TTTTATCGTGTTTAAGCCGAACT 57.072 34.783 6.90 0.00 33.89 3.01
148 149 5.927954 TTTATCGTGTTTAAGCCGAACTT 57.072 34.783 6.90 0.00 42.76 2.66
149 150 5.520022 TTATCGTGTTTAAGCCGAACTTC 57.480 39.130 6.90 0.00 39.97 3.01
150 151 3.102052 TCGTGTTTAAGCCGAACTTCT 57.898 42.857 1.58 0.00 39.97 2.85
151 152 3.460103 TCGTGTTTAAGCCGAACTTCTT 58.540 40.909 1.58 0.00 39.97 2.52
152 153 3.872771 TCGTGTTTAAGCCGAACTTCTTT 59.127 39.130 1.58 0.00 39.97 2.52
153 154 4.333372 TCGTGTTTAAGCCGAACTTCTTTT 59.667 37.500 1.58 0.00 39.97 2.27
154 155 5.523188 TCGTGTTTAAGCCGAACTTCTTTTA 59.477 36.000 1.58 0.00 39.97 1.52
155 156 6.203338 TCGTGTTTAAGCCGAACTTCTTTTAT 59.797 34.615 1.58 0.00 39.97 1.40
156 157 6.854381 CGTGTTTAAGCCGAACTTCTTTTATT 59.146 34.615 0.00 0.00 39.97 1.40
157 158 7.377662 CGTGTTTAAGCCGAACTTCTTTTATTT 59.622 33.333 0.00 0.00 39.97 1.40
158 159 9.027129 GTGTTTAAGCCGAACTTCTTTTATTTT 57.973 29.630 0.00 0.00 39.97 1.82
164 165 8.277270 AGCCGAACTTCTTTTATTTTAAAACG 57.723 30.769 1.97 0.00 0.00 3.60
165 166 7.916977 AGCCGAACTTCTTTTATTTTAAAACGT 59.083 29.630 1.97 0.00 0.00 3.99
166 167 7.994343 GCCGAACTTCTTTTATTTTAAAACGTG 59.006 33.333 1.97 0.00 0.00 4.49
167 168 7.994343 CCGAACTTCTTTTATTTTAAAACGTGC 59.006 33.333 1.97 0.00 0.00 5.34
168 169 7.994343 CGAACTTCTTTTATTTTAAAACGTGCC 59.006 33.333 1.97 0.00 0.00 5.01
169 170 8.936070 AACTTCTTTTATTTTAAAACGTGCCT 57.064 26.923 1.97 0.00 0.00 4.75
170 171 8.347729 ACTTCTTTTATTTTAAAACGTGCCTG 57.652 30.769 1.97 0.00 0.00 4.85
171 172 7.436970 ACTTCTTTTATTTTAAAACGTGCCTGG 59.563 33.333 1.97 0.00 0.00 4.45
172 173 6.217294 TCTTTTATTTTAAAACGTGCCTGGG 58.783 36.000 1.97 0.00 0.00 4.45
173 174 4.522722 TTATTTTAAAACGTGCCTGGGG 57.477 40.909 1.97 0.00 0.00 4.96
212 213 2.266055 GGGACCAACTCGCTCCAG 59.734 66.667 0.00 0.00 0.00 3.86
213 214 2.283529 GGGACCAACTCGCTCCAGA 61.284 63.158 0.00 0.00 0.00 3.86
214 215 1.079750 GGACCAACTCGCTCCAGAC 60.080 63.158 0.00 0.00 0.00 3.51
215 216 1.079750 GACCAACTCGCTCCAGACC 60.080 63.158 0.00 0.00 0.00 3.85
216 217 2.266055 CCAACTCGCTCCAGACCC 59.734 66.667 0.00 0.00 0.00 4.46
217 218 2.583441 CCAACTCGCTCCAGACCCA 61.583 63.158 0.00 0.00 0.00 4.51
218 219 1.371183 CAACTCGCTCCAGACCCAA 59.629 57.895 0.00 0.00 0.00 4.12
219 220 0.036010 CAACTCGCTCCAGACCCAAT 60.036 55.000 0.00 0.00 0.00 3.16
220 221 0.693049 AACTCGCTCCAGACCCAATT 59.307 50.000 0.00 0.00 0.00 2.32
221 222 0.693049 ACTCGCTCCAGACCCAATTT 59.307 50.000 0.00 0.00 0.00 1.82
222 223 1.073923 ACTCGCTCCAGACCCAATTTT 59.926 47.619 0.00 0.00 0.00 1.82
223 224 2.162681 CTCGCTCCAGACCCAATTTTT 58.837 47.619 0.00 0.00 0.00 1.94
224 225 3.244770 ACTCGCTCCAGACCCAATTTTTA 60.245 43.478 0.00 0.00 0.00 1.52
225 226 3.078837 TCGCTCCAGACCCAATTTTTAC 58.921 45.455 0.00 0.00 0.00 2.01
226 227 2.159572 CGCTCCAGACCCAATTTTTACG 60.160 50.000 0.00 0.00 0.00 3.18
227 228 2.415491 GCTCCAGACCCAATTTTTACGC 60.415 50.000 0.00 0.00 0.00 4.42
