Multiple sequence alignment - TraesCS7D01G312100

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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 TraesCS7D01G312100 chr7D 100.000 4934 0 0 1 4934 395601550 395606483 0.000000e+00 9112.0
1 TraesCS7D01G312100 chr7A 94.302 2387 87 24 2178 4526 448728605 448730980 0.000000e+00 3609.0
2 TraesCS7D01G312100 chr7A 93.064 2004 74 28 217 2178 448726585 448728565 0.000000e+00 2870.0
3 TraesCS7D01G312100 chr7A 92.614 352 20 4 4588 4934 448731694 448732044 7.370000e-138 501.0
4 TraesCS7D01G312100 chr7B 93.149 1810 64 21 1642 3413 395244438 395246225 0.000000e+00 2601.0
5 TraesCS7D01G312100 chr7B 93.805 1259 37 17 400 1646 395243053 395244282 0.000000e+00 1855.0
6 TraesCS7D01G312100 chr7B 92.497 933 54 10 3412 4343 395246349 395247266 0.000000e+00 1321.0
7 TraesCS7D01G312100 chr7B 93.220 236 14 1 4699 4934 395260307 395260540 3.660000e-91 346.0
8 TraesCS7D01G312100 chr7B 94.054 185 9 2 159 341 395242646 395242830 3.760000e-71 279.0
9 TraesCS7D01G312100 chr2D 80.864 162 22 5 4529 4682 478122227 478122387 8.680000e-23 119.0
10 TraesCS7D01G312100 chr2B 93.590 78 4 1 4527 4604 53413370 53413294 1.120000e-21 115.0
11 TraesCS7D01G312100 chr2B 82.500 80 13 1 4527 4606 94204035 94203957 8.860000e-08 69.4
12 TraesCS7D01G312100 chr5A 79.503 161 27 4 4527 4682 698194819 698194660 5.220000e-20 110.0
13 TraesCS7D01G312100 chr5A 93.023 43 3 0 4482 4524 428970744 428970702 4.120000e-06 63.9
14 TraesCS7D01G312100 chr4B 81.651 109 14 3 4531 4633 168565477 168565585 8.800000e-13 86.1
15 TraesCS7D01G312100 chr4B 89.552 67 5 1 4527 4593 645894720 645894784 3.160000e-12 84.2
16 TraesCS7D01G312100 chr4B 88.710 62 7 0 4462 4523 119272761 119272822 5.300000e-10 76.8
17 TraesCS7D01G312100 chr5D 83.158 95 12 3 4431 4524 9593587 9593496 3.160000e-12 84.2
18 TraesCS7D01G312100 chr6D 86.667 75 9 1 4533 4607 380804892 380804819 1.140000e-11 82.4
19 TraesCS7D01G312100 chr1B 86.486 74 8 2 4532 4605 469061655 469061584 4.090000e-11 80.5
20 TraesCS7D01G312100 chr1B 91.111 45 4 0 4480 4524 221562356 221562400 1.480000e-05 62.1
21 TraesCS7D01G312100 chr3D 82.292 96 9 5 4431 4524 45408457 45408368 5.300000e-10 76.8
22 TraesCS7D01G312100 chr6B 83.784 74 12 0 4531 4604 666901147 666901074 2.460000e-08 71.3
