Multiple sequence alignment - TraesCS5D01G242800

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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 TraesCS5D01G242800 chr5D 100.000 3332 0 0 858 4189 351007511 351004180 0.000000e+00 6154.0
1 TraesCS5D01G242800 chr5D 100.000 511 0 0 1 511 351008368 351007858 0.000000e+00 944.0
2 TraesCS5D01G242800 chr5D 84.416 231 33 3 3612 3840 518917273 518917502 1.520000e-54 224.0
3 TraesCS5D01G242800 chr5D 89.844 128 13 0 25 152 275606289 275606416 9.320000e-37 165.0
4 TraesCS5D01G242800 chr5D 77.737 274 44 13 1924 2195 475510338 475510080 7.250000e-33 152.0
5 TraesCS5D01G242800 chr5D 88.608 79 9 0 997 1075 475511503 475511425 3.450000e-16 97.1
6 TraesCS5D01G242800 chr5D 97.619 42 1 0 4147 4188 533115705 533115664 5.810000e-09 73.1
7 TraesCS5D01G242800 chr5B 93.305 3331 148 36 873 4162 411932133 411928837 0.000000e+00 4846.0
8 TraesCS5D01G242800 chr5B 90.223 358 17 5 154 509 411932471 411932130 6.390000e-123 451.0
9 TraesCS5D01G242800 chr5B 87.407 135 16 1 19 152 377183097 377183231 2.020000e-33 154.0
10 TraesCS5D01G242800 chr5B 83.019 106 17 1 997 1102 582891329 582891225 1.240000e-15 95.3
11 TraesCS5D01G242800 chr5A 92.236 2808 113 36 858 3616 451481116 451478365 0.000000e+00 3880.0
12 TraesCS5D01G242800 chr5A 93.056 360 22 3 154 511 451481468 451481110 1.330000e-144 523.0
13 TraesCS5D01G242800 chr5A 79.927 274 42 10 1924 2195 594963143 594962881 5.530000e-44 189.0
14 TraesCS5D01G242800 chr5A 81.690 213 34 5 3612 3821 100066924 100067134 5.570000e-39 172.0
15 TraesCS5D01G242800 chr5A 87.912 91 11 0 62 152 364418922 364419012 1.590000e-19 108.0
16 TraesCS5D01G242800 chr5A 88.608 79 9 0 997 1075 594964352 594964274 3.450000e-16 97.1
17 TraesCS5D01G242800 chr1A 92.143 140 11 0 19 158 540137718 540137579 9.190000e-47 198.0
18 TraesCS5D01G242800 chr1A 88.000 150 18 0 3617 3766 481503796 481503945 1.200000e-40 178.0
19 TraesCS5D01G242800 chr2D 90.647 139 13 0 19 157 590802293 590802155 7.150000e-43 185.0
20 TraesCS5D01G242800 chr7B 90.000 140 13 1 19 157 66415518 66415379 3.330000e-41 180.0
21 TraesCS5D01G242800 chr2A 83.582 201 24 6 3612 3805 142895187 142895385 3.330000e-41 180.0
22 TraesCS5D01G242800 chr2A 84.277 159 22 3 3614 3771 452311823 452311667 7.250000e-33 152.0
23 TraesCS5D01G242800 chr2A 85.926 135 19 0 3606 3740 81014759 81014893 1.210000e-30 145.0
24 TraesCS5D01G242800 chr2B 84.000 150 22 2 3613 3761 406880919 406881067 4.370000e-30 143.0
25 TraesCS5D01G242800 chr2B 82.051 78 14 0 20 97 373765003 373764926 2.700000e-07 67.6
26 TraesCS5D01G242800 chr4B 82.692 156 27 0 3613 3768 273981543 273981698 5.650000e-29 139.0
27 TraesCS5D01G242800 chr4B 95.238 42 2 0 4147 4188 454515535 454515494 2.700000e-07 67.6
28 TraesCS5D01G242800 chrUn 97.500 40 1 0 4148 4187 31863539 31863578 7.510000e-08 69.4
29 TraesCS5D01G242800 chr4A 93.478 46 3 0 4143 4188 605008626 605008671 7.510000e-08 69.4
30 TraesCS5D01G242800 chr3B 95.349 43 2 0 4146 4188 43273691 43273733 7.510000e-08 69.4
31 TraesCS5D01G242800 chr1B 97.500 40 1 0 4149 4188 151363747 151363708 7.510000e-08 69.4
32 TraesCS5D01G242800 chr7D 93.478 46 2 1 4143 4188 34378739 34378783 2.700000e-07 67.6
33 TraesCS5D01G242800 chr3D 93.478 46 1 2 4144 4188 365114215 365114259 2.700000e-07 67.6
34 TraesCS5D01G242800 chr3A 91.837 49 2 2 4141 4188 596487008 596487055 2.700000e-07 67.6


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 TraesCS5D01G242800 chr5D 351004180 351008368 4188 True 3549.0 6154 100.000 1 4189 2 chr5D.!!$R2 4188
1 TraesCS5D01G242800 chr5B 411928837 411932471 3634 True 2648.5 4846 91.764 154 4162 2 chr5B.!!$R2 4008
2 TraesCS5D01G242800 chr5A 451478365 451481468 3103 True 2201.5 3880 92.646 154 3616 2 chr5A.!!$R1 3462

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
92 93 0.256464 TCCACCCCGTGTTTTCAACT 59.744 50.000 0.00 0.00 0.00 3.16 F
93 94 0.383949 CCACCCCGTGTTTTCAACTG 59.616 55.000 0.00 0.00 0.00 3.16 F
968 980 0.393537 CGCCCAATCCAGCTCTTCTT 60.394 55.000 0.00 0.00 0.00 2.52 F
2104 2127 1.132721 AGGATATGGGCTACAGCTCCA 60.133 52.381 12.05 12.05 41.95 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 1302 0.460459 GCGGCTTGGAGGAAGAGTAC 60.460 60.000 0.00 0.0 32.82 2.73 R