228 229 2.163613 CTCCAGACCCAATTTTTACGCC 59.836 50.000 0.00 0.00 0.00 5.68
229 230 1.135517 CCAGACCCAATTTTTACGCCG 60.136 52.381 0.00 0.00 0.00 6.46
230 231 1.135517 CAGACCCAATTTTTACGCCGG 60.136 52.381 0.00 0.00 0.00 6.13
231 232 0.457166 GACCCAATTTTTACGCCGGC 60.457 55.000 19.07 19.07 0.00 6.13
232 233 0.896479 ACCCAATTTTTACGCCGGCT 60.896 50.000 26.68 14.27 0.00 5.52
233 234 0.179148 CCCAATTTTTACGCCGGCTC 60.179 55.000 26.68 0.00 0.00 4.70
234 235 0.523966 CCAATTTTTACGCCGGCTCA 59.476 50.000 26.68 9.08 0.00 4.26
235 236 1.613270 CAATTTTTACGCCGGCTCAC 58.387 50.000 26.68 0.00 0.00 3.51
236 237 0.524414 AATTTTTACGCCGGCTCACC 59.476 50.000 26.68 0.00 0.00 4.02
237 238 1.310216 ATTTTTACGCCGGCTCACCC 61.310 55.000 26.68 0.00 0.00 4.61
238 239 3.905437 TTTTACGCCGGCTCACCCC 62.905 63.158 26.68 0.00 0.00 4.95
253 254 2.124487 CCCCAGGCGGCGATTTTA 60.124 61.111 12.98 0.00 0.00 1.52
254 255 2.186826 CCCCAGGCGGCGATTTTAG 61.187 63.158 12.98 0.00 0.00 1.85
255 256 2.186826 CCCAGGCGGCGATTTTAGG 61.187 63.158 12.98 2.42 0.00 2.69
256 257 2.715624 CAGGCGGCGATTTTAGGC 59.284 61.111 12.98 0.00 0.00 3.93
262 263 3.592814 GCGATTTTAGGCGCCCCC 61.593 66.667 26.15 5.00 46.93 5.40
264 265 2.186826 CGATTTTAGGCGCCCCCTG 61.187 63.158 26.15 2.62 45.91 4.45
265 266 1.226262 GATTTTAGGCGCCCCCTGA 59.774 57.895 26.15 6.15 45.91 3.86
266 267 0.395173 GATTTTAGGCGCCCCCTGAA 60.395 55.000 26.15 11.81 45.91 3.02
267 268 0.395724 ATTTTAGGCGCCCCCTGAAG 60.396 55.000 26.15 0.00 45.91 3.02
268 269 2.493273 TTTTAGGCGCCCCCTGAAGG 62.493 60.000 26.15 0.00 45.91 3.46
306 307 2.680339 GCCCTAACACTCTCATTTGCTC 59.320 50.000 0.00 0.00 0.00 4.26
321 323 8.443176 TCTCATTTGCTCATCCTAAATTCCTAT 58.557 33.333 0.00 0.00 0.00 2.57
345 347 2.140717 AGCACCGTTTCCTTAGTTTCG 58.859 47.619 0.00 0.00 0.00 3.46
366 368 3.310774 CGTGATTTCATCTCATGTCACCC 59.689 47.826 0.00 0.00 32.99 4.61
411 413 6.391227 TTTTGAAGGTGAGGAACAAATCTC 57.609 37.500 0.00 0.00 32.05 2.75
447 449 2.032054 CACTCGTTTGAAGCAGCAAAGA 59.968 45.455 4.49 4.58 38.33 2.52
448 450 2.682856 ACTCGTTTGAAGCAGCAAAGAA 59.317 40.909 4.49 0.00 38.33 2.52
449 451 3.128589 ACTCGTTTGAAGCAGCAAAGAAA 59.871 39.130 4.49 0.00 38.33 2.52
492 494 3.080319 GCTGCTGAGATCTCTTTTTGGT 58.920 45.455 22.95 0.00 0.00 3.67
511 513 4.331968 TGGTAAAAATGCCGATCTTCTGT 58.668 39.130 0.00 0.00 0.00 3.41
512 514 4.155826 TGGTAAAAATGCCGATCTTCTGTG 59.844 41.667 0.00 0.00 0.00 3.66
610 621 4.715130 TACTCGGCCAGCACCCCT 62.715 66.667 2.24 0.00 0.00 4.79
632 643 3.730761 GAGCAGCAGCAACACCGG 61.731 66.667 3.17 0.00 45.49 5.28
914 935 2.186384 CGCCAGCTTCCTCCTCAG 59.814 66.667 0.00 0.00 0.00 3.35
932 953 2.897326 TCAGGACGAATCTTGGACTTGA 59.103 45.455 0.00 0.00 32.82 3.02
933 954 3.056536 TCAGGACGAATCTTGGACTTGAG 60.057 47.826 0.00 0.00 32.82 3.02
953 974 1.886542 GGGCGGAGAAACTGAAAATGT 59.113 47.619 0.00 0.00 0.00 2.71
