Multiple sequence alignment - TraesCS6B01G262000

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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 TraesCS6B01G262000 chr6B 100.000 3137 0 0 1 3137 471677867 471674731 0.000000e+00 5794.0
1 TraesCS6B01G262000 chr6A 93.039 2902 95 43 272 3137 409433063 409430233 0.000000e+00 4141.0
2 TraesCS6B01G262000 chr6A 85.882 85 8 1 2640 2720 88080388 88080304 1.550000e-13 87.9
3 TraesCS6B01G262000 chr6D 93.538 2445 68 33 272 2677 305171898 305174291 0.000000e+00 3557.0
4 TraesCS6B01G262000 chr6D 94.203 414 16 4 2724 3137 305174293 305174698 2.660000e-175 625.0
5 TraesCS6B01G262000 chr6D 89.474 76 7 1 2370 2444 305174073 305173998 9.260000e-16 95.3
6 TraesCS6B01G262000 chr6D 85.185 81 7 4 2354 2433 57176666 57176742 9.330000e-11 78.7
7 TraesCS6B01G262000 chr2A 86.726 678 69 12 1139 1813 618982493 618981834 0.000000e+00 734.0
8 TraesCS6B01G262000 chr2A 85.259 251 27 7 23 271 675574152 675573910 1.870000e-62 250.0
9 TraesCS6B01G262000 chr2B 88.305 590 65 4 1226 1813 557815959 557815372 0.000000e+00 704.0
10 TraesCS6B01G262000 chr2D 85.546 678 77 14 1139 1813 476696894 476696235 0.000000e+00 689.0
11 TraesCS6B01G262000 chr2D 86.747 249 27 1 23 271 531194978 531194736 3.990000e-69 272.0
12 TraesCS6B01G262000 chr2D 90.000 80 4 3 2640 2715 548076875 548076796 1.990000e-17 100.0
13 TraesCS6B01G262000 chr5A 89.157 249 21 1 23 271 590035758 590035516 3.930000e-79 305.0
14 TraesCS6B01G262000 chr5A 89.069 247 21 1 23 269 589939817 589939577 5.080000e-78 302.0
15 TraesCS6B01G262000 chr5A 87.952 249 24 1 23 271 589881882 589881640 3.960000e-74 289.0
16 TraesCS6B01G262000 chr5A 90.000 80 4 3 2640 2715 185649702 185649781 1.990000e-17 100.0
17 TraesCS6B01G262000 chr5A 84.211 76 8 4 2370 2444 676888980 676888908 1.560000e-08 71.3
18 TraesCS6B01G262000 chr5B 88.353 249 18 2 23 271 489565714 489565477 3.960000e-74 289.0
19 TraesCS6B01G262000 chr5B 90.000 80 4 3 2640 2715 187046448 187046369 1.990000e-17 100.0
20 TraesCS6B01G262000 chr5B 86.301 73 7 3 2368 2440 660148660 660148591 3.350000e-10 76.8
21 TraesCS6B01G262000 chr4A 86.697 218 29 0 23 240 581866652 581866869 3.130000e-60 243.0
22 TraesCS6B01G262000 chr3B 85.455 220 28 3 23 240 811156418 811156201 3.150000e-55 226.0
23 TraesCS6B01G262000 chr3B 91.803 61 3 2 2355 2415 73692410 73692352 2.000000e-12 84.2
24 TraesCS6B01G262000 chr1A 85.388 219 30 2 23 240 117820145 117819928 3.150000e-55 226.0
25 TraesCS6B01G262000 chr1A 89.024 82 5 1 2640 2717 307037678 307037759 7.160000e-17 99.0
26 TraesCS6B01G262000 chr1B 90.588 85 4 1 2640 2720 332083873 332083789 3.310000e-20 110.0
27 TraesCS6B01G262000 chr5D 96.721 61 2 0 2637 2697 354256737 354256797 5.540000e-18 102.0
28 TraesCS6B01G262000 chr3D 87.500 88 7 3 2632 2715 515667215 515667302 7.160000e-17 99.0
29 TraesCS6B01G262000 chr7D 89.024 82 4 2 2368 2444 5041166 5041247 2.580000e-16 97.1
30 TraesCS6B01G262000 chr7D 88.462 78 3 3 2368 2439 299594514 299594591 4.310000e-14 89.8
31 TraesCS6B01G262000 chr3A 100.000 28 0 0 2368 2395 36231378 36231351 6.000000e-03 52.8


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 TraesCS6B01G262000 chr6B 471674731 471677867 3136 True 5794 5794 100.0000 1 3137 1 chr6B.!!$R1 3136
1 TraesCS6B01G262000 chr6A 409430233 409433063 2830 True 4141 4141 93.0390 272 3137 1 chr6A.!!$R2 2865
2 TraesCS6B01G262000 chr6D 305171898 305174698 2800 False 2091 3557 93.8705 272 3137 2 chr6D.!!$F2 2865
3 TraesCS6B01G262000 chr2A 618981834 618982493 659 True 734 734 86.7260 1139 1813 1 chr2A.!!$R1 674
4 TraesCS6B01G262000 chr2B 557815372 557815959 587 True 704 704 88.3050 1226 1813 1 chr2B.!!$R1 587
5 TraesCS6B01G262000 chr2D 476696235 476696894 659 True 689 689 85.5460 1139 1813 1 chr2D.!!$R1 674

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
535 544 0.17576 TCTCATTACCGAGCCTGCAC 59.824 55.0 0.0 0.0 32.75 4.57 F
930 953 1.05666 TTTCACACTCTCCTCACCCC 58.943 55.0 0.0 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2089 2.289010 GGCAATTGAAACAACAGGGAGG 60.289 50.000 10.34 0.0 0.0 4.3 R
2712 2775 3.135895 ACACCACAAGCTACTTACAACCT 59.864 43.478 0.00 0.0 0.0 3.5 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
30 31 2.142356 TTTTGCGGGGATCATCATGT 57.858 45.000 0.00 0.00 0.00 3.21
31 32 1.679139 TTTGCGGGGATCATCATGTC 58.321 50.000 0.00 0.00 0.00 3.06
32 33 0.179020 TTGCGGGGATCATCATGTCC 60.179 55.000 0.00 0.00 0.00 4.02
33 34 1.344191 TGCGGGGATCATCATGTCCA 61.344 55.000 8.11 0.00 36.19 4.02
34 35 0.604780 GCGGGGATCATCATGTCCAG 60.605 60.000 8.11 3.79 36.19 3.86
35 36 0.761187 CGGGGATCATCATGTCCAGT 59.239 55.000 8.11 0.00 36.19 4.00
36 37 1.141657 CGGGGATCATCATGTCCAGTT 59.858 52.381 8.11 0.00 36.19 3.16
37 38 2.421952 CGGGGATCATCATGTCCAGTTT 60.422 50.000 8.11 0.00 36.19 2.66
38 39 3.181455 CGGGGATCATCATGTCCAGTTTA 60.181 47.826 8.11 0.00 36.19 2.01
39 40 4.685848 CGGGGATCATCATGTCCAGTTTAA 60.686 45.833 8.11 0.00 36.19 1.52
40 41 4.580580 GGGGATCATCATGTCCAGTTTAAC 59.419 45.833 8.11 0.00 36.19 2.01
41 42 5.192927 GGGATCATCATGTCCAGTTTAACA 58.807 41.667 8.11 0.00 36.19 2.41
