Multiple sequence alignment - TraesCS5D01G104900

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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 TraesCS5D01G104900 chr5D 100.000 5127 0 0 1 5127 118834141 118839267 0.000000e+00 9468.0
1 TraesCS5D01G104900 chr5D 76.367 567 57 31 4598 5127 47857639 47858165 3.090000e-57 233.0
2 TraesCS5D01G104900 chr5D 78.509 228 28 14 4909 5127 47851957 47852172 4.170000e-26 130.0
3 TraesCS5D01G104900 chr5D 91.781 73 4 2 4354 4425 278272905 278272976 3.270000e-17 100.0
4 TraesCS5D01G104900 chr5A 94.388 5025 149 49 168 5127 128426010 128430966 0.000000e+00 7594.0
5 TraesCS5D01G104900 chr5A 80.440 409 38 14 4730 5127 37974889 37975266 1.820000e-69 274.0
6 TraesCS5D01G104900 chr5A 83.824 136 20 2 2805 2938 94920763 94920628 1.500000e-25 128.0
7 TraesCS5D01G104900 chr5A 83.824 136 20 2 2805 2938 99084597 99084732 1.500000e-25 128.0
8 TraesCS5D01G104900 chr5A 94.203 69 3 1 4357 4425 35260289 35260222 2.530000e-18 104.0
9 TraesCS5D01G104900 chr5B 95.943 4042 106 17 280 4297 130910560 130914567 0.000000e+00 6503.0
10 TraesCS5D01G104900 chr5B 86.287 649 50 17 4501 5127 130914725 130915356 0.000000e+00 669.0
11 TraesCS5D01G104900 chr5B 86.034 179 19 4 4954 5127 50510839 50511016 2.440000e-43 187.0
12 TraesCS5D01G104900 chr5B 89.231 130 5 5 162 287 130895613 130895737 2.470000e-33 154.0
13 TraesCS5D01G104900 chr5B 92.593 108 5 3 4595 4702 50510480 50510584 8.890000e-33 152.0
14 TraesCS5D01G104900 chr5B 83.942 137 19 3 2805 2938 606705542 606705678 1.500000e-25 128.0
15 TraesCS5D01G104900 chr1B 86.486 148 20 0 3068 3215 389535051 389534904 4.110000e-36 163.0
16 TraesCS5D01G104900 chr1B 93.651 63 4 0 9 71 677620955 677620893 1.520000e-15 95.3
17 TraesCS5D01G104900 chr1D 86.806 144 19 0 2795 2938 287831115 287830972 1.480000e-35 161.0
18 TraesCS5D01G104900 chr1A 85.294 136 18 2 2805 2938 592524491 592524626 6.920000e-29 139.0
19 TraesCS5D01G104900 chr7B 83.824 136 20 2 2805 2938 33979693 33979558 1.500000e-25 128.0
20 TraesCS5D01G104900 chr7B 90.278 72 6 1 4354 4425 257651318 257651388 5.470000e-15 93.5
21 TraesCS5D01G104900 chr6B 83.824 136 20 2 2805 2938 63717473 63717608 1.500000e-25 128.0
22 TraesCS5D01G104900 chr7A 89.474 95 6 2 2143 2236 503779648 503779557 3.240000e-22 117.0
23 TraesCS5D01G104900 chr4A 84.615 117 18 0 3100 3216 549001775 549001659 3.240000e-22 117.0
24 TraesCS5D01G104900 chr4A 95.161 62 3 0 9 70 611979951 611980012 1.170000e-16 99.0
25 TraesCS5D01G104900 chr3B 90.361 83 8 0 3279 3361 400527820 400527738 5.430000e-20 110.0
26 TraesCS5D01G104900 chr3B 89.157 83 9 0 3100 3182 660066368 660066450 2.530000e-18 104.0
27 TraesCS5D01G104900 chr3D 95.161 62 3 0 9 70 268071192 268071131 1.170000e-16 99.0
28 TraesCS5D01G104900 chr3D 95.161 62 3 0 9 70 268096109 268096170 1.170000e-16 99.0
29 TraesCS5D01G104900 chr4B 93.651 63 4 0 9 71 630090817 630090755 1.520000e-15 95.3
30 TraesCS5D01G104900 chr4B 91.304 69 5 1 4357 4425 22464678 22464611 5.470000e-15 93.5
31 TraesCS5D01G104900 chr2D 93.651 63 4 0 9 71 28963608 28963546 1.520000e-15 95.3
32 TraesCS5D01G104900 chr2D 91.304 69 5 1 4357 4425 556200593 556200660 5.470000e-15 93.5
33 TraesCS5D01G104900 chr2D 90.278 72 6 1 4354 4425 564584807 564584877 5.470000e-15 93.5
34 TraesCS5D01G104900 chr2D 85.393 89 12 1 3068 3156 128105612 128105699 1.970000e-14 91.6
35 TraesCS5D01G104900 chr2B 93.651 63 4 0 9 71 763031569 763031631 1.520000e-15 95.3
36 TraesCS5D01G104900 chrUn 93.548 62 4 0 9 70 68320119 68320180 5.470000e-15 93.5
37 TraesCS5D01G104900 chrUn 88.000 75 8 1 9 82 22755489 22755415 2.540000e-13 87.9
38 TraesCS5D01G104900 chr6A 91.429 70 3 3 4357 4425 561651217 561651150 5.470000e-15 93.5
39 TraesCS5D01G104900 chr6D 84.270 89 12 2 3068 3156 411386813 411386727 9.150000e-13 86.1
40 TraesCS5D01G104900 chr7D 80.165 121 15 7 4309 4424 14149852 14149968 1.180000e-11 82.4
41 TraesCS5D01G104900 chr3A 86.111 72 10 0 1406 1477 401684538 401684609 1.530000e-10 78.7
42 TraesCS5D01G104900 chr3A 91.111 45 1 2 2328 2372 477682152 477682111 1.990000e-04 58.4


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 TraesCS5D01G104900 chr5D 118834141 118839267 5126 False 9468 9468 100.000 1 5127 1 chr5D.!!$F3 5126
1 TraesCS5D01G104900 chr5D 47857639 47858165 526 False 233 233 76.367 4598 5127 1 chr5D.!!$F2 529
2 TraesCS5D01G104900 chr5A 128426010 128430966 4956 False 7594 7594 94.388 168 5127 1 chr5A.!!$F3 4959
3 TraesCS5D01G104900 chr5B 130910560 130915356 4796 False 3586 6503 91.115 280 5127 2 chr5B.!!$F4 4847