954 975 2.296190 GGGCGGAGAAACTGAAAATGTT 59.704 45.455 0.00 0.00 0.00 2.71
955 976 3.308530 GGCGGAGAAACTGAAAATGTTG 58.691 45.455 0.00 0.00 0.00 3.33
956 977 3.243401 GGCGGAGAAACTGAAAATGTTGT 60.243 43.478 0.00 0.00 0.00 3.32
997 1018 0.035458 AGAAGCTTGGACGGTGGAAG 59.965 55.000 2.10 0.00 0.00 3.46
1041 1062 1.186200 ACACGGAGAAGCAGCTCATA 58.814 50.000 0.00 0.00 36.62 2.15
1085 1106 1.743772 CGCGAACCCCAAGATCAGATT 60.744 52.381 0.00 0.00 0.00 2.40
1088 1109 2.681976 CGAACCCCAAGATCAGATTGCT 60.682 50.000 0.00 0.00 0.00 3.91
1104 1146 2.202362 CTGTCACTCGCCGTCTCG 60.202 66.667 0.00 0.00 0.00 4.04
1149 1191 2.617274 GGAGAACAAGCCCACACGC 61.617 63.158 0.00 0.00 0.00 5.34
1196 1238 0.824109 CCGGAGCTCCAACATGAGTA 59.176 55.000 31.67 0.00 34.74 2.59
1289 1331 2.425312 CAGACTGCCAGGTACTAGTGAG 59.575 54.545 5.39 0.00 36.02 3.51
1290 1332 1.751924 GACTGCCAGGTACTAGTGAGG 59.248 57.143 5.39 3.10 36.02 3.86
1308 1350 1.156645 GGCATCTGATCGTGCTGGAC 61.157 60.000 14.58 0.00 41.04 4.02
1341 1383 2.203015 GCGCACCGGATGTACCAT 60.203 61.111 9.46 0.00 38.90 3.55
1401 1443 2.320781 GAAGCAGATAGGGTCAGCCTA 58.679 52.381 4.72 4.72 39.96 3.93
1474 1516 1.878522 ATCGTCGTCGCCATGAAGC 60.879 57.895 0.00 0.00 36.96 3.86
1527 1569 2.100603 CTCGCCGTCTTCGAGTCC 59.899 66.667 4.44 0.00 45.86 3.85
1579 1621 2.222027 AGAACTGGAAACCAAAGCTCG 58.778 47.619 0.00 0.00 30.80 5.03
1649 1691 6.547141 AGTCCAGATGTTGTTTTCTGAATCAA 59.453 34.615 1.63 0.00 41.53 2.57
1656 1698 7.448588 TGTTGTTTTCTGAATCAACATTTCG 57.551 32.000 24.16 0.00 44.42 3.46
1732 1774 2.554032 CAGGAAGCAACGGAAGAACAAT 59.446 45.455 0.00 0.00 0.00 2.71
1820 1864 5.010314 ACCATAGACAACACGACTACAAAGA 59.990 40.000 0.00 0.00 0.00 2.52
1892 1936 2.103263 GCCAATATCCTCCGAAGACAGT 59.897 50.000 0.00 0.00 0.00 3.55
1949 1993 6.183360 GCACCATCTACCCTTGAAGTAGAATA 60.183 42.308 4.86 0.00 46.84 1.75
1974 2018 0.965866 AGATGGCGGAACTCAGTCGA 60.966 55.000 0.00 0.00 0.00 4.20
2014 2059 0.829990 TGGACTTATCAGCGATGGCA 59.170 50.000 0.00 0.00 43.41 4.92
2355 2403 1.289066 CATGTCCGACTCACACCGT 59.711 57.895 0.00 0.00 0.00 4.83
2446 2494 3.564218 GATCGGGCCCTGCATCCT 61.564 66.667 22.43 0.00 0.00 3.24
2497 2545 2.115910 CAAGTGCAGCCCTCCCAA 59.884 61.111 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 7.329588 TCTAAAGGAAAAACTGGTTGAAGTC 57.670 36.000 0.00 0.00 0.00 3.01
1 2 7.898014 ATCTAAAGGAAAAACTGGTTGAAGT 57.102 32.000 0.00 0.00 0.00 3.01
2 3 9.899226 CTAATCTAAAGGAAAAACTGGTTGAAG 57.101 33.333 0.00 0.00 0.00 3.02
34 35 9.973246 CGGATTTTCATTACATAGCACATATAC 57.027 33.333 0.00 0.00 0.00 1.47
35 36 9.719355 ACGGATTTTCATTACATAGCACATATA 57.281 29.630 0.00 0.00 0.00 0.86
36 37 8.506437 CACGGATTTTCATTACATAGCACATAT 58.494 33.333 0.00 0.00 0.00 1.78
37 38 7.713073 TCACGGATTTTCATTACATAGCACATA 59.287 33.333 0.00 0.00 0.00 2.29
38 39 6.542005 TCACGGATTTTCATTACATAGCACAT 59.458 34.615 0.00 0.00 0.00 3.21