42 43 5.297776 GGGATCATCATGTCCAGTTTAACAG 59.702 44.000 8.11 0.00 36.19 3.16
43 44 5.220931 GGATCATCATGTCCAGTTTAACAGC 60.221 44.000 0.00 0.00 34.57 4.40
44 45 4.650734 TCATCATGTCCAGTTTAACAGCA 58.349 39.130 0.00 0.00 0.00 4.41
45 46 4.455533 TCATCATGTCCAGTTTAACAGCAC 59.544 41.667 0.00 0.00 0.00 4.40
46 47 3.814625 TCATGTCCAGTTTAACAGCACA 58.185 40.909 0.00 0.00 0.00 4.57
47 48 4.203226 TCATGTCCAGTTTAACAGCACAA 58.797 39.130 0.00 0.00 0.00 3.33
48 49 4.642437 TCATGTCCAGTTTAACAGCACAAA 59.358 37.500 0.00 0.00 0.00 2.83
49 50 5.126222 TCATGTCCAGTTTAACAGCACAAAA 59.874 36.000 0.00 0.00 0.00 2.44
50 51 5.590530 TGTCCAGTTTAACAGCACAAAAT 57.409 34.783 0.00 0.00 0.00 1.82
51 52 5.587289 TGTCCAGTTTAACAGCACAAAATC 58.413 37.500 0.00 0.00 0.00 2.17
52 53 5.359576 TGTCCAGTTTAACAGCACAAAATCT 59.640 36.000 0.00 0.00 0.00 2.40
53 54 6.544197 TGTCCAGTTTAACAGCACAAAATCTA 59.456 34.615 0.00 0.00 0.00 1.98
54 55 7.230510 TGTCCAGTTTAACAGCACAAAATCTAT 59.769 33.333 0.00 0.00 0.00 1.98
55 56 8.082242 GTCCAGTTTAACAGCACAAAATCTATT 58.918 33.333 0.00 0.00 0.00 1.73
56 57 8.296713 TCCAGTTTAACAGCACAAAATCTATTC 58.703 33.333 0.00 0.00 0.00 1.75
57 58 7.542130 CCAGTTTAACAGCACAAAATCTATTCC 59.458 37.037 0.00 0.00 0.00 3.01
58 59 8.299570 CAGTTTAACAGCACAAAATCTATTCCT 58.700 33.333 0.00 0.00 0.00 3.36
59 60 8.515414 AGTTTAACAGCACAAAATCTATTCCTC 58.485 33.333 0.00 0.00 0.00 3.71
60 61 8.515414 GTTTAACAGCACAAAATCTATTCCTCT 58.485 33.333 0.00 0.00 0.00 3.69
61 62 6.506500 AACAGCACAAAATCTATTCCTCTG 57.493 37.500 0.00 0.00 0.00 3.35
62 63 5.809001 ACAGCACAAAATCTATTCCTCTGA 58.191 37.500 0.00 0.00 0.00 3.27
63 64 5.879223 ACAGCACAAAATCTATTCCTCTGAG 59.121 40.000 0.00 0.00 0.00 3.35
64 65 4.880696 AGCACAAAATCTATTCCTCTGAGC 59.119 41.667 0.00 0.00 0.00 4.26
65 66 4.880696 GCACAAAATCTATTCCTCTGAGCT 59.119 41.667 0.00 0.00 0.00 4.09
66 67 5.356470 GCACAAAATCTATTCCTCTGAGCTT 59.644 40.000 0.00 0.00 0.00 3.74
67 68 6.127786 GCACAAAATCTATTCCTCTGAGCTTT 60.128 38.462 0.00 0.00 0.00 3.51
68 69 7.249147 CACAAAATCTATTCCTCTGAGCTTTG 58.751 38.462 0.00 0.00 0.00 2.77
69 70 6.944862 ACAAAATCTATTCCTCTGAGCTTTGT 59.055 34.615 0.00 0.00 31.13 2.83
70 71 7.449704 ACAAAATCTATTCCTCTGAGCTTTGTT 59.550 33.333 0.00 0.00 31.54 2.83
71 72 8.302438 CAAAATCTATTCCTCTGAGCTTTGTTT 58.698 33.333 0.00 0.00 0.00 2.83
72 73 7.622893 AATCTATTCCTCTGAGCTTTGTTTC 57.377 36.000 0.00 0.00 0.00 2.78
73 74 6.365970 TCTATTCCTCTGAGCTTTGTTTCT 57.634 37.500 0.00 0.00 0.00 2.52
74 75 6.773638 TCTATTCCTCTGAGCTTTGTTTCTT 58.226 36.000 0.00 0.00 0.00 2.52
75 76 7.227156 TCTATTCCTCTGAGCTTTGTTTCTTT 58.773 34.615 0.00 0.00 0.00 2.52
76 77 6.721704 ATTCCTCTGAGCTTTGTTTCTTTT 57.278 33.333 0.00 0.00 0.00 2.27
77 78 5.757850 TCCTCTGAGCTTTGTTTCTTTTC 57.242 39.130 0.00 0.00 0.00 2.29
78 79 5.192927 TCCTCTGAGCTTTGTTTCTTTTCA 58.807 37.500 0.00 0.00 0.00 2.69
79 80 5.829924 TCCTCTGAGCTTTGTTTCTTTTCAT 59.170 36.000 0.00 0.00 0.00 2.57
80 81 6.998074 TCCTCTGAGCTTTGTTTCTTTTCATA 59.002 34.615 0.00 0.00 0.00 2.15
81 82 7.502226 TCCTCTGAGCTTTGTTTCTTTTCATAA 59.498 33.333 0.00 0.00 0.00 1.90
82 83 8.137437 CCTCTGAGCTTTGTTTCTTTTCATAAA 58.863 33.333 0.00 0.00 0.00 1.40
83 84 9.520204 CTCTGAGCTTTGTTTCTTTTCATAAAA 57.480 29.630 0.00 0.00 0.00 1.52
86 87 8.550376 TGAGCTTTGTTTCTTTTCATAAAATGC 58.450 29.630 0.00 0.00 0.00 3.56
87 88 8.436046 AGCTTTGTTTCTTTTCATAAAATGCA 57.564 26.923 0.00 0.00 0.00 3.96
88 89 8.891720 AGCTTTGTTTCTTTTCATAAAATGCAA 58.108 25.926 0.00 0.00 0.00 4.08
89 90 9.161684 GCTTTGTTTCTTTTCATAAAATGCAAG 57.838 29.630 0.00 0.00 0.00 4.01
90 91 9.161684 CTTTGTTTCTTTTCATAAAATGCAAGC 57.838 29.630 0.00 0.00 0.00 4.01
91 92 7.783090 TGTTTCTTTTCATAAAATGCAAGCA 57.217 28.000 0.00 0.00 0.00 3.91
92 93 8.380743 TGTTTCTTTTCATAAAATGCAAGCAT 57.619 26.923 0.86 0.86 38.46 3.79
94 95 9.321590 GTTTCTTTTCATAAAATGCAAGCATTC 57.678 29.630 19.42 0.08 44.86 2.67
95 96 7.280730 TCTTTTCATAAAATGCAAGCATTCG 57.719 32.000 19.42 9.61 44.86 3.34
96 97 6.867816 TCTTTTCATAAAATGCAAGCATTCGT 59.132 30.769 19.42 13.24 44.86 3.85
97 98 8.026026 TCTTTTCATAAAATGCAAGCATTCGTA 58.974 29.630 19.42 14.75 44.86 3.43
98 99 8.526218 TTTTCATAAAATGCAAGCATTCGTAA 57.474 26.923 19.42 8.30 44.86 3.18
99 100 7.739022 TTCATAAAATGCAAGCATTCGTAAG 57.261 32.000 19.42 12.09 44.86 2.34
100 101 5.743398 TCATAAAATGCAAGCATTCGTAAGC 59.257 36.000 19.42 0.00 44.86 3.09
101 102 3.574284 AAATGCAAGCATTCGTAAGCA 57.426 38.095 19.42 0.00 44.86 3.91
102 103 2.838386 ATGCAAGCATTCGTAAGCAG 57.162 45.000 0.86 0.00 35.26 4.24
103 104 1.522668 TGCAAGCATTCGTAAGCAGT 58.477 45.000 0.00 0.00 37.18 4.40
104 105 2.694213 TGCAAGCATTCGTAAGCAGTA 58.306 42.857 0.00 0.00 37.18 2.74
105 106 3.070748 TGCAAGCATTCGTAAGCAGTAA 58.929 40.909 0.00 0.00 37.18 2.24
106 107 3.689161 TGCAAGCATTCGTAAGCAGTAAT 59.311 39.130 0.00 0.00 37.18 1.89
107 108 4.873259 TGCAAGCATTCGTAAGCAGTAATA 59.127 37.500 0.00 0.00 37.18 0.98
108 109 5.352846 TGCAAGCATTCGTAAGCAGTAATAA 59.647 36.000 0.00 0.00 37.18 1.40
109 110 6.038161 TGCAAGCATTCGTAAGCAGTAATAAT 59.962 34.615 0.00 0.00 37.18 1.28
110 111 7.225734 TGCAAGCATTCGTAAGCAGTAATAATA 59.774 33.333 0.00 0.00 37.18 0.98
