Multiple sequence alignment - TraesCS6B01G066100

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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 TraesCS6B01G066100 chr6B 100.000 3031 0 0 1 3031 44060777 44063807 0.000000e+00 5598
1 TraesCS6B01G066100 chr6B 94.196 2774 112 3 158 2903 43867504 43870256 0.000000e+00 4185
2 TraesCS6B01G066100 chr6B 92.877 1797 98 16 1110 2903 43922841 43924610 0.000000e+00 2582
3 TraesCS6B01G066100 chr6B 95.279 1504 55 3 158 1645 43857159 43858662 0.000000e+00 2370
4 TraesCS6B01G066100 chr6B 95.260 1498 61 4 158 1645 43819164 43820661 0.000000e+00 2364
5 TraesCS6B01G066100 chr6B 95.458 1431 65 0 1473 2903 43843262 43844692 0.000000e+00 2283
6 TraesCS6B01G066100 chr6B 93.083 1518 79 3 158 1674 43931319 43932811 0.000000e+00 2198
7 TraesCS6B01G066100 chr6B 94.309 1230 70 0 1674 2903 43895216 43896445 0.000000e+00 1884
8 TraesCS6B01G066100 chr6B 89.725 1489 107 16 1412 2878 43481169 43482633 0.000000e+00 1860
9 TraesCS6B01G066100 chr6B 93.851 1236 70 3 158 1392 43951799 43953029 0.000000e+00 1857
10 TraesCS6B01G066100 chr6B 94.937 158 6 1 3 158 280943703 280943860 2.330000e-61 246
11 TraesCS6B01G066100 chr6B 92.073 164 10 2 3 163 280955478 280955641 8.450000e-56 228
12 TraesCS6B01G066100 chr6B 94.488 127 7 0 2881 3007 503545624 503545750 2.380000e-46 196
13 TraesCS6B01G066100 chrUn 95.397 2759 114 2 158 2903 181047910 181050668 0.000000e+00 4379
14 TraesCS6B01G066100 chrUn 94.817 2759 112 4 158 2903 181032192 181034932 0.000000e+00 4274
15 TraesCS6B01G066100 chrUn 94.434 2767 118 5 158 2903 180993495 180996246 0.000000e+00 4224
16 TraesCS6B01G066100 chrUn 95.360 1487 60 3 168 1645 300786432 300784946 0.000000e+00 2355
17 TraesCS6B01G066100 chrUn 95.354 1485 58 3 168 1641 395593292 395591808 0.000000e+00 2350
18 TraesCS6B01G066100 chrUn 94.655 1478 64 1 1426 2903 387096604 387098066 0.000000e+00 2278
19 TraesCS6B01G066100 chrUn 94.308 1423 60 1 1481 2903 181008365 181009766 0.000000e+00 2159
20 TraesCS6B01G066100 chrUn 91.871 1304 84 12 395 1680 94214043 94215342 0.000000e+00 1801
21 TraesCS6B01G066100 chrUn 91.852 135 10 1 2880 3014 191163435 191163302 1.430000e-43 187
22 TraesCS6B01G066100 chr5B 97.484 159 4 0 1 159 602652027 602651869 3.850000e-69 272
23 TraesCS6B01G066100 chr5A 91.772 158 11 1 1 158 647113985 647113830 5.090000e-53 219
24 TraesCS6B01G066100 chr5A 91.139 158 12 1 1 158 647122668 647122513 2.370000e-51 213
25 TraesCS6B01G066100 chr1B 95.489 133 5 1 2880 3012 653879103 653879234 8.510000e-51 211
26 TraesCS6B01G066100 chr1B 93.798 129 8 0 2881 3009 642926700 642926828 8.570000e-46 195
27 TraesCS6B01G066100 chr1B 93.750 128 8 0 2881 3008 273653285 273653412 3.080000e-45 193
28 TraesCS6B01G066100 chr1A 90.000 160 14 2 1 158 589656228 589656387 3.960000e-49 206
29 TraesCS6B01G066100 chr1A 91.912 136 11 0 2880 3015 352843671 352843536 1.110000e-44 191
30 TraesCS6B01G066100 chr1D 89.937 159 14 1 1 159 48737372 48737528 1.420000e-48 204
31 TraesCS6B01G066100 chr2B 89.744 156 16 0 1 156 651984644 651984799 1.840000e-47 200
32 TraesCS6B01G066100 chr3B 93.130 131 9 0 2880 3010 530239414 530239544 3.080000e-45 193
33 TraesCS6B01G066100 chr3B 93.750 128 8 0 2881 3008 650361301 650361174 3.080000e-45 193
34 TraesCS6B01G066100 chr3B 91.852 135 10 1 2880 3014 778740082 778739949 1.430000e-43 187
35 TraesCS6B01G066100 chr2A 88.820 161 12 6 1 156 371535406 371535565 3.080000e-45 193


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 TraesCS6B01G066100 chr6B 44060777 44063807 3030 False 5598 5598 100.000 1 3031 1 chr6B.!!$F10 3030
1 TraesCS6B01G066100 chr6B 43867504 43870256 2752 False 4185 4185 94.196 158 2903 1 chr6B.!!$F5 2745
2 TraesCS6B01G066100 chr6B 43922841 43924610 1769 False 2582 2582 92.877 1110 2903 1 chr6B.!!$F7 1793
3 TraesCS6B01G066100 chr6B 43857159 43858662 1503 False 2370 2370 95.279 158 1645 1 chr6B.!!$F4 1487
4 TraesCS6B01G066100 chr6B 43819164 43820661 1497 False 2364 2364 95.260 158 1645 1 chr6B.!!$F2 1487
5 TraesCS6B01G066100 chr6B 43843262 43844692 1430 False 2283 2283 95.458 1473 2903 1 chr6B.!!$F3 1430
6 TraesCS6B01G066100 chr6B 43931319 43932811 1492 False 2198 2198 93.083 158 1674 1 chr6B.!!$F8 1516
7 TraesCS6B01G066100 chr6B 43895216 43896445 1229 False 1884 1884 94.309 1674 2903 1 chr6B.!!$F6 1229
8 TraesCS6B01G066100 chr6B 43481169 43482633 1464 False 1860 1860 89.725 1412 2878 1 chr6B.!!$F1 1466
9 TraesCS6B01G066100 chr6B 43951799 43953029 1230 False 1857 1857 93.851 158 1392 1 chr6B.!!$F9 1234
10 TraesCS6B01G066100 chrUn 181047910 181050668 2758 False 4379 4379 95.397 158 2903 1 chrUn.!!$F5 2745
11 TraesCS6B01G066100 chrUn 181032192 181034932 2740 False 4274 4274 94.817 158 2903 1 chrUn.!!$F4 2745
12 TraesCS6B01G066100 chrUn 180993495 180996246 2751 False 4224 4224 94.434 158 2903 1 chrUn.!!$F2 2745