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
76 77 0.036388 ATGCAATTCACTCGGACCGT 60.036 50.0 14.79 0.00 0.00 4.83 F
162 163 0.248784 GGACCTATTCGTAGCGCGTT 60.249 55.0 8.43 3.54 42.13 4.84 F
202 203 0.392706 CCACGGTAGCAGCCATCATA 59.607 55.0 0.00 0.00 0.00 2.15 F
2137 2186 0.235926 GCCGTGCTTTCACTCTTGAC 59.764 55.0 0.00 0.00 40.99 3.18 F
3497 3556 0.733566 GCCCGTGTGTGCATCAATTG 60.734 55.0 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2025 0.752658 CTACCTGCCGGATGACATCA 59.247 55.000 17.08 0.00 0.00 3.07 R
2069 2118 9.242477 GTTTTCTTCAAGAGAATTTTCAGAAGG 57.758 33.333 20.85 10.18 43.65 3.46 R
2276 2325 5.188434 ACATCAGGATGGTTATCAGTGTTG 58.812 41.667 13.40 0.00 42.91 3.33 R
3994 4058 0.027586 GCGTGTTGCATATTCCGGTC 59.972 55.000 0.00 0.00 45.45 4.79 R
4816 4919 0.034089 CCACCCATTCAGGTTCCCTC 60.034 60.000 0.00 0.00 38.39 4.30 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
20 21 3.994204 GGTTTTGGTCCGTAAATGTGT 57.006 42.857 0.00 0.00 0.00 3.72
21 22 3.634283 GGTTTTGGTCCGTAAATGTGTG 58.366 45.455 0.00 0.00 0.00 3.82
22 23 3.551250 GGTTTTGGTCCGTAAATGTGTGG 60.551 47.826 0.00 0.00 0.00 4.17
23 24 2.642154 TTGGTCCGTAAATGTGTGGT 57.358 45.000 0.00 0.00 0.00 4.16
24 25 2.642154 TGGTCCGTAAATGTGTGGTT 57.358 45.000 0.00 0.00 0.00 3.67
25 26 2.496111 TGGTCCGTAAATGTGTGGTTC 58.504 47.619 0.00 0.00 0.00 3.62
26 27 1.808343 GGTCCGTAAATGTGTGGTTCC 59.192 52.381 0.00 0.00 0.00 3.62
27 28 2.551504 GGTCCGTAAATGTGTGGTTCCT 60.552 50.000 0.00 0.00 0.00 3.36
28 29 2.482721 GTCCGTAAATGTGTGGTTCCTG 59.517 50.000 0.00 0.00 0.00 3.86
29 30 1.199097 CCGTAAATGTGTGGTTCCTGC 59.801 52.381 0.00 0.00 0.00 4.85
30 31 1.876799 CGTAAATGTGTGGTTCCTGCA 59.123 47.619 0.00 0.00 0.00 4.41
31 32 2.292016 CGTAAATGTGTGGTTCCTGCAA 59.708 45.455 0.00 0.00 0.00 4.08
32 33 3.243234 CGTAAATGTGTGGTTCCTGCAAA 60.243 43.478 0.00 0.00 0.00 3.68
33 34 2.888834 AATGTGTGGTTCCTGCAAAC 57.111 45.000 0.00 0.00 0.00 2.93
40 41 2.979814 GGTTCCTGCAAACCTTGTTT 57.020 45.000 12.26 0.00 44.45 2.83
41 42 2.549926 GGTTCCTGCAAACCTTGTTTG 58.450 47.619 12.26 13.83 44.45 2.93
42 43 2.167487 GGTTCCTGCAAACCTTGTTTGA 59.833 45.455 20.53 7.48 44.45 2.69
43 44 3.368948 GGTTCCTGCAAACCTTGTTTGAA 60.369 43.478 20.53 11.27 44.45 2.69
44 45 3.799281 TCCTGCAAACCTTGTTTGAAG 57.201 42.857 20.53 18.81 35.34 3.02
45 46 3.096092 TCCTGCAAACCTTGTTTGAAGT 58.904 40.909 20.71 0.00 34.06 3.01
46 47 3.119173 TCCTGCAAACCTTGTTTGAAGTG 60.119 43.478 20.71 14.35 34.06 3.16
47 48 3.368323 CCTGCAAACCTTGTTTGAAGTGT 60.368 43.478 20.71 0.00 34.06 3.55
48 49 3.843999 TGCAAACCTTGTTTGAAGTGTC 58.156 40.909 20.53 5.22 0.00 3.67
49 50 2.851824 GCAAACCTTGTTTGAAGTGTCG 59.148 45.455 20.53 0.00 0.00 4.35
50 51 3.426963 GCAAACCTTGTTTGAAGTGTCGA 60.427 43.478 20.53 0.00 0.00 4.20
51 52 4.733523 GCAAACCTTGTTTGAAGTGTCGAT 60.734 41.667 20.53 0.00 0.00 3.59
52 53 5.504994 GCAAACCTTGTTTGAAGTGTCGATA 60.505 40.000 20.53 0.00 0.00 2.92
53 54 6.668323 CAAACCTTGTTTGAAGTGTCGATAT 58.332 36.000 13.07 0.00 0.00 1.63
54 55 6.877611 AACCTTGTTTGAAGTGTCGATATT 57.122 33.333 0.00 0.00 0.00 1.28
55 56 6.877611 ACCTTGTTTGAAGTGTCGATATTT 57.122 33.333 0.00 0.00 0.00 1.40
56 57 7.272037 ACCTTGTTTGAAGTGTCGATATTTT 57.728 32.000 0.00 0.00 0.00 1.82
57 58 8.385898 ACCTTGTTTGAAGTGTCGATATTTTA 57.614 30.769 0.00 0.00 0.00 1.52
58 59 9.010029 ACCTTGTTTGAAGTGTCGATATTTTAT 57.990 29.630 0.00 0.00 0.00 1.40
59 60 9.277565 CCTTGTTTGAAGTGTCGATATTTTATG 57.722 33.333 0.00 0.00 0.00 1.90
60 61 8.667987 TTGTTTGAAGTGTCGATATTTTATGC 57.332 30.769 0.00 0.00 0.00 3.14
61 62 7.811653 TGTTTGAAGTGTCGATATTTTATGCA 58.188 30.769 0.00 0.00 0.00 3.96
62 63 8.293157 TGTTTGAAGTGTCGATATTTTATGCAA 58.707 29.630 0.00 0.00 0.00 4.08
63 64 9.289303 GTTTGAAGTGTCGATATTTTATGCAAT 57.711 29.630 0.00 0.00 0.00 3.56
64 65 9.853555 TTTGAAGTGTCGATATTTTATGCAATT 57.146 25.926 0.00 0.00 0.00 2.32
65 66 9.502145 TTGAAGTGTCGATATTTTATGCAATTC 57.498 29.630 0.00 0.00 32.44 2.17
66 67 8.672815 TGAAGTGTCGATATTTTATGCAATTCA 58.327 29.630 5.89 5.89 37.21 2.57
67 68 8.841444 AAGTGTCGATATTTTATGCAATTCAC 57.159 30.769 0.00 0.00 0.00 3.18
68 69 8.213518 AGTGTCGATATTTTATGCAATTCACT 57.786 30.769 0.00 0.00 0.00 3.41
69 70 8.338259 AGTGTCGATATTTTATGCAATTCACTC 58.662 33.333 0.00 0.00 0.00 3.51
70 71 7.318909 GTGTCGATATTTTATGCAATTCACTCG 59.681 37.037 0.00 0.00 0.00 4.18
71 72 6.792250 GTCGATATTTTATGCAATTCACTCGG 59.208 38.462 0.00 0.00 0.00 4.63
72 73 6.704050 TCGATATTTTATGCAATTCACTCGGA 59.296 34.615 0.00 0.00 0.00 4.55