1809 1827 1.008767 CTCGGCGAGAATACGGTCC 60.009 63.158 32.07 0.0 0.00 4.46 R
2482 2517 1.454572 ATTCAGCACAGCAACCGCAA 61.455 50.000 0.00 0.0 42.27 4.85 R
3238 3283 1.048601 AAGAGGACTGAAACTCGGCA 58.951 50.000 0.00 0.0 38.72 5.69 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
26 27 7.705325 TCAGTTAGTAATAAAGATCTGTTCGGC 59.295 37.037 0.00 0.00 0.00 5.54
27 28 7.491372 CAGTTAGTAATAAAGATCTGTTCGGCA 59.509 37.037 0.00 0.00 0.00 5.69
28 29 8.038944 AGTTAGTAATAAAGATCTGTTCGGCAA 58.961 33.333 0.00 0.00 0.00 4.52
29 30 8.827677 GTTAGTAATAAAGATCTGTTCGGCAAT 58.172 33.333 0.00 0.00 0.00 3.56
30 31 7.484035 AGTAATAAAGATCTGTTCGGCAATC 57.516 36.000 0.00 0.00 0.00 2.67
31 32 7.047891 AGTAATAAAGATCTGTTCGGCAATCA 58.952 34.615 0.00 0.00 0.00 2.57
32 33 6.757897 AATAAAGATCTGTTCGGCAATCAA 57.242 33.333 0.00 0.00 0.00 2.57
33 34 4.425577 AAAGATCTGTTCGGCAATCAAC 57.574 40.909 0.00 0.00 0.00 3.18
34 35 2.359900 AGATCTGTTCGGCAATCAACC 58.640 47.619 0.00 0.00 0.00 3.77
40 41 2.098298 CGGCAATCAACCGCTTCG 59.902 61.111 0.00 0.00 44.90 3.79
41 42 2.387445 CGGCAATCAACCGCTTCGA 61.387 57.895 0.00 0.00 44.90 3.71
42 43 1.425428 GGCAATCAACCGCTTCGAG 59.575 57.895 0.00 0.00 0.00 4.04
43 44 1.019278 GGCAATCAACCGCTTCGAGA 61.019 55.000 0.00 0.00 0.00 4.04
44 45 0.796312 GCAATCAACCGCTTCGAGAA 59.204 50.000 0.00 0.00 0.00 2.87
45 46 1.196808 GCAATCAACCGCTTCGAGAAA 59.803 47.619 0.00 0.00 0.00 2.52
46 47 2.159517 GCAATCAACCGCTTCGAGAAAT 60.160 45.455 0.00 0.00 0.00 2.17
47 48 3.063452 GCAATCAACCGCTTCGAGAAATA 59.937 43.478 0.00 0.00 0.00 1.40
48 49 4.578601 CAATCAACCGCTTCGAGAAATAC 58.421 43.478 0.00 0.00 0.00 1.89
49 50 2.256174 TCAACCGCTTCGAGAAATACG 58.744 47.619 0.00 0.00 0.00 3.06
50 51 2.095110 TCAACCGCTTCGAGAAATACGA 60.095 45.455 0.00 0.00 37.99 3.43
51 52 2.190325 ACCGCTTCGAGAAATACGAG 57.810 50.000 0.00 0.00 40.72 4.18
52 53 1.741706 ACCGCTTCGAGAAATACGAGA 59.258 47.619 0.00 0.00 40.72 4.04
53 54 2.163010 ACCGCTTCGAGAAATACGAGAA 59.837 45.455 0.00 0.00 40.72 2.87
54 55 3.181489 ACCGCTTCGAGAAATACGAGAAT 60.181 43.478 0.00 0.00 40.72 2.40
55 56 3.422546 CCGCTTCGAGAAATACGAGAATC 59.577 47.826 0.00 0.00 40.72 2.52
56 57 4.283678 CGCTTCGAGAAATACGAGAATCT 58.716 43.478 0.00 0.00 40.72 2.40
57 58 4.145585 CGCTTCGAGAAATACGAGAATCTG 59.854 45.833 0.00 0.00 40.72 2.90
58 59 5.038033 GCTTCGAGAAATACGAGAATCTGT 58.962 41.667 0.00 0.00 40.72 3.41
59 60 5.052040 GCTTCGAGAAATACGAGAATCTGTG 60.052 44.000 0.00 0.00 40.72 3.66
60 61 5.813080 TCGAGAAATACGAGAATCTGTGA 57.187 39.130 0.00 0.00 34.85 3.58
61 62 6.190954 TCGAGAAATACGAGAATCTGTGAA 57.809 37.500 0.00 0.00 34.85 3.18
62 63 6.258899 TCGAGAAATACGAGAATCTGTGAAG 58.741 40.000 0.00 0.00 34.85 3.02
63 64 5.052040 CGAGAAATACGAGAATCTGTGAAGC 60.052 44.000 0.00 0.00 0.00 3.86
64 65 5.724328 AGAAATACGAGAATCTGTGAAGCA 58.276 37.500 0.00 0.00 0.00 3.91
65 66 6.344500 AGAAATACGAGAATCTGTGAAGCAT 58.656 36.000 0.00 0.00 0.00 3.79
66 67 6.478344 AGAAATACGAGAATCTGTGAAGCATC 59.522 38.462 0.00 0.00 0.00 3.91
67 68 3.883830 ACGAGAATCTGTGAAGCATCT 57.116 42.857 0.00 0.00 0.00 2.90
68 69 4.199432 ACGAGAATCTGTGAAGCATCTT 57.801 40.909 0.00 0.00 0.00 2.40
69 70 4.573900 ACGAGAATCTGTGAAGCATCTTT 58.426 39.130 0.00 0.00 0.00 2.52
70 71 4.999950 ACGAGAATCTGTGAAGCATCTTTT 59.000 37.500 0.00 0.00 0.00 2.27
71 72 5.471456 ACGAGAATCTGTGAAGCATCTTTTT 59.529 36.000 0.00 0.00 0.00 1.94
72 73 6.020372 CGAGAATCTGTGAAGCATCTTTTTC 58.980 40.000 0.00 0.00 0.00 2.29
73 74 6.128336 CGAGAATCTGTGAAGCATCTTTTTCT 60.128 38.462 0.00 0.00 0.00 2.52
74 75 7.143514 AGAATCTGTGAAGCATCTTTTTCTC 57.856 36.000 0.00 0.00 0.00 2.87
75 76 5.893897 ATCTGTGAAGCATCTTTTTCTCC 57.106 39.130 0.00 0.00 0.00 3.71
76 77 4.717877 TCTGTGAAGCATCTTTTTCTCCA 58.282 39.130 0.00 0.00 0.00 3.86
77 78 4.516698 TCTGTGAAGCATCTTTTTCTCCAC 59.483 41.667 0.00 0.00 0.00 4.02
78 79 3.569701 TGTGAAGCATCTTTTTCTCCACC 59.430 43.478 0.00 0.00 0.00 4.61
79 80 3.057245 GTGAAGCATCTTTTTCTCCACCC 60.057 47.826 0.00 0.00 0.00 4.61
80 81 2.222227 AGCATCTTTTTCTCCACCCC 57.778 50.000 0.00 0.00 0.00 4.95