13 TraesCS6B01G066100 chrUn 300784946 300786432 1486 True 2355 2355 95.360 168 1645 1 chrUn.!!$R2 1477
14 TraesCS6B01G066100 chrUn 395591808 395593292 1484 True 2350 2350 95.354 168 1641 1 chrUn.!!$R3 1473
15 TraesCS6B01G066100 chrUn 387096604 387098066 1462 False 2278 2278 94.655 1426 2903 1 chrUn.!!$F6 1477
16 TraesCS6B01G066100 chrUn 181008365 181009766 1401 False 2159 2159 94.308 1481 2903 1 chrUn.!!$F3 1422
17 TraesCS6B01G066100 chrUn 94214043 94215342 1299 False 1801 1801 91.871 395 1680 1 chrUn.!!$F1 1285

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
126 127 0.038709 TGCACCTAAAATGCCAACGC 60.039 50.000 0.0 0.0 42.69 4.84 F
264 267 2.031012 CAGCTGCACTCGGAACCA 59.969 61.111 0.0 0.0 0.00 3.67 F
1238 1243 2.356665 TCTAGGGCAGCAACAACAAA 57.643 45.000 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1243 0.832983 TGCTGCTGCCCTGGAAATTT 60.833 50.000 13.47 0.0 38.71 1.82 R
1255 1260 1.137872 TGTTGTGGTGGAAATGGTTGC 59.862 47.619 0.00 0.0 0.00 4.17 R
2986 3148 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.0 44.66 1.40 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
25 26 8.773033 ATGTGAAATAGAAATAGGCAATCCTT 57.227 30.769 0.00 0.00 40.66 3.36
26 27 8.593945 TGTGAAATAGAAATAGGCAATCCTTT 57.406 30.769 0.00 0.00 40.66 3.11
27 28 8.469200 TGTGAAATAGAAATAGGCAATCCTTTG 58.531 33.333 0.00 0.00 40.66 2.77
28 29 8.686334 GTGAAATAGAAATAGGCAATCCTTTGA 58.314 33.333 0.00 0.00 40.66 2.69
29 30 9.425248 TGAAATAGAAATAGGCAATCCTTTGAT 57.575 29.630 0.00 0.00 40.66 2.57
35 36 8.571336 AGAAATAGGCAATCCTTTGATAATTCG 58.429 33.333 0.00 0.00 40.66 3.34
36 37 8.463930 AAATAGGCAATCCTTTGATAATTCGA 57.536 30.769 0.00 0.00 40.66 3.71
37 38 8.641498 AATAGGCAATCCTTTGATAATTCGAT 57.359 30.769 0.00 0.00 40.66 3.59
38 39 9.739276 AATAGGCAATCCTTTGATAATTCGATA 57.261 29.630 0.00 0.00 40.66 2.92
39 40 9.739276 ATAGGCAATCCTTTGATAATTCGATAA 57.261 29.630 0.00 0.00 40.66 1.75
40 41 8.463930 AGGCAATCCTTTGATAATTCGATAAA 57.536 30.769 0.00 0.00 40.66 1.40
41 42 8.571336 AGGCAATCCTTTGATAATTCGATAAAG 58.429 33.333 0.00 0.00 40.66 1.85
42 43 8.352942 GGCAATCCTTTGATAATTCGATAAAGT 58.647 33.333 0.00 0.00 34.60 2.66
43 44 9.173939 GCAATCCTTTGATAATTCGATAAAGTG 57.826 33.333 0.00 0.00 34.60 3.16
46 47 9.613428 ATCCTTTGATAATTCGATAAAGTGTGA 57.387 29.630 0.00 0.00 0.00 3.58
47 48 9.098355 TCCTTTGATAATTCGATAAAGTGTGAG 57.902 33.333 0.00 0.00 0.00 3.51
48 49 8.883731 CCTTTGATAATTCGATAAAGTGTGAGT 58.116 33.333 0.00 0.00 0.00 3.41
49 50 9.907576 CTTTGATAATTCGATAAAGTGTGAGTC 57.092 33.333 0.00 0.00 0.00 3.36
50 51 9.653287 TTTGATAATTCGATAAAGTGTGAGTCT 57.347 29.630 0.00 0.00 0.00 3.24
51 52 8.858003 TGATAATTCGATAAAGTGTGAGTCTC 57.142 34.615 0.00 0.00 0.00 3.36
52 53 7.921214 TGATAATTCGATAAAGTGTGAGTCTCC 59.079 37.037 0.00 0.00 0.00 3.71
53 54 5.923733 ATTCGATAAAGTGTGAGTCTCCT 57.076 39.130 0.00 0.00 0.00 3.69
54 55 7.406031 AATTCGATAAAGTGTGAGTCTCCTA 57.594 36.000 0.00 0.00 0.00 2.94
55 56 7.589958 ATTCGATAAAGTGTGAGTCTCCTAT 57.410 36.000 0.00 0.00 0.00 2.57
56 57 7.406031 TTCGATAAAGTGTGAGTCTCCTATT 57.594 36.000 0.00 0.00 0.00 1.73
57 58 7.406031 TCGATAAAGTGTGAGTCTCCTATTT 57.594 36.000 0.00 0.00 0.00 1.40
58 59 7.481642 TCGATAAAGTGTGAGTCTCCTATTTC 58.518 38.462 0.00 0.00 0.00 2.17
59 60 6.697892 CGATAAAGTGTGAGTCTCCTATTTCC 59.302 42.308 0.00 0.00 0.00 3.13
60 61 4.457834 AAGTGTGAGTCTCCTATTTCCG 57.542 45.455 0.00 0.00 0.00 4.30
61 62 3.432378 AGTGTGAGTCTCCTATTTCCGT 58.568 45.455 0.00 0.00 0.00 4.69
62 63 3.193691 AGTGTGAGTCTCCTATTTCCGTG 59.806 47.826 0.00 0.00 0.00 4.94
63 64 3.056749 GTGTGAGTCTCCTATTTCCGTGT 60.057 47.826 0.00 0.00 0.00 4.49
64 65 4.157289 GTGTGAGTCTCCTATTTCCGTGTA 59.843 45.833 0.00 0.00 0.00 2.90
65 66 4.954202 TGTGAGTCTCCTATTTCCGTGTAT 59.046 41.667 0.00 0.00 0.00 2.29
66 67 5.421056 TGTGAGTCTCCTATTTCCGTGTATT 59.579 40.000 0.00 0.00 0.00 1.89
67 68 5.978322 GTGAGTCTCCTATTTCCGTGTATTC 59.022 44.000 0.00 0.00 0.00 1.75
68 69 5.184340 AGTCTCCTATTTCCGTGTATTCG 57.816 43.478 0.00 0.00 0.00 3.34
69 70 4.885907 AGTCTCCTATTTCCGTGTATTCGA 59.114 41.667 0.00 0.00 0.00 3.71
70 71 5.359009 AGTCTCCTATTTCCGTGTATTCGAA 59.641 40.000 0.00 0.00 0.00 3.71
71 72 5.686397 GTCTCCTATTTCCGTGTATTCGAAG 59.314 44.000 3.35 0.00 0.00 3.79
72 73 5.359009 TCTCCTATTTCCGTGTATTCGAAGT 59.641 40.000 3.35 0.00 0.00 3.01
73 74 6.543465 TCTCCTATTTCCGTGTATTCGAAGTA 59.457 38.462 3.35 0.00 0.00 2.24
74 75 7.067372 TCTCCTATTTCCGTGTATTCGAAGTAA 59.933 37.037 3.35 0.00 0.00 2.24
75 76 7.719483 TCCTATTTCCGTGTATTCGAAGTAAT 58.281 34.615 3.35 0.00 0.00 1.89
76 77 7.650504 TCCTATTTCCGTGTATTCGAAGTAATG 59.349 37.037 3.35 0.00 0.00 1.90
77 78 7.650504 CCTATTTCCGTGTATTCGAAGTAATGA 59.349 37.037 3.35 0.00 0.00 2.57
78 79 7.837202 ATTTCCGTGTATTCGAAGTAATGAA 57.163 32.000 3.35 0.00 0.00 2.57
79 80 7.837202 TTTCCGTGTATTCGAAGTAATGAAT 57.163 32.000 3.35 0.00 38.34 2.57