73 74 6.792250 CGATATTTTATGCAATTCACTCGGAC 59.208 38.462 0.00 0.00 0.00 4.79
74 75 4.695217 TTTTATGCAATTCACTCGGACC 57.305 40.909 0.00 0.00 0.00 4.46
75 76 1.934589 TATGCAATTCACTCGGACCG 58.065 50.000 7.84 7.84 0.00 4.79
76 77 0.036388 ATGCAATTCACTCGGACCGT 60.036 50.000 14.79 0.00 0.00 4.83
77 78 0.604073 TGCAATTCACTCGGACCGTA 59.396 50.000 14.79 0.00 0.00 4.02
78 79 1.278238 GCAATTCACTCGGACCGTAG 58.722 55.000 14.79 12.27 0.00 3.51
79 80 1.135199 GCAATTCACTCGGACCGTAGA 60.135 52.381 14.79 7.64 0.00 2.59
80 81 2.798680 CAATTCACTCGGACCGTAGAG 58.201 52.381 14.79 6.66 40.16 2.43
84 85 3.336122 ACTCGGACCGTAGAGTGTT 57.664 52.632 14.79 0.00 45.03 3.32
85 86 2.479566 ACTCGGACCGTAGAGTGTTA 57.520 50.000 14.79 0.00 45.03 2.41
86 87 2.996631 ACTCGGACCGTAGAGTGTTAT 58.003 47.619 14.79 0.00 45.03 1.89
87 88 2.681848 ACTCGGACCGTAGAGTGTTATG 59.318 50.000 14.79 0.00 45.03 1.90
88 89 2.681848 CTCGGACCGTAGAGTGTTATGT 59.318 50.000 14.79 0.00 0.00 2.29
89 90 3.872696 TCGGACCGTAGAGTGTTATGTA 58.127 45.455 14.79 0.00 0.00 2.29
90 91 4.454678 TCGGACCGTAGAGTGTTATGTAT 58.545 43.478 14.79 0.00 0.00 2.29
91 92 4.883585 TCGGACCGTAGAGTGTTATGTATT 59.116 41.667 14.79 0.00 0.00 1.89
92 93 6.054941 TCGGACCGTAGAGTGTTATGTATTA 58.945 40.000 14.79 0.00 0.00 0.98
93 94 6.712095 TCGGACCGTAGAGTGTTATGTATTAT 59.288 38.462 14.79 0.00 0.00 1.28
94 95 7.229306 TCGGACCGTAGAGTGTTATGTATTATT 59.771 37.037 14.79 0.00 0.00 1.40
95 96 7.325338 CGGACCGTAGAGTGTTATGTATTATTG 59.675 40.741 5.48 0.00 0.00 1.90
96 97 8.139989 GGACCGTAGAGTGTTATGTATTATTGT 58.860 37.037 0.00 0.00 0.00 2.71
125 126 8.860780 TGCATGTATATAGGAATTGTATTGCA 57.139 30.769 0.00 0.00 28.06 4.08
126 127 8.949177 TGCATGTATATAGGAATTGTATTGCAG 58.051 33.333 0.00 0.00 27.75 4.41
127 128 8.950210 GCATGTATATAGGAATTGTATTGCAGT 58.050 33.333 0.00 0.00 0.00 4.40
130 131 9.845740 TGTATATAGGAATTGTATTGCAGTGTT 57.154 29.630 0.00 0.00 0.00 3.32
133 134 7.944729 ATAGGAATTGTATTGCAGTGTTTCT 57.055 32.000 0.00 0.00 0.00 2.52
134 135 6.259550 AGGAATTGTATTGCAGTGTTTCTC 57.740 37.500 0.00 0.00 0.00 2.87
135 136 5.088739 GGAATTGTATTGCAGTGTTTCTCG 58.911 41.667 0.00 0.00 0.00 4.04
136 137 5.106712 GGAATTGTATTGCAGTGTTTCTCGA 60.107 40.000 0.00 0.00 0.00 4.04
137 138 5.940192 ATTGTATTGCAGTGTTTCTCGAA 57.060 34.783 0.00 0.00 0.00 3.71
138 139 5.940192 TTGTATTGCAGTGTTTCTCGAAT 57.060 34.783 0.00 0.00 0.00 3.34
139 140 5.940192 TGTATTGCAGTGTTTCTCGAATT 57.060 34.783 0.00 0.00 0.00 2.17
140 141 5.688823 TGTATTGCAGTGTTTCTCGAATTG 58.311 37.500 0.00 0.00 0.00 2.32
141 142 4.836125 ATTGCAGTGTTTCTCGAATTGT 57.164 36.364 0.00 0.00 0.00 2.71
142 143 3.607422 TGCAGTGTTTCTCGAATTGTG 57.393 42.857 0.00 0.00 0.00 3.33
143 144 2.290367 TGCAGTGTTTCTCGAATTGTGG 59.710 45.455 0.00 0.00 0.00 4.17
144 145 2.350772 GCAGTGTTTCTCGAATTGTGGG 60.351 50.000 0.00 0.00 0.00 4.61
145 146 3.138304 CAGTGTTTCTCGAATTGTGGGA 58.862 45.455 0.00 0.00 0.00 4.37
146 147 3.058914 CAGTGTTTCTCGAATTGTGGGAC 60.059 47.826 0.00 0.00 0.00 4.46
147 148 2.225727 GTGTTTCTCGAATTGTGGGACC 59.774 50.000 0.00 0.00 0.00 4.46
148 149 2.105821 TGTTTCTCGAATTGTGGGACCT 59.894 45.455 0.00 0.00 0.00 3.85
149 150 3.325425 TGTTTCTCGAATTGTGGGACCTA 59.675 43.478 0.00 0.00 0.00 3.08
150 151 4.019681 TGTTTCTCGAATTGTGGGACCTAT 60.020 41.667 0.00 0.00 0.00 2.57
151 152 4.837093 TTCTCGAATTGTGGGACCTATT 57.163 40.909 0.00 0.00 0.00 1.73
152 153 4.402056 TCTCGAATTGTGGGACCTATTC 57.598 45.455 0.00 0.00 0.00 1.75
153 154 3.123804 CTCGAATTGTGGGACCTATTCG 58.876 50.000 18.65 18.65 46.38 3.34
154 155 2.498481 TCGAATTGTGGGACCTATTCGT 59.502 45.455 21.30 0.00 45.63 3.85
155 156 3.700539 TCGAATTGTGGGACCTATTCGTA 59.299 43.478 21.30 12.60 45.63 3.43
156 157 4.049186 CGAATTGTGGGACCTATTCGTAG 58.951 47.826 17.48 0.00 42.46 3.51
157 158 2.973694 TTGTGGGACCTATTCGTAGC 57.026 50.000 0.00 0.00 0.00 3.58
158 159 0.742505 TGTGGGACCTATTCGTAGCG 59.257 55.000 0.00 0.00 0.00 4.26
159 160 0.596859 GTGGGACCTATTCGTAGCGC 60.597 60.000 0.00 0.00 0.00 5.92
160 161 1.371389 GGGACCTATTCGTAGCGCG 60.371 63.158 0.00 0.00 43.01 6.86
161 162 1.358046 GGACCTATTCGTAGCGCGT 59.642 57.895 8.43 0.00 42.13 6.01
162 163 0.248784 GGACCTATTCGTAGCGCGTT 60.249 55.000 8.43 3.54 42.13 4.84
163 164 1.002468 GGACCTATTCGTAGCGCGTTA 60.002 52.381 8.43 2.16 42.13 3.18
164 165 2.305291 GACCTATTCGTAGCGCGTTAG 58.695 52.381 8.43 0.36 42.13 2.34
165 166 1.942657 ACCTATTCGTAGCGCGTTAGA 59.057 47.619 8.43 2.98 42.13 2.10
166 167 2.032204 ACCTATTCGTAGCGCGTTAGAG 60.032 50.000 8.43 3.35 42.13 2.43