81 82 0.811281 GCATCTTTTTCTCCACCCCG 59.189 55.000 0.00 0.00 0.00 5.73
82 83 1.886655 GCATCTTTTTCTCCACCCCGT 60.887 52.381 0.00 0.00 0.00 5.28
83 84 1.812571 CATCTTTTTCTCCACCCCGTG 59.187 52.381 0.00 0.00 0.00 4.94
84 85 0.841289 TCTTTTTCTCCACCCCGTGT 59.159 50.000 0.00 0.00 0.00 4.49
85 86 1.213430 TCTTTTTCTCCACCCCGTGTT 59.787 47.619 0.00 0.00 0.00 3.32
86 87 2.028876 CTTTTTCTCCACCCCGTGTTT 58.971 47.619 0.00 0.00 0.00 2.83
87 88 2.146920 TTTTCTCCACCCCGTGTTTT 57.853 45.000 0.00 0.00 0.00 2.43
88 89 1.682740 TTTCTCCACCCCGTGTTTTC 58.317 50.000 0.00 0.00 0.00 2.29
89 90 0.547075 TTCTCCACCCCGTGTTTTCA 59.453 50.000 0.00 0.00 0.00 2.69
90 91 0.547075 TCTCCACCCCGTGTTTTCAA 59.453 50.000 0.00 0.00 0.00 2.69
91 92 0.666374 CTCCACCCCGTGTTTTCAAC 59.334 55.000 0.00 0.00 0.00 3.18
92 93 0.256464 TCCACCCCGTGTTTTCAACT 59.744 50.000 0.00 0.00 0.00 3.16
93 94 0.383949 CCACCCCGTGTTTTCAACTG 59.616 55.000 0.00 0.00 0.00 3.16
94 95 1.384525 CACCCCGTGTTTTCAACTGA 58.615 50.000 0.00 0.00 0.00 3.41
95 96 1.746220 CACCCCGTGTTTTCAACTGAA 59.254 47.619 0.00 0.00 0.00 3.02
96 97 2.021457 ACCCCGTGTTTTCAACTGAAG 58.979 47.619 0.00 0.00 35.21 3.02
97 98 1.336755 CCCCGTGTTTTCAACTGAAGG 59.663 52.381 0.00 0.00 35.21 3.46
98 99 2.021457 CCCGTGTTTTCAACTGAAGGT 58.979 47.619 0.00 0.00 35.21 3.50
99 100 2.032924 CCCGTGTTTTCAACTGAAGGTC 59.967 50.000 0.00 0.00 35.21 3.85
100 101 2.286184 CCGTGTTTTCAACTGAAGGTCG 60.286 50.000 0.00 0.00 35.21 4.79
101 102 2.286184 CGTGTTTTCAACTGAAGGTCGG 60.286 50.000 0.00 0.00 35.21 4.79
102 103 2.032924 GTGTTTTCAACTGAAGGTCGGG 59.967 50.000 0.00 0.00 35.21 5.14
103 104 1.001706 GTTTTCAACTGAAGGTCGGGC 60.002 52.381 0.00 0.00 35.21 6.13
104 105 0.536460 TTTCAACTGAAGGTCGGGCC 60.536 55.000 0.00 0.00 35.21 5.80
105 106 1.701031 TTCAACTGAAGGTCGGGCCA 61.701 55.000 4.39 0.00 40.61 5.36
106 107 1.966451 CAACTGAAGGTCGGGCCAC 60.966 63.158 4.39 0.37 40.61 5.01
107 108 2.147387 AACTGAAGGTCGGGCCACT 61.147 57.895 4.39 0.00 40.61 4.00
108 109 2.113243 AACTGAAGGTCGGGCCACTC 62.113 60.000 4.39 0.00 40.61 3.51
109 110 3.316573 CTGAAGGTCGGGCCACTCC 62.317 68.421 4.39 2.75 40.61 3.85
129 130 4.838486 GAGCGGAGTCGTGCGGAG 62.838 72.222 0.90 0.00 38.11 4.63
132 133 4.778415 CGGAGTCGTGCGGAGTGG 62.778 72.222 0.00 0.00 33.08 4.00
139 140 4.057428 GTGCGGAGTGGCGAGACT 62.057 66.667 0.00 0.00 35.06 3.24
140 141 3.749064 TGCGGAGTGGCGAGACTC 61.749 66.667 5.85 5.85 41.55 3.36
144 145 3.275088 GAGTGGCGAGACTCCGAA 58.725 61.111 0.00 0.00 37.05 4.30
145 146 1.153997 GAGTGGCGAGACTCCGAAC 60.154 63.158 0.00 0.00 37.05 3.95
146 147 1.863662 GAGTGGCGAGACTCCGAACA 61.864 60.000 0.00 0.00 37.05 3.18
147 148 1.215647 GTGGCGAGACTCCGAACAT 59.784 57.895 0.00 0.00 0.00 2.71
148 149 1.078759 GTGGCGAGACTCCGAACATG 61.079 60.000 0.00 0.00 0.00 3.21
149 150 2.167861 GGCGAGACTCCGAACATGC 61.168 63.158 0.00 0.00 0.00 4.06
150 151 2.167861 GCGAGACTCCGAACATGCC 61.168 63.158 0.00 0.00 0.00 4.40
151 152 1.519455 CGAGACTCCGAACATGCCC 60.519 63.158 0.00 0.00 0.00 5.36
152 153 1.153349 GAGACTCCGAACATGCCCC 60.153 63.158 0.00 0.00 0.00 5.80
166 167 0.968405 TGCCCCAAGTTTGCTCATTC 59.032 50.000 0.00 0.00 0.00 2.67
197 199 1.275291 TCCTCTGTCGTTGAACCCATC 59.725 52.381 0.00 0.00 0.00 3.51
225 227 9.563748 CCAATAGTAATTACCGGGAAAATTCTA 57.436 33.333 1.37 3.77 0.00 2.10
364 368 2.192175 CTACCCCATTGACCGCCC 59.808 66.667 0.00 0.00 0.00 6.13
925 937 1.167155 ATCAGTAGCCGATCGCGTCT 61.167 55.000 10.32 8.67 44.76 4.18
968 980 0.393537 CGCCCAATCCAGCTCTTCTT 60.394 55.000 0.00 0.00 0.00 2.52
1288 1300 2.563179 CACTCTCTTTTCCCTTCGAGGA 59.437 50.000 0.00 0.00 37.67 3.71
1290 1302 1.544691 TCTCTTTTCCCTTCGAGGACG 59.455 52.381 0.00 0.00 37.67 4.79
1299 1311 1.401199 CCTTCGAGGACGTACTCTTCC 59.599 57.143 24.96 3.18 37.67 3.46
1602 1620 4.394712 CCAACCGCCGGAGCTTCT 62.395 66.667 11.71 0.00 36.60 2.85
1620 1638 3.052082 GCTTCTGCTTCTGGCGCA 61.052 61.111 10.83 0.00 45.43 6.09
1644 1662 1.883084 CCGGAACATCGGTGCTAGC 60.883 63.158 8.10 8.10 44.60 3.42
1844 1862 8.945140 TCTCGCCGAGAAGGTAAAACATTTTAC 61.945 40.741 15.58 15.80 41.92 2.01
1865 1885 9.929180 TTTTACGGAGGATTATCTGATGATTAG 57.071 33.333 0.00 0.00 34.32 1.73