80 81 7.837202 TTCCGTGTATTCGAAGTAATGAATT 57.163 32.000 3.35 0.00 36.32 2.17
81 82 7.459394 TCCGTGTATTCGAAGTAATGAATTC 57.541 36.000 3.35 0.00 36.32 2.17
83 84 6.020121 CCGTGTATTCGAAGTAATGAATTCGT 60.020 38.462 12.13 0.00 46.34 3.85
84 85 7.166307 CCGTGTATTCGAAGTAATGAATTCGTA 59.834 37.037 12.13 3.56 46.34 3.43
85 86 8.688184 CGTGTATTCGAAGTAATGAATTCGTAT 58.312 33.333 12.13 10.62 46.34 3.06
89 90 6.664978 TCGAAGTAATGAATTCGTATACGC 57.335 37.500 20.42 7.01 46.34 4.42
90 91 6.432936 TCGAAGTAATGAATTCGTATACGCT 58.567 36.000 20.42 7.34 46.34 5.07
91 92 6.576313 TCGAAGTAATGAATTCGTATACGCTC 59.424 38.462 20.42 15.58 46.34 5.03
92 93 6.449515 CGAAGTAATGAATTCGTATACGCTCG 60.450 42.308 20.42 18.62 42.47 5.03
93 94 5.755813 AGTAATGAATTCGTATACGCTCGT 58.244 37.500 20.42 13.89 39.60 4.18
94 95 6.891624 AGTAATGAATTCGTATACGCTCGTA 58.108 36.000 20.42 4.53 39.60 3.43
95 96 7.524912 AGTAATGAATTCGTATACGCTCGTAT 58.475 34.615 20.42 17.45 43.04 3.06
96 97 8.659491 AGTAATGAATTCGTATACGCTCGTATA 58.341 33.333 20.42 15.64 41.12 1.47
103 104 2.701073 ATACGCTCGTATACTGGCAC 57.299 50.000 12.62 0.00 39.29 5.01
104 105 0.305617 TACGCTCGTATACTGGCACG 59.694 55.000 14.27 7.91 39.48 5.34
105 106 2.293627 CGCTCGTATACTGGCACGC 61.294 63.158 14.27 2.76 38.05 5.34
106 107 1.949631 GCTCGTATACTGGCACGCC 60.950 63.158 0.00 0.00 38.05 5.68
107 108 1.734137 CTCGTATACTGGCACGCCT 59.266 57.895 9.92 0.00 38.05 5.52
108 109 0.595053 CTCGTATACTGGCACGCCTG 60.595 60.000 12.87 12.87 38.05 4.85
109 110 2.237751 CGTATACTGGCACGCCTGC 61.238 63.158 14.21 0.00 43.41 4.85
110 111 1.153449 GTATACTGGCACGCCTGCA 60.153 57.895 14.21 2.60 46.28 4.41
111 112 1.153449 TATACTGGCACGCCTGCAC 60.153 57.895 14.21 0.33 46.28 4.57
112 113 2.587322 TATACTGGCACGCCTGCACC 62.587 60.000 14.21 0.00 46.28 5.01
114 115 4.393155 CTGGCACGCCTGCACCTA 62.393 66.667 9.92 0.00 46.28 3.08
115 116 3.899981 CTGGCACGCCTGCACCTAA 62.900 63.158 9.92 0.00 46.28 2.69
116 117 2.671619 GGCACGCCTGCACCTAAA 60.672 61.111 9.92 0.00 46.28 1.85
117 118 2.265182 GGCACGCCTGCACCTAAAA 61.265 57.895 9.92 0.00 46.28 1.52
118 119 1.595093 GGCACGCCTGCACCTAAAAT 61.595 55.000 9.92 0.00 46.28 1.82
119 120 0.456653 GCACGCCTGCACCTAAAATG 60.457 55.000 2.56 0.00 43.62 2.32
120 121 0.456653 CACGCCTGCACCTAAAATGC 60.457 55.000 0.00 0.00 43.68 3.56
121 122 1.139520 CGCCTGCACCTAAAATGCC 59.860 57.895 0.00 0.00 42.69 4.40
122 123 1.594194 CGCCTGCACCTAAAATGCCA 61.594 55.000 0.00 0.00 42.69 4.92
123 124 0.607620 GCCTGCACCTAAAATGCCAA 59.392 50.000 0.00 0.00 42.69 4.52
124 125 1.672737 GCCTGCACCTAAAATGCCAAC 60.673 52.381 0.00 0.00 42.69 3.77
125 126 1.402720 CCTGCACCTAAAATGCCAACG 60.403 52.381 0.00 0.00 42.69 4.10
126 127 0.038709 TGCACCTAAAATGCCAACGC 60.039 50.000 0.00 0.00 42.69 4.84
136 137 3.642938 TGCCAACGCAGGTAGATTT 57.357 47.368 0.00 0.00 41.12 2.17
137 138 2.772077 TGCCAACGCAGGTAGATTTA 57.228 45.000 0.00 0.00 41.12 1.40
138 139 3.060736 TGCCAACGCAGGTAGATTTAA 57.939 42.857 0.00 0.00 41.12 1.52
139 140 3.616219 TGCCAACGCAGGTAGATTTAAT 58.384 40.909 0.00 0.00 41.12 1.40
140 141 4.771903 TGCCAACGCAGGTAGATTTAATA 58.228 39.130 0.00 0.00 41.12 0.98
141 142 5.373222 TGCCAACGCAGGTAGATTTAATAT 58.627 37.500 0.00 0.00 41.12 1.28
142 143 5.825679 TGCCAACGCAGGTAGATTTAATATT 59.174 36.000 0.00 0.00 41.12 1.28
143 144 6.320164 TGCCAACGCAGGTAGATTTAATATTT 59.680 34.615 0.00 0.00 41.12 1.40
144 145 7.499563 TGCCAACGCAGGTAGATTTAATATTTA 59.500 33.333 0.00 0.00 41.12 1.40
145 146 8.512138 GCCAACGCAGGTAGATTTAATATTTAT 58.488 33.333 0.00 0.00 34.03 1.40
150 151 9.760660 CGCAGGTAGATTTAATATTTATCTTGC 57.239 33.333 14.40 15.47 31.28 4.01
151 152 9.760660 GCAGGTAGATTTAATATTTATCTTGCG 57.239 33.333 14.40 6.35 31.46 4.85
264 267 2.031012 CAGCTGCACTCGGAACCA 59.969 61.111 0.00 0.00 0.00 3.67
374 377 3.129287 ACACATTGCAAGCCATACTAAGC 59.871 43.478 4.94 0.00 0.00 3.09
450 453 5.587844 AGCAATTTGATGAGTCATGGTCTAC 59.412 40.000 11.20 0.00 33.56 2.59
465 468 4.020372 GGTCTACCAAAGCAAGCTGCAG 62.020 54.545 10.11 10.11 40.17 4.41
545 548 7.413109 GCAAGTCAAGCTTATCTAGTTTACACC 60.413 40.741 0.00 0.00 35.27 4.16
658 661 6.034683 GTCATGACCTACTAAAGCAAGTTACG 59.965 42.308 15.31 0.00 0.00 3.18
908 913 6.633856 ACCAAATTATGATTTCAGGAAGCAC 58.366 36.000 6.38 0.00 36.31 4.40
979 984 4.080356 CCATGGCAGCTATAAATAGGCCTA 60.080 45.833 16.60 16.60 38.07 3.93
1000 1005 6.631992 GCCTATAGCATGATGATCATCCTTCA 60.632 42.308 28.61 15.18 42.97 3.02
1001 1006 6.987404 CCTATAGCATGATGATCATCCTTCAG 59.013 42.308 28.61 17.83 34.28 3.02
1076 1081 5.418840 GGTCAATACAAATCCACCATGAAGT 59.581 40.000 0.00 0.00 0.00 3.01
1078 1083 6.150976 GTCAATACAAATCCACCATGAAGTCA 59.849 38.462 0.00 0.00 0.00 3.41
1238 1243 2.356665 TCTAGGGCAGCAACAACAAA 57.643 45.000 0.00 0.00 0.00 2.83
1255 1260 2.224354 ACAAAAATTTCCAGGGCAGCAG 60.224 45.455 0.00 0.00 0.00 4.24
1317 1358 3.511146 CCATTTCTGCCACAACTACCATT 59.489 43.478 0.00 0.00 0.00 3.16