178 179 3.482833 GCGCGTTAGAGAGTTCAGTAATC 59.517 47.826 8.43 0.00 0.00 1.75
193 194 3.130516 CAGTAATCTTCTCCACGGTAGCA 59.869 47.826 0.00 0.00 0.00 3.49
194 195 2.969628 AATCTTCTCCACGGTAGCAG 57.030 50.000 0.00 0.00 0.00 4.24
195 196 0.461961 ATCTTCTCCACGGTAGCAGC 59.538 55.000 0.00 0.00 0.00 5.25
198 199 1.264749 TTCTCCACGGTAGCAGCCAT 61.265 55.000 0.00 0.00 0.00 4.40
199 200 1.227380 CTCCACGGTAGCAGCCATC 60.227 63.158 0.00 0.00 0.00 3.51
200 201 1.960040 CTCCACGGTAGCAGCCATCA 61.960 60.000 0.00 0.00 0.00 3.07
201 202 1.146930 CCACGGTAGCAGCCATCAT 59.853 57.895 0.00 0.00 0.00 2.45
202 203 0.392706 CCACGGTAGCAGCCATCATA 59.607 55.000 0.00 0.00 0.00 2.15
203 204 1.202639 CCACGGTAGCAGCCATCATAA 60.203 52.381 0.00 0.00 0.00 1.90
252 253 1.029947 CCTCCCCCGAATTGTTTCCG 61.030 60.000 0.00 0.00 0.00 4.30
277 282 1.967535 CGTCCTCCTTGTCAGCTCA 59.032 57.895 0.00 0.00 0.00 4.26
384 389 2.534019 CGCATCAAATACGCCGCCT 61.534 57.895 0.00 0.00 0.00 5.52
389 394 1.887707 CAAATACGCCGCCTCCTCC 60.888 63.158 0.00 0.00 0.00 4.30
523 532 2.505819 ACAACAAGTCCAAGAGAGGTGT 59.494 45.455 0.00 0.00 0.00 4.16
551 560 4.534168 CTGCAATTCGATCATGGTGATTC 58.466 43.478 0.00 0.00 37.20 2.52
572 581 1.237285 CCTTGCTTCTGTCGGGGTTG 61.237 60.000 0.00 0.00 0.00 3.77
592 601 6.350949 GGGTTGGGTACGTCTGTATTTTACTA 60.351 42.308 0.00 0.00 32.11 1.82
745 756 4.037923 ACCATGGTTTCACATGTTCTGTTC 59.962 41.667 13.00 0.00 45.21 3.18
852 868 3.883489 ACTTTCAGCTGGTTACTTTGTCC 59.117 43.478 15.13 0.00 0.00 4.02
853 869 2.561478 TCAGCTGGTTACTTTGTCCC 57.439 50.000 15.13 0.00 0.00 4.46
854 870 1.073284 TCAGCTGGTTACTTTGTCCCC 59.927 52.381 15.13 0.00 0.00 4.81
855 871 1.073923 CAGCTGGTTACTTTGTCCCCT 59.926 52.381 5.57 0.00 0.00 4.79
856 872 1.073923 AGCTGGTTACTTTGTCCCCTG 59.926 52.381 0.00 0.00 0.00 4.45
914 930 1.392589 ACAGTTGAGTTGCTGTTGGG 58.607 50.000 0.00 0.00 42.61 4.12
927 943 2.887152 GCTGTTGGGAAATCTGTGAACT 59.113 45.455 0.00 0.00 0.00 3.01
1127 1163 7.449395 TGGATATGGAAATAAATCAAGAGCAGG 59.551 37.037 0.00 0.00 0.00 4.85
1533 1582 3.270433 AGACATGGATCAAACTCCCCATT 59.730 43.478 0.00 0.00 37.30 3.16
1543 1592 7.201911 GGATCAAACTCCCCATTAATTACTTGG 60.202 40.741 6.64 6.64 0.00 3.61
1976 2025 1.272147 GGACTTTGCCCTGGTCTCAAT 60.272 52.381 0.00 0.00 0.00 2.57
2137 2186 0.235926 GCCGTGCTTTCACTCTTGAC 59.764 55.000 0.00 0.00 40.99 3.18
2306 2355 8.768397 ACTGATAACCATCCTGATGTAAGTTTA 58.232 33.333 6.40 0.00 37.11 2.01
2649 2698 2.746362 CAGAGCAAGACATGTCTTTCCC 59.254 50.000 33.46 22.31 46.95 3.97
2685 2734 9.220767 AGACTAGATTGTACCAGAAACATTTTC 57.779 33.333 0.00 0.00 0.00 2.29
2822 2871 5.758784 CCGGAAGAGAAAACTAAAAGTGTCT 59.241 40.000 0.00 0.00 0.00 3.41
2980 3029 6.363882 TCTCAGACTCTCATCTCATGTGTAT 58.636 40.000 0.00 0.00 0.00 2.29
2981 3030 7.512992 TCTCAGACTCTCATCTCATGTGTATA 58.487 38.462 0.00 0.00 0.00 1.47
2982 3031 8.162746 TCTCAGACTCTCATCTCATGTGTATAT 58.837 37.037 0.00 0.00 0.00 0.86
2997 3046 5.660460 TGTGTATATATATCTGCAAGCGGG 58.340 41.667 0.00 0.00 0.00 6.13
3014 3064 4.460263 AGCGGGCAAAGAATATATTGTCA 58.540 39.130 1.78 0.00 32.88 3.58
3066 3116 1.141019 TGGTTCGCGCTCTATGGTC 59.859 57.895 5.56 0.00 0.00 4.02
3077 3127 2.158842 GCTCTATGGTCAGGCACATTCT 60.159 50.000 0.00 0.00 0.00 2.40
3161 3211 3.551496 TTCCCTGTCAAGCGGGCAG 62.551 63.158 6.11 6.11 42.42 4.85
3235 3285 3.906720 TGCCCTTCCAACTCACTATAC 57.093 47.619 0.00 0.00 0.00 1.47
3413 3472 9.911788 AGATACCTTCACATACAAGATCAATTT 57.088 29.630 0.00 0.00 0.00 1.82
3477 3536 2.959707 GGATCTCTTGACGTAGGGATGT 59.040 50.000 5.42 0.00 35.49 3.06
3497 3556 0.733566 GCCCGTGTGTGCATCAATTG 60.734 55.000 0.00 0.00 0.00 2.32
3498 3557 0.880441 CCCGTGTGTGCATCAATTGA 59.120 50.000 11.26 11.26 0.00 2.57
3687 3751 5.003804 GTGTTCTTCACCATGATGTAGGTT 58.996 41.667 0.00 0.00 40.84 3.50
3938 4002 5.554070 TCTGTTTTCTGAGATGAGCATTGA 58.446 37.500 0.00 0.00 0.00 2.57
3994 4058 3.499737 GGGTTCAGCGGCATCACG 61.500 66.667 1.45 0.00 0.00 4.35
4036 4100 0.108520 ACGTGTACCTGCCAATACCG 60.109 55.000 0.00 0.00 0.00 4.02
4177 4242 2.211250 AGTGCTAGAAGTACCGGTGA 57.789 50.000 19.93 0.00 30.68 4.02
4249 4314 2.489073 GGTATGCCCTGTAATTCCTGGG 60.489 54.545 8.46 8.46 44.29 4.45
4367 4432 8.818141 ATGTATAATAGACACATTTCAGTCCG 57.182 34.615 0.00 0.00 35.38 4.79
4376 4441 1.131126 CATTTCAGTCCGCATGTGGTC 59.869 52.381 24.28 18.99 0.00 4.02
4393 4458 5.879763 TGTGGTCCCATATTGGAATATCAG 58.120 41.667 0.00 0.00 40.96 2.90
4425 4490 8.696374 TCTTATATTTGTGAACAGAGGGAGTAG 58.304 37.037 0.00 0.00 0.00 2.57
4481 4546 4.692155 GCCAAAGCTGTTATCTGCAAAAAT 59.308 37.500 5.59 0.00 40.25 1.82