1895 1915 2.543777 TGCTCGCTCTACTTGGTTTT 57.456 45.000 0.00 0.00 0.00 2.43
1900 1920 4.630069 GCTCGCTCTACTTGGTTTTTGATA 59.370 41.667 0.00 0.00 0.00 2.15
2022 2042 6.118170 TGATGATTTCCAGTCTCTCCAATTC 58.882 40.000 0.00 0.00 0.00 2.17
2045 2068 5.355071 TCAGTGTTTCCATGATTCATACTGC 59.645 40.000 15.51 3.68 34.56 4.40
2046 2069 4.641989 AGTGTTTCCATGATTCATACTGCC 59.358 41.667 0.00 0.00 0.00 4.85
2047 2070 4.398988 GTGTTTCCATGATTCATACTGCCA 59.601 41.667 0.00 0.00 0.00 4.92
2071 2094 8.461222 CCAGTGAATTTGATGCTAATTTGAGTA 58.539 33.333 0.00 0.00 0.00 2.59
2104 2127 1.132721 AGGATATGGGCTACAGCTCCA 60.133 52.381 12.05 12.05 41.95 3.86
2208 2231 2.766970 TGTTTCTTTGCGTTGCTACC 57.233 45.000 0.00 0.00 0.00 3.18
2238 2269 3.060070 GCTGTGCTGCAAAAAGTTTGATC 60.060 43.478 2.77 0.00 0.00 2.92
2270 2301 2.281762 GCCGAGCTATAACAGTTGTTCG 59.718 50.000 0.00 0.00 39.31 3.95
2292 2323 1.448985 TGGTTCTTTGATAGGTGCGC 58.551 50.000 0.00 0.00 0.00 6.09
2385 2416 6.777580 AGATGGAACCATTGGTATGTTTATCC 59.222 38.462 9.20 10.83 36.70 2.59
2443 2474 2.549064 TTGTATGCTGTGAGCTGTGT 57.451 45.000 0.00 0.00 42.97 3.72
2444 2475 3.676291 TTGTATGCTGTGAGCTGTGTA 57.324 42.857 0.00 0.00 42.97 2.90
2445 2476 2.959516 TGTATGCTGTGAGCTGTGTAC 58.040 47.619 0.00 0.00 42.97 2.90
2446 2477 2.298729 TGTATGCTGTGAGCTGTGTACA 59.701 45.455 0.00 0.00 42.97 2.90
2447 2478 2.775911 ATGCTGTGAGCTGTGTACAT 57.224 45.000 0.00 0.00 42.97 2.29
2448 2479 2.549064 TGCTGTGAGCTGTGTACATT 57.451 45.000 0.00 0.00 42.97 2.71
2449 2480 3.676291 TGCTGTGAGCTGTGTACATTA 57.324 42.857 0.00 0.00 42.97 1.90
2451 2482 5.337578 TGCTGTGAGCTGTGTACATTATA 57.662 39.130 0.00 0.00 42.97 0.98
2452 2483 5.109210 TGCTGTGAGCTGTGTACATTATAC 58.891 41.667 0.00 0.00 42.97 1.47
2453 2484 5.105351 TGCTGTGAGCTGTGTACATTATACT 60.105 40.000 0.00 0.00 42.97 2.12
2454 2485 5.233050 GCTGTGAGCTGTGTACATTATACTG 59.767 44.000 0.00 0.45 38.45 2.74
2532 2567 6.043938 TGAATTCTGGGACCTGTAGTTAGTTT 59.956 38.462 7.05 0.00 0.00 2.66
2533 2568 7.236019 TGAATTCTGGGACCTGTAGTTAGTTTA 59.764 37.037 7.05 0.00 0.00 2.01
2535 2570 5.021458 TCTGGGACCTGTAGTTAGTTTAGG 58.979 45.833 0.00 0.00 34.70 2.69
2537 2572 3.453717 GGGACCTGTAGTTAGTTTAGGGG 59.546 52.174 0.00 0.00 32.81 4.79
2605 2647 8.624776 AGAAGAAATCTTTCTAACCAACTGTTG 58.375 33.333 13.50 13.50 46.22 3.33
2664 2706 1.442017 GCCACCGCGATGACAAAAC 60.442 57.895 8.23 0.00 0.00 2.43
2702 2744 8.308851 ACATGATCCCATTGAAATGTTTGATA 57.691 30.769 0.00 0.00 33.04 2.15
2810 2852 1.342819 AGAGAATATCTCACCCAGCGC 59.657 52.381 0.00 0.00 45.73 5.92
2874 2916 2.859165 TGTCAGCCTTTCCGATTTCT 57.141 45.000 0.00 0.00 0.00 2.52
2879 2921 0.375106 GCCTTTCCGATTTCTGCGAG 59.625 55.000 0.00 0.00 0.00 5.03
2885 2927 3.179443 TCCGATTTCTGCGAGCTAATT 57.821 42.857 0.00 0.00 0.00 1.40
2988 3030 0.981183 ACTGGTATGCTTCCGAACCA 59.019 50.000 0.00 0.00 39.66 3.67
2995 3037 2.391389 GCTTCCGAACCAAGCTCCG 61.391 63.158 0.00 0.00 42.63 4.63
3005 3047 1.073923 ACCAAGCTCCGTTTTCATCCT 59.926 47.619 0.00 0.00 0.00 3.24
3034 3079 2.103771 TCAGCTGCATAGAATCCAGGTC 59.896 50.000 9.47 0.00 35.36 3.85
3101 3146 4.407296 GTGAGGAACATACTTGGGAGATCT 59.593 45.833 0.00 0.00 0.00 2.75
3158 3203 3.881937 ACAAGATACTACCAACCCGAC 57.118 47.619 0.00 0.00 0.00 4.79
3250 3295 1.970917 GCCGATGTGCCGAGTTTCAG 61.971 60.000 0.00 0.00 0.00 3.02
3310 3355 2.823924 TGAATTCCTGTTCCGTTCGA 57.176 45.000 2.27 0.00 0.00 3.71
3430 3485 4.500375 GCTTCAGAGCTGGACAATTTTTGT 60.500 41.667 0.00 0.00 45.59 2.83
3431 3486 5.594926 CTTCAGAGCTGGACAATTTTTGTT 58.405 37.500 0.00 0.00 45.52 2.83
3432 3487 5.186996 TCAGAGCTGGACAATTTTTGTTC 57.813 39.130 0.00 0.00 45.52 3.18
3433 3488 4.889409 TCAGAGCTGGACAATTTTTGTTCT 59.111 37.500 0.00 0.00 45.52 3.01
3434 3489 4.980434 CAGAGCTGGACAATTTTTGTTCTG 59.020 41.667 0.00 3.30 45.52 3.02
3471 3526 0.179034 CTGGCTGGGAGATGTAAGGC 60.179 60.000 0.00 0.00 35.87 4.35
3723 3796 3.799366 TCCGAAGCTGACTGTTTGTTTA 58.201 40.909 0.00 0.00 0.00 2.01
3747 3820 4.142381 CCCTGCTATAGAAAAACCACAAGC 60.142 45.833 3.21 0.00 0.00 4.01
3779 3852 9.378551 GTAATGTCCACAATGACTAGAATACAA 57.621 33.333 0.00 0.00 36.21 2.41
3788 3861 8.450964 ACAATGACTAGAATACAAAAATGGTCG 58.549 33.333 0.00 0.00 0.00 4.79