1378 1419 0.398696 AACCGCAACCACAGTATCCA 59.601 50.000 0.00 0.00 0.00 3.41
1479 1565 4.370049 CAACAACAACTGATTCCATGCAA 58.630 39.130 0.00 0.00 0.00 4.08
1591 1680 2.075355 AATTGTGGCAGACCCCCGAA 62.075 55.000 0.00 0.00 33.59 4.30
1624 1713 1.135603 CAAGCCATCCACAATGTCGTG 60.136 52.381 0.00 0.00 36.61 4.35
1689 1841 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1690 1842 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1691 1843 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
1692 1844 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1693 1845 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1694 1846 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
1748 1900 1.340405 CCTACCAGCAGCCTCAACAAT 60.340 52.381 0.00 0.00 0.00 2.71
1759 1911 5.391310 GCAGCCTCAACAATAATATCCATCG 60.391 44.000 0.00 0.00 0.00 3.84
1858 2010 4.028131 TCGAGGAAATAAGGAACCTAGCA 58.972 43.478 0.00 0.00 32.53 3.49
1873 2025 0.965866 TAGCACTGCAGACGCTACCT 60.966 55.000 27.46 14.52 39.64 3.08
1920 2072 2.779755 TATTGCTCGACCACCATTGT 57.220 45.000 0.00 0.00 0.00 2.71
2015 2169 3.863681 CCATGGTTTGGTCGTTGTG 57.136 52.632 2.57 0.00 40.99 3.33
2039 2194 5.457140 GCGGTGAAAAATAAAGTGACATGA 58.543 37.500 0.00 0.00 0.00 3.07
2040 2195 6.092748 GCGGTGAAAAATAAAGTGACATGAT 58.907 36.000 0.00 0.00 0.00 2.45
2324 2485 1.826720 TGGCTTGCCCTTGATCAATTC 59.173 47.619 8.96 1.94 0.00 2.17
2333 2494 5.248934 TGCCCTTGATCAATTCTTTCCAAAT 59.751 36.000 8.96 0.00 0.00 2.32
2404 2565 5.506686 TCTCCTCAACATGAGTATCTTCG 57.493 43.478 0.00 0.00 42.80 3.79
2459 2620 7.564793 TGAAGCATTAATAGCACTCTTCCTTA 58.435 34.615 10.96 0.00 0.00 2.69
2467 2628 6.798427 ATAGCACTCTTCCTTACATCAAGA 57.202 37.500 0.00 0.00 36.22 3.02
2717 2879 5.242838 TGCACCAAAATACTCTTAACTTGGG 59.757 40.000 3.88 0.00 38.09 4.12
2723 2885 8.852135 CCAAAATACTCTTAACTTGGGTTGTAA 58.148 33.333 0.00 0.00 36.92 2.41
2878 3040 3.690460 ACCCATGACCAAATGTTCTCTC 58.310 45.455 0.00 0.00 0.00 3.20
2903 3065 2.238898 CTCCCTCCGTCCCAAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
2904 3066 2.026636 TCCCTCCGTCCCAAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
2905 3067 2.290705 CCCTCCGTCCCAAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
2906 3068 3.007635 CCTCCGTCCCAAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
2907 3069 3.558321 CCTCCGTCCCAAAATACTTGTCA 60.558 47.826 0.00 0.00 0.00 3.58
2908 3070 4.261801 CTCCGTCCCAAAATACTTGTCAT 58.738 43.478 0.00 0.00 0.00 3.06
2909 3071 4.658063 TCCGTCCCAAAATACTTGTCATT 58.342 39.130 0.00 0.00 0.00 2.57
2910 3072 5.806818 TCCGTCCCAAAATACTTGTCATTA 58.193 37.500 0.00 0.00 0.00 1.90
2911 3073 6.239396 TCCGTCCCAAAATACTTGTCATTAA 58.761 36.000 0.00 0.00 0.00 1.40
2912 3074 6.715718 TCCGTCCCAAAATACTTGTCATTAAA 59.284 34.615 0.00 0.00 0.00 1.52
2913 3075 7.230913 TCCGTCCCAAAATACTTGTCATTAAAA 59.769 33.333 0.00 0.00 0.00 1.52
2914 3076 8.032451 CCGTCCCAAAATACTTGTCATTAAAAT 58.968 33.333 0.00 0.00 0.00 1.82
2915 3077 8.859156 CGTCCCAAAATACTTGTCATTAAAATG 58.141 33.333 0.00 0.00 37.75 2.32
2916 3078 9.150348 GTCCCAAAATACTTGTCATTAAAATGG 57.850 33.333 3.00 0.00 37.03 3.16
2917 3079 9.094578 TCCCAAAATACTTGTCATTAAAATGGA 57.905 29.630 3.00 0.00 37.03 3.41
2918 3080 9.889128 CCCAAAATACTTGTCATTAAAATGGAT 57.111 29.630 3.00 0.00 37.03 3.41
2926 3088 8.458843 ACTTGTCATTAAAATGGATAAACGAGG 58.541 33.333 3.00 0.00 37.03 4.63
2927 3089 8.568676 TTGTCATTAAAATGGATAAACGAGGA 57.431 30.769 3.00 0.00 37.03 3.71
2928 3090 8.746052 TGTCATTAAAATGGATAAACGAGGAT 57.254 30.769 3.00 0.00 37.03 3.24
2929 3091 8.620416 TGTCATTAAAATGGATAAACGAGGATG 58.380 33.333 3.00 0.00 37.03 3.51
2930 3092 8.621286 GTCATTAAAATGGATAAACGAGGATGT 58.379 33.333 3.00 0.00 37.03 3.06
2931 3093 9.839817 TCATTAAAATGGATAAACGAGGATGTA 57.160 29.630 3.00 0.00 37.03 2.29
2936 3098 9.712305 AAAATGGATAAACGAGGATGTATCTAG 57.288 33.333 0.00 0.00 0.00 2.43
2937 3099 8.651589 AATGGATAAACGAGGATGTATCTAGA 57.348 34.615 0.00 0.00 0.00 2.43
2938 3100 8.830915 ATGGATAAACGAGGATGTATCTAGAT 57.169 34.615 10.73 10.73 0.00 1.98
2939 3101 8.056407 TGGATAAACGAGGATGTATCTAGATG 57.944 38.462 15.79 0.00 0.00 2.90
2940 3102 7.670140 TGGATAAACGAGGATGTATCTAGATGT 59.330 37.037 15.79 1.25 0.00 3.06
2941 3103 7.971168 GGATAAACGAGGATGTATCTAGATGTG 59.029 40.741 15.79 0.00 0.00 3.21
2942 3104 6.716934 AAACGAGGATGTATCTAGATGTGT 57.283 37.500 15.79 0.52 0.00 3.72
2943 3105 6.716934 AACGAGGATGTATCTAGATGTGTT 57.283 37.500 15.79 5.47 0.00 3.32
2944 3106 6.716934 ACGAGGATGTATCTAGATGTGTTT 57.283 37.500 15.79 0.00 0.00 2.83
2945 3107 7.113658 ACGAGGATGTATCTAGATGTGTTTT 57.886 36.000 15.79 0.00 0.00 2.43
2946 3108 8.234136 ACGAGGATGTATCTAGATGTGTTTTA 57.766 34.615 15.79 0.00 0.00 1.52
2947 3109 8.353684 ACGAGGATGTATCTAGATGTGTTTTAG 58.646 37.037 15.79 4.33 0.00 1.85
2948 3110 8.353684 CGAGGATGTATCTAGATGTGTTTTAGT 58.646 37.037 15.79 0.00 0.00 2.24