39 40 5.877564 TCACGGATTTTCATTACATAGCACA 59.122 36.000 0.00 0.00 0.00 4.57
40 41 6.358118 TCACGGATTTTCATTACATAGCAC 57.642 37.500 0.00 0.00 0.00 4.40
41 42 6.597672 AGTTCACGGATTTTCATTACATAGCA 59.402 34.615 0.00 0.00 0.00 3.49
42 43 7.016361 AGTTCACGGATTTTCATTACATAGC 57.984 36.000 0.00 0.00 0.00 2.97
43 44 7.846107 CGAAGTTCACGGATTTTCATTACATAG 59.154 37.037 3.32 0.00 0.00 2.23
44 45 7.675403 GCGAAGTTCACGGATTTTCATTACATA 60.675 37.037 3.32 0.00 0.00 2.29
45 46 6.542852 CGAAGTTCACGGATTTTCATTACAT 58.457 36.000 3.32 0.00 0.00 2.29
46 47 5.615984 GCGAAGTTCACGGATTTTCATTACA 60.616 40.000 3.32 0.00 0.00 2.41
47 48 4.786575 GCGAAGTTCACGGATTTTCATTAC 59.213 41.667 3.32 0.00 0.00 1.89
48 49 4.142773 GGCGAAGTTCACGGATTTTCATTA 60.143 41.667 3.32 0.00 0.00 1.90
49 50 3.365969 GGCGAAGTTCACGGATTTTCATT 60.366 43.478 3.32 0.00 0.00 2.57
50 51 2.161609 GGCGAAGTTCACGGATTTTCAT 59.838 45.455 3.32 0.00 0.00 2.57
51 52 1.533731 GGCGAAGTTCACGGATTTTCA 59.466 47.619 3.32 0.00 0.00 2.69
52 53 1.463528 CGGCGAAGTTCACGGATTTTC 60.464 52.381 0.00 0.00 0.00 2.29
53 54 0.515564 CGGCGAAGTTCACGGATTTT 59.484 50.000 0.00 0.00 0.00 1.82
54 55 0.320073 TCGGCGAAGTTCACGGATTT 60.320 50.000 7.35 0.00 0.00 2.17
55 56 0.320073 TTCGGCGAAGTTCACGGATT 60.320 50.000 19.83 0.00 0.00 3.01
56 57 0.320073 TTTCGGCGAAGTTCACGGAT 60.320 50.000 22.52 0.00 0.00 4.18
57 58 0.320073 ATTTCGGCGAAGTTCACGGA 60.320 50.000 22.52 5.60 0.00 4.69
58 59 0.179225 CATTTCGGCGAAGTTCACGG 60.179 55.000 22.52 3.78 0.00 4.94
59 60 0.511221 ACATTTCGGCGAAGTTCACG 59.489 50.000 22.52 10.22 0.00 4.35
60 61 1.950472 CACATTTCGGCGAAGTTCAC 58.050 50.000 22.52 0.00 0.00 3.18
61 62 0.237235 GCACATTTCGGCGAAGTTCA 59.763 50.000 22.52 8.39 0.00 3.18
62 63 0.454452 GGCACATTTCGGCGAAGTTC 60.454 55.000 22.52 12.21 0.00 3.01
63 64 1.579429 GGCACATTTCGGCGAAGTT 59.421 52.632 22.52 11.63 0.00 2.66
64 65 3.263941 GGCACATTTCGGCGAAGT 58.736 55.556 22.52 17.44 0.00 3.01
69 70 1.708822 AAATTTCGGCACATTTCGGC 58.291 45.000 0.00 0.00 0.00 5.54
70 71 3.723764 CGATAAATTTCGGCACATTTCGG 59.276 43.478 0.00 0.00 35.50 4.30
71 72 4.202158 CACGATAAATTTCGGCACATTTCG 59.798 41.667 4.68 0.00 43.33 3.46
72 73 5.092781 ACACGATAAATTTCGGCACATTTC 58.907 37.500 4.68 0.00 43.33 2.17
73 74 5.054390 ACACGATAAATTTCGGCACATTT 57.946 34.783 4.68 0.00 43.33 2.32
74 75 4.695217 ACACGATAAATTTCGGCACATT 57.305 36.364 4.68 0.00 43.33 2.71
75 76 4.695217 AACACGATAAATTTCGGCACAT 57.305 36.364 4.68 0.00 43.33 3.21
76 77 4.222886 CAAACACGATAAATTTCGGCACA 58.777 39.130 4.68 0.00 43.33 4.57
77 78 3.606346 CCAAACACGATAAATTTCGGCAC 59.394 43.478 4.68 0.00 43.33 5.01
78 79 3.827625 CCAAACACGATAAATTTCGGCA 58.172 40.909 4.68 0.00 43.33 5.69
79 80 2.596862 GCCAAACACGATAAATTTCGGC 59.403 45.455 4.68 0.00 43.33 5.54
80 81 3.175929 GGCCAAACACGATAAATTTCGG 58.824 45.455 0.00 0.00 43.33 4.30
81 82 2.843643 CGGCCAAACACGATAAATTTCG 59.156 45.455 2.24 0.00 44.56 3.46