23 TraesCS7D01G312100 chr6B 91.111 45 4 0 4480 4524 11192637 11192681 1.480000e-05 62.1
24 TraesCS7D01G312100 chr2A 97.561 41 1 0 1276 1316 699511902 699511942 2.460000e-08 71.3


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 TraesCS7D01G312100 chr7D 395601550 395606483 4933 False 9112.000000 9112 100.000000 1 4934 1 chr7D.!!$F1 4933
1 TraesCS7D01G312100 chr7A 448726585 448732044 5459 False 2326.666667 3609 93.326667 217 4934 3 chr7A.!!$F1 4717
2 TraesCS7D01G312100 chr7B 395242646 395247266 4620 False 1514.000000 2601 93.376250 159 4343 4 chr7B.!!$F2 4184

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
153 154 0.322975 TCAACCCAGAAGAGCAGCTC 59.677 55.0 15.25 15.25 0.00 4.09 F
154 155 0.324285 CAACCCAGAAGAGCAGCTCT 59.676 55.0 20.04 20.04 43.37 4.09 F
898 1093 0.616891 GCGGGTTTTAAGGAGGGAGA 59.383 55.0 0.00 0.00 0.00 3.71 F
2110 2501 0.969917 AGTCATCGCTGTCTCTGCCT 60.970 55.0 0.00 0.00 0.00 4.75 F
2630 3075 0.392327 CTCACACCACCACACACACA 60.392 55.0 0.00 0.00 0.00 3.72 F
3747 4342 0.108233 CTCCTGCTGTTCAGCTCTCC 60.108 60.0 22.44 0.00 41.50 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 2237 1.064654 GCTTCGAATCTTGCATGACCC 59.935 52.381 4.14 0.0 0.00 4.46 R
2110 2501 2.050533 GTTGCGCGTTGCCATCAA 60.051 55.556 8.43 0.0 45.60 2.57 R
2158 2549 0.106149 ACTCACAAACCGGGTCTGTC 59.894 55.000 2.41 0.0 0.00 3.51 R
3378 3828 0.815734 GAACAGGACTAGCCGCTACA 59.184 55.000 0.00 0.0 43.43 2.74 R
3828 4423 1.591703 CCAGTTCTGGTCTGCGCTA 59.408 57.895 9.73 0.0 0.00 4.26 R
4891 6143 0.321564 CATGCACGGGAGGAAGTTCA 60.322 55.000 5.01 0.0 0.00 3.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.128138 ACAAATTAGGGGCATATACTCTCC 57.872 41.667 0.00 0.00 0.00 3.71
26 27 5.610982 ACAAATTAGGGGCATATACTCTCCA 59.389 40.000 0.00 0.00 0.00 3.86
27 28 6.275618 ACAAATTAGGGGCATATACTCTCCAT 59.724 38.462 0.00 0.00 0.00 3.41
28 29 6.567602 AATTAGGGGCATATACTCTCCATC 57.432 41.667 0.00 0.00 0.00 3.51
29 30 3.567375 AGGGGCATATACTCTCCATCA 57.433 47.619 0.00 0.00 0.00 3.07
30 31 3.177228 AGGGGCATATACTCTCCATCAC 58.823 50.000 0.00 0.00 0.00 3.06
31 32 2.906389 GGGGCATATACTCTCCATCACA 59.094 50.000 0.00 0.00 0.00 3.58
32 33 3.521126 GGGGCATATACTCTCCATCACAT 59.479 47.826 0.00 0.00 0.00 3.21
33 34 4.018960 GGGGCATATACTCTCCATCACATT 60.019 45.833 0.00 0.00 0.00 2.71