2972 3134 9.793259 AGTTCTAAATACATCTCTTTTTGTCCA 57.207 29.630 0.00 0.00 0.00 4.02
2980 3142 9.865321 ATACATCTCTTTTTGTCCATTTTGATG 57.135 29.630 0.00 0.00 35.23 3.07
2981 3143 7.954835 ACATCTCTTTTTGTCCATTTTGATGA 58.045 30.769 0.00 0.00 33.85 2.92
2982 3144 7.869429 ACATCTCTTTTTGTCCATTTTGATGAC 59.131 33.333 0.00 0.00 33.85 3.06
2983 3145 7.345422 TCTCTTTTTGTCCATTTTGATGACA 57.655 32.000 0.00 0.00 0.00 3.58
2984 3146 7.780064 TCTCTTTTTGTCCATTTTGATGACAA 58.220 30.769 0.00 0.00 34.47 3.18
2985 3147 8.256605 TCTCTTTTTGTCCATTTTGATGACAAA 58.743 29.630 11.70 11.70 43.10 2.83
2986 3148 8.961294 TCTTTTTGTCCATTTTGATGACAAAT 57.039 26.923 15.28 0.00 43.99 2.32
2992 3154 9.434420 TTGTCCATTTTGATGACAAATATTTCC 57.566 29.630 0.00 0.00 43.99 3.13
2993 3155 7.758980 TGTCCATTTTGATGACAAATATTTCCG 59.241 33.333 0.00 0.00 43.99 4.30
2994 3156 7.222611 GTCCATTTTGATGACAAATATTTCCGG 59.777 37.037 0.00 0.00 43.99 5.14
2995 3157 7.123397 TCCATTTTGATGACAAATATTTCCGGA 59.877 33.333 0.00 0.00 43.99 5.14
2996 3158 7.222611 CCATTTTGATGACAAATATTTCCGGAC 59.777 37.037 1.83 0.00 43.99 4.79
2997 3159 5.478233 TTGATGACAAATATTTCCGGACG 57.522 39.130 1.83 0.00 32.73 4.79
2998 3160 3.874543 TGATGACAAATATTTCCGGACGG 59.125 43.478 1.83 3.96 0.00 4.79
2999 3161 3.613494 TGACAAATATTTCCGGACGGA 57.387 42.857 1.83 9.76 43.52 4.69
3000 3162 3.527533 TGACAAATATTTCCGGACGGAG 58.472 45.455 13.64 3.15 46.06 4.63
3001 3163 2.870411 GACAAATATTTCCGGACGGAGG 59.130 50.000 13.64 0.00 46.06 4.30
3002 3164 2.218603 CAAATATTTCCGGACGGAGGG 58.781 52.381 13.64 0.00 46.06 4.30
3003 3165 1.797320 AATATTTCCGGACGGAGGGA 58.203 50.000 13.64 4.95 46.06 4.20
3004 3166 1.339097 ATATTTCCGGACGGAGGGAG 58.661 55.000 13.64 0.00 46.06 4.30
3005 3167 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
3006 3168 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
3007 3169 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
3008 3170 2.044650 CCGGACGGAGGGAGTACA 60.045 66.667 4.40 0.00 37.50 2.90
3009 3171 1.455217 CCGGACGGAGGGAGTACAT 60.455 63.158 4.40 0.00 37.50 2.29
3010 3172 1.041447 CCGGACGGAGGGAGTACATT 61.041 60.000 4.40 0.00 37.50 2.71
3011 3173 1.683943 CGGACGGAGGGAGTACATTA 58.316 55.000 0.00 0.00 0.00 1.90
3012 3174 2.236766 CGGACGGAGGGAGTACATTAT 58.763 52.381 0.00 0.00 0.00 1.28
3013 3175 2.626743 CGGACGGAGGGAGTACATTATT 59.373 50.000 0.00 0.00 0.00 1.40
3014 3176 3.069158 CGGACGGAGGGAGTACATTATTT 59.931 47.826 0.00 0.00 0.00 1.40
3015 3177 4.377897 GGACGGAGGGAGTACATTATTTG 58.622 47.826 0.00 0.00 0.00 2.32
3016 3178 4.377897 GACGGAGGGAGTACATTATTTGG 58.622 47.826 0.00 0.00 0.00 3.28
3017 3179 3.778629 ACGGAGGGAGTACATTATTTGGT 59.221 43.478 0.00 0.00 0.00 3.67
3018 3180 4.141779 ACGGAGGGAGTACATTATTTGGTC 60.142 45.833 0.00 0.00 0.00 4.02
3019 3181 4.377897 GGAGGGAGTACATTATTTGGTCG 58.622 47.826 0.00 0.00 0.00 4.79
3020 3182 4.141779 GGAGGGAGTACATTATTTGGTCGT 60.142 45.833 0.00 0.00 0.00 4.34
3021 3183 4.766375 AGGGAGTACATTATTTGGTCGTG 58.234 43.478 0.00 0.00 0.00 4.35
3022 3184 3.875134 GGGAGTACATTATTTGGTCGTGG 59.125 47.826 0.00 0.00 0.00 4.94
3023 3185 3.311596 GGAGTACATTATTTGGTCGTGGC 59.688 47.826 0.00 0.00 0.00 5.01
3024 3186 3.936453 GAGTACATTATTTGGTCGTGGCA 59.064 43.478 0.00 0.00 0.00 4.92
3025 3187 4.523083 AGTACATTATTTGGTCGTGGCAT 58.477 39.130 0.00 0.00 0.00 4.40
3026 3188 5.676552 AGTACATTATTTGGTCGTGGCATA 58.323 37.500 0.00 0.00 0.00 3.14
3027 3189 6.296026 AGTACATTATTTGGTCGTGGCATAT 58.704 36.000 0.00 0.00 0.00 1.78
3028 3190 6.770785 AGTACATTATTTGGTCGTGGCATATT 59.229 34.615 0.00 0.00 0.00 1.28
3029 3191 7.934665 AGTACATTATTTGGTCGTGGCATATTA 59.065 33.333 0.00 0.00 0.00 0.98
3030 3192 7.575414 ACATTATTTGGTCGTGGCATATTAA 57.425 32.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.773033 AAGGATTGCCTATTTCTATTTCACAT 57.227 30.769 0.00 0.00 46.28 3.21
1 2 8.469200 CAAAGGATTGCCTATTTCTATTTCACA 58.531 33.333 0.00 0.00 46.28 3.58
2 3 8.686334 TCAAAGGATTGCCTATTTCTATTTCAC 58.314 33.333 0.00 0.00 46.28 3.18
3 4 8.821686 TCAAAGGATTGCCTATTTCTATTTCA 57.178 30.769 0.00 0.00 46.28 2.69
9 10 8.571336 CGAATTATCAAAGGATTGCCTATTTCT 58.429 33.333 0.00 0.00 46.28 2.52
10 11 8.567948 TCGAATTATCAAAGGATTGCCTATTTC 58.432 33.333 0.00 0.00 46.28 2.17
11 12 8.463930 TCGAATTATCAAAGGATTGCCTATTT 57.536 30.769 0.00 0.00 46.28 1.40
12 13 8.641498 ATCGAATTATCAAAGGATTGCCTATT 57.359 30.769 0.00 0.00 46.28 1.73
13 14 9.739276 TTATCGAATTATCAAAGGATTGCCTAT 57.261 29.630 0.00 0.00 46.28 2.57
14 15 9.567776 TTTATCGAATTATCAAAGGATTGCCTA 57.432 29.630 0.00 0.00 46.28 3.93
16 17 8.352942 ACTTTATCGAATTATCAAAGGATTGCC 58.647 33.333 0.00 0.00 36.45 4.52
17 18 9.173939 CACTTTATCGAATTATCAAAGGATTGC 57.826 33.333 0.00 0.00 36.45 3.56
20 21 9.613428 TCACACTTTATCGAATTATCAAAGGAT 57.387 29.630 0.00 0.00 37.55 3.24
21 22 9.098355 CTCACACTTTATCGAATTATCAAAGGA 57.902 33.333 0.00 0.00 31.89 3.36