82 83 4.086199 TCGGCCAAACACGATAAATTTC 57.914 40.909 2.24 0.00 33.69 2.17
83 84 4.506886 TTCGGCCAAACACGATAAATTT 57.493 36.364 2.24 0.00 39.06 1.82
84 85 4.506886 TTTCGGCCAAACACGATAAATT 57.493 36.364 2.24 0.00 39.06 1.82
85 86 4.712122 ATTTCGGCCAAACACGATAAAT 57.288 36.364 2.24 0.00 39.06 1.40
86 87 4.506886 AATTTCGGCCAAACACGATAAA 57.493 36.364 2.24 0.00 39.06 1.40
87 88 4.506886 AAATTTCGGCCAAACACGATAA 57.493 36.364 2.24 0.00 39.06 1.75
88 89 5.821516 ATAAATTTCGGCCAAACACGATA 57.178 34.783 2.24 0.00 39.06 2.92
89 90 4.712122 ATAAATTTCGGCCAAACACGAT 57.288 36.364 2.24 0.00 39.06 3.73
90 91 4.230657 CAATAAATTTCGGCCAAACACGA 58.769 39.130 2.24 0.00 37.33 4.35
91 92 3.984633 ACAATAAATTTCGGCCAAACACG 59.015 39.130 2.24 0.00 0.00 4.49
92 93 4.747605 ACACAATAAATTTCGGCCAAACAC 59.252 37.500 2.24 0.00 0.00 3.32
93 94 4.950050 ACACAATAAATTTCGGCCAAACA 58.050 34.783 2.24 0.00 0.00 2.83
94 95 5.915812 AACACAATAAATTTCGGCCAAAC 57.084 34.783 2.24 0.00 0.00 2.93
95 96 5.237344 CCAAACACAATAAATTTCGGCCAAA 59.763 36.000 2.24 2.92 0.00 3.28
96 97 4.752101 CCAAACACAATAAATTTCGGCCAA 59.248 37.500 2.24 0.00 0.00 4.52
97 98 4.310769 CCAAACACAATAAATTTCGGCCA 58.689 39.130 2.24 0.00 0.00 5.36
98 99 3.124466 GCCAAACACAATAAATTTCGGCC 59.876 43.478 0.00 0.00 0.00 6.13
99 100 3.124466 GGCCAAACACAATAAATTTCGGC 59.876 43.478 0.00 0.00 32.96 5.54
100 101 3.366422 CGGCCAAACACAATAAATTTCGG 59.634 43.478 2.24 0.00 0.00 4.30
101 102 4.230657 TCGGCCAAACACAATAAATTTCG 58.769 39.130 2.24 0.00 0.00 3.46
102 103 6.720012 ATTCGGCCAAACACAATAAATTTC 57.280 33.333 2.24 0.00 0.00 2.17
103 104 7.503521 AAATTCGGCCAAACACAATAAATTT 57.496 28.000 2.24 0.00 0.00 1.82
104 105 7.503521 AAAATTCGGCCAAACACAATAAATT 57.496 28.000 2.24 0.00 0.00 1.82
105 106 8.785329 ATAAAATTCGGCCAAACACAATAAAT 57.215 26.923 2.24 0.00 0.00 1.40
106 107 7.062371 CGATAAAATTCGGCCAAACACAATAAA 59.938 33.333 2.24 0.00 35.50 1.40
107 108 6.528423 CGATAAAATTCGGCCAAACACAATAA 59.472 34.615 2.24 0.00 35.50 1.40
108 109 6.030849 CGATAAAATTCGGCCAAACACAATA 58.969 36.000 2.24 0.00 35.50 1.90
109 110 4.862018 CGATAAAATTCGGCCAAACACAAT 59.138 37.500 2.24 0.00 35.50 2.71
110 111 4.230657 CGATAAAATTCGGCCAAACACAA 58.769 39.130 2.24 0.00 35.50 3.33
111 112 3.253677 ACGATAAAATTCGGCCAAACACA 59.746 39.130 2.24 0.00 43.33 3.72
112 113 3.606346 CACGATAAAATTCGGCCAAACAC 59.394 43.478 2.24 0.00 43.33 3.32
113 114 3.253677 ACACGATAAAATTCGGCCAAACA 59.746 39.130 2.24 0.00 43.33 2.83
114 115 3.828786 ACACGATAAAATTCGGCCAAAC 58.171 40.909 2.24 0.00 43.33 2.93
115 116 4.506886 AACACGATAAAATTCGGCCAAA 57.493 36.364 2.24 0.00 43.33 3.28
116 117 4.506886 AAACACGATAAAATTCGGCCAA 57.493 36.364 2.24 0.00 43.33 4.52
117 118 5.624344 TTAAACACGATAAAATTCGGCCA 57.376 34.783 2.24 0.00 43.33 5.36
118 119 4.497966 GCTTAAACACGATAAAATTCGGCC 59.502 41.667 0.00 0.00 43.33 6.13