111 112 8.230486 GCAAGCATTCGTAAGCAGTAATAATAT 58.770 33.333 0.00 0.00 37.18 1.28
128 129 9.907576 GTAATAATATTATCAGTGATCAAGCGC 57.092 33.333 9.42 0.00 0.00 5.92
129 130 5.869753 AATATTATCAGTGATCAAGCGCC 57.130 39.130 9.42 0.00 0.00 6.53
130 131 1.570813 TTATCAGTGATCAAGCGCCG 58.429 50.000 9.42 0.00 0.00 6.46
131 132 0.744281 TATCAGTGATCAAGCGCCGA 59.256 50.000 9.42 0.31 0.00 5.54
132 133 0.529337 ATCAGTGATCAAGCGCCGAG 60.529 55.000 2.29 0.00 0.00 4.63
133 134 2.169789 CAGTGATCAAGCGCCGAGG 61.170 63.158 2.29 0.00 0.00 4.63
134 135 2.892425 GTGATCAAGCGCCGAGGG 60.892 66.667 2.29 0.00 0.00 4.30
135 136 3.074369 TGATCAAGCGCCGAGGGA 61.074 61.111 2.29 0.00 0.00 4.20
136 137 2.586357 GATCAAGCGCCGAGGGAC 60.586 66.667 2.29 0.00 0.00 4.46
137 138 3.371097 GATCAAGCGCCGAGGGACA 62.371 63.158 2.29 0.00 0.00 4.02
138 139 2.852495 GATCAAGCGCCGAGGGACAA 62.852 60.000 2.29 0.00 0.00 3.18
139 140 2.463589 ATCAAGCGCCGAGGGACAAA 62.464 55.000 2.29 0.00 0.00 2.83
140 141 2.358737 AAGCGCCGAGGGACAAAG 60.359 61.111 2.29 0.00 0.00 2.77
141 142 3.901797 AAGCGCCGAGGGACAAAGG 62.902 63.158 2.29 0.00 0.00 3.11
145 146 3.068881 CCGAGGGACAAAGGCAGA 58.931 61.111 0.00 0.00 0.00 4.26
146 147 1.376037 CCGAGGGACAAAGGCAGAC 60.376 63.158 0.00 0.00 0.00 3.51
147 148 1.674057 CGAGGGACAAAGGCAGACT 59.326 57.895 0.00 0.00 0.00 3.24
148 149 0.671781 CGAGGGACAAAGGCAGACTG 60.672 60.000 0.00 0.00 0.00 3.51
149 150 0.957888 GAGGGACAAAGGCAGACTGC 60.958 60.000 19.55 19.55 44.08 4.40
150 151 1.073897 GGGACAAAGGCAGACTGCT 59.926 57.895 25.92 10.19 44.28 4.24
151 152 0.538287 GGGACAAAGGCAGACTGCTT 60.538 55.000 25.92 17.13 44.28 3.91
152 153 0.877743 GGACAAAGGCAGACTGCTTC 59.122 55.000 25.92 11.26 44.28 3.86
153 154 0.514691 GACAAAGGCAGACTGCTTCG 59.485 55.000 25.92 15.77 44.28 3.79
154 155 1.208614 CAAAGGCAGACTGCTTCGC 59.791 57.895 25.92 10.16 44.28 4.70
155 156 1.227943 AAAGGCAGACTGCTTCGCA 60.228 52.632 25.92 0.00 44.28 5.10
169 170 5.712152 TGCTTCGCAGAGATAATATCAGA 57.288 39.130 2.84 0.00 38.43 3.27
170 171 6.089249 TGCTTCGCAGAGATAATATCAGAA 57.911 37.500 2.84 0.50 38.43 3.02
171 172 6.515832 TGCTTCGCAGAGATAATATCAGAAA 58.484 36.000 2.84 0.00 38.43 2.52
172 173 6.644181 TGCTTCGCAGAGATAATATCAGAAAG 59.356 38.462 2.84 0.00 38.43 2.62
173 174 6.865726 GCTTCGCAGAGATAATATCAGAAAGA 59.134 38.462 2.84 0.00 38.43 2.52
174 175 7.383572 GCTTCGCAGAGATAATATCAGAAAGAA 59.616 37.037 2.84 2.62 38.43 2.52
175 176 9.421806 CTTCGCAGAGATAATATCAGAAAGAAT 57.578 33.333 2.84 0.00 38.43 2.40
176 177 9.770097 TTCGCAGAGATAATATCAGAAAGAATT 57.230 29.630 2.84 0.00 38.43 2.17
177 178 9.770097 TCGCAGAGATAATATCAGAAAGAATTT 57.230 29.630 2.84 0.00 43.98 1.82
178 179 9.808808 CGCAGAGATAATATCAGAAAGAATTTG 57.191 33.333 2.84 0.00 39.27 2.32
186 187 8.992835 AATATCAGAAAGAATTTGTTTCAGCC 57.007 30.769 18.05 0.00 39.27 4.85
187 188 6.661304 ATCAGAAAGAATTTGTTTCAGCCT 57.339 33.333 18.05 2.59 39.27 4.58
188 189 7.765695 ATCAGAAAGAATTTGTTTCAGCCTA 57.234 32.000 18.05 0.00 39.27 3.93
189 190 7.765695 TCAGAAAGAATTTGTTTCAGCCTAT 57.234 32.000 18.05 0.00 39.27 2.57
190 191 8.181904 TCAGAAAGAATTTGTTTCAGCCTATT 57.818 30.769 18.05 0.00 39.27 1.73
191 192 9.295825 TCAGAAAGAATTTGTTTCAGCCTATTA 57.704 29.630 18.05 0.00 39.27 0.98
192 193 9.565213 CAGAAAGAATTTGTTTCAGCCTATTAG 57.435 33.333 18.05 0.00 39.27 1.73
193 194 9.520515 AGAAAGAATTTGTTTCAGCCTATTAGA 57.479 29.630 18.05 0.00 39.27 2.10
201 202 9.528489 TTTGTTTCAGCCTATTAGATAAAACCT 57.472 29.630 0.00 0.00 0.00 3.50
202 203 9.528489 TTGTTTCAGCCTATTAGATAAAACCTT 57.472 29.630 0.00 0.00 0.00 3.50
203 204 8.956426 TGTTTCAGCCTATTAGATAAAACCTTG 58.044 33.333 0.00 0.00 0.00 3.61
204 205 8.406297 GTTTCAGCCTATTAGATAAAACCTTGG 58.594 37.037 0.00 0.00 0.00 3.61
205 206 7.446106 TCAGCCTATTAGATAAAACCTTGGA 57.554 36.000 0.00 0.00 0.00 3.53
206 207 7.867921 TCAGCCTATTAGATAAAACCTTGGAA 58.132 34.615 0.00 0.00 0.00 3.53
207 208 7.993183 TCAGCCTATTAGATAAAACCTTGGAAG 59.007 37.037 0.00 0.00 0.00 3.46
208 209 6.773200 AGCCTATTAGATAAAACCTTGGAAGC 59.227 38.462 0.00 0.00 0.00 3.86
209 210 6.546034 GCCTATTAGATAAAACCTTGGAAGCA 59.454 38.462 0.00 0.00 0.00 3.91
210 211 7.068226 GCCTATTAGATAAAACCTTGGAAGCAA 59.932 37.037 0.00 0.00 0.00 3.91
211 212 9.136323 CCTATTAGATAAAACCTTGGAAGCAAT 57.864 33.333 0.00 0.00 0.00 3.56
215 216 7.967890 AGATAAAACCTTGGAAGCAATTTTG 57.032 32.000 0.00 0.00 0.00 2.44
216 217 7.508687 AGATAAAACCTTGGAAGCAATTTTGT 58.491 30.769 0.00 0.00 0.00 2.83
217 218 8.646900 AGATAAAACCTTGGAAGCAATTTTGTA 58.353 29.630 0.00 0.00 0.00 2.41
218 219 8.831715 ATAAAACCTTGGAAGCAATTTTGTAG 57.168 30.769 0.00 0.00 0.00 2.74
219 220 6.478512 AAACCTTGGAAGCAATTTTGTAGA 57.521 33.333 0.00 0.00 0.00 2.59
220 221 6.478512 AACCTTGGAAGCAATTTTGTAGAA 57.521 33.333 0.00 0.00 0.00 2.10
221 222 6.670695 ACCTTGGAAGCAATTTTGTAGAAT 57.329 33.333 0.00 0.00 0.00 2.40
222 223 7.775053 ACCTTGGAAGCAATTTTGTAGAATA 57.225 32.000 0.00 0.00 0.00 1.75
223 224 7.602753 ACCTTGGAAGCAATTTTGTAGAATAC 58.397 34.615 0.00 0.00 43.42 1.89
241 242 9.632969 GTAGAATACATTGCACAAACTAATACG 57.367 33.333 0.00 0.00 42.43 3.06
242 243 8.487313 AGAATACATTGCACAAACTAATACGA 57.513 30.769 0.00 0.00 0.00 3.43