22 23 8.883731 ACTCACACTTTATCGAATTATCAAAGG 58.116 33.333 0.00 0.00 31.89 3.11
23 24 9.907576 GACTCACACTTTATCGAATTATCAAAG 57.092 33.333 0.00 0.00 33.45 2.77
24 25 9.653287 AGACTCACACTTTATCGAATTATCAAA 57.347 29.630 0.00 0.00 0.00 2.69
25 26 9.302345 GAGACTCACACTTTATCGAATTATCAA 57.698 33.333 0.00 0.00 0.00 2.57
26 27 7.921214 GGAGACTCACACTTTATCGAATTATCA 59.079 37.037 4.53 0.00 0.00 2.15
27 28 8.138712 AGGAGACTCACACTTTATCGAATTATC 58.861 37.037 4.53 0.00 32.90 1.75
28 29 8.012957 AGGAGACTCACACTTTATCGAATTAT 57.987 34.615 4.53 0.00 32.90 1.28
29 30 7.406031 AGGAGACTCACACTTTATCGAATTA 57.594 36.000 4.53 0.00 32.90 1.40
30 31 6.287589 AGGAGACTCACACTTTATCGAATT 57.712 37.500 4.53 0.00 32.90 2.17
31 32 5.923733 AGGAGACTCACACTTTATCGAAT 57.076 39.130 4.53 0.00 32.90 3.34
32 33 7.406031 AATAGGAGACTCACACTTTATCGAA 57.594 36.000 4.53 0.00 43.67 3.71
33 34 7.406031 AAATAGGAGACTCACACTTTATCGA 57.594 36.000 4.53 0.00 43.67 3.59
34 35 6.697892 GGAAATAGGAGACTCACACTTTATCG 59.302 42.308 4.53 0.00 43.67 2.92
35 36 6.697892 CGGAAATAGGAGACTCACACTTTATC 59.302 42.308 4.53 0.00 43.67 1.75
36 37 6.154706 ACGGAAATAGGAGACTCACACTTTAT 59.845 38.462 4.53 0.00 43.67 1.40
37 38 5.479375 ACGGAAATAGGAGACTCACACTTTA 59.521 40.000 4.53 0.00 43.67 1.85
38 39 4.283722 ACGGAAATAGGAGACTCACACTTT 59.716 41.667 4.53 0.00 43.67 2.66
39 40 3.833070 ACGGAAATAGGAGACTCACACTT 59.167 43.478 4.53 0.00 43.67 3.16
40 41 3.193691 CACGGAAATAGGAGACTCACACT 59.806 47.826 4.53 0.00 43.67 3.55
41 42 3.056749 ACACGGAAATAGGAGACTCACAC 60.057 47.826 4.53 0.00 43.67 3.82
42 43 3.162666 ACACGGAAATAGGAGACTCACA 58.837 45.455 4.53 0.00 43.67 3.58
43 44 3.870633 ACACGGAAATAGGAGACTCAC 57.129 47.619 4.53 0.00 43.67 3.51
44 45 5.220989 CGAATACACGGAAATAGGAGACTCA 60.221 44.000 4.53 0.00 43.67 3.41
45 46 5.008415 TCGAATACACGGAAATAGGAGACTC 59.992 44.000 0.00 0.00 43.67 3.36
47 48 5.179045 TCGAATACACGGAAATAGGAGAC 57.821 43.478 0.00 0.00 0.00 3.36
48 49 5.359009 ACTTCGAATACACGGAAATAGGAGA 59.641 40.000 0.00 0.00 0.00 3.71
49 50 5.589192 ACTTCGAATACACGGAAATAGGAG 58.411 41.667 0.00 0.00 0.00 3.69
50 51 5.587388 ACTTCGAATACACGGAAATAGGA 57.413 39.130 0.00 0.00 0.00 2.94
51 52 7.650504 TCATTACTTCGAATACACGGAAATAGG 59.349 37.037 0.00 0.00 0.00 2.57
52 53 8.570096 TCATTACTTCGAATACACGGAAATAG 57.430 34.615 0.00 0.00 0.00 1.73
53 54 8.929827 TTCATTACTTCGAATACACGGAAATA 57.070 30.769 0.00 0.00 0.00 1.40
54 55 7.837202 TTCATTACTTCGAATACACGGAAAT 57.163 32.000 0.00 0.00 0.00 2.17
55 56 7.837202 ATTCATTACTTCGAATACACGGAAA 57.163 32.000 0.00 0.00 30.12 3.13
56 57 7.253850 CGAATTCATTACTTCGAATACACGGAA 60.254 37.037 6.22 0.00 45.31 4.30
57 58 6.197655 CGAATTCATTACTTCGAATACACGGA 59.802 38.462 6.22 0.00 45.31 4.69
58 59 6.020121 ACGAATTCATTACTTCGAATACACGG 60.020 38.462 11.18 0.00 45.31 4.94
59 60 6.919188 ACGAATTCATTACTTCGAATACACG 58.081 36.000 11.18 0.00 45.31 4.49
63 64 8.843733 GCGTATACGAATTCATTACTTCGAATA 58.156 33.333 28.66 0.00 45.31 1.75
64 65 7.594015 AGCGTATACGAATTCATTACTTCGAAT 59.406 33.333 28.66 0.00 45.31 3.34
65 66 6.914215 AGCGTATACGAATTCATTACTTCGAA 59.086 34.615 28.66 0.00 45.31 3.71
66 67 6.432936 AGCGTATACGAATTCATTACTTCGA 58.567 36.000 28.66 0.00 45.31 3.71
68 69 6.359087 ACGAGCGTATACGAATTCATTACTTC 59.641 38.462 28.66 6.05 43.02 3.01
69 70 6.204359 ACGAGCGTATACGAATTCATTACTT 58.796 36.000 28.66 0.00 43.02 2.24
70 71 5.755813 ACGAGCGTATACGAATTCATTACT 58.244 37.500 28.66 12.22 43.02 2.24
71 72 7.716738 ATACGAGCGTATACGAATTCATTAC 57.283 36.000 28.66 7.49 43.02 1.89
83 84 2.158254 CGTGCCAGTATACGAGCGTATA 59.842 50.000 16.27 16.27 42.54 1.47
84 85 1.069432 CGTGCCAGTATACGAGCGTAT 60.069 52.381 18.12 18.12 42.54 3.06
85 86 0.305617 CGTGCCAGTATACGAGCGTA 59.694 55.000 5.12 5.12 42.54 4.42
86 87 1.063649 CGTGCCAGTATACGAGCGT 59.936 57.895 13.32 0.00 42.54 5.07
87 88 2.293627 GCGTGCCAGTATACGAGCG 61.294 63.158 13.32 8.94 42.54 5.03
88 89 1.949631 GGCGTGCCAGTATACGAGC 60.950 63.158 5.89 11.84 42.54 5.03
89 90 0.595053 CAGGCGTGCCAGTATACGAG 60.595 60.000 14.29 0.00 42.54 4.18
90 91 1.435925 CAGGCGTGCCAGTATACGA 59.564 57.895 14.29 0.00 42.54 3.43
91 92 2.237751 GCAGGCGTGCCAGTATACG 61.238 63.158 20.50 0.00 44.72 3.06
92 93 3.719214 GCAGGCGTGCCAGTATAC 58.281 61.111 20.50 0.00 44.72 1.47
101 102 0.456653 GCATTTTAGGTGCAGGCGTG 60.457 55.000 1.01 1.01 42.08 5.34
102 103 1.595093 GGCATTTTAGGTGCAGGCGT 61.595 55.000 0.00 0.00 44.25 5.68
103 104 1.139520 GGCATTTTAGGTGCAGGCG 59.860 57.895 0.00 0.00 44.25 5.52
104 105 0.607620 TTGGCATTTTAGGTGCAGGC 59.392 50.000 0.00 0.00 44.25 4.85
105 106 1.402720 CGTTGGCATTTTAGGTGCAGG 60.403 52.381 0.00 0.00 44.25 4.85
106 107 1.981254 CGTTGGCATTTTAGGTGCAG 58.019 50.000 0.00 0.00 44.25 4.41
107 108 0.038709 GCGTTGGCATTTTAGGTGCA 60.039 50.000 0.00 0.00 44.25 4.57
108 109 0.038709 TGCGTTGGCATTTTAGGTGC 60.039 50.000 0.00 0.00 46.21 5.01
119 120 5.941948 ATATTAAATCTACCTGCGTTGGC 57.058 39.130 0.00 0.00 40.52 4.52