119 120 4.497966 GGCTTAAACACGATAAAATTCGGC 59.502 41.667 0.00 0.00 43.33 5.54
120 121 4.726704 CGGCTTAAACACGATAAAATTCGG 59.273 41.667 0.00 0.00 43.33 4.30
121 122 5.552807 TCGGCTTAAACACGATAAAATTCG 58.447 37.500 0.00 0.00 44.56 3.34
122 123 7.019418 AGTTCGGCTTAAACACGATAAAATTC 58.981 34.615 0.00 0.00 36.43 2.17
123 124 6.905578 AGTTCGGCTTAAACACGATAAAATT 58.094 32.000 0.00 0.00 36.43 1.82
124 125 6.490566 AGTTCGGCTTAAACACGATAAAAT 57.509 33.333 0.00 0.00 36.43 1.82
125 126 5.927954 AGTTCGGCTTAAACACGATAAAA 57.072 34.783 0.00 0.00 36.43 1.52
126 127 5.697633 AGAAGTTCGGCTTAAACACGATAAA 59.302 36.000 0.00 0.00 37.59 1.40
127 128 5.232463 AGAAGTTCGGCTTAAACACGATAA 58.768 37.500 0.00 0.00 37.59 1.75
128 129 4.813027 AGAAGTTCGGCTTAAACACGATA 58.187 39.130 0.00 0.00 37.59 2.92
129 130 3.660865 AGAAGTTCGGCTTAAACACGAT 58.339 40.909 0.00 0.00 37.59 3.73
130 131 3.102052 AGAAGTTCGGCTTAAACACGA 57.898 42.857 0.00 0.00 37.59 4.35
131 132 3.872560 AAGAAGTTCGGCTTAAACACG 57.127 42.857 0.00 0.00 37.59 4.49
132 133 8.570096 AAATAAAAGAAGTTCGGCTTAAACAC 57.430 30.769 0.00 0.00 37.59 3.32
138 139 8.748582 CGTTTTAAAATAAAAGAAGTTCGGCTT 58.251 29.630 3.52 0.00 40.76 4.35
139 140 7.916977 ACGTTTTAAAATAAAAGAAGTTCGGCT 59.083 29.630 3.52 0.00 0.00 5.52
140 141 7.994343 CACGTTTTAAAATAAAAGAAGTTCGGC 59.006 33.333 3.52 0.00 0.00 5.54
141 142 7.994343 GCACGTTTTAAAATAAAAGAAGTTCGG 59.006 33.333 3.52 0.00 0.00 4.30
142 143 7.994343 GGCACGTTTTAAAATAAAAGAAGTTCG 59.006 33.333 3.52 1.24 0.00 3.95
143 144 9.027129 AGGCACGTTTTAAAATAAAAGAAGTTC 57.973 29.630 3.52 0.00 0.00 3.01
144 145 8.813282 CAGGCACGTTTTAAAATAAAAGAAGTT 58.187 29.630 3.52 0.00 0.00 2.66
145 146 7.436970 CCAGGCACGTTTTAAAATAAAAGAAGT 59.563 33.333 3.52 0.00 0.00 3.01
146 147 7.095816 CCCAGGCACGTTTTAAAATAAAAGAAG 60.096 37.037 3.52 0.00 0.00 2.85
147 148 6.702282 CCCAGGCACGTTTTAAAATAAAAGAA 59.298 34.615 3.52 0.00 0.00 2.52
148 149 6.217294 CCCAGGCACGTTTTAAAATAAAAGA 58.783 36.000 3.52 0.00 0.00 2.52
149 150 5.407084 CCCCAGGCACGTTTTAAAATAAAAG 59.593 40.000 3.52 0.00 0.00 2.27
150 151 5.298347 CCCCAGGCACGTTTTAAAATAAAA 58.702 37.500 3.52 0.00 0.00 1.52
151 152 4.884247 CCCCAGGCACGTTTTAAAATAAA 58.116 39.130 3.52 0.00 0.00 1.40
152 153 4.522722 CCCCAGGCACGTTTTAAAATAA 57.477 40.909 3.52 0.00 0.00 1.40
187 188 3.607370 GAGTTGGTCCCCAGCCGTC 62.607 68.421 0.00 0.00 35.27 4.79
188 189 3.637273 GAGTTGGTCCCCAGCCGT 61.637 66.667 0.00 0.00 35.27 5.68
189 190 4.760047 CGAGTTGGTCCCCAGCCG 62.760 72.222 0.00 0.00 35.27 5.52
191 192 3.959991 GAGCGAGTTGGTCCCCAGC 62.960 68.421 0.00 0.00 39.22 4.85
192 193 2.266055 GAGCGAGTTGGTCCCCAG 59.734 66.667 0.00 0.00 39.22 4.45
197 198 1.079750 GGTCTGGAGCGAGTTGGTC 60.080 63.158 0.52 0.52 44.49 4.02
198 199 2.584391 GGGTCTGGAGCGAGTTGGT 61.584 63.158 0.00 0.00 0.00 3.67
199 200 2.111999 TTGGGTCTGGAGCGAGTTGG 62.112 60.000 0.00 0.00 0.00 3.77
200 201 0.036010 ATTGGGTCTGGAGCGAGTTG 60.036 55.000 0.00 0.00 0.00 3.16