243 244 8.604035 AGAATACATTGCACAAACTAATACGAG 58.396 33.333 0.00 0.00 0.00 4.18
244 245 7.843490 ATACATTGCACAAACTAATACGAGT 57.157 32.000 0.00 0.00 0.00 4.18
245 246 8.936070 ATACATTGCACAAACTAATACGAGTA 57.064 30.769 0.00 0.00 0.00 2.59
246 247 7.290857 ACATTGCACAAACTAATACGAGTAG 57.709 36.000 0.00 0.00 0.00 2.57
247 248 6.312918 ACATTGCACAAACTAATACGAGTAGG 59.687 38.462 0.00 0.00 0.00 3.18
248 249 5.395682 TGCACAAACTAATACGAGTAGGT 57.604 39.130 0.00 0.00 0.00 3.08
249 250 5.404946 TGCACAAACTAATACGAGTAGGTC 58.595 41.667 0.00 0.00 0.00 3.85
250 251 5.184479 TGCACAAACTAATACGAGTAGGTCT 59.816 40.000 0.00 0.00 0.00 3.85
251 252 5.515626 GCACAAACTAATACGAGTAGGTCTG 59.484 44.000 0.00 0.00 0.00 3.51
252 253 6.624423 GCACAAACTAATACGAGTAGGTCTGA 60.624 42.308 0.00 0.00 0.00 3.27
253 254 7.310664 CACAAACTAATACGAGTAGGTCTGAA 58.689 38.462 0.00 0.00 0.00 3.02
254 255 7.974501 CACAAACTAATACGAGTAGGTCTGAAT 59.025 37.037 0.00 0.00 0.00 2.57
255 256 8.529476 ACAAACTAATACGAGTAGGTCTGAATT 58.471 33.333 0.00 0.00 0.00 2.17
256 257 8.808529 CAAACTAATACGAGTAGGTCTGAATTG 58.191 37.037 0.00 0.00 0.00 2.32
257 258 7.876936 ACTAATACGAGTAGGTCTGAATTGA 57.123 36.000 0.00 0.00 0.00 2.57
258 259 7.932335 ACTAATACGAGTAGGTCTGAATTGAG 58.068 38.462 0.00 0.00 0.00 3.02
259 260 6.777213 AATACGAGTAGGTCTGAATTGAGT 57.223 37.500 0.00 0.00 0.00 3.41
260 261 4.442375 ACGAGTAGGTCTGAATTGAGTG 57.558 45.455 0.00 0.00 0.00 3.51
261 262 4.079970 ACGAGTAGGTCTGAATTGAGTGA 58.920 43.478 0.00 0.00 0.00 3.41
262 263 4.156922 ACGAGTAGGTCTGAATTGAGTGAG 59.843 45.833 0.00 0.00 0.00 3.51
263 264 4.396478 CGAGTAGGTCTGAATTGAGTGAGA 59.604 45.833 0.00 0.00 0.00 3.27
264 265 5.067153 CGAGTAGGTCTGAATTGAGTGAGAT 59.933 44.000 0.00 0.00 0.00 2.75
265 266 6.405286 CGAGTAGGTCTGAATTGAGTGAGATT 60.405 42.308 0.00 0.00 0.00 2.40
266 267 7.201741 CGAGTAGGTCTGAATTGAGTGAGATTA 60.202 40.741 0.00 0.00 0.00 1.75
267 268 8.006298 AGTAGGTCTGAATTGAGTGAGATTAG 57.994 38.462 0.00 0.00 0.00 1.73
268 269 6.865834 AGGTCTGAATTGAGTGAGATTAGT 57.134 37.500 0.00 0.00 0.00 2.24
269 270 6.638610 AGGTCTGAATTGAGTGAGATTAGTG 58.361 40.000 0.00 0.00 0.00 2.74
270 271 5.814705 GGTCTGAATTGAGTGAGATTAGTGG 59.185 44.000 0.00 0.00 0.00 4.00
279 280 1.483424 GAGATTAGTGGCTCACGCGC 61.483 60.000 5.73 0.00 39.64 6.86
281 282 1.756375 GATTAGTGGCTCACGCGCAG 61.756 60.000 5.73 3.06 39.64 5.18
346 347 4.847444 GAGGCGCTGCTTCCCTCC 62.847 72.222 7.64 1.31 39.36 4.30
429 438 0.821517 AGACACGTATCGGGATGCAA 59.178 50.000 0.00 0.00 32.98 4.08
440 449 2.680841 TCGGGATGCAATTTTAACGGAG 59.319 45.455 0.00 0.00 0.00 4.63
466 475 0.586802 GGTTGCTTCACCACTCGTTC 59.413 55.000 0.00 0.00 36.73 3.95
492 501 2.257371 GCGTGTGCTCGTCTACCA 59.743 61.111 0.00 0.00 38.39 3.25
508 517 1.034838 ACCAGTGCAGAAAAACGCCA 61.035 50.000 0.00 0.00 0.00 5.69
529 538 0.394565 AGCCCATCTCATTACCGAGC 59.605 55.000 0.00 0.00 32.75 5.03
530 539 0.603975 GCCCATCTCATTACCGAGCC 60.604 60.000 0.00 0.00 32.75 4.70
531 540 1.051812 CCCATCTCATTACCGAGCCT 58.948 55.000 0.00 0.00 32.75 4.58
535 544 0.175760 TCTCATTACCGAGCCTGCAC 59.824 55.000 0.00 0.00 32.75 4.57
537 546 1.409064 CTCATTACCGAGCCTGCACTA 59.591 52.381 0.00 0.00 0.00 2.74
539 548 1.134818 CATTACCGAGCCTGCACTACA 60.135 52.381 0.00 0.00 0.00 2.74
553 562 2.033299 GCACTACACACACAGCAACAAT 59.967 45.455 0.00 0.00 0.00 2.71
606 615 1.320507 GGGCTAGTAGAACTCTCCCG 58.679 60.000 0.00 0.00 32.63 5.14
703 712 1.308998 AAGCCCAGACGTTCTTTGTG 58.691 50.000 0.00 0.00 0.00 3.33
807 823 3.966543 CACTCCACCCCACCCCAC 61.967 72.222 0.00 0.00 0.00 4.61
814 830 4.715130 CCCCACCCCACGGAGAGA 62.715 72.222 0.00 0.00 0.00 3.10
834 857 4.860022 AGAAGGAGAGGAGAAGAGAAGAG 58.140 47.826 0.00 0.00 0.00 2.85
926 949 1.613925 CTCCGTTTCACACTCTCCTCA 59.386 52.381 0.00 0.00 0.00 3.86
927 950 1.340248 TCCGTTTCACACTCTCCTCAC 59.660 52.381 0.00 0.00 0.00 3.51
928 951 1.605712 CCGTTTCACACTCTCCTCACC 60.606 57.143 0.00 0.00 0.00 4.02
929 952 1.605712 CGTTTCACACTCTCCTCACCC 60.606 57.143 0.00 0.00 0.00 4.61
930 953 1.056660 TTTCACACTCTCCTCACCCC 58.943 55.000 0.00 0.00 0.00 4.95
931 954 1.185618 TTCACACTCTCCTCACCCCG 61.186 60.000 0.00 0.00 0.00 5.73
932 955 1.908793 CACACTCTCCTCACCCCGT 60.909 63.158 0.00 0.00 0.00 5.28
933 956 1.152312 ACACTCTCCTCACCCCGTT 60.152 57.895 0.00 0.00 0.00 4.44
934 957 1.186267 ACACTCTCCTCACCCCGTTC 61.186 60.000 0.00 0.00 0.00 3.95
1228 1278 3.217743 GGCTACTCCTCCGTCCGG 61.218 72.222 0.00 0.00 0.00 5.14
1708 1758 3.876589 CTACGCCAAGCACACGGGT 62.877 63.158 0.00 0.00 0.00 5.28
2034 2089 4.642429 ACAACAGGTCAACTTGGTATCTC 58.358 43.478 0.00 0.00 0.00 2.75
2101 2158 4.759516 TTGCAACTCGTAAAAGGGATTC 57.240 40.909 0.00 0.00 0.00 2.52
2179 2236 8.149647 TCAATTTCAGGTTACAGCATCAAAAAT 58.850 29.630 0.00 0.00 0.00 1.82
2186 2243 7.062605 CAGGTTACAGCATCAAAAATCATGTTC 59.937 37.037 0.00 0.00 0.00 3.18
2401 2458 5.176958 CCGTCCCACAATATAAGATCGTTTC 59.823 44.000 0.00 0.00 0.00 2.78
2409 2466 9.249457 CACAATATAAGATCGTTTCTCAAGCTA 57.751 33.333 0.00 0.00 31.78 3.32
2410 2467 9.817809 ACAATATAAGATCGTTTCTCAAGCTAA 57.182 29.630 0.00 0.00 31.78 3.09