124 125 9.760660 GCAAGATAAATATTAAATCTACCTGCG 57.239 33.333 11.64 0.00 29.89 5.18
125 126 9.760660 CGCAAGATAAATATTAAATCTACCTGC 57.239 33.333 16.76 16.76 43.02 4.85
140 141 9.177671 GGTGGTACCTGTTTTCGCAAGATAAAT 62.178 40.741 14.36 0.00 40.34 1.40
141 142 7.952000 GGTGGTACCTGTTTTCGCAAGATAAA 61.952 42.308 14.36 0.00 40.34 1.40
142 143 6.542386 GGTGGTACCTGTTTTCGCAAGATAA 61.542 44.000 14.36 0.00 40.34 1.75
143 144 5.099163 GGTGGTACCTGTTTTCGCAAGATA 61.099 45.833 14.36 0.00 40.34 1.98
144 145 4.364389 GGTGGTACCTGTTTTCGCAAGAT 61.364 47.826 14.36 0.00 40.34 2.40
145 146 3.066463 GGTGGTACCTGTTTTCGCAAGA 61.066 50.000 14.36 0.00 39.30 3.02
146 147 1.265905 GGTGGTACCTGTTTTCGCAAG 59.734 52.381 14.36 0.00 34.73 4.01
147 148 1.310904 GGTGGTACCTGTTTTCGCAA 58.689 50.000 14.36 0.00 34.73 4.85
148 149 0.180642 TGGTGGTACCTGTTTTCGCA 59.819 50.000 14.36 0.00 39.58 5.10
149 150 1.310904 TTGGTGGTACCTGTTTTCGC 58.689 50.000 14.36 0.00 39.58 4.70
150 151 4.373348 TTTTTGGTGGTACCTGTTTTCG 57.627 40.909 14.36 0.00 39.58 3.46
194 197 1.747355 GGGATGGCATGAGTTCTTGTG 59.253 52.381 3.81 0.00 0.00 3.33
259 262 8.025445 GCAAATGATCATCTATGGTAATGGTTC 58.975 37.037 9.06 0.00 0.00 3.62
262 265 7.457024 TGCAAATGATCATCTATGGTAATGG 57.543 36.000 9.06 0.00 0.00 3.16
264 267 8.873186 TCATGCAAATGATCATCTATGGTAAT 57.127 30.769 9.06 0.00 0.00 1.89
450 453 3.441572 AGTAATACTGCAGCTTGCTTTGG 59.558 43.478 15.27 0.00 45.31 3.28
599 602 8.415950 TTCCTTTTACATGTCAATTGGTGTAT 57.584 30.769 0.00 0.00 0.00 2.29
604 607 8.830201 TCAAATTCCTTTTACATGTCAATTGG 57.170 30.769 0.00 3.88 0.00 3.16
607 610 9.865321 CTCATCAAATTCCTTTTACATGTCAAT 57.135 29.630 0.00 0.00 0.00 2.57
738 741 9.980780 GTTTGTAATGTTTTGCAAGTTGTTATT 57.019 25.926 4.48 0.00 38.43 1.40
899 904 0.825010 AAGTGCTTGGGTGCTTCCTG 60.825 55.000 0.00 0.00 36.25 3.86
908 913 1.610522 CTTGTCTGGAAAGTGCTTGGG 59.389 52.381 0.00 0.00 0.00 4.12
1000 1005 7.235193 ACTCTACTTATGAGAATGATGGATGCT 59.765 37.037 0.00 0.00 35.66 3.79
1001 1006 7.331440 CACTCTACTTATGAGAATGATGGATGC 59.669 40.741 0.00 0.00 35.66 3.91
1076 1081 2.092212 GGAGGGCAAGGATGAGAAATGA 60.092 50.000 0.00 0.00 0.00 2.57
1078 1083 2.212420 AGGAGGGCAAGGATGAGAAAT 58.788 47.619 0.00 0.00 0.00 2.17
1238 1243 0.832983 TGCTGCTGCCCTGGAAATTT 60.833 50.000 13.47 0.00 38.71 1.82
1255 1260 1.137872 TGTTGTGGTGGAAATGGTTGC 59.862 47.619 0.00 0.00 0.00 4.17
1378 1419 3.516615 CGAAATTGGTTGTTGTGGTTGT 58.483 40.909 0.00 0.00 0.00 3.32
1479 1565 1.873591 GTTGTTGCAAGACGACATCCT 59.126 47.619 0.00 0.00 42.43 3.24
1516 1602 3.586100 TGTTGCGATACTTGTGAGCTA 57.414 42.857 0.00 0.00 0.00 3.32
1591 1680 2.591715 GCTTGGCACCGTGACTGT 60.592 61.111 5.82 0.00 0.00 3.55
1689 1841 5.220681 GGTTGTTGTTGTTGTTGTTGTTGTT 60.221 36.000 0.00 0.00 0.00 2.83
1690 1842 4.271291 GGTTGTTGTTGTTGTTGTTGTTGT 59.729 37.500 0.00 0.00 0.00 3.32
1691 1843 4.607114 CGGTTGTTGTTGTTGTTGTTGTTG 60.607 41.667 0.00 0.00 0.00 3.33
1692 1844 3.491267 CGGTTGTTGTTGTTGTTGTTGTT 59.509 39.130 0.00 0.00 0.00 2.83
1693 1845 3.053455 CGGTTGTTGTTGTTGTTGTTGT 58.947 40.909 0.00 0.00 0.00 3.32
1694 1846 3.053455 ACGGTTGTTGTTGTTGTTGTTG 58.947 40.909 0.00 0.00 0.00 3.33
1748 1900 1.285280 CCCTGGGCCGATGGATATTA 58.715 55.000 2.71 0.00 0.00 0.98
2015 2169 4.231718 TGTCACTTTATTTTTCACCGCC 57.768 40.909 0.00 0.00 0.00 6.13
2039 2194 6.732896 AGTTCGGGTTCTTACATGATAGAT 57.267 37.500 0.00 0.00 0.00 1.98
2040 2195 7.834881 ATAGTTCGGGTTCTTACATGATAGA 57.165 36.000 0.00 0.00 0.00 1.98
2105 2260 7.660112 ACTCAAACAAACAATCATATGCAGAA 58.340 30.769 0.00 0.00 0.00 3.02
2260 2416 8.242053 CACTATCAATGCTCAATTTGAAAGTCT 58.758 33.333 0.01 0.00 0.00 3.24
2324 2485 9.373603 TGATGAATTGAATGCTTATTTGGAAAG 57.626 29.630 0.00 0.00 0.00 2.62
2404 2565 1.666189 GAGATTTGGAGTAGCCGCAAC 59.334 52.381 0.00 0.00 40.66 4.17
2459 2620 8.915057 ATCTTCGATCCATATTTTCTTGATGT 57.085 30.769 0.00 0.00 0.00 3.06
2487 2648 2.554032 CACCCAGAAACATGGTCAAGAC 59.446 50.000 0.00 0.00 38.81 3.01
2717 2879 1.601166 ACGGAAGCTTGGGTTACAAC 58.399 50.000 2.10 0.00 34.76 3.32
2723 2885 2.597510 GGCAACGGAAGCTTGGGT 60.598 61.111 2.10 0.00 0.00 4.51
2726 2888 3.363341 TTAAAAGGCAACGGAAGCTTG 57.637 42.857 2.10 0.00 46.39 4.01
2733 2895 6.293190 GGGAAGAAAAATTTAAAAGGCAACGG 60.293 38.462 0.00 0.00 46.39 4.44
2848 3010 6.201591 ACATTTGGTCATGGGTATGGTAAAT 58.798 36.000 0.00 0.00 34.97 1.40
2878 3040 0.616679 TTTGGGACGGAGGGAGTAGG 60.617 60.000 0.00 0.00 0.00 3.18
2903 3065 8.620416 CATCCTCGTTTATCCATTTTAATGACA 58.380 33.333 4.07 0.00 38.70 3.58
2904 3066 8.621286 ACATCCTCGTTTATCCATTTTAATGAC 58.379 33.333 4.07 0.00 38.70 3.06
2905 3067 8.746052 ACATCCTCGTTTATCCATTTTAATGA 57.254 30.769 4.07 0.00 38.70 2.57
2910 3072 9.712305 CTAGATACATCCTCGTTTATCCATTTT 57.288 33.333 0.00 0.00 0.00 1.82
2911 3073 9.090103 TCTAGATACATCCTCGTTTATCCATTT 57.910 33.333 0.00 0.00 0.00 2.32