4511 4581 4.464597 GGTAGGTTCCCATTTTGCATGTAA 59.535 41.667 0.00 0.00 0.00 2.41
4513 4583 6.322712 GGTAGGTTCCCATTTTGCATGTAATA 59.677 38.462 0.00 0.00 0.00 0.98
4528 4599 5.516339 GCATGTAATATGCCAAACTTGTGTC 59.484 40.000 0.54 0.00 39.01 3.67
4533 4604 2.363306 TGCCAAACTTGTGTCCAGAT 57.637 45.000 0.00 0.00 0.00 2.90
4534 4605 2.665165 TGCCAAACTTGTGTCCAGATT 58.335 42.857 0.00 0.00 0.00 2.40
4557 4628 9.180678 GATTTACATAAAACTGGAATAATGGCG 57.819 33.333 0.00 0.00 0.00 5.69
4592 4664 3.769739 TGTCTGCCATTTGAGTACAGT 57.230 42.857 0.00 0.00 0.00 3.55
4751 4854 5.863397 CACATTTGCGATTTTGTACTGGATT 59.137 36.000 0.00 0.00 0.00 3.01
4764 4867 9.562408 TTTTGTACTGGATTGTTACATTACTCA 57.438 29.630 0.00 0.00 0.00 3.41
4813 4916 3.991773 TGCGTCATGGTTTAAGACACTAC 59.008 43.478 0.00 0.00 32.68 2.73
4815 4918 5.047872 TGCGTCATGGTTTAAGACACTACTA 60.048 40.000 0.00 0.00 32.68 1.82
4816 4919 5.515626 GCGTCATGGTTTAAGACACTACTAG 59.484 44.000 0.00 0.00 32.68 2.57
4817 4920 6.624423 GCGTCATGGTTTAAGACACTACTAGA 60.624 42.308 0.00 0.00 32.68 2.43
4897 5000 6.428159 GGTGAAACGATGCTATGGAGATTTAT 59.572 38.462 0.00 0.00 38.12 1.40
4921 5024 4.096682 GGATATAGGCTCGTACTAAGGCAG 59.903 50.000 17.23 0.00 41.51 4.85
4945 5048 4.157656 AGTTCAAACTGCAACTGTAAGCAA 59.842 37.500 8.81 0.00 40.73 3.91
4946 5049 4.710423 TCAAACTGCAACTGTAAGCAAA 57.290 36.364 8.81 0.00 40.73 3.68
4947 5050 4.671377 TCAAACTGCAACTGTAAGCAAAG 58.329 39.130 8.81 2.29 40.73 2.77
4948 5051 3.715628 AACTGCAACTGTAAGCAAAGG 57.284 42.857 8.81 1.71 40.73 3.11
4949 5052 2.930950 ACTGCAACTGTAAGCAAAGGA 58.069 42.857 8.81 0.00 40.73 3.36
4950 5053 3.287222 ACTGCAACTGTAAGCAAAGGAA 58.713 40.909 8.81 0.00 40.73 3.36
4951 5054 3.316308 ACTGCAACTGTAAGCAAAGGAAG 59.684 43.478 8.81 0.55 40.73 3.46
4952 5055 3.287222 TGCAACTGTAAGCAAAGGAAGT 58.713 40.909 5.51 0.00 37.90 3.01
4968 5071 6.936968 AAGGAAGTAAGGAACTCTACATGT 57.063 37.500 2.69 2.69 38.49 3.21
5027 5130 0.462937 CCGTGGACCTGTTTGTGACA 60.463 55.000 0.00 0.00 36.65 3.58
5083 5202 1.860676 TGTGTAGCGGTGAACTTGAC 58.139 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.551250 CCACACATTTACGGACCAAAACC 60.551 47.826 0.00 0.00 0.00 3.27
1 2 3.067040 ACCACACATTTACGGACCAAAAC 59.933 43.478 0.00 0.00 0.00 2.43
2 3 3.288964 ACCACACATTTACGGACCAAAA 58.711 40.909 0.00 0.00 0.00 2.44
3 4 2.933573 ACCACACATTTACGGACCAAA 58.066 42.857 0.00 0.00 0.00 3.28
4 5 2.642154 ACCACACATTTACGGACCAA 57.358 45.000 0.00 0.00 0.00 3.67
5 6 2.496111 GAACCACACATTTACGGACCA 58.504 47.619 0.00 0.00 0.00 4.02
6 7 1.808343 GGAACCACACATTTACGGACC 59.192 52.381 0.00 0.00 0.00 4.46
7 8 2.482721 CAGGAACCACACATTTACGGAC 59.517 50.000 0.00 0.00 0.00 4.79
8 9 2.773487 CAGGAACCACACATTTACGGA 58.227 47.619 0.00 0.00 0.00 4.69
9 10 1.199097 GCAGGAACCACACATTTACGG 59.801 52.381 0.00 0.00 0.00 4.02
10 11 1.876799 TGCAGGAACCACACATTTACG 59.123 47.619 0.00 0.00 0.00 3.18
11 12 4.048504 GTTTGCAGGAACCACACATTTAC 58.951 43.478 0.00 0.00 0.00 2.01
12 13 3.068873 GGTTTGCAGGAACCACACATTTA 59.931 43.478 14.26 0.00 46.66 1.40
13 14 2.158971 GGTTTGCAGGAACCACACATTT 60.159 45.455 14.26 0.00 46.66 2.32
14 15 1.412343 GGTTTGCAGGAACCACACATT 59.588 47.619 14.26 0.00 46.66 2.71
15 16 1.039856 GGTTTGCAGGAACCACACAT 58.960 50.000 14.26 0.00 46.66 3.21
16 17 2.499214 GGTTTGCAGGAACCACACA 58.501 52.632 14.26 0.00 46.66 3.72
22 23 3.518634 TCAAACAAGGTTTGCAGGAAC 57.481 42.857 15.12 0.00 0.00 3.62
23 24 3.513515 ACTTCAAACAAGGTTTGCAGGAA 59.486 39.130 20.01 8.96 29.12 3.36
24 25 3.096092 ACTTCAAACAAGGTTTGCAGGA 58.904 40.909 20.01 2.73 29.12 3.86
25 26 3.189285 CACTTCAAACAAGGTTTGCAGG 58.811 45.455 20.01 13.08 29.12 4.85
26 27 3.848726 ACACTTCAAACAAGGTTTGCAG 58.151 40.909 16.24 16.24 0.00 4.41
27 28 3.671971 CGACACTTCAAACAAGGTTTGCA 60.672 43.478 15.12 5.64 0.00 4.08
28 29 2.851824 CGACACTTCAAACAAGGTTTGC 59.148 45.455 15.12 2.07 0.00 3.68
29 30 4.349663 TCGACACTTCAAACAAGGTTTG 57.650 40.909 14.05 14.05 0.00 2.93
30 31 6.877611 ATATCGACACTTCAAACAAGGTTT 57.122 33.333 0.00 0.00 0.00 3.27
31 32 6.877611 AATATCGACACTTCAAACAAGGTT 57.122 33.333 0.00 0.00 0.00 3.50
32 33 6.877611 AAATATCGACACTTCAAACAAGGT 57.122 33.333 0.00 0.00 0.00 3.50
33 34 9.277565 CATAAAATATCGACACTTCAAACAAGG 57.722 33.333 0.00 0.00 0.00 3.61
34 35 8.788813 GCATAAAATATCGACACTTCAAACAAG 58.211 33.333 0.00 0.00 0.00 3.16
35 36 8.293157 TGCATAAAATATCGACACTTCAAACAA 58.707 29.630 0.00 0.00 0.00 2.83
36 37 7.811653 TGCATAAAATATCGACACTTCAAACA 58.188 30.769 0.00 0.00 0.00 2.83