2413 2470 9.988815 ATATAAGATCGTTTCTCAAGCTAACAT 57.011 29.630 0.00 0.00 31.78 2.71
2435 2493 8.190326 ACATAAGATCTTATATTGTGGGACGA 57.810 34.615 24.24 0.00 34.27 4.20
2441 2499 4.717778 TCTTATATTGTGGGACGAAGGGAA 59.282 41.667 0.00 0.00 0.00 3.97
2472 2530 4.691860 AATTTCCAGAATCACTCAAGCG 57.308 40.909 0.00 0.00 0.00 4.68
2712 2775 7.656137 GTCTCTAAAACCTCATTTGTGTACAGA 59.344 37.037 0.00 0.00 0.00 3.41
2713 2776 7.872993 TCTCTAAAACCTCATTTGTGTACAGAG 59.127 37.037 0.00 0.00 0.00 3.35
2741 2804 3.886123 AGTAGCTTGTGGTGTTGAGTTT 58.114 40.909 0.00 0.00 0.00 2.66
2847 2910 3.593442 TGAACCAGACCAAGTTCCATT 57.407 42.857 0.00 0.00 41.36 3.16
2860 2923 4.640771 AGTTCCATTCCTAGAAACAGCA 57.359 40.909 0.00 0.00 0.00 4.41
2981 3044 6.311935 GCAGCTTTCATAATTTGAATTGCTCA 59.688 34.615 17.53 0.00 44.98 4.26
3028 3091 5.864418 ATATGCATTCTGGATGTTTGCTT 57.136 34.783 3.54 0.00 38.07 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.426738 GACATGATGATCCCCGCAAAAA 59.573 45.455 0.00 0.00 0.00 1.94
11 12 2.023673 GACATGATGATCCCCGCAAAA 58.976 47.619 0.00 0.00 0.00 2.44
12 13 1.679139 GACATGATGATCCCCGCAAA 58.321 50.000 0.00 0.00 0.00 3.68
13 14 0.179020 GGACATGATGATCCCCGCAA 60.179 55.000 0.00 0.00 0.00 4.85
14 15 1.344191 TGGACATGATGATCCCCGCA 61.344 55.000 0.00 0.00 33.69 5.69
15 16 0.604780 CTGGACATGATGATCCCCGC 60.605 60.000 0.00 0.00 33.69 6.13
16 17 0.761187 ACTGGACATGATGATCCCCG 59.239 55.000 0.00 0.16 33.69 5.73
17 18 3.303351 AAACTGGACATGATGATCCCC 57.697 47.619 0.00 0.00 33.69 4.81
18 19 5.192927 TGTTAAACTGGACATGATGATCCC 58.807 41.667 0.00 0.00 33.69 3.85
19 20 5.220931 GCTGTTAAACTGGACATGATGATCC 60.221 44.000 0.00 3.30 35.37 3.36
20 21 5.355071 TGCTGTTAAACTGGACATGATGATC 59.645 40.000 0.00 0.00 0.00 2.92
21 22 5.124457 GTGCTGTTAAACTGGACATGATGAT 59.876 40.000 0.00 0.00 38.06 2.45
22 23 4.455533 GTGCTGTTAAACTGGACATGATGA 59.544 41.667 0.00 0.00 38.06 2.92
23 24 4.216042 TGTGCTGTTAAACTGGACATGATG 59.784 41.667 0.00 0.00 41.72 3.07
24 25 4.397420 TGTGCTGTTAAACTGGACATGAT 58.603 39.130 0.00 0.00 41.72 2.45
25 26 3.814625 TGTGCTGTTAAACTGGACATGA 58.185 40.909 0.00 0.00 41.72 3.07
26 27 4.566545 TTGTGCTGTTAAACTGGACATG 57.433 40.909 0.00 0.00 44.70 3.21
27 28 5.590530 TTTTGTGCTGTTAAACTGGACAT 57.409 34.783 0.00 0.00 44.70 3.06
28 29 5.359576 AGATTTTGTGCTGTTAAACTGGACA 59.640 36.000 0.00 0.00 43.98 4.02
29 30 5.831997 AGATTTTGTGCTGTTAAACTGGAC 58.168 37.500 0.00 0.00 38.50 4.02
30 31 7.759489 ATAGATTTTGTGCTGTTAAACTGGA 57.241 32.000 0.00 0.00 0.00 3.86
31 32 7.542130 GGAATAGATTTTGTGCTGTTAAACTGG 59.458 37.037 0.00 0.00 0.00 4.00
32 33 8.299570 AGGAATAGATTTTGTGCTGTTAAACTG 58.700 33.333 0.00 0.00 0.00 3.16
33 34 8.409358 AGGAATAGATTTTGTGCTGTTAAACT 57.591 30.769 0.00 0.00 0.00 2.66
34 35 8.515414 AGAGGAATAGATTTTGTGCTGTTAAAC 58.485 33.333 0.00 0.00 0.00 2.01
35 36 8.514594 CAGAGGAATAGATTTTGTGCTGTTAAA 58.485 33.333 0.00 0.00 0.00 1.52
36 37 7.882791 TCAGAGGAATAGATTTTGTGCTGTTAA 59.117 33.333 0.00 0.00 0.00 2.01
37 38 7.394016 TCAGAGGAATAGATTTTGTGCTGTTA 58.606 34.615 0.00 0.00 0.00 2.41
38 39 6.240894 TCAGAGGAATAGATTTTGTGCTGTT 58.759 36.000 0.00 0.00 0.00 3.16
39 40 5.809001 TCAGAGGAATAGATTTTGTGCTGT 58.191 37.500 0.00 0.00 0.00 4.40
40 41 5.220815 GCTCAGAGGAATAGATTTTGTGCTG 60.221 44.000 0.00 0.00 0.00 4.41
41 42 4.880696 GCTCAGAGGAATAGATTTTGTGCT 59.119 41.667 0.00 0.00 0.00 4.40
42 43 4.880696 AGCTCAGAGGAATAGATTTTGTGC 59.119 41.667 0.00 0.00 0.00 4.57
43 44 6.998968 AAGCTCAGAGGAATAGATTTTGTG 57.001 37.500 0.00 0.00 0.00 3.33
44 45 6.944862 ACAAAGCTCAGAGGAATAGATTTTGT 59.055 34.615 0.00 0.00 26.99 2.83
45 46 7.388460 ACAAAGCTCAGAGGAATAGATTTTG 57.612 36.000 0.00 0.00 26.99 2.44
46 47 8.414629 AAACAAAGCTCAGAGGAATAGATTTT 57.585 30.769 0.00 0.00 26.99 1.82
47 48 7.887495 AGAAACAAAGCTCAGAGGAATAGATTT 59.113 33.333 0.00 0.00 29.44 2.17
48 49 7.401246 AGAAACAAAGCTCAGAGGAATAGATT 58.599 34.615 0.00 0.00 0.00 2.40
49 50 6.956497 AGAAACAAAGCTCAGAGGAATAGAT 58.044 36.000 0.00 0.00 0.00 1.98
50 51 6.365970 AGAAACAAAGCTCAGAGGAATAGA 57.634 37.500 0.00 0.00 0.00 1.98
51 52 7.446001 AAAGAAACAAAGCTCAGAGGAATAG 57.554 36.000 0.00 0.00 0.00 1.73
52 53 7.502226 TGAAAAGAAACAAAGCTCAGAGGAATA 59.498 33.333 0.00 0.00 0.00 1.75
53 54 6.322201 TGAAAAGAAACAAAGCTCAGAGGAAT 59.678 34.615 0.00 0.00 0.00 3.01
54 55 5.652014 TGAAAAGAAACAAAGCTCAGAGGAA 59.348 36.000 0.00 0.00 0.00 3.36
55 56 5.192927 TGAAAAGAAACAAAGCTCAGAGGA 58.807 37.500 0.00 0.00 0.00 3.71
56 57 5.505173 TGAAAAGAAACAAAGCTCAGAGG 57.495 39.130 0.00 0.00 0.00 3.69
57 58 9.520204 TTTTATGAAAAGAAACAAAGCTCAGAG 57.480 29.630 0.00 0.00 0.00 3.35
60 61 8.550376 GCATTTTATGAAAAGAAACAAAGCTCA 58.450 29.630 0.00 0.00 33.22 4.26
61 62 8.550376 TGCATTTTATGAAAAGAAACAAAGCTC 58.450 29.630 0.00 0.00 33.22 4.09
62 63 8.436046 TGCATTTTATGAAAAGAAACAAAGCT 57.564 26.923 0.00 0.00 33.22 3.74
63 64 9.161684 CTTGCATTTTATGAAAAGAAACAAAGC 57.838 29.630 0.00 0.00 33.22 3.51
64 65 9.161684 GCTTGCATTTTATGAAAAGAAACAAAG 57.838 29.630 0.00 0.00 33.22 2.77
65 66 8.671921 TGCTTGCATTTTATGAAAAGAAACAAA 58.328 25.926 0.00 0.00 33.22 2.83
66 67 8.206325 TGCTTGCATTTTATGAAAAGAAACAA 57.794 26.923 0.00 0.00 33.22 2.83