2912 3074 8.651589 TCTAGATACATCCTCGTTTATCCATT 57.348 34.615 0.00 0.00 0.00 3.16
2913 3075 8.690884 CATCTAGATACATCCTCGTTTATCCAT 58.309 37.037 4.54 0.00 0.00 3.41
2914 3076 7.670140 ACATCTAGATACATCCTCGTTTATCCA 59.330 37.037 4.54 0.00 0.00 3.41
2915 3077 7.971168 CACATCTAGATACATCCTCGTTTATCC 59.029 40.741 4.54 0.00 0.00 2.59
2916 3078 8.516234 ACACATCTAGATACATCCTCGTTTATC 58.484 37.037 4.54 0.00 0.00 1.75
2917 3079 8.410673 ACACATCTAGATACATCCTCGTTTAT 57.589 34.615 4.54 0.00 0.00 1.40
2918 3080 7.818997 ACACATCTAGATACATCCTCGTTTA 57.181 36.000 4.54 0.00 0.00 2.01
2919 3081 6.716934 ACACATCTAGATACATCCTCGTTT 57.283 37.500 4.54 0.00 0.00 3.60
2920 3082 6.716934 AACACATCTAGATACATCCTCGTT 57.283 37.500 4.54 0.00 0.00 3.85
2921 3083 6.716934 AAACACATCTAGATACATCCTCGT 57.283 37.500 4.54 0.00 0.00 4.18
2922 3084 8.353684 ACTAAAACACATCTAGATACATCCTCG 58.646 37.037 4.54 0.00 0.00 4.63
2946 3108 9.793259 TGGACAAAAAGAGATGTATTTAGAACT 57.207 29.630 0.00 0.00 0.00 3.01
2954 3116 9.865321 CATCAAAATGGACAAAAAGAGATGTAT 57.135 29.630 0.00 0.00 0.00 2.29
2955 3117 9.076781 TCATCAAAATGGACAAAAAGAGATGTA 57.923 29.630 0.00 0.00 33.42 2.29
2956 3118 7.869429 GTCATCAAAATGGACAAAAAGAGATGT 59.131 33.333 0.00 0.00 33.42 3.06
2957 3119 7.868922 TGTCATCAAAATGGACAAAAAGAGATG 59.131 33.333 0.00 0.00 33.42 2.90
2958 3120 7.954835 TGTCATCAAAATGGACAAAAAGAGAT 58.045 30.769 0.00 0.00 33.42 2.75
2959 3121 7.345422 TGTCATCAAAATGGACAAAAAGAGA 57.655 32.000 0.00 0.00 33.42 3.10
2960 3122 8.422973 TTTGTCATCAAAATGGACAAAAAGAG 57.577 30.769 14.59 0.00 40.08 2.85
2961 3123 8.961294 ATTTGTCATCAAAATGGACAAAAAGA 57.039 26.923 19.13 1.83 44.97 2.52
2966 3128 9.434420 GGAAATATTTGTCATCAAAATGGACAA 57.566 29.630 5.17 0.00 44.97 3.18
2967 3129 7.758980 CGGAAATATTTGTCATCAAAATGGACA 59.241 33.333 5.17 0.00 44.97 4.02
2968 3130 7.222611 CCGGAAATATTTGTCATCAAAATGGAC 59.777 37.037 5.17 0.00 44.97 4.02
2969 3131 7.123397 TCCGGAAATATTTGTCATCAAAATGGA 59.877 33.333 0.00 0.00 44.97 3.41
2970 3132 7.222611 GTCCGGAAATATTTGTCATCAAAATGG 59.777 37.037 5.23 0.00 44.97 3.16
2971 3133 7.044117 CGTCCGGAAATATTTGTCATCAAAATG 60.044 37.037 5.23 0.00 44.97 2.32
2972 3134 6.972328 CGTCCGGAAATATTTGTCATCAAAAT 59.028 34.615 5.23 0.00 44.97 1.82
2973 3135 6.318628 CGTCCGGAAATATTTGTCATCAAAA 58.681 36.000 5.23 0.00 44.97 2.44
2974 3136 5.163703 CCGTCCGGAAATATTTGTCATCAAA 60.164 40.000 5.23 0.00 41.49 2.69
2975 3137 4.334203 CCGTCCGGAAATATTTGTCATCAA 59.666 41.667 5.23 0.00 37.50 2.57
2976 3138 3.874543 CCGTCCGGAAATATTTGTCATCA 59.125 43.478 5.23 0.00 37.50 3.07
2977 3139 4.124238 TCCGTCCGGAAATATTTGTCATC 58.876 43.478 5.23 0.00 42.05 2.92
2978 3140 4.127171 CTCCGTCCGGAAATATTTGTCAT 58.873 43.478 5.23 0.00 44.66 3.06
2979 3141 3.527533 CTCCGTCCGGAAATATTTGTCA 58.472 45.455 5.23 0.00 44.66 3.58
2980 3142 2.870411 CCTCCGTCCGGAAATATTTGTC 59.130 50.000 5.23 0.00 44.66 3.18
2981 3143 2.420967 CCCTCCGTCCGGAAATATTTGT 60.421 50.000 5.23 0.00 44.66 2.83
2982 3144 2.158871 TCCCTCCGTCCGGAAATATTTG 60.159 50.000 5.23 0.00 44.66 2.32
2983 3145 2.104281 CTCCCTCCGTCCGGAAATATTT 59.896 50.000 5.23 0.00 44.66 1.40
2984 3146 1.692519 CTCCCTCCGTCCGGAAATATT 59.307 52.381 5.23 0.00 44.66 1.28
2985 3147 1.339097 CTCCCTCCGTCCGGAAATAT 58.661 55.000 5.23 0.00 44.66 1.28
2986 3148 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2987 3149 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2988 3150 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2989 3151 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2990 3152 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
2991 3153 1.041447 AATGTACTCCCTCCGTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
2992 3154 1.683943 TAATGTACTCCCTCCGTCCG 58.316 55.000 0.00 0.00 0.00 4.79
2993 3155 4.377897 CAAATAATGTACTCCCTCCGTCC 58.622 47.826 0.00 0.00 0.00 4.79
2994 3156 4.141779 ACCAAATAATGTACTCCCTCCGTC 60.142 45.833 0.00 0.00 0.00 4.79
2995 3157 3.778629 ACCAAATAATGTACTCCCTCCGT 59.221 43.478 0.00 0.00 0.00 4.69
2996 3158 4.377897 GACCAAATAATGTACTCCCTCCG 58.622 47.826 0.00 0.00 0.00 4.63
2997 3159 4.141779 ACGACCAAATAATGTACTCCCTCC 60.142 45.833 0.00 0.00 0.00 4.30
2998 3160 4.809426 CACGACCAAATAATGTACTCCCTC 59.191 45.833 0.00 0.00 0.00 4.30
2999 3161 4.383770 CCACGACCAAATAATGTACTCCCT 60.384 45.833 0.00 0.00 0.00 4.20
3000 3162 3.875134 CCACGACCAAATAATGTACTCCC 59.125 47.826 0.00 0.00 0.00 4.30
3001 3163 3.311596 GCCACGACCAAATAATGTACTCC 59.688 47.826 0.00 0.00 0.00 3.85
3002 3164 3.936453 TGCCACGACCAAATAATGTACTC 59.064 43.478 0.00 0.00 0.00 2.59
3003 3165 3.945346 TGCCACGACCAAATAATGTACT 58.055 40.909 0.00 0.00 0.00 2.73
3004 3166 4.893424 ATGCCACGACCAAATAATGTAC 57.107 40.909 0.00 0.00 0.00 2.90
3005 3167 8.678593 TTAATATGCCACGACCAAATAATGTA 57.321 30.769 0.00 0.00 0.00 2.29
3006 3168 7.575414 TTAATATGCCACGACCAAATAATGT 57.425 32.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.