37 38 8.667987 TTGCATAAAATATCGACACTTCAAAC 57.332 30.769 0.00 0.00 0.00 2.93
38 39 9.853555 AATTGCATAAAATATCGACACTTCAAA 57.146 25.926 0.00 0.00 0.00 2.69
39 40 9.502145 GAATTGCATAAAATATCGACACTTCAA 57.498 29.630 0.00 0.00 0.00 2.69
40 41 8.672815 TGAATTGCATAAAATATCGACACTTCA 58.327 29.630 0.00 0.00 0.00 3.02
41 42 8.947940 GTGAATTGCATAAAATATCGACACTTC 58.052 33.333 0.00 0.00 0.00 3.01
42 43 8.677300 AGTGAATTGCATAAAATATCGACACTT 58.323 29.630 0.00 0.00 0.00 3.16
43 44 8.213518 AGTGAATTGCATAAAATATCGACACT 57.786 30.769 0.00 0.00 0.00 3.55
44 45 7.318909 CGAGTGAATTGCATAAAATATCGACAC 59.681 37.037 0.00 0.00 0.00 3.67
45 46 7.344441 CGAGTGAATTGCATAAAATATCGACA 58.656 34.615 0.00 0.00 0.00 4.35
46 47 6.792250 CCGAGTGAATTGCATAAAATATCGAC 59.208 38.462 0.00 0.00 0.00 4.20
47 48 6.704050 TCCGAGTGAATTGCATAAAATATCGA 59.296 34.615 0.00 0.00 0.00 3.59
48 49 6.792250 GTCCGAGTGAATTGCATAAAATATCG 59.208 38.462 0.00 0.00 0.00 2.92
49 50 7.078228 GGTCCGAGTGAATTGCATAAAATATC 58.922 38.462 0.00 0.00 0.00 1.63
50 51 6.293407 CGGTCCGAGTGAATTGCATAAAATAT 60.293 38.462 4.91 0.00 0.00 1.28
51 52 5.007234 CGGTCCGAGTGAATTGCATAAAATA 59.993 40.000 4.91 0.00 0.00 1.40
52 53 4.201910 CGGTCCGAGTGAATTGCATAAAAT 60.202 41.667 4.91 0.00 0.00 1.82
53 54 3.126171 CGGTCCGAGTGAATTGCATAAAA 59.874 43.478 4.91 0.00 0.00 1.52
54 55 2.675844 CGGTCCGAGTGAATTGCATAAA 59.324 45.455 4.91 0.00 0.00 1.40
55 56 2.276201 CGGTCCGAGTGAATTGCATAA 58.724 47.619 4.91 0.00 0.00 1.90
56 57 1.206132 ACGGTCCGAGTGAATTGCATA 59.794 47.619 20.51 0.00 0.00 3.14
57 58 0.036388 ACGGTCCGAGTGAATTGCAT 60.036 50.000 20.51 0.00 0.00 3.96
58 59 0.604073 TACGGTCCGAGTGAATTGCA 59.396 50.000 20.51 0.00 0.00 4.08
59 60 1.135199 TCTACGGTCCGAGTGAATTGC 60.135 52.381 20.51 0.00 0.00 3.56
60 61 2.163815 ACTCTACGGTCCGAGTGAATTG 59.836 50.000 20.51 4.11 38.94 2.32
61 62 2.444421 ACTCTACGGTCCGAGTGAATT 58.556 47.619 20.51 0.00 38.94 2.17
62 63 2.125773 ACTCTACGGTCCGAGTGAAT 57.874 50.000 20.51 0.00 38.94 2.57
63 64 3.639099 ACTCTACGGTCCGAGTGAA 57.361 52.632 20.51 0.00 38.94 3.18
66 67 2.479566 TAACACTCTACGGTCCGAGT 57.520 50.000 20.51 8.41 40.92 4.18
67 68 2.681848 ACATAACACTCTACGGTCCGAG 59.318 50.000 20.51 11.15 0.00 4.63
68 69 2.715046 ACATAACACTCTACGGTCCGA 58.285 47.619 20.51 0.31 0.00 4.55
69 70 4.825546 ATACATAACACTCTACGGTCCG 57.174 45.455 10.48 10.48 0.00 4.79
70 71 8.139989 ACAATAATACATAACACTCTACGGTCC 58.860 37.037 0.00 0.00 0.00 4.46
99 100 9.294614 TGCAATACAATTCCTATATACATGCAA 57.705 29.630 0.00 0.00 34.96 4.08
100 101 8.860780 TGCAATACAATTCCTATATACATGCA 57.139 30.769 0.00 0.00 35.45 3.96
101 102 8.950210 ACTGCAATACAATTCCTATATACATGC 58.050 33.333 0.00 0.00 0.00 4.06
104 105 9.845740 AACACTGCAATACAATTCCTATATACA 57.154 29.630 0.00 0.00 0.00 2.29
107 108 9.632638 AGAAACACTGCAATACAATTCCTATAT 57.367 29.630 0.00 0.00 0.00 0.86
108 109 9.109393 GAGAAACACTGCAATACAATTCCTATA 57.891 33.333 0.00 0.00 0.00 1.31
109 110 7.201644 CGAGAAACACTGCAATACAATTCCTAT 60.202 37.037 0.00 0.00 0.00 2.57
110 111 6.092122 CGAGAAACACTGCAATACAATTCCTA 59.908 38.462 0.00 0.00 0.00 2.94
111 112 5.106555 CGAGAAACACTGCAATACAATTCCT 60.107 40.000 0.00 0.00 0.00 3.36
112 113 5.088739 CGAGAAACACTGCAATACAATTCC 58.911 41.667 0.00 0.00 0.00 3.01
113 114 5.927030 TCGAGAAACACTGCAATACAATTC 58.073 37.500 0.00 0.00 0.00 2.17
114 115 5.940192 TCGAGAAACACTGCAATACAATT 57.060 34.783 0.00 0.00 0.00 2.32
115 116 5.940192 TTCGAGAAACACTGCAATACAAT 57.060 34.783 0.00 0.00 0.00 2.71
116 117 5.940192 ATTCGAGAAACACTGCAATACAA 57.060 34.783 0.00 0.00 0.00 2.41
117 118 5.238432 ACAATTCGAGAAACACTGCAATACA 59.762 36.000 0.00 0.00 0.00 2.29
118 119 5.565259 CACAATTCGAGAAACACTGCAATAC 59.435 40.000 0.00 0.00 0.00 1.89
119 120 5.334802 CCACAATTCGAGAAACACTGCAATA 60.335 40.000 0.00 0.00 0.00 1.90
120 121 4.539870 CACAATTCGAGAAACACTGCAAT 58.460 39.130 0.00 0.00 0.00 3.56
121 122 3.243035 CCACAATTCGAGAAACACTGCAA 60.243 43.478 0.00 0.00 0.00 4.08
122 123 2.290367 CCACAATTCGAGAAACACTGCA 59.710 45.455 0.00 0.00 0.00 4.41
123 124 2.350772 CCCACAATTCGAGAAACACTGC 60.351 50.000 0.00 0.00 0.00 4.40
124 125 3.058914 GTCCCACAATTCGAGAAACACTG 60.059 47.826 0.00 0.00 0.00 3.66
125 126 3.139077 GTCCCACAATTCGAGAAACACT 58.861 45.455 0.00 0.00 0.00 3.55
126 127 2.225727 GGTCCCACAATTCGAGAAACAC 59.774 50.000 0.00 0.00 0.00 3.32
127 128 2.105821 AGGTCCCACAATTCGAGAAACA 59.894 45.455 0.00 0.00 0.00 2.83
128 129 2.779506 AGGTCCCACAATTCGAGAAAC 58.220 47.619 0.00 0.00 0.00 2.78
129 130 4.837093 ATAGGTCCCACAATTCGAGAAA 57.163 40.909 0.00 0.00 0.00 2.52