3864 3937 5.305644 ACTCCAAGTGTAGTGAAGTCTGAAT 59.694 40.000 0.00 0.00 0.00 2.57
3962 4035 8.969267 AGAATTACATTCTCTTTTAGTATCGCG 58.031 33.333 0.00 0.00 46.17 5.87
4013 4086 7.703621 AGTTGCAAATATGATAACTTGTGATGC 59.296 33.333 0.00 0.00 34.09 3.91
4028 4101 1.737236 TGATGCTAACGTGTTCATGGC 59.263 47.619 0.00 0.00 0.00 4.40
4042 4115 6.038356 GTGTTCATGGCAGAAATAGAAATGG 58.962 40.000 0.00 0.00 0.00 3.16
4043 4116 4.924305 TCATGGCAGAAATAGAAATGGC 57.076 40.909 0.00 0.00 38.60 4.40
4047 4122 4.343231 TGGCAGAAATAGAAATGGCTTCA 58.657 39.130 0.00 0.00 38.88 3.02
4066 4141 8.359642 TGGCTTCATATATGCCTTGTTTTTATC 58.640 33.333 7.92 0.00 46.33 1.75
4093 4168 9.567776 TGAACAAATAAACTCTTGACATCCTAA 57.432 29.630 0.00 0.00 0.00 2.69
4102 4177 7.617041 ACTCTTGACATCCTAAAATGCTAAC 57.383 36.000 0.00 0.00 0.00 2.34
4105 4180 8.402798 TCTTGACATCCTAAAATGCTAACAAA 57.597 30.769 0.00 0.00 0.00 2.83
4106 4181 8.855110 TCTTGACATCCTAAAATGCTAACAAAA 58.145 29.630 0.00 0.00 0.00 2.44
4107 4182 9.474920 CTTGACATCCTAAAATGCTAACAAAAA 57.525 29.630 0.00 0.00 0.00 1.94
4162 4237 7.506328 AAATGTTGTTGTTTACTACTCCCTC 57.494 36.000 0.00 0.00 34.20 4.30
4163 4238 4.964593 TGTTGTTGTTTACTACTCCCTCC 58.035 43.478 0.00 0.00 34.20 4.30
4164 4239 3.947910 TGTTGTTTACTACTCCCTCCG 57.052 47.619 0.00 0.00 0.00 4.63
4165 4240 3.233507 TGTTGTTTACTACTCCCTCCGT 58.766 45.455 0.00 0.00 0.00 4.69
4166 4241 4.406456 TGTTGTTTACTACTCCCTCCGTA 58.594 43.478 0.00 0.00 0.00 4.02
4167 4242 4.832266 TGTTGTTTACTACTCCCTCCGTAA 59.168 41.667 0.00 0.00 0.00 3.18
4168 4243 5.304101 TGTTGTTTACTACTCCCTCCGTAAA 59.696 40.000 0.00 0.00 31.56 2.01
4169 4244 5.391312 TGTTTACTACTCCCTCCGTAAAC 57.609 43.478 13.83 13.83 45.76 2.01
4170 4245 5.391312 GTTTACTACTCCCTCCGTAAACA 57.609 43.478 15.14 0.00 45.29 2.83
4171 4246 5.783111 GTTTACTACTCCCTCCGTAAACAA 58.217 41.667 15.14 0.00 45.29 2.83
4172 4247 6.223120 GTTTACTACTCCCTCCGTAAACAAA 58.777 40.000 15.14 0.00 45.29 2.83
4173 4248 6.610075 TTACTACTCCCTCCGTAAACAAAT 57.390 37.500 0.00 0.00 0.00 2.32
4174 4249 7.716799 TTACTACTCCCTCCGTAAACAAATA 57.283 36.000 0.00 0.00 0.00 1.40
4175 4250 6.803366 ACTACTCCCTCCGTAAACAAATAT 57.197 37.500 0.00 0.00 0.00 1.28
4176 4251 7.902920 ACTACTCCCTCCGTAAACAAATATA 57.097 36.000 0.00 0.00 0.00 0.86
4177 4252 8.310122 ACTACTCCCTCCGTAAACAAATATAA 57.690 34.615 0.00 0.00 0.00 0.98
4178 4253 8.419442 ACTACTCCCTCCGTAAACAAATATAAG 58.581 37.037 0.00 0.00 0.00 1.73
4179 4254 7.427989 ACTCCCTCCGTAAACAAATATAAGA 57.572 36.000 0.00 0.00 0.00 2.10
4180 4255 7.498443 ACTCCCTCCGTAAACAAATATAAGAG 58.502 38.462 0.00 0.00 0.00 2.85
4181 4256 6.285990 TCCCTCCGTAAACAAATATAAGAGC 58.714 40.000 0.00 0.00 0.00 4.09
4182 4257 5.176958 CCCTCCGTAAACAAATATAAGAGCG 59.823 44.000 0.00 0.00 0.00 5.03
4183 4258 5.751990 CCTCCGTAAACAAATATAAGAGCGT 59.248 40.000 0.00 0.00 0.00 5.07
4184 4259 6.257193 CCTCCGTAAACAAATATAAGAGCGTT 59.743 38.462 0.00 0.00 0.00 4.84
4185 4260 7.201582 CCTCCGTAAACAAATATAAGAGCGTTT 60.202 37.037 0.00 0.00 0.00 3.60
4186 4261 8.700722 TCCGTAAACAAATATAAGAGCGTTTA 57.299 30.769 0.00 0.00 0.00 2.01
4187 4262 8.810427 TCCGTAAACAAATATAAGAGCGTTTAG 58.190 33.333 0.00 0.00 31.53 1.85
4188 4263 8.060090 CCGTAAACAAATATAAGAGCGTTTAGG 58.940 37.037 0.00 0.00 35.81 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.705325 GCCGAACAGATCTTTATTACTAACTGA 59.295 37.037 0.00 0.00 0.00 3.41
1 2 7.491372 TGCCGAACAGATCTTTATTACTAACTG 59.509 37.037 0.00 0.00 0.00 3.16
2 3 7.553334 TGCCGAACAGATCTTTATTACTAACT 58.447 34.615 0.00 0.00 0.00 2.24
3 4 7.766219 TGCCGAACAGATCTTTATTACTAAC 57.234 36.000 0.00 0.00 0.00 2.34
4 5 8.958119 ATTGCCGAACAGATCTTTATTACTAA 57.042 30.769 0.00 0.00 0.00 2.24
5 6 8.201464 TGATTGCCGAACAGATCTTTATTACTA 58.799 33.333 0.00 0.00 0.00 1.82
6 7 7.047891 TGATTGCCGAACAGATCTTTATTACT 58.952 34.615 0.00 0.00 0.00 2.24
7 8 7.246674 TGATTGCCGAACAGATCTTTATTAC 57.753 36.000 0.00 0.00 0.00 1.89
8 9 7.201696 GGTTGATTGCCGAACAGATCTTTATTA 60.202 37.037 0.00 0.00 0.00 0.98
9 10 6.404734 GGTTGATTGCCGAACAGATCTTTATT 60.405 38.462 0.00 0.00 0.00 1.40
10 11 5.066505 GGTTGATTGCCGAACAGATCTTTAT 59.933 40.000 0.00 0.00 0.00 1.40
11 12 4.394920 GGTTGATTGCCGAACAGATCTTTA 59.605 41.667 0.00 0.00 0.00 1.85