34 35 5.189736 GGGGCATATACTCTCCATCACATTA 59.810 44.000 0.00 0.00 0.00 1.90
35 36 6.126652 GGGGCATATACTCTCCATCACATTAT 60.127 42.308 0.00 0.00 0.00 1.28
36 37 6.765036 GGGCATATACTCTCCATCACATTATG 59.235 42.308 0.00 0.00 0.00 1.90
37 38 7.334090 GGCATATACTCTCCATCACATTATGT 58.666 38.462 0.00 0.00 0.00 2.29
38 39 8.478066 GGCATATACTCTCCATCACATTATGTA 58.522 37.037 0.00 0.00 0.00 2.29
39 40 9.526713 GCATATACTCTCCATCACATTATGTAG 57.473 37.037 0.00 0.00 0.00 2.74
40 41 9.526713 CATATACTCTCCATCACATTATGTAGC 57.473 37.037 0.00 0.00 0.00 3.58
41 42 7.789202 ATACTCTCCATCACATTATGTAGCT 57.211 36.000 0.00 0.00 0.00 3.32
42 43 5.851720 ACTCTCCATCACATTATGTAGCTG 58.148 41.667 0.00 0.00 0.00 4.24
43 44 5.600069 ACTCTCCATCACATTATGTAGCTGA 59.400 40.000 0.00 0.00 0.00 4.26
44 45 6.098838 ACTCTCCATCACATTATGTAGCTGAA 59.901 38.462 0.00 0.00 0.00 3.02
45 46 6.888105 TCTCCATCACATTATGTAGCTGAAA 58.112 36.000 0.00 0.00 0.00 2.69
46 47 7.337938 TCTCCATCACATTATGTAGCTGAAAA 58.662 34.615 0.00 0.00 0.00 2.29
47 48 7.828717 TCTCCATCACATTATGTAGCTGAAAAA 59.171 33.333 0.00 0.00 0.00 1.94
48 49 8.523915 TCCATCACATTATGTAGCTGAAAAAT 57.476 30.769 0.00 0.00 0.00 1.82
49 50 8.970020 TCCATCACATTATGTAGCTGAAAAATT 58.030 29.630 0.00 0.00 0.00 1.82
50 51 9.590451 CCATCACATTATGTAGCTGAAAAATTT 57.410 29.630 0.00 0.00 0.00 1.82
52 53 9.807649 ATCACATTATGTAGCTGAAAAATTTCC 57.192 29.630 0.00 0.00 36.36 3.13
53 54 8.801299 TCACATTATGTAGCTGAAAAATTTCCA 58.199 29.630 0.00 0.00 36.36 3.53
54 55 9.079833 CACATTATGTAGCTGAAAAATTTCCAG 57.920 33.333 13.29 13.29 36.36 3.86
55 56 9.023962 ACATTATGTAGCTGAAAAATTTCCAGA 57.976 29.630 18.98 4.35 36.36 3.86
56 57 9.859427 CATTATGTAGCTGAAAAATTTCCAGAA 57.141 29.630 18.98 7.96 36.36 3.02
60 61 8.647143 TGTAGCTGAAAAATTTCCAGAAAAAG 57.353 30.769 18.98 0.00 36.36 2.27
61 62 8.474025 TGTAGCTGAAAAATTTCCAGAAAAAGA 58.526 29.630 18.98 3.06 36.36 2.52
62 63 9.313118 GTAGCTGAAAAATTTCCAGAAAAAGAA 57.687 29.630 18.98 0.00 36.36 2.52
63 64 8.969260 AGCTGAAAAATTTCCAGAAAAAGAAT 57.031 26.923 18.98 0.00 36.36 2.40
64 65 9.399797 AGCTGAAAAATTTCCAGAAAAAGAATT 57.600 25.926 18.98 0.00 36.36 2.17
74 75 9.520515 TTTCCAGAAAAAGAATTATGTAGCTCT 57.479 29.630 0.00 0.00 0.00 4.09
75 76 8.723942 TCCAGAAAAAGAATTATGTAGCTCTC 57.276 34.615 0.00 0.00 0.00 3.20
76 77 8.543774 TCCAGAAAAAGAATTATGTAGCTCTCT 58.456 33.333 0.00 0.00 0.00 3.10