67 68 7.783090 TGCTTGCATTTTATGAAAAGAAACA 57.217 28.000 0.00 0.00 33.22 2.83
68 69 9.321590 GAATGCTTGCATTTTATGAAAAGAAAC 57.678 29.630 19.90 1.30 33.22 2.78
69 70 8.222433 CGAATGCTTGCATTTTATGAAAAGAAA 58.778 29.630 19.90 0.00 33.22 2.52
70 71 7.384660 ACGAATGCTTGCATTTTATGAAAAGAA 59.615 29.630 19.90 0.00 33.22 2.52
71 72 6.867816 ACGAATGCTTGCATTTTATGAAAAGA 59.132 30.769 19.90 0.00 33.22 2.52
72 73 7.052565 ACGAATGCTTGCATTTTATGAAAAG 57.947 32.000 19.90 7.72 33.22 2.27
73 74 8.526218 TTACGAATGCTTGCATTTTATGAAAA 57.474 26.923 19.90 7.39 34.41 2.29
74 75 7.201427 GCTTACGAATGCTTGCATTTTATGAAA 60.201 33.333 19.90 9.52 0.00 2.69
75 76 6.253298 GCTTACGAATGCTTGCATTTTATGAA 59.747 34.615 19.90 10.45 0.00 2.57
76 77 5.743398 GCTTACGAATGCTTGCATTTTATGA 59.257 36.000 19.90 6.90 0.00 2.15
77 78 5.515982 TGCTTACGAATGCTTGCATTTTATG 59.484 36.000 19.90 15.90 0.00 1.90
78 79 5.649557 TGCTTACGAATGCTTGCATTTTAT 58.350 33.333 19.90 11.91 0.00 1.40
79 80 5.053140 TGCTTACGAATGCTTGCATTTTA 57.947 34.783 19.90 12.46 0.00 1.52
80 81 3.911868 TGCTTACGAATGCTTGCATTTT 58.088 36.364 19.90 13.30 0.00 1.82
81 82 3.057315 ACTGCTTACGAATGCTTGCATTT 60.057 39.130 19.90 9.44 0.00 2.32
82 83 2.489329 ACTGCTTACGAATGCTTGCATT 59.511 40.909 19.16 19.16 0.00 3.56
83 84 2.086869 ACTGCTTACGAATGCTTGCAT 58.913 42.857 1.81 1.81 0.00 3.96
84 85 1.522668 ACTGCTTACGAATGCTTGCA 58.477 45.000 0.00 0.00 0.00 4.08
85 86 3.740044 TTACTGCTTACGAATGCTTGC 57.260 42.857 0.00 0.00 0.00 4.01
102 103 9.907576 GCGCTTGATCACTGATAATATTATTAC 57.092 33.333 9.33 0.00 0.00 1.89
103 104 9.098355 GGCGCTTGATCACTGATAATATTATTA 57.902 33.333 7.64 4.74 0.00 0.98
104 105 7.201556 CGGCGCTTGATCACTGATAATATTATT 60.202 37.037 7.64 0.00 0.00 1.40
105 106 6.256539 CGGCGCTTGATCACTGATAATATTAT 59.743 38.462 7.64 7.72 0.00 1.28
106 107 5.576774 CGGCGCTTGATCACTGATAATATTA 59.423 40.000 7.64 0.00 0.00 0.98
107 108 4.389992 CGGCGCTTGATCACTGATAATATT 59.610 41.667 7.64 0.00 0.00 1.28
108 109 3.928992 CGGCGCTTGATCACTGATAATAT 59.071 43.478 7.64 0.00 0.00 1.28
109 110 3.005367 TCGGCGCTTGATCACTGATAATA 59.995 43.478 7.64 0.00 0.00 0.98
110 111 2.138320 CGGCGCTTGATCACTGATAAT 58.862 47.619 7.64 0.00 0.00 1.28
111 112 1.136110 TCGGCGCTTGATCACTGATAA 59.864 47.619 7.64 0.00 0.00 1.75
112 113 0.744281 TCGGCGCTTGATCACTGATA 59.256 50.000 7.64 0.00 0.00 2.15
113 114 0.529337 CTCGGCGCTTGATCACTGAT 60.529 55.000 7.64 0.00 0.00 2.90
114 115 1.153765 CTCGGCGCTTGATCACTGA 60.154 57.895 7.64 0.00 0.00 3.41
115 116 2.169789 CCTCGGCGCTTGATCACTG 61.170 63.158 7.64 0.00 0.00 3.66
116 117 2.185350 CCTCGGCGCTTGATCACT 59.815 61.111 7.64 0.00 0.00 3.41
117 118 2.892425 CCCTCGGCGCTTGATCAC 60.892 66.667 7.64 0.00 0.00 3.06
118 119 3.074369 TCCCTCGGCGCTTGATCA 61.074 61.111 7.64 0.00 0.00 2.92
119 120 2.586357 GTCCCTCGGCGCTTGATC 60.586 66.667 7.64 0.00 0.00 2.92
120 121 2.463589 TTTGTCCCTCGGCGCTTGAT 62.464 55.000 7.64 0.00 0.00 2.57
121 122 3.171828 TTTGTCCCTCGGCGCTTGA 62.172 57.895 7.64 4.88 0.00 3.02
122 123 2.668212 TTTGTCCCTCGGCGCTTG 60.668 61.111 7.64 0.00 0.00 4.01
123 124 2.358737 CTTTGTCCCTCGGCGCTT 60.359 61.111 7.64 0.00 0.00 4.68
124 125 4.394712 CCTTTGTCCCTCGGCGCT 62.395 66.667 7.64 0.00 0.00 5.92
126 127 4.697756 TGCCTTTGTCCCTCGGCG 62.698 66.667 0.00 0.00 45.36 6.46
127 128 2.747855 CTGCCTTTGTCCCTCGGC 60.748 66.667 0.00 0.00 42.78 5.54
128 129 1.376037 GTCTGCCTTTGTCCCTCGG 60.376 63.158 0.00 0.00 0.00 4.63
129 130 0.671781 CAGTCTGCCTTTGTCCCTCG 60.672 60.000 0.00 0.00 0.00 4.63
130 131 0.957888 GCAGTCTGCCTTTGTCCCTC 60.958 60.000 14.27 0.00 37.42 4.30
131 132 1.073897 GCAGTCTGCCTTTGTCCCT 59.926 57.895 14.27 0.00 37.42 4.20
132 133 0.538287 AAGCAGTCTGCCTTTGTCCC 60.538 55.000 21.32 0.00 46.52 4.46
133 134 0.877743 GAAGCAGTCTGCCTTTGTCC 59.122 55.000 21.32 0.00 46.52 4.02
134 135 0.514691 CGAAGCAGTCTGCCTTTGTC 59.485 55.000 21.32 9.97 46.52 3.18
135 136 2.621763 CGAAGCAGTCTGCCTTTGT 58.378 52.632 21.32 0.00 46.52 2.83
149 150 8.809159 TTCTTTCTGATATTATCTCTGCGAAG 57.191 34.615 5.33 0.00 0.00 3.79
150 151 9.770097 AATTCTTTCTGATATTATCTCTGCGAA 57.230 29.630 5.33 3.90 0.00 4.70
151 152 9.770097 AAATTCTTTCTGATATTATCTCTGCGA 57.230 29.630 5.33 0.00 0.00 5.10
152 153 9.808808 CAAATTCTTTCTGATATTATCTCTGCG 57.191 33.333 5.33 0.00 0.00 5.18
161 162 8.810041 AGGCTGAAACAAATTCTTTCTGATATT 58.190 29.630 14.59 0.00 38.92 1.28
162 163 8.358582 AGGCTGAAACAAATTCTTTCTGATAT 57.641 30.769 14.59 0.00 38.92 1.63
163 164 7.765695 AGGCTGAAACAAATTCTTTCTGATA 57.234 32.000 14.59 0.00 38.92 2.15
164 165 6.661304 AGGCTGAAACAAATTCTTTCTGAT 57.339 33.333 14.59 4.85 38.92 2.90
165 166 7.765695 ATAGGCTGAAACAAATTCTTTCTGA 57.234 32.000 14.59 1.59 38.92 3.27
166 167 9.565213 CTAATAGGCTGAAACAAATTCTTTCTG 57.435 33.333 0.00 9.23 38.92 3.02
167 168 9.520515 TCTAATAGGCTGAAACAAATTCTTTCT 57.479 29.630 0.00 0.00 38.92 2.52
175 176 9.528489 AGGTTTTATCTAATAGGCTGAAACAAA 57.472 29.630 0.00 0.00 0.00 2.83
176 177 9.528489 AAGGTTTTATCTAATAGGCTGAAACAA 57.472 29.630 0.00 0.00 0.00 2.83
177 178 8.956426 CAAGGTTTTATCTAATAGGCTGAAACA 58.044 33.333 0.00 0.00 0.00 2.83
178 179 8.406297 CCAAGGTTTTATCTAATAGGCTGAAAC 58.594 37.037 0.00 0.00 0.00 2.78