12 13 3.191371 GGTTGATTGCCGAACAGATCTTT 59.809 43.478 0.00 0.00 0.00 2.52
13 14 2.749621 GGTTGATTGCCGAACAGATCTT 59.250 45.455 0.00 0.00 0.00 2.40
14 15 2.359900 GGTTGATTGCCGAACAGATCT 58.640 47.619 0.00 0.00 0.00 2.75
15 16 2.832672 GGTTGATTGCCGAACAGATC 57.167 50.000 0.00 0.00 0.00 2.75
24 25 1.019278 TCTCGAAGCGGTTGATTGCC 61.019 55.000 3.70 0.00 0.00 4.52
25 26 0.796312 TTCTCGAAGCGGTTGATTGC 59.204 50.000 3.70 0.00 0.00 3.56
26 27 3.747099 ATTTCTCGAAGCGGTTGATTG 57.253 42.857 3.70 0.00 0.00 2.67
27 28 3.306166 CGTATTTCTCGAAGCGGTTGATT 59.694 43.478 3.70 0.00 0.00 2.57
28 29 2.858344 CGTATTTCTCGAAGCGGTTGAT 59.142 45.455 3.70 0.00 0.00 2.57
29 30 2.095110 TCGTATTTCTCGAAGCGGTTGA 60.095 45.455 3.70 1.85 34.36 3.18
30 31 2.256174 TCGTATTTCTCGAAGCGGTTG 58.744 47.619 3.70 0.00 34.36 3.77
31 32 2.163010 TCTCGTATTTCTCGAAGCGGTT 59.837 45.455 0.00 0.00 36.89 4.44
32 33 1.741706 TCTCGTATTTCTCGAAGCGGT 59.258 47.619 0.00 0.00 36.89 5.68
33 34 2.470196 TCTCGTATTTCTCGAAGCGG 57.530 50.000 0.00 0.00 36.89 5.52
34 35 4.145585 CAGATTCTCGTATTTCTCGAAGCG 59.854 45.833 0.00 0.00 36.89 4.68
35 36 5.038033 ACAGATTCTCGTATTTCTCGAAGC 58.962 41.667 0.00 0.00 36.89 3.86
36 37 6.258899 TCACAGATTCTCGTATTTCTCGAAG 58.741 40.000 0.00 0.00 36.89 3.79
37 38 6.190954 TCACAGATTCTCGTATTTCTCGAA 57.809 37.500 0.00 0.00 36.89 3.71
38 39 5.813080 TCACAGATTCTCGTATTTCTCGA 57.187 39.130 0.00 0.00 35.96 4.04
39 40 5.052040 GCTTCACAGATTCTCGTATTTCTCG 60.052 44.000 0.00 0.00 0.00 4.04
40 41 5.807520 TGCTTCACAGATTCTCGTATTTCTC 59.192 40.000 0.00 0.00 0.00 2.87
41 42 5.724328 TGCTTCACAGATTCTCGTATTTCT 58.276 37.500 0.00 0.00 0.00 2.52
42 43 6.478344 AGATGCTTCACAGATTCTCGTATTTC 59.522 38.462 2.07 0.00 0.00 2.17
43 44 6.344500 AGATGCTTCACAGATTCTCGTATTT 58.656 36.000 2.07 0.00 0.00 1.40
44 45 5.911752 AGATGCTTCACAGATTCTCGTATT 58.088 37.500 2.07 0.00 0.00 1.89
45 46 5.528043 AGATGCTTCACAGATTCTCGTAT 57.472 39.130 2.07 0.00 0.00 3.06
46 47 4.991153 AGATGCTTCACAGATTCTCGTA 57.009 40.909 2.07 0.00 0.00 3.43
47 48 3.883830 AGATGCTTCACAGATTCTCGT 57.116 42.857 2.07 0.00 0.00 4.18
48 49 5.542616 AAAAGATGCTTCACAGATTCTCG 57.457 39.130 2.07 0.00 0.00 4.04
49 50 7.143514 AGAAAAAGATGCTTCACAGATTCTC 57.856 36.000 2.07 0.00 0.00 2.87
50 51 6.150809 GGAGAAAAAGATGCTTCACAGATTCT 59.849 38.462 2.07 4.59 0.00 2.40
51 52 6.072286 TGGAGAAAAAGATGCTTCACAGATTC 60.072 38.462 2.07 0.28 0.00 2.52
52 53 5.771666 TGGAGAAAAAGATGCTTCACAGATT 59.228 36.000 2.07 0.00 0.00 2.40
53 54 5.182760 GTGGAGAAAAAGATGCTTCACAGAT 59.817 40.000 2.07 0.00 37.92 2.90
54 55 4.516698 GTGGAGAAAAAGATGCTTCACAGA 59.483 41.667 2.07 0.00 37.92 3.41
55 56 4.320788 GGTGGAGAAAAAGATGCTTCACAG 60.321 45.833 0.00 0.00 39.40 3.66
56 57 3.569701 GGTGGAGAAAAAGATGCTTCACA 59.430 43.478 0.00 0.00 39.40 3.58
57 58 3.057245 GGGTGGAGAAAAAGATGCTTCAC 60.057 47.826 2.07 0.00 37.41 3.18
58 59 3.157087 GGGTGGAGAAAAAGATGCTTCA 58.843 45.455 2.07 0.00 0.00 3.02
59 60 2.493675 GGGGTGGAGAAAAAGATGCTTC 59.506 50.000 0.00 0.00 0.00 3.86
60 61 2.529632 GGGGTGGAGAAAAAGATGCTT 58.470 47.619 0.00 0.00 0.00 3.91
61 62 1.614317 CGGGGTGGAGAAAAAGATGCT 60.614 52.381 0.00 0.00 0.00 3.79
62 63 0.811281 CGGGGTGGAGAAAAAGATGC 59.189 55.000 0.00 0.00 0.00 3.91
63 64 1.812571 CACGGGGTGGAGAAAAAGATG 59.187 52.381 0.00 0.00 0.00 2.90
64 65 1.423921 ACACGGGGTGGAGAAAAAGAT 59.576 47.619 0.42 0.00 37.94 2.40
65 66 0.841289 ACACGGGGTGGAGAAAAAGA 59.159 50.000 0.42 0.00 37.94 2.52
66 67 1.687563 AACACGGGGTGGAGAAAAAG 58.312 50.000 0.42 0.00 37.94 2.27
67 68 2.146920 AAACACGGGGTGGAGAAAAA 57.853 45.000 0.42 0.00 37.94 1.94
68 69 2.025898 GAAAACACGGGGTGGAGAAAA 58.974 47.619 0.42 0.00 37.94 2.29
69 70 1.064611 TGAAAACACGGGGTGGAGAAA 60.065 47.619 0.42 0.00 37.94 2.52
70 71 0.547075 TGAAAACACGGGGTGGAGAA 59.453 50.000 0.42 0.00 37.94 2.87
71 72 0.547075 TTGAAAACACGGGGTGGAGA 59.453 50.000 0.42 0.00 37.94 3.71
72 73 3.103637 TTGAAAACACGGGGTGGAG 57.896 52.632 0.42 0.00 37.94 3.86
83 84 4.214061 GGCCCGACCTTCAGTTGAAAAC 62.214 54.545 0.00 0.00 41.06 2.43
84 85 1.314730 GCCCGACCTTCAGTTGAAAA 58.685 50.000 0.00 0.00 33.07 2.29
85 86 0.536460 GGCCCGACCTTCAGTTGAAA 60.536 55.000 0.00 0.00 33.07 2.69