77 78 8.610896 CCAGAAAAAGAATTATGTAGCTCTCTG 58.389 37.037 0.00 0.00 0.00 3.35
78 79 8.610896 CAGAAAAAGAATTATGTAGCTCTCTGG 58.389 37.037 0.00 0.00 0.00 3.86
79 80 8.325046 AGAAAAAGAATTATGTAGCTCTCTGGT 58.675 33.333 0.00 0.00 0.00 4.00
80 81 8.870075 AAAAAGAATTATGTAGCTCTCTGGTT 57.130 30.769 0.00 0.00 0.00 3.67
81 82 7.856145 AAAGAATTATGTAGCTCTCTGGTTG 57.144 36.000 0.00 0.00 0.00 3.77
82 83 6.552445 AGAATTATGTAGCTCTCTGGTTGT 57.448 37.500 0.00 0.00 0.00 3.32
83 84 6.951971 AGAATTATGTAGCTCTCTGGTTGTT 58.048 36.000 0.00 0.00 0.00 2.83
84 85 7.044798 AGAATTATGTAGCTCTCTGGTTGTTC 58.955 38.462 0.00 0.00 0.00 3.18
85 86 6.552445 ATTATGTAGCTCTCTGGTTGTTCT 57.448 37.500 0.00 0.00 0.00 3.01
86 87 7.661536 ATTATGTAGCTCTCTGGTTGTTCTA 57.338 36.000 0.00 0.00 0.00 2.10
87 88 7.661536 TTATGTAGCTCTCTGGTTGTTCTAT 57.338 36.000 0.00 0.00 0.00 1.98
88 89 8.762481 TTATGTAGCTCTCTGGTTGTTCTATA 57.238 34.615 0.00 0.00 0.00 1.31
89 90 6.452494 TGTAGCTCTCTGGTTGTTCTATAC 57.548 41.667 0.00 0.00 0.00 1.47
90 91 5.949952 TGTAGCTCTCTGGTTGTTCTATACA 59.050 40.000 0.00 0.00 34.12 2.29
91 92 5.590530 AGCTCTCTGGTTGTTCTATACAG 57.409 43.478 0.00 0.00 38.19 2.74
92 93 5.020132 AGCTCTCTGGTTGTTCTATACAGT 58.980 41.667 0.00 0.00 38.19 3.55
93 94 5.482175 AGCTCTCTGGTTGTTCTATACAGTT 59.518 40.000 0.00 0.00 38.19 3.16
94 95 6.014156 AGCTCTCTGGTTGTTCTATACAGTTT 60.014 38.462 0.00 0.00 38.19 2.66
95 96 6.311690 GCTCTCTGGTTGTTCTATACAGTTTC 59.688 42.308 0.00 0.00 38.19 2.78
96 97 7.540474 TCTCTGGTTGTTCTATACAGTTTCT 57.460 36.000 0.00 0.00 38.19 2.52
97 98 7.963532 TCTCTGGTTGTTCTATACAGTTTCTT 58.036 34.615 0.00 0.00 38.19 2.52
98 99 8.429641 TCTCTGGTTGTTCTATACAGTTTCTTT 58.570 33.333 0.00 0.00 38.19 2.52
99 100 8.974060 TCTGGTTGTTCTATACAGTTTCTTTT 57.026 30.769 0.00 0.00 38.19 2.27
103 104 9.556030 GGTTGTTCTATACAGTTTCTTTTATGC 57.444 33.333 0.00 0.00 38.19 3.14
127 128 9.781425 TGCATATATATAAATTTTGGATGGGGT 57.219 29.630 0.00 0.00 0.00 4.95
132 133 7.839680 ATATAAATTTTGGATGGGGTCAGAC 57.160 36.000 0.00 0.00 0.00 3.51
133 134 3.833559 AATTTTGGATGGGGTCAGACT 57.166 42.857 0.00 0.00 0.00 3.24
134 135 3.833559 ATTTTGGATGGGGTCAGACTT 57.166 42.857 0.00 0.00 0.00 3.01
135 136 2.879103 TTTGGATGGGGTCAGACTTC 57.121 50.000 0.00 0.00 0.00 3.01
136 137 1.741028 TTGGATGGGGTCAGACTTCA 58.259 50.000 0.00 0.00 0.00 3.02