130 131 4.766375 GAATAGGTCCCACAATTCGAGAA 58.234 43.478 0.00 0.00 0.00 2.87
131 132 4.402056 GAATAGGTCCCACAATTCGAGA 57.598 45.455 0.00 0.00 0.00 4.04
135 136 3.808174 GCTACGAATAGGTCCCACAATTC 59.192 47.826 0.00 0.00 0.00 2.17
136 137 3.740141 CGCTACGAATAGGTCCCACAATT 60.740 47.826 0.00 0.00 0.00 2.32
137 138 2.223971 CGCTACGAATAGGTCCCACAAT 60.224 50.000 0.00 0.00 0.00 2.71
138 139 1.135527 CGCTACGAATAGGTCCCACAA 59.864 52.381 0.00 0.00 0.00 3.33
139 140 0.742505 CGCTACGAATAGGTCCCACA 59.257 55.000 0.00 0.00 0.00 4.17
140 141 0.596859 GCGCTACGAATAGGTCCCAC 60.597 60.000 0.00 0.00 0.00 4.61
141 142 1.737816 GCGCTACGAATAGGTCCCA 59.262 57.895 0.00 0.00 0.00 4.37
142 143 4.649618 GCGCTACGAATAGGTCCC 57.350 61.111 0.00 0.00 0.00 4.46
153 154 2.159544 ACTGAACTCTCTAACGCGCTAC 60.160 50.000 5.73 0.00 0.00 3.58
154 155 2.082231 ACTGAACTCTCTAACGCGCTA 58.918 47.619 5.73 0.00 0.00 4.26
155 156 0.882474 ACTGAACTCTCTAACGCGCT 59.118 50.000 5.73 0.00 0.00 5.92
156 157 2.539346 TACTGAACTCTCTAACGCGC 57.461 50.000 5.73 0.00 0.00 6.86
157 158 4.911053 AGATTACTGAACTCTCTAACGCG 58.089 43.478 3.53 3.53 0.00 6.01
158 159 6.557110 AGAAGATTACTGAACTCTCTAACGC 58.443 40.000 0.00 0.00 0.00 4.84
159 160 7.148222 TGGAGAAGATTACTGAACTCTCTAACG 60.148 40.741 0.00 0.00 0.00 3.18
160 161 7.971722 GTGGAGAAGATTACTGAACTCTCTAAC 59.028 40.741 0.00 0.00 0.00 2.34
161 162 7.148222 CGTGGAGAAGATTACTGAACTCTCTAA 60.148 40.741 0.00 0.00 0.00 2.10
162 163 6.316640 CGTGGAGAAGATTACTGAACTCTCTA 59.683 42.308 0.00 0.00 0.00 2.43
163 164 5.124776 CGTGGAGAAGATTACTGAACTCTCT 59.875 44.000 0.00 0.00 0.00 3.10
164 165 5.336744 CGTGGAGAAGATTACTGAACTCTC 58.663 45.833 0.00 0.00 0.00 3.20
165 166 4.158764 CCGTGGAGAAGATTACTGAACTCT 59.841 45.833 0.00 0.00 0.00 3.24
166 167 4.082136 ACCGTGGAGAAGATTACTGAACTC 60.082 45.833 0.00 0.00 0.00 3.01
178 179 1.153549 GGCTGCTACCGTGGAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
193 194 1.063183 GGAGGAGGCTTATGATGGCT 58.937 55.000 0.00 0.00 43.15 4.75
194 195 0.767375 TGGAGGAGGCTTATGATGGC 59.233 55.000 0.00 0.00 0.00 4.40
195 196 2.290768 CCATGGAGGAGGCTTATGATGG 60.291 54.545 5.56 0.00 41.22 3.51
198 199 2.494888 TCCATGGAGGAGGCTTATGA 57.505 50.000 11.44 0.00 43.07 2.15
252 253 2.747855 CAAGGAGGACGCCCAAGC 60.748 66.667 0.00 0.00 33.88 4.01
260 261 2.550830 TTTGAGCTGACAAGGAGGAC 57.449 50.000 0.00 0.00 0.00 3.85
317 322 1.077334 ACGGGGAGAAAGAGAGGAGAA 59.923 52.381 0.00 0.00 0.00 2.87
384 389 2.042843 GGGAGAGGAAGCGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
389 394 0.747852 GGAGTAAGGGAGAGGAAGCG 59.252 60.000 0.00 0.00 0.00 4.68
505 510 2.119495 ACACACCTCTCTTGGACTTGT 58.881 47.619 0.00 0.00 0.00 3.16
523 532 3.129113 CCATGATCGAATTGCAGGAAACA 59.871 43.478 0.00 0.00 0.00 2.83
551 560 2.045926 CCCGACAGAAGCAAGGGG 60.046 66.667 0.00 0.00 38.44 4.79
572 581 6.867550 ACCTTAGTAAAATACAGACGTACCC 58.132 40.000 0.00 0.00 0.00 3.69
592 601 4.274950 CCAACCATCGCGATTTTATACCTT 59.725 41.667 21.14 0.00 0.00 3.50
745 756 5.871396 TTATCTGGGTGCTAGTAGAAAGG 57.129 43.478 0.00 0.00 0.00 3.11
852 868 1.604378 CCTTCACTACAGGGCAGGG 59.396 63.158 0.00 0.00 0.00 4.45
853 869 1.604378 CCCTTCACTACAGGGCAGG 59.396 63.158 0.00 0.00 45.00 4.85
914 930 5.642063 TGTAAATCGGGAGTTCACAGATTTC 59.358 40.000 13.46 8.95 40.58 2.17
927 943 7.505258 TGATGATAACAGATTGTAAATCGGGA 58.495 34.615 5.36 0.00 30.08 5.14
1127 1163 2.760374 CTCTGACAACCAAGTGACCTC 58.240 52.381 0.00 0.00 0.00 3.85
1166 1202 3.496884 CGGATTCGAAAAGTCCAGTTTCA 59.503 43.478 14.90 0.00 39.00 2.69
1533 1582 8.956426 CAGCCAAAGAAACTATCCAAGTAATTA 58.044 33.333 0.00 0.00 37.50 1.40
1543 1592 6.749923 ATTCAGACAGCCAAAGAAACTATC 57.250 37.500 0.00 0.00 0.00 2.08
1700 1749 9.349713 ACCTGAAGAATCAACAACTTTGTAATA 57.650 29.630 0.00 0.00 41.31 0.98
1976 2025 0.752658 CTACCTGCCGGATGACATCA 59.247 55.000 17.08 0.00 0.00 3.07
2069 2118 9.242477 GTTTTCTTCAAGAGAATTTTCAGAAGG 57.758 33.333 20.85 10.18 43.65 3.46
2276 2325 5.188434 ACATCAGGATGGTTATCAGTGTTG 58.812 41.667 13.40 0.00 42.91 3.33
2306 2355 4.017126 GCTGGGTTAAGTAAAAGAGCCAT 58.983 43.478 0.00 0.00 38.79 4.40
2321 2370 4.081087 ACGACATGTCTATTAAGCTGGGTT 60.081 41.667 22.95 0.00 0.00 4.11
2372 2421 2.416162 GCCACGAGACACTCCTAAGAAG 60.416 54.545 0.00 0.00 0.00 2.85
2649 2698 5.472137 GGTACAATCTAGTCTAGGAGCTGAG 59.528 48.000 7.05 0.00 0.00 3.35
2685 2734 2.792890 CGTCATAGTTGAGCGAGACCAG 60.793 54.545 0.00 0.00 32.01 4.00
2980 3029 3.694043 TTGCCCGCTTGCAGATATATA 57.306 42.857 0.00 0.00 43.21 0.86