179 180 8.333235 TCCAAGGTTTTATCTAATAGGCTGAAA 58.667 33.333 0.00 0.00 0.00 2.69
180 181 7.867921 TCCAAGGTTTTATCTAATAGGCTGAA 58.132 34.615 0.00 0.00 0.00 3.02
181 182 7.446106 TCCAAGGTTTTATCTAATAGGCTGA 57.554 36.000 0.00 0.00 0.00 4.26
182 183 7.255277 GCTTCCAAGGTTTTATCTAATAGGCTG 60.255 40.741 0.00 0.00 0.00 4.85
183 184 6.773200 GCTTCCAAGGTTTTATCTAATAGGCT 59.227 38.462 0.00 0.00 0.00 4.58
184 185 6.546034 TGCTTCCAAGGTTTTATCTAATAGGC 59.454 38.462 0.00 0.00 0.00 3.93
185 186 8.519799 TTGCTTCCAAGGTTTTATCTAATAGG 57.480 34.615 0.00 0.00 0.00 2.57
189 190 9.487790 CAAAATTGCTTCCAAGGTTTTATCTAA 57.512 29.630 0.00 0.00 33.80 2.10
190 191 8.646900 ACAAAATTGCTTCCAAGGTTTTATCTA 58.353 29.630 0.00 0.00 33.80 1.98
191 192 7.508687 ACAAAATTGCTTCCAAGGTTTTATCT 58.491 30.769 0.00 0.00 33.80 1.98
192 193 7.728847 ACAAAATTGCTTCCAAGGTTTTATC 57.271 32.000 0.00 0.00 33.80 1.75
193 194 8.646900 TCTACAAAATTGCTTCCAAGGTTTTAT 58.353 29.630 0.00 0.00 33.80 1.40
194 195 8.012957 TCTACAAAATTGCTTCCAAGGTTTTA 57.987 30.769 0.00 0.00 33.80 1.52
195 196 6.883744 TCTACAAAATTGCTTCCAAGGTTTT 58.116 32.000 0.00 0.00 33.80 2.43
196 197 6.478512 TCTACAAAATTGCTTCCAAGGTTT 57.521 33.333 0.00 0.00 33.80 3.27
197 198 6.478512 TTCTACAAAATTGCTTCCAAGGTT 57.521 33.333 0.00 0.00 33.80 3.50
198 199 6.670695 ATTCTACAAAATTGCTTCCAAGGT 57.329 33.333 0.00 0.00 33.80 3.50
199 200 7.601856 TGTATTCTACAAAATTGCTTCCAAGG 58.398 34.615 0.00 0.00 35.38 3.61
200 201 9.643693 AATGTATTCTACAAAATTGCTTCCAAG 57.356 29.630 0.00 0.00 42.76 3.61
201 202 9.421806 CAATGTATTCTACAAAATTGCTTCCAA 57.578 29.630 0.00 0.00 42.76 3.53
202 203 7.545265 GCAATGTATTCTACAAAATTGCTTCCA 59.455 33.333 13.10 0.00 43.51 3.53
203 204 7.545265 TGCAATGTATTCTACAAAATTGCTTCC 59.455 33.333 17.84 0.23 45.42 3.46
204 205 8.375465 GTGCAATGTATTCTACAAAATTGCTTC 58.625 33.333 17.84 11.24 45.42 3.86
205 206 7.871973 TGTGCAATGTATTCTACAAAATTGCTT 59.128 29.630 17.84 0.00 45.42 3.91
206 207 7.377398 TGTGCAATGTATTCTACAAAATTGCT 58.623 30.769 17.84 0.00 45.42 3.91
207 208 7.579589 TGTGCAATGTATTCTACAAAATTGC 57.420 32.000 13.33 13.33 45.42 3.56
208 209 9.796062 GTTTGTGCAATGTATTCTACAAAATTG 57.204 29.630 13.19 0.00 42.76 2.32
209 210 9.762933 AGTTTGTGCAATGTATTCTACAAAATT 57.237 25.926 13.19 6.59 42.76 1.82
215 216 9.632969 CGTATTAGTTTGTGCAATGTATTCTAC 57.367 33.333 0.00 0.00 0.00 2.59
216 217 9.589111 TCGTATTAGTTTGTGCAATGTATTCTA 57.411 29.630 0.00 0.00 0.00 2.10
217 218 8.487313 TCGTATTAGTTTGTGCAATGTATTCT 57.513 30.769 0.00 0.00 0.00 2.40
218 219 8.388103 ACTCGTATTAGTTTGTGCAATGTATTC 58.612 33.333 0.00 0.00 0.00 1.75
219 220 8.263940 ACTCGTATTAGTTTGTGCAATGTATT 57.736 30.769 0.00 0.00 0.00 1.89
220 221 7.843490 ACTCGTATTAGTTTGTGCAATGTAT 57.157 32.000 0.00 0.00 0.00 2.29
221 222 7.490079 CCTACTCGTATTAGTTTGTGCAATGTA 59.510 37.037 0.00 0.00 0.00 2.29
222 223 6.312918 CCTACTCGTATTAGTTTGTGCAATGT 59.687 38.462 0.00 0.00 0.00 2.71
223 224 6.312918 ACCTACTCGTATTAGTTTGTGCAATG 59.687 38.462 0.00 0.00 0.00 2.82
224 225 6.403878 ACCTACTCGTATTAGTTTGTGCAAT 58.596 36.000 0.00 0.00 0.00 3.56
225 226 5.786311 ACCTACTCGTATTAGTTTGTGCAA 58.214 37.500 0.00 0.00 0.00 4.08
226 227 5.184479 AGACCTACTCGTATTAGTTTGTGCA 59.816 40.000 0.00 0.00 0.00 4.57
227 228 5.515626 CAGACCTACTCGTATTAGTTTGTGC 59.484 44.000 0.00 0.00 0.00 4.57
228 229 6.849502 TCAGACCTACTCGTATTAGTTTGTG 58.150 40.000 0.00 0.00 0.00 3.33
229 230 7.458409 TTCAGACCTACTCGTATTAGTTTGT 57.542 36.000 0.00 0.00 0.00 2.83
230 231 8.808529 CAATTCAGACCTACTCGTATTAGTTTG 58.191 37.037 0.00 0.00 0.00 2.93
231 232 8.746530 TCAATTCAGACCTACTCGTATTAGTTT 58.253 33.333 0.00 0.00 0.00 2.66
232 233 8.289939 TCAATTCAGACCTACTCGTATTAGTT 57.710 34.615 0.00 0.00 0.00 2.24
233 234 7.556996 ACTCAATTCAGACCTACTCGTATTAGT 59.443 37.037 0.00 0.00 0.00 2.24
234 235 7.858382 CACTCAATTCAGACCTACTCGTATTAG 59.142 40.741 0.00 0.00 0.00 1.73
235 236 7.555195 TCACTCAATTCAGACCTACTCGTATTA 59.445 37.037 0.00 0.00 0.00 0.98
236 237 6.377429 TCACTCAATTCAGACCTACTCGTATT 59.623 38.462 0.00 0.00 0.00 1.89
237 238 5.886474 TCACTCAATTCAGACCTACTCGTAT 59.114 40.000 0.00 0.00 0.00 3.06
238 239 5.250982 TCACTCAATTCAGACCTACTCGTA 58.749 41.667 0.00 0.00 0.00 3.43
239 240 4.079970 TCACTCAATTCAGACCTACTCGT 58.920 43.478 0.00 0.00 0.00 4.18
240 241 4.396478 TCTCACTCAATTCAGACCTACTCG 59.604 45.833 0.00 0.00 0.00 4.18
241 242 5.906113 TCTCACTCAATTCAGACCTACTC 57.094 43.478 0.00 0.00 0.00 2.59
242 243 6.865834 AATCTCACTCAATTCAGACCTACT 57.134 37.500 0.00 0.00 0.00 2.57
243 244 7.704472 CACTAATCTCACTCAATTCAGACCTAC 59.296 40.741 0.00 0.00 0.00 3.18
244 245 7.147828 CCACTAATCTCACTCAATTCAGACCTA 60.148 40.741 0.00 0.00 0.00 3.08
245 246 6.351711 CCACTAATCTCACTCAATTCAGACCT 60.352 42.308 0.00 0.00 0.00 3.85
246 247 5.814705 CCACTAATCTCACTCAATTCAGACC 59.185 44.000 0.00 0.00 0.00 3.85
247 248 5.293079 GCCACTAATCTCACTCAATTCAGAC 59.707 44.000 0.00 0.00 0.00 3.51
248 249 5.188555 AGCCACTAATCTCACTCAATTCAGA 59.811 40.000 0.00 0.00 0.00 3.27
249 250 5.426504 AGCCACTAATCTCACTCAATTCAG 58.573 41.667 0.00 0.00 0.00 3.02
250 251 5.046376 TGAGCCACTAATCTCACTCAATTCA 60.046 40.000 0.00 0.00 34.69 2.57