137 138 1.741028 TGGATGGGGTCAGACTTCAA 58.259 50.000 0.00 0.00 0.00 2.69
138 139 1.351017 TGGATGGGGTCAGACTTCAAC 59.649 52.381 0.00 0.00 0.00 3.18
139 140 1.340114 GGATGGGGTCAGACTTCAACC 60.340 57.143 0.00 4.20 0.00 3.77
144 145 2.930826 GGTCAGACTTCAACCCAGAA 57.069 50.000 0.00 0.00 0.00 3.02
146 147 2.368875 GGTCAGACTTCAACCCAGAAGA 59.631 50.000 10.37 0.00 46.18 2.87
147 148 3.556004 GGTCAGACTTCAACCCAGAAGAG 60.556 52.174 10.37 1.29 46.18 2.85
148 149 2.037772 TCAGACTTCAACCCAGAAGAGC 59.962 50.000 10.37 2.85 46.18 4.09
149 150 2.050144 AGACTTCAACCCAGAAGAGCA 58.950 47.619 10.37 0.00 46.18 4.26
150 151 2.038295 AGACTTCAACCCAGAAGAGCAG 59.962 50.000 10.37 0.00 46.18 4.24
151 152 1.163554 CTTCAACCCAGAAGAGCAGC 58.836 55.000 0.00 0.00 46.18 5.25
152 153 0.767375 TTCAACCCAGAAGAGCAGCT 59.233 50.000 0.00 0.00 0.00 4.24
153 154 0.322975 TCAACCCAGAAGAGCAGCTC 59.677 55.000 15.25 15.25 0.00 4.09
154 155 0.324285 CAACCCAGAAGAGCAGCTCT 59.676 55.000 20.04 20.04 43.37 4.09
155 156 1.552337 CAACCCAGAAGAGCAGCTCTA 59.448 52.381 25.66 0.00 40.28 2.43
156 157 1.484038 ACCCAGAAGAGCAGCTCTAG 58.516 55.000 25.66 17.11 40.28 2.43
157 158 1.006519 ACCCAGAAGAGCAGCTCTAGA 59.993 52.381 25.66 0.00 40.28 2.43
158 159 2.106566 CCCAGAAGAGCAGCTCTAGAA 58.893 52.381 25.66 0.00 40.28 2.10
159 160 2.699846 CCCAGAAGAGCAGCTCTAGAAT 59.300 50.000 25.66 9.86 40.28 2.40
160 161 3.134442 CCCAGAAGAGCAGCTCTAGAATT 59.866 47.826 25.66 9.44 40.28 2.17
161 162 4.383989 CCCAGAAGAGCAGCTCTAGAATTT 60.384 45.833 25.66 8.64 40.28 1.82
162 163 4.810491 CCAGAAGAGCAGCTCTAGAATTTC 59.190 45.833 25.66 17.15 40.28 2.17
163 164 4.810491 CAGAAGAGCAGCTCTAGAATTTCC 59.190 45.833 25.66 7.44 40.28 3.13
172 173 6.094603 GCAGCTCTAGAATTTCCTTCATTTCA 59.905 38.462 0.00 0.00 36.24 2.69
182 183 9.136952 GAATTTCCTTCATTTCATTTCAGACAG 57.863 33.333 0.00 0.00 33.78 3.51
203 204 2.480845 GACTAGCCGTTGAAACACACT 58.519 47.619 0.00 0.00 0.00 3.55
210 211 3.719924 CCGTTGAAACACACTACCAGTA 58.280 45.455 0.00 0.00 0.00 2.74
240 241 1.116536 TGCTTCCACACGGACCAGTA 61.117 55.000 0.00 0.00 42.67 2.74
282 283 1.133294 TCCACTGTACAGTCTGTCCCA 60.133 52.381 25.63 6.91 40.20 4.37
348 349 3.889692 CCAGCCCACACCCACAGT 61.890 66.667 0.00 0.00 0.00 3.55
433 599 3.211045 TCAAGCCCAGTAATTTATCCGC 58.789 45.455 0.00 0.00 0.00 5.54