86 87 1.072505 GGCCCGACCTTCAGTTGAA 59.927 57.895 0.00 0.00 34.51 2.69
87 88 2.144078 TGGCCCGACCTTCAGTTGA 61.144 57.895 0.00 0.00 40.22 3.18
88 89 1.966451 GTGGCCCGACCTTCAGTTG 60.966 63.158 0.00 0.00 40.22 3.16
89 90 2.113243 GAGTGGCCCGACCTTCAGTT 62.113 60.000 0.00 0.00 40.22 3.16
90 91 2.526873 AGTGGCCCGACCTTCAGT 60.527 61.111 0.00 0.00 40.22 3.41
91 92 2.266055 GAGTGGCCCGACCTTCAG 59.734 66.667 0.00 0.00 40.22 3.02
92 93 3.319198 GGAGTGGCCCGACCTTCA 61.319 66.667 0.00 0.00 40.22 3.02
112 113 4.838486 CTCCGCACGACTCCGCTC 62.838 72.222 0.00 0.00 39.95 5.03
115 116 4.778415 CCACTCCGCACGACTCCG 62.778 72.222 0.00 0.00 42.50 4.63
122 123 3.973267 GAGTCTCGCCACTCCGCAC 62.973 68.421 2.91 0.00 37.43 5.34
123 124 3.749064 GAGTCTCGCCACTCCGCA 61.749 66.667 2.91 0.00 37.43 5.69
127 128 1.153997 GTTCGGAGTCTCGCCACTC 60.154 63.158 5.29 5.29 41.99 3.51
128 129 1.251527 ATGTTCGGAGTCTCGCCACT 61.252 55.000 0.00 0.00 0.00 4.00
129 130 1.078759 CATGTTCGGAGTCTCGCCAC 61.079 60.000 0.00 0.00 0.00 5.01
130 131 1.215382 CATGTTCGGAGTCTCGCCA 59.785 57.895 0.00 0.00 0.00 5.69
131 132 2.167861 GCATGTTCGGAGTCTCGCC 61.168 63.158 0.00 0.00 0.00 5.54
132 133 2.167861 GGCATGTTCGGAGTCTCGC 61.168 63.158 0.00 0.00 0.00 5.03
133 134 1.519455 GGGCATGTTCGGAGTCTCG 60.519 63.158 0.00 0.00 0.00 4.04
134 135 1.153349 GGGGCATGTTCGGAGTCTC 60.153 63.158 0.00 0.00 0.00 3.36
135 136 1.488705 TTGGGGCATGTTCGGAGTCT 61.489 55.000 0.00 0.00 0.00 3.24
136 137 1.002624 TTGGGGCATGTTCGGAGTC 60.003 57.895 0.00 0.00 0.00 3.36
137 138 1.002134 CTTGGGGCATGTTCGGAGT 60.002 57.895 0.00 0.00 0.00 3.85
138 139 0.609131 AACTTGGGGCATGTTCGGAG 60.609 55.000 0.00 0.00 27.86 4.63
139 140 0.178975 AAACTTGGGGCATGTTCGGA 60.179 50.000 0.00 0.00 31.99 4.55
140 141 0.038343 CAAACTTGGGGCATGTTCGG 60.038 55.000 0.00 0.00 31.99 4.30
141 142 0.667184 GCAAACTTGGGGCATGTTCG 60.667 55.000 0.00 0.00 31.99 3.95
142 143 0.681175 AGCAAACTTGGGGCATGTTC 59.319 50.000 0.00 0.00 31.99 3.18
143 144 0.681175 GAGCAAACTTGGGGCATGTT 59.319 50.000 0.00 0.00 34.07 2.71
144 145 0.469705 TGAGCAAACTTGGGGCATGT 60.470 50.000 0.00 0.00 0.00 3.21
145 146 0.899720 ATGAGCAAACTTGGGGCATG 59.100 50.000 0.00 0.00 0.00 4.06
146 147 1.551883 GAATGAGCAAACTTGGGGCAT 59.448 47.619 0.00 0.00 0.00 4.40
147 148 0.968405 GAATGAGCAAACTTGGGGCA 59.032 50.000 0.00 0.00 0.00 5.36
148 149 0.247460 GGAATGAGCAAACTTGGGGC 59.753 55.000 0.00 0.00 0.00 5.80
149 150 1.821136 GAGGAATGAGCAAACTTGGGG 59.179 52.381 0.00 0.00 0.00 4.96
150 151 2.229784 GTGAGGAATGAGCAAACTTGGG 59.770 50.000 0.00 0.00 0.00 4.12
151 152 3.152341 AGTGAGGAATGAGCAAACTTGG 58.848 45.455 0.00 0.00 0.00 3.61
152 153 4.070716 AGAGTGAGGAATGAGCAAACTTG 58.929 43.478 0.00 0.00 0.00 3.16
166 167 2.297597 ACGACAGAGGAAAAGAGTGAGG 59.702 50.000 0.00 0.00 0.00 3.86
197 199 8.459911 AATTTTCCCGGTAATTACTATTGGAG 57.540 34.615 15.05 7.04 0.00 3.86
309 313 4.404098 GGGGAGGGAAAGCGCGAA 62.404 66.667 12.10 0.00 0.00 4.70
364 368 4.452733 GAGGGCGAGGTCAACGGG 62.453 72.222 0.00 0.00 0.00 5.28
891 903 1.134401 ACTGATTGCAGACCATACCGG 60.134 52.381 0.00 0.00 45.17 5.28
968 980 1.180029 GAGGAGCCGTAGTGTTACCA 58.820 55.000 0.00 0.00 0.00 3.25
1116 1128 3.801997 CAGAAGGGGCGCCAGGAT 61.802 66.667 30.85 11.24 0.00 3.24
1119 1131 4.809496 ATGCAGAAGGGGCGCCAG 62.809 66.667 30.85 11.19 0.00 4.85
1288 1300 0.896226 GGCTTGGAGGAAGAGTACGT 59.104 55.000 0.00 0.00 32.82 3.57
1290 1302 0.460459 GCGGCTTGGAGGAAGAGTAC 60.460 60.000 0.00 0.00 32.82 2.73
1323 1341 3.484806 ACCGACAGCAACCCCACA 61.485 61.111 0.00 0.00 0.00 4.17
1518 1536 2.760385 GTGGGAGGAGGGGACGAG 60.760 72.222 0.00 0.00 0.00 4.18
1602 1620 3.052082 GCGCCAGAAGCAGAAGCA 61.052 61.111 0.00 0.00 45.49 3.91
1620 1638 3.918544 CCGATGTTCCGGGCAATT 58.081 55.556 0.00 0.00 45.43 2.32
1644 1662 2.758089 GCTCCTGCTCATTGTGGCG 61.758 63.158 0.00 0.00 36.03 5.69
1809 1827 1.008767 CTCGGCGAGAATACGGTCC 60.009 63.158 32.07 0.00 0.00 4.46
1815 1833 4.082081 TGTTTTACCTTCTCGGCGAGAATA 60.082 41.667 41.87 31.77 45.84 1.75
1844 1862 7.875041 ACAAACTAATCATCAGATAATCCTCCG 59.125 37.037 0.00 0.00 33.08 4.63
1865 1885 3.273919 AGAGCGAGCAAAATGACAAAC 57.726 42.857 0.00 0.00 0.00 2.93