251 252 5.423015 TGAGCCACTAATCTCACTCAATTC 58.577 41.667 0.00 0.00 34.69 2.17
252 253 5.426689 TGAGCCACTAATCTCACTCAATT 57.573 39.130 0.00 0.00 34.69 2.32
279 280 3.842602 CGTGCACGTAGTCACCTG 58.157 61.111 30.50 0.00 41.61 4.00
383 384 2.125832 ACGCCACGACCATTACCG 60.126 61.111 0.00 0.00 0.00 4.02
429 438 5.944007 AGCAACCATTCTACTCCGTTAAAAT 59.056 36.000 0.00 0.00 0.00 1.82
492 501 1.802508 GCTTTGGCGTTTTTCTGCACT 60.803 47.619 0.00 0.00 0.00 4.40
508 517 2.746472 GCTCGGTAATGAGATGGGCTTT 60.746 50.000 0.00 0.00 38.28 3.51
529 538 0.532640 TGCTGTGTGTGTAGTGCAGG 60.533 55.000 0.00 0.00 0.00 4.85
530 539 1.003545 GTTGCTGTGTGTGTAGTGCAG 60.004 52.381 0.00 0.00 0.00 4.41
531 540 1.013596 GTTGCTGTGTGTGTAGTGCA 58.986 50.000 0.00 0.00 0.00 4.57
535 544 5.416862 TTGTATTGTTGCTGTGTGTGTAG 57.583 39.130 0.00 0.00 0.00 2.74
537 546 4.710423 TTTGTATTGTTGCTGTGTGTGT 57.290 36.364 0.00 0.00 0.00 3.72
539 548 4.560819 CGTTTTTGTATTGTTGCTGTGTGT 59.439 37.500 0.00 0.00 0.00 3.72
553 562 6.205853 ACCATGCTAGTGATTTCGTTTTTGTA 59.794 34.615 0.00 0.00 0.00 2.41
587 596 1.320507 CGGGAGAGTTCTACTAGCCC 58.679 60.000 0.00 0.00 37.94 5.19
588 597 0.669619 GCGGGAGAGTTCTACTAGCC 59.330 60.000 0.00 0.00 0.00 3.93
591 600 3.199508 ACAGTAGCGGGAGAGTTCTACTA 59.800 47.826 0.00 0.00 39.55 1.82
592 601 2.026075 ACAGTAGCGGGAGAGTTCTACT 60.026 50.000 0.00 0.00 41.51 2.57
593 602 2.097791 CACAGTAGCGGGAGAGTTCTAC 59.902 54.545 0.00 0.00 33.48 2.59
606 615 5.358160 AGAATTCAATTTAGCCCACAGTAGC 59.642 40.000 8.44 0.00 0.00 3.58
660 669 5.698832 TCGCTTGTTTTCCATGTTATGAAG 58.301 37.500 0.00 0.00 0.00 3.02
665 674 4.295051 GCTTTCGCTTGTTTTCCATGTTA 58.705 39.130 0.00 0.00 0.00 2.41
666 675 3.123050 GCTTTCGCTTGTTTTCCATGTT 58.877 40.909 0.00 0.00 0.00 2.71
667 676 2.545742 GGCTTTCGCTTGTTTTCCATGT 60.546 45.455 0.00 0.00 36.09 3.21
668 677 2.061028 GGCTTTCGCTTGTTTTCCATG 58.939 47.619 0.00 0.00 36.09 3.66
669 678 1.000843 GGGCTTTCGCTTGTTTTCCAT 59.999 47.619 0.00 0.00 36.09 3.41
806 822 1.291109 TCTCCTCTCCTTCTCTCCGT 58.709 55.000 0.00 0.00 0.00 4.69
807 823 2.092646 TCTTCTCCTCTCCTTCTCTCCG 60.093 54.545 0.00 0.00 0.00 4.63
808 824 3.202151 TCTCTTCTCCTCTCCTTCTCTCC 59.798 52.174 0.00 0.00 0.00 3.71
812 828 4.540099 TCTCTTCTCTTCTCCTCTCCTTCT 59.460 45.833 0.00 0.00 0.00 2.85
813 829 4.855340 TCTCTTCTCTTCTCCTCTCCTTC 58.145 47.826 0.00 0.00 0.00 3.46
814 830 4.946160 TCTCTTCTCTTCTCCTCTCCTT 57.054 45.455 0.00 0.00 0.00 3.36
926 949 2.121644 AAGGAAGGGGAACGGGGT 60.122 61.111 0.00 0.00 0.00 4.95
927 950 2.355115 CAAGGAAGGGGAACGGGG 59.645 66.667 0.00 0.00 0.00 5.73
928 951 1.202769 TACCAAGGAAGGGGAACGGG 61.203 60.000 0.00 0.00 0.00 5.28
929 952 0.916809 ATACCAAGGAAGGGGAACGG 59.083 55.000 0.00 0.00 0.00 4.44
930 953 3.199289 ACTTATACCAAGGAAGGGGAACG 59.801 47.826 0.00 0.00 0.00 3.95
931 954 4.384978 GGACTTATACCAAGGAAGGGGAAC 60.385 50.000 0.00 0.00 0.00 3.62
932 955 3.784202 GGACTTATACCAAGGAAGGGGAA 59.216 47.826 0.00 0.00 0.00 3.97
933 956 3.014807 AGGACTTATACCAAGGAAGGGGA 59.985 47.826 0.00 0.00 0.00 4.81
934 957 3.391626 GAGGACTTATACCAAGGAAGGGG 59.608 52.174 0.00 0.00 0.00 4.79
1009 1052 3.336568 ATGGCTGCTGCTGGTCCT 61.337 61.111 15.64 0.00 39.59 3.85
1010 1053 3.138798 CATGGCTGCTGCTGGTCC 61.139 66.667 15.64 2.81 39.59 4.46
1012 1055 2.360852 GTCATGGCTGCTGCTGGT 60.361 61.111 15.64 0.00 39.59 4.00
1013 1056 3.506096 CGTCATGGCTGCTGCTGG 61.506 66.667 15.64 5.55 39.59 4.85
2034 2089 2.289010 GGCAATTGAAACAACAGGGAGG 60.289 50.000 10.34 0.00 0.00 4.30
2196 2253 7.042523 ACACAAAGCAAAGAAAATCTTATGTGC 60.043 33.333 15.17 11.78 37.77 4.57
2198 2255 8.196771 TGACACAAAGCAAAGAAAATCTTATGT 58.803 29.630 0.00 0.00 35.27 2.29
2348 2405 7.278868 GGAGTAGTGAATAAGAACATTGGACAG 59.721 40.741 0.00 0.00 0.00 3.51
2409 2466 8.647796 TCGTCCCACAATATAAGATCTTATGTT 58.352 33.333 30.14 27.05 37.35 2.71
2410 2467 8.190326 TCGTCCCACAATATAAGATCTTATGT 57.810 34.615 30.14 23.65 36.52 2.29
2411 2468 9.144747 CTTCGTCCCACAATATAAGATCTTATG 57.855 37.037 30.14 20.78 36.52 1.90
2413 2470 7.256190 CCCTTCGTCCCACAATATAAGATCTTA 60.256 40.741 17.32 17.32 0.00 2.10
2472 2530 3.604582 ACACTTCTGCTAATGCCTCTTC 58.395 45.455 0.00 0.00 38.71 2.87
2513 2571 6.852420 ACACTAAGCTCCTAATAACAGTGA 57.148 37.500 0.00 0.00 36.51 3.41
2563 2625 7.615582 TCTAGACATGCTAAACCATTCTTTG 57.384 36.000 0.00 0.00 0.00 2.77
2564 2626 7.885399 ACTTCTAGACATGCTAAACCATTCTTT 59.115 33.333 0.00 0.00 0.00 2.52
2627 2690 5.844601 ACAGAGGGAGTAGAATTCTACCTT 58.155 41.667 32.51 20.58 45.38 3.50
2712 2775 3.135895 ACACCACAAGCTACTTACAACCT 59.864 43.478 0.00 0.00 0.00 3.50
2713 2776 3.473625 ACACCACAAGCTACTTACAACC 58.526 45.455 0.00 0.00 0.00 3.77
2741 2804 7.330262 TGAATCACATAGCTTGTATCTGAACA 58.670 34.615 0.00 0.00 36.57 3.18
2847 2910 7.039011 TCACTCTTTAGAATGCTGTTTCTAGGA 60.039 37.037 0.00 6.75 38.92 2.94
2860 2923 3.944015 GCACAGGCATCACTCTTTAGAAT 59.056 43.478 0.00 0.00 40.72 2.40
2981 3044 8.837099 TTCCACTATATCCAATTCACCAAAAT 57.163 30.769 0.00 0.00 0.00 1.82
2987 3050 8.565896 TGCATATTCCACTATATCCAATTCAC 57.434 34.615 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.