660 837 2.612251 CTCTCCTCTCCCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
729 907 2.988688 TTTTGCATTCCGGCCTCGC 61.989 57.895 0.00 0.00 34.56 5.03
730 908 3.918253 TTTGCATTCCGGCCTCGCT 62.918 57.895 0.00 0.00 34.56 4.93
731 909 4.838152 TGCATTCCGGCCTCGCTC 62.838 66.667 0.00 0.00 34.56 5.03
789 982 1.226128 GCTGCGGATTCTCGTTTGC 60.226 57.895 0.00 0.00 0.00 3.68
790 983 1.059369 CTGCGGATTCTCGTTTGCG 59.941 57.895 0.00 0.00 39.92 4.85
794 987 1.662026 GCGGATTCTCGTTTGCGTTTT 60.662 47.619 0.00 0.00 39.49 2.43
831 1026 6.733145 TGTGGATTTTTGCTTTATTTTTGCC 58.267 32.000 0.00 0.00 0.00 4.52
898 1093 0.616891 GCGGGTTTTAAGGAGGGAGA 59.383 55.000 0.00 0.00 0.00 3.71
1035 1230 2.411504 GGAAGCGAGCTCTCCGACT 61.412 63.158 12.85 0.00 0.00 4.18
1282 1477 1.064825 GGTCAAGGTGGGGAAGAAGA 58.935 55.000 0.00 0.00 0.00 2.87
1603 1801 9.578439 AAAATGTTCAGAAAAATCTAGCATAGC 57.422 29.630 0.00 0.00 38.99 2.97
1604 1802 7.870509 ATGTTCAGAAAAATCTAGCATAGCA 57.129 32.000 0.00 0.00 38.99 3.49
1605 1803 7.076842 TGTTCAGAAAAATCTAGCATAGCAC 57.923 36.000 0.00 0.00 38.99 4.40
1606 1804 6.881065 TGTTCAGAAAAATCTAGCATAGCACT 59.119 34.615 0.00 0.00 38.99 4.40
1607 1805 7.391554 TGTTCAGAAAAATCTAGCATAGCACTT 59.608 33.333 0.00 0.00 38.99 3.16
1608 1806 7.928307 TCAGAAAAATCTAGCATAGCACTTT 57.072 32.000 0.00 0.00 38.99 2.66
1646 2013 6.352394 CCAATCCACAAATCCTCCATGAAAAT 60.352 38.462 0.00 0.00 0.00 1.82
1650 2017 8.378115 TCCACAAATCCTCCATGAAAATAATT 57.622 30.769 0.00 0.00 0.00 1.40
1679 2046 6.069705 TGGATTATTCCCTAAAGTTTCCGT 57.930 37.500 1.24 0.00 41.83 4.69
1758 2139 4.493747 GAAGTCGGGCGTCCCTCG 62.494 72.222 0.00 0.00 42.67 4.63
1827 2208 8.144478 TCTTATCCGAATATTTCTTGTCTCCTG 58.856 37.037 0.00 0.00 0.00 3.86
1856 2237 3.339141 CTCCATCCATGATCAGATGCAG 58.661 50.000 16.01 9.58 38.85 4.41
1879 2260 1.929169 TCATGCAAGATTCGAAGCTCG 59.071 47.619 17.46 6.71 42.10 5.03
1946 2327 1.583477 GGCCTCTTTGCTGTTCTGC 59.417 57.895 0.00 0.00 0.00 4.26
1955 2336 4.641989 TCTTTGCTGTTCTGCTCTTTTCTT 59.358 37.500 3.65 0.00 0.00 2.52
2110 2501 0.969917 AGTCATCGCTGTCTCTGCCT 60.970 55.000 0.00 0.00 0.00 4.75
2157 2548 1.488705 AATTGTCCCGGCTCCTGTCA 61.489 55.000 0.00 0.00 0.00 3.58
2158 2549 1.903877 ATTGTCCCGGCTCCTGTCAG 61.904 60.000 0.00 0.00 0.00 3.51
2159 2550 2.680352 GTCCCGGCTCCTGTCAGA 60.680 66.667 0.00 0.00 0.00 3.27