1900 1920 8.469200 CCTGTGGATCACATTATTACAACAAAT 58.531 33.333 0.98 0.00 43.71 2.32
1921 1941 2.672874 CGGAACACATATGACACCTGTG 59.327 50.000 10.38 14.59 44.51 3.66
1922 1942 2.354704 CCGGAACACATATGACACCTGT 60.355 50.000 10.38 0.00 0.00 4.00
1923 1943 2.279741 CCGGAACACATATGACACCTG 58.720 52.381 10.38 0.00 0.00 4.00
1949 1969 6.405176 GGAAGATCACAATGTCCAAGATTTCC 60.405 42.308 0.00 0.00 0.00 3.13
2022 2042 5.449588 GGCAGTATGAATCATGGAAACACTG 60.450 44.000 14.10 14.10 41.77 3.66
2045 2068 7.318141 ACTCAAATTAGCATCAAATTCACTGG 58.682 34.615 0.00 0.00 0.00 4.00
2046 2069 9.282247 GTACTCAAATTAGCATCAAATTCACTG 57.718 33.333 0.00 0.00 0.00 3.66
2047 2070 9.013229 TGTACTCAAATTAGCATCAAATTCACT 57.987 29.630 0.00 0.00 0.00 3.41
2071 2094 4.410099 CCCATATCCTGCCATAACATTGT 58.590 43.478 0.00 0.00 0.00 2.71
2104 2127 3.328931 ACCCTCTTGATGAACACATCACT 59.671 43.478 11.60 0.00 46.37 3.41
2270 2301 2.159517 CGCACCTATCAAAGAACCAAGC 60.160 50.000 0.00 0.00 0.00 4.01
2292 2323 2.093306 TGACCAGTAACTTGCCATCG 57.907 50.000 0.00 0.00 0.00 3.84
2385 2416 5.730550 AGACACTAGAGACTAGACACAGAG 58.269 45.833 11.94 0.00 0.00 3.35
2451 2482 7.831193 AGCCTAAATGTTCAAAGATCATACAGT 59.169 33.333 0.00 0.00 0.00 3.55
2452 2483 8.218338 AGCCTAAATGTTCAAAGATCATACAG 57.782 34.615 0.00 0.00 0.00 2.74
2453 2484 8.579850 AAGCCTAAATGTTCAAAGATCATACA 57.420 30.769 0.00 0.00 0.00 2.29
2454 2485 9.860898 AAAAGCCTAAATGTTCAAAGATCATAC 57.139 29.630 0.00 0.00 0.00 2.39
2482 2517 1.454572 ATTCAGCACAGCAACCGCAA 61.455 50.000 0.00 0.00 42.27 4.85
2533 2568 8.945193 TCTTACTTGCATTAGTAAATATCCCCT 58.055 33.333 11.21 0.00 39.43 4.79
2879 2921 4.501921 GCAAGAATAACAGCAGCAATTAGC 59.498 41.667 0.00 0.00 46.19 3.09
2988 3030 4.816925 GCTTATAGGATGAAAACGGAGCTT 59.183 41.667 0.00 0.00 0.00 3.74
3019 3061 5.619220 AGAAATCAGACCTGGATTCTATGC 58.381 41.667 0.00 0.00 35.62 3.14
3034 3079 7.591165 ACATCACAGATCACAAAAGAAATCAG 58.409 34.615 0.00 0.00 0.00 2.90
3101 3146 2.141448 TGGCCAGTACCGGAACACA 61.141 57.895 9.46 0.00 0.00 3.72
3164 3209 2.043248 ATCCCCACCGCGTAGAGT 60.043 61.111 4.92 0.00 0.00 3.24
3238 3283 1.048601 AAGAGGACTGAAACTCGGCA 58.951 50.000 0.00 0.00 38.72 5.69
3241 3286 4.119862 TGAAACAAGAGGACTGAAACTCG 58.880 43.478 0.00 0.00 38.72 4.18
3245 3290 6.356556 TCTCAATGAAACAAGAGGACTGAAA 58.643 36.000 0.00 0.00 0.00 2.69
3250 3295 6.038714 ACAAACTCTCAATGAAACAAGAGGAC 59.961 38.462 3.55 0.00 39.64 3.85
3592 3665 4.942761 ATCACAATGCCAACTCAGTTTT 57.057 36.364 0.00 0.00 0.00 2.43
3723 3796 4.650972 TGTGGTTTTTCTATAGCAGGGT 57.349 40.909 0.00 0.00 0.00 4.34
3768 3841 8.964476 ATGATCGACCATTTTTGTATTCTAGT 57.036 30.769 0.00 0.00 0.00 2.57
3779 3852 6.266168 TGCAAGTTTATGATCGACCATTTT 57.734 33.333 0.00 0.00 0.00 1.82
3833 3906 7.736893 ACTTCACTACACTTGGAGTAAGATTT 58.263 34.615 13.43 0.00 39.76 2.17
3840 3913 4.215908 TCAGACTTCACTACACTTGGAGT 58.784 43.478 0.00 0.00 35.34 3.85
3864 3937 3.230743 TCGCTCGTGATTCAGATGAAA 57.769 42.857 0.00 0.00 37.61 2.69
3939 4012 7.919091 TCACGCGATACTAAAAGAGAATGTAAT 59.081 33.333 15.93 0.00 0.00 1.89
3944 4017 5.892568 ACTCACGCGATACTAAAAGAGAAT 58.107 37.500 15.93 0.00 0.00 2.40
4013 4086 4.685169 ATTTCTGCCATGAACACGTTAG 57.315 40.909 0.00 0.00 0.00 2.34
4028 4101 9.784680 GCATATATGAAGCCATTTCTATTTCTG 57.215 33.333 17.10 0.00 36.71 3.02
4042 4115 9.403110 CAGATAAAAACAAGGCATATATGAAGC 57.597 33.333 17.10 0.79 0.00 3.86
4066 4141 8.103948 AGGATGTCAAGAGTTTATTTGTTCAG 57.896 34.615 0.00 0.00 0.00 3.02
4074 4149 8.814038 AGCATTTTAGGATGTCAAGAGTTTAT 57.186 30.769 0.00 0.00 0.00 1.40
4075 4150 9.733556 TTAGCATTTTAGGATGTCAAGAGTTTA 57.266 29.630 0.00 0.00 0.00 2.01
4108 4183 9.787532 CAAATAACATCATTCAACGGTAGATTT 57.212 29.630 0.00 0.00 0.00 2.17
4109 4184 9.173021 TCAAATAACATCATTCAACGGTAGATT 57.827 29.630 0.00 0.00 0.00 2.40
4110 4185 8.731275 TCAAATAACATCATTCAACGGTAGAT 57.269 30.769 0.00 0.00 0.00 1.98
4162 4237 8.060090 CCTAAACGCTCTTATATTTGTTTACGG 58.940 37.037 0.00 0.00 32.41 4.02
4163 4238 8.967445 CCTAAACGCTCTTATATTTGTTTACG 57.033 34.615 0.00 0.00 32.41 3.18


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

AutoCloner maintained by Alex Coulton.