2981 3030 2.566833 TTGCCCGCTTGCAGATATAT 57.433 45.000 0.00 0.00 43.21 0.86
2982 3031 2.158827 TCTTTGCCCGCTTGCAGATATA 60.159 45.455 0.00 0.00 43.21 0.86
3053 3103 2.659897 GCCTGACCATAGAGCGCG 60.660 66.667 0.00 0.00 0.00 6.86
3054 3104 1.884926 GTGCCTGACCATAGAGCGC 60.885 63.158 0.00 0.00 0.00 5.92
3077 3127 1.694844 ATCCGATGCCATGAAATGCA 58.305 45.000 0.00 0.00 44.97 3.96
3161 3211 1.940613 GGTATCAGGCAAATGTCGACC 59.059 52.381 14.12 0.00 0.00 4.79
3199 3249 1.068333 GGGCATACACAGCACAAGTTG 60.068 52.381 0.00 0.00 34.91 3.16
3235 3285 5.636903 TTAAATCAATCAGAGGAGAGGGG 57.363 43.478 0.00 0.00 0.00 4.79
3413 3472 3.888930 CTGGCAGTTAAGTTTCCCAAGAA 59.111 43.478 6.28 0.00 0.00 2.52
3477 3536 1.177895 AATTGATGCACACACGGGCA 61.178 50.000 0.00 0.00 45.23 5.36
3497 3556 9.593134 AACAGAACAGAATATTGTATGTCTCTC 57.407 33.333 0.00 0.00 32.89 3.20
3758 3822 3.895041 TGTACTTCACATCAGAGTGGACA 59.105 43.478 0.00 0.00 39.93 4.02
3824 3888 1.450848 CGTGCACAGGATGGCATCT 60.451 57.895 25.48 10.14 42.55 2.90
3938 4002 2.731572 CTGCAAGGTTCAATCAGGGAT 58.268 47.619 0.00 0.00 0.00 3.85
3994 4058 0.027586 GCGTGTTGCATATTCCGGTC 59.972 55.000 0.00 0.00 45.45 4.79
4036 4100 2.678336 CCTTGGCGTCTTGATAACTTCC 59.322 50.000 0.00 0.00 0.00 3.46
4177 4242 7.114754 AGAATGACATTGACAATCCTGTACAT 58.885 34.615 5.14 0.02 35.30 2.29
4249 4314 1.413445 AGCAGATGAGCTCAGGATCAC 59.587 52.381 22.96 10.92 42.18 3.06
4340 4405 9.988815 GGACTGAAATGTGTCTATTATACATCT 57.011 33.333 0.00 0.00 38.83 2.90
4341 4406 8.916654 CGGACTGAAATGTGTCTATTATACATC 58.083 37.037 0.00 0.00 38.83 3.06
4342 4407 7.385205 GCGGACTGAAATGTGTCTATTATACAT 59.615 37.037 0.00 0.00 41.27 2.29
4343 4408 6.700081 GCGGACTGAAATGTGTCTATTATACA 59.300 38.462 0.00 0.00 33.31 2.29
4344 4409 6.700081 TGCGGACTGAAATGTGTCTATTATAC 59.300 38.462 0.00 0.00 34.01 1.47
4346 4411 5.670485 TGCGGACTGAAATGTGTCTATTAT 58.330 37.500 0.00 0.00 34.01 1.28
4348 4413 3.937814 TGCGGACTGAAATGTGTCTATT 58.062 40.909 0.00 0.00 34.01 1.73
4349 4414 3.610040 TGCGGACTGAAATGTGTCTAT 57.390 42.857 0.00 0.00 34.01 1.98
4352 4417 1.806542 ACATGCGGACTGAAATGTGTC 59.193 47.619 0.00 0.00 32.18 3.67
4356 4421 1.131126 GACCACATGCGGACTGAAATG 59.869 52.381 6.80 0.00 0.00 2.32
4367 4432 2.363306 TCCAATATGGGACCACATGC 57.637 50.000 0.00 0.00 38.32 4.06
4376 4441 8.874744 AGATGTTTCTGATATTCCAATATGGG 57.125 34.615 0.00 0.00 38.32 4.00
4393 4458 9.994432 CCTCTGTTCACAAATATAAGATGTTTC 57.006 33.333 0.00 0.00 0.00 2.78
4408 4473 2.310779 AGCTACTCCCTCTGTTCACA 57.689 50.000 0.00 0.00 0.00 3.58
4511 4581 4.032960 TCTGGACACAAGTTTGGCATAT 57.967 40.909 0.00 0.00 0.00 1.78
4513 4583 2.363306 TCTGGACACAAGTTTGGCAT 57.637 45.000 0.00 0.00 0.00 4.40
4533 4604 8.282455 TCGCCATTATTCCAGTTTTATGTAAA 57.718 30.769 0.00 0.00 0.00 2.01
4534 4605 7.867305 TCGCCATTATTCCAGTTTTATGTAA 57.133 32.000 0.00 0.00 0.00 2.41
4557 4628 5.957798 TGGCAGACATCTTTGATCATTTTC 58.042 37.500 0.00 0.00 0.00 2.29
4592 4664 9.905713 AAGAAATTAGAGGCAATGTATGTCTTA 57.094 29.630 0.00 0.00 46.26 2.10
4751 4854 6.220930 GTGTCCTGACTTGAGTAATGTAACA 58.779 40.000 0.00 0.00 0.00 2.41
4764 4867 4.271696 TCAATGAATCGTGTCCTGACTT 57.728 40.909 0.00 0.00 0.00 3.01
4813 4916 2.171448 CACCCATTCAGGTTCCCTCTAG 59.829 54.545 0.00 0.00 38.39 2.43
4815 4918 0.995024 CACCCATTCAGGTTCCCTCT 59.005 55.000 0.00 0.00 38.39 3.69
4816 4919 0.034089 CCACCCATTCAGGTTCCCTC 60.034 60.000 0.00 0.00 38.39 4.30
4817 4920 0.776080 ACCACCCATTCAGGTTCCCT 60.776 55.000 0.00 0.00 38.39 4.20
4897 5000 4.015084 GCCTTAGTACGAGCCTATATCCA 58.985 47.826 0.00 0.00 0.00 3.41
4921 5024 4.201910 TGCTTACAGTTGCAGTTTGAACTC 60.202 41.667 0.00 0.00 37.08 3.01
4945 5048 6.270231 ACACATGTAGAGTTCCTTACTTCCTT 59.730 38.462 0.00 0.00 37.17 3.36
4946 5049 5.780793 ACACATGTAGAGTTCCTTACTTCCT 59.219 40.000 0.00 0.00 37.17 3.36
4947 5050 6.038997 ACACATGTAGAGTTCCTTACTTCC 57.961 41.667 0.00 0.00 37.17 3.46
4948 5051 7.329717 CAGAACACATGTAGAGTTCCTTACTTC 59.670 40.741 18.78 0.00 45.43 3.01
4949 5052 7.155328 CAGAACACATGTAGAGTTCCTTACTT 58.845 38.462 18.78 2.73 45.43 2.24
4950 5053 6.295349 CCAGAACACATGTAGAGTTCCTTACT 60.295 42.308 18.78 3.29 45.43 2.24
4951 5054 5.869888 CCAGAACACATGTAGAGTTCCTTAC 59.130 44.000 18.78 1.19 45.43 2.34
4952 5055 5.568825 GCCAGAACACATGTAGAGTTCCTTA 60.569 44.000 18.78 0.00 45.43 2.69
4968 5071 1.067295 AGAAGGATGGTGCCAGAACA 58.933 50.000 0.00 0.00 0.00 3.18
5083 5202 1.522668 TCACCGAAACTGCAGATTGG 58.477 50.000 23.35 22.24 0.00 3.16


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

AutoCloner maintained by Alex Coulton.