2160 2551 2.680352 TCCCGGCTCCTGTCAGAC 60.680 66.667 0.00 0.00 0.00 3.51
2161 2552 2.997315 CCCGGCTCCTGTCAGACA 60.997 66.667 2.48 2.48 0.00 3.41
2477 2909 3.758554 TGCTTCCTTTTAAGTCATGGCTC 59.241 43.478 0.00 0.00 0.00 4.70
2557 2997 4.759782 AGACTAGCATGCGTTTTATCTGT 58.240 39.130 13.01 1.99 0.00 3.41
2589 3030 8.807667 AACTTATTTTTCAGAAGCACAGATTG 57.192 30.769 0.00 0.00 0.00 2.67
2630 3075 0.392327 CTCACACCACCACACACACA 60.392 55.000 0.00 0.00 0.00 3.72
2656 3101 2.036475 CACACAGCACCTACTGAAGACT 59.964 50.000 0.00 0.00 40.25 3.24
2659 3104 1.620819 CAGCACCTACTGAAGACTGGT 59.379 52.381 0.00 0.00 40.25 4.00
2889 3337 7.601886 TCAGACTTGTCTCTCTCAAATTTGATC 59.398 37.037 20.76 11.29 36.46 2.92
3058 3508 0.882927 TTTCTCAACAAGGACCGCGG 60.883 55.000 26.86 26.86 0.00 6.46
3182 3632 8.080417 TCACTCTAATGCACGTAATACCTTATC 58.920 37.037 0.00 0.00 0.00 1.75
3378 3828 0.538287 GTGGAGTTGCTGGCCTTCTT 60.538 55.000 3.32 0.00 0.00 2.52
3489 4064 9.737427 AATTCTCCGCTTATCTTGATATATACG 57.263 33.333 0.00 0.00 0.00 3.06
3491 4066 8.678593 TCTCCGCTTATCTTGATATATACGAT 57.321 34.615 0.00 0.00 0.00 3.73
3493 4068 9.737427 CTCCGCTTATCTTGATATATACGATTT 57.263 33.333 0.00 0.00 0.00 2.17
3509 4101 4.165779 ACGATTTTGACCATTCGATTTGC 58.834 39.130 0.00 0.00 35.64 3.68
3517 4109 4.912766 TGACCATTCGATTTGCGTAAAAAC 59.087 37.500 1.94 0.00 41.80 2.43
3518 4110 4.861210 ACCATTCGATTTGCGTAAAAACA 58.139 34.783 1.94 0.00 41.80 2.83
3525 4117 4.487408 CGATTTGCGTAAAAACAGTCGATC 59.513 41.667 11.79 0.00 34.64 3.69
3540 4135 4.330074 CAGTCGATCTACACATTTTGACCC 59.670 45.833 0.00 0.00 0.00 4.46
3700 4295 1.975327 CAGAAGAAGGCGAGGGTGA 59.025 57.895 0.00 0.00 0.00 4.02
3701 4296 0.108424 CAGAAGAAGGCGAGGGTGAG 60.108 60.000 0.00 0.00 0.00 3.51
3729 4324 3.017581 CCCCTTAGCCAGGCACCT 61.018 66.667 15.80 0.00 42.29 4.00
3747 4342 0.108233 CTCCTGCTGTTCAGCTCTCC 60.108 60.000 22.44 0.00 41.50 3.71
3828 4423 3.120060 ACGTCGTAACTTCTTCAGCGTAT 60.120 43.478 0.00 0.00 0.00 3.06
3892 4487 0.037160 TGCTGAGGCATCAAGAAGCA 59.963 50.000 8.70 8.70 44.28 3.91
4037 4632 6.800072 TCCACTAGGTTGGTTTTCAAAAAT 57.200 33.333 0.00 0.00 37.93 1.82
4113 4708 1.536766 TGTGACGTTAGTACCTGTCGG 59.463 52.381 0.00 0.00 34.11 4.79
4124 4719 1.056660 ACCTGTCGGTCTTGTTGGAT 58.943 50.000 0.00 0.00 40.27 3.41