201 202 0.693049 AATTGGGTCTGGAGCGAGTT 59.307 50.000 0.00 0.00 0.00 3.01
202 203 0.693049 AAATTGGGTCTGGAGCGAGT 59.307 50.000 0.00 0.00 0.00 4.18
203 204 1.826385 AAAATTGGGTCTGGAGCGAG 58.174 50.000 0.00 0.00 0.00 5.03
204 205 2.286365 AAAAATTGGGTCTGGAGCGA 57.714 45.000 0.00 0.00 0.00 4.93
205 206 2.159572 CGTAAAAATTGGGTCTGGAGCG 60.160 50.000 0.00 0.00 0.00 5.03
206 207 2.415491 GCGTAAAAATTGGGTCTGGAGC 60.415 50.000 0.00 0.00 0.00 4.70
207 208 2.163613 GGCGTAAAAATTGGGTCTGGAG 59.836 50.000 0.00 0.00 0.00 3.86
208 209 2.164338 GGCGTAAAAATTGGGTCTGGA 58.836 47.619 0.00 0.00 0.00 3.86
209 210 1.135517 CGGCGTAAAAATTGGGTCTGG 60.136 52.381 0.00 0.00 0.00 3.86
210 211 1.135517 CCGGCGTAAAAATTGGGTCTG 60.136 52.381 6.01 0.00 0.00 3.51
211 212 1.170442 CCGGCGTAAAAATTGGGTCT 58.830 50.000 6.01 0.00 0.00 3.85
212 213 0.457166 GCCGGCGTAAAAATTGGGTC 60.457 55.000 12.58 0.00 0.00 4.46
213 214 0.896479 AGCCGGCGTAAAAATTGGGT 60.896 50.000 23.20 0.00 0.00 4.51
214 215 0.179148 GAGCCGGCGTAAAAATTGGG 60.179 55.000 23.20 0.00 0.00 4.12
215 216 0.523966 TGAGCCGGCGTAAAAATTGG 59.476 50.000 23.20 0.00 0.00 3.16
216 217 1.613270 GTGAGCCGGCGTAAAAATTG 58.387 50.000 23.20 0.00 0.00 2.32
217 218 0.524414 GGTGAGCCGGCGTAAAAATT 59.476 50.000 23.20 0.00 0.00 1.82
218 219 1.310216 GGGTGAGCCGGCGTAAAAAT 61.310 55.000 23.20 0.00 34.97 1.82
219 220 1.967494 GGGTGAGCCGGCGTAAAAA 60.967 57.895 23.20 0.72 34.97 1.94
220 221 2.358984 GGGTGAGCCGGCGTAAAA 60.359 61.111 23.20 2.78 34.97 1.52
221 222 4.397832 GGGGTGAGCCGGCGTAAA 62.398 66.667 23.20 4.88 34.97 2.01
237 238 2.186826 CCTAAAATCGCCGCCTGGG 61.187 63.158 0.00 0.00 39.58 4.45
238 239 2.834618 GCCTAAAATCGCCGCCTGG 61.835 63.158 0.00 0.00 38.77 4.45
239 240 2.715624 GCCTAAAATCGCCGCCTG 59.284 61.111 0.00 0.00 0.00 4.85
240 241 2.895372 CGCCTAAAATCGCCGCCT 60.895 61.111 0.00 0.00 0.00 5.52
241 242 4.607606 GCGCCTAAAATCGCCGCC 62.608 66.667 0.00 0.00 45.01 6.13
246 247 2.186826 CAGGGGGCGCCTAAAATCG 61.187 63.158 28.56 5.85 0.00 3.34
247 248 0.395173 TTCAGGGGGCGCCTAAAATC 60.395 55.000 28.56 8.16 0.00 2.17
248 249 0.395724 CTTCAGGGGGCGCCTAAAAT 60.396 55.000 28.56 5.30 0.00 1.82
249 250 1.001393 CTTCAGGGGGCGCCTAAAA 60.001 57.895 28.56 18.20 0.00 1.52
250 251 2.674754 CTTCAGGGGGCGCCTAAA 59.325 61.111 28.56 14.87 0.00 1.85
251 252 3.407967 CCTTCAGGGGGCGCCTAA 61.408 66.667 28.56 5.93 0.00 2.69
276 277 0.543749 AGTGTTAGGGCATCTCCAGC 59.456 55.000 0.00 0.00 36.21 4.85
277 278 2.102252 GAGAGTGTTAGGGCATCTCCAG 59.898 54.545 0.00 0.00 36.21 3.86
278 279 2.111384 GAGAGTGTTAGGGCATCTCCA 58.889 52.381 0.00 0.00 36.21 3.86
279 280 2.111384 TGAGAGTGTTAGGGCATCTCC 58.889 52.381 0.00 0.00 36.42 3.71
280 281 4.414337 AATGAGAGTGTTAGGGCATCTC 57.586 45.455 0.00 0.00 37.50 2.75
281 282 4.521146 CAAATGAGAGTGTTAGGGCATCT 58.479 43.478 0.00 0.00 0.00 2.90
282 283 3.065925 GCAAATGAGAGTGTTAGGGCATC 59.934 47.826 0.00 0.00 0.00 3.91
283 284 3.019564 GCAAATGAGAGTGTTAGGGCAT 58.980 45.455 0.00 0.00 0.00 4.40
284 285 2.040278 AGCAAATGAGAGTGTTAGGGCA 59.960 45.455 0.00 0.00 0.00 5.36
285 286 2.680339 GAGCAAATGAGAGTGTTAGGGC 59.320 50.000 0.00 0.00 0.00 5.19
286 287 3.942829 TGAGCAAATGAGAGTGTTAGGG 58.057 45.455 0.00 0.00 0.00 3.53
287 288 4.574013 GGATGAGCAAATGAGAGTGTTAGG 59.426 45.833 0.00 0.00 0.00 2.69
291 292 3.996921 AGGATGAGCAAATGAGAGTGT 57.003 42.857 0.00 0.00 0.00 3.55
306 307 5.474876 GGTGCTCCAATAGGAATTTAGGATG 59.525 44.000 0.00 0.00 45.19 3.51
321 323 1.418637 ACTAAGGAAACGGTGCTCCAA 59.581 47.619 5.52 0.35 33.83 3.53
345 347 8.055710 CTGTGGGTGACATGAGATGAAATCAC 62.056 46.154 0.00 0.00 39.01 3.06
366 368 1.247567 GTGGGGTCCATTTGTCTGTG 58.752 55.000 0.00 0.00 35.28 3.66
411 413 2.438434 GTGGATGGGGCGACAAGG 60.438 66.667 0.00 0.00 0.00 3.61
492 494 4.009675 AGCACAGAAGATCGGCATTTTTA 58.990 39.130 0.00 0.00 0.00 1.52
914 935 2.622436 CCTCAAGTCCAAGATTCGTCC 58.378 52.381 0.00 0.00 0.00 4.79
932 953 2.162681 CATTTTCAGTTTCTCCGCCCT 58.837 47.619 0.00 0.00 0.00 5.19
933 954 1.886542 ACATTTTCAGTTTCTCCGCCC 59.113 47.619 0.00 0.00 0.00 6.13
953 974 3.283684 CGGCACCGGCTTCAACAA 61.284 61.111 0.00 0.00 40.87 2.83
974 995 0.671781 CACCGTCCAAGCTTCTCCAG 60.672 60.000 0.00 0.00 0.00 3.86
997 1018 1.303561 TGGAGCACTTGTCCATGGC 60.304 57.895 6.96 2.72 39.28 4.40
1085 1106 3.268965 GAGACGGCGAGTGACAGCA 62.269 63.158 16.62 0.00 34.54 4.41
1088 1109 2.255881 TTCGAGACGGCGAGTGACA 61.256 57.895 16.62 0.00 41.79 3.58
1132 1174 1.845809 CTGCGTGTGGGCTTGTTCTC 61.846 60.000 0.00 0.00 0.00 2.87
1149 1191 2.684843 GGCTTCTTCGCCTGTGCTG 61.685 63.158 0.00 0.00 46.63 4.41
1196 1238 2.421739 GCGGTATGGCGATGGAGT 59.578 61.111 0.00 0.00 0.00 3.85
1289 1331 1.144716 TCCAGCACGATCAGATGCC 59.855 57.895 9.37 0.00 43.12 4.40
1290 1332 2.305405 GTCCAGCACGATCAGATGC 58.695 57.895 5.64 5.64 42.39 3.91
1341 1383 1.001764 CTGCAGCCATGGGTTCTCA 60.002 57.895 15.37 11.52 0.00 3.27
1401 1443 2.134287 ATGCCTCACCTCGCCGTAT 61.134 57.895 0.00 0.00 0.00 3.06
1474 1516 3.522731 CTCGTCCTCCCCGAGCTG 61.523 72.222 0.00 0.00 44.42 4.24
1512 1554 1.874019 CATGGACTCGAAGACGGCG 60.874 63.158 4.80 4.80 40.21 6.46
1579 1621 9.127277 AGTCCAGAGAAATTACTACTATGACTC 57.873 37.037 0.00 0.00 0.00 3.36
1820 1864 0.704664 CCTAGGACAGGCCCCTTTTT 59.295 55.000 1.05 0.00 37.70 1.94
1892 1936 1.930251 AGTCTCAGTTGGAGCTGCTA 58.070 50.000 6.82 0.00 43.70 3.49
1949 1993 2.045926 GTTCCGCCATCTGCCTGT 60.046 61.111 0.00 0.00 36.24 4.00
2028 2073 1.202405 CCGCTGTTTTTGGTGAAGCTT 60.202 47.619 0.00 0.00 0.00 3.74
2152 2197 2.313051 GAAAGCCTAGGTCCGGAGCC 62.313 65.000 29.33 20.68 0.00 4.70
2446 2494 1.960040 CTCCAGCCGTGGTAGATGCA 61.960 60.000 0.00 0.00 45.28 3.96
2530 2578 3.379445 GGAGGGCGACGAGTGGAA 61.379 66.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.