4196 4791 7.210873 CCTACTACTTCATCTGTTGGATTACC 58.789 42.308 0.00 0.00 31.27 2.85
4276 4871 0.032540 TCGCTGATCATGATCCACCG 59.967 55.000 28.61 25.36 37.02 4.94
4297 4892 6.470235 CACCGATCAATCTGAAATTGCTTTAC 59.530 38.462 0.00 0.00 0.00 2.01
4326 4921 3.149005 AGGCTTCATTTACCAAACCGA 57.851 42.857 0.00 0.00 0.00 4.69
4358 4953 8.833493 CATGCTCATGTTGATCTTATGTTTAGA 58.167 33.333 1.84 0.00 34.23 2.10
4363 4958 8.677300 TCATGTTGATCTTATGTTTAGAAAGCC 58.323 33.333 0.00 0.00 0.00 4.35
4385 4980 3.811722 TGCGAGAAACATCATGTTGAC 57.188 42.857 3.07 1.90 40.14 3.18
4502 5097 9.982651 ACAACTATATAAGGATGTGATGTGTAC 57.017 33.333 0.00 0.00 30.71 2.90
4503 5098 9.129209 CAACTATATAAGGATGTGATGTGTACG 57.871 37.037 0.00 0.00 0.00 3.67
4509 5104 3.508402 AGGATGTGATGTGTACGTGTGTA 59.492 43.478 0.00 0.00 0.00 2.90
4521 5116 6.483974 TGTGTACGTGTGTAAAATTTCAGGAT 59.516 34.615 0.00 0.00 30.94 3.24
4553 5541 9.294030 GCACTCATTTTAATCTATTTTGTCCTG 57.706 33.333 0.00 0.00 0.00 3.86
4648 5895 8.847196 TGAATTTTGATCATTTCAATTTTGGCA 58.153 25.926 11.64 0.00 43.73 4.92
4650 5897 9.849166 AATTTTGATCATTTCAATTTTGGCATC 57.151 25.926 0.00 0.00 43.73 3.91
4651 5898 6.650239 TTGATCATTTCAATTTTGGCATCG 57.350 33.333 0.00 0.00 39.44 3.84
4654 5901 6.477360 TGATCATTTCAATTTTGGCATCGATG 59.523 34.615 21.27 21.27 0.00 3.84
4655 5902 5.110598 TCATTTCAATTTTGGCATCGATGG 58.889 37.500 26.00 8.82 0.00 3.51
4672 5919 3.564027 GCGGCCGAGTTCCATTCG 61.564 66.667 33.48 0.00 37.78 3.34
4686 5933 5.997129 AGTTCCATTCGGCATTTTTGAAAAT 59.003 32.000 0.00 0.00 39.07 1.82
4688 5935 7.331687 AGTTCCATTCGGCATTTTTGAAAATAG 59.668 33.333 1.69 0.00 36.52 1.73
4690 5937 5.874261 CCATTCGGCATTTTTGAAAATAGGT 59.126 36.000 1.69 0.00 36.52 3.08
4744 5991 1.271597 GGCCATATCACCCAGCTAAGG 60.272 57.143 0.00 0.35 0.00 2.69
4745 5992 1.699634 GCCATATCACCCAGCTAAGGA 59.300 52.381 8.92 0.00 0.00 3.36
4764 6013 1.954382 GAAGGTGTGGTCAAAACCCTC 59.046 52.381 0.00 0.00 45.83 4.30
4783 6032 1.071542 TCAAAAGAGGTCATGGTCGCA 59.928 47.619 0.00 0.00 0.00 5.10
4920 6172 1.580942 CCGTGCATGGTGGAAACAG 59.419 57.895 17.42 0.00 44.46 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.102615 TGGAGAGTATATGCCCCTAATTTGTT 59.897 38.462 0.00 0.00 0.00 2.83
2 3 5.610982 TGGAGAGTATATGCCCCTAATTTGT 59.389 40.000 0.00 0.00 0.00 2.83
3 4 6.126863 TGGAGAGTATATGCCCCTAATTTG 57.873 41.667 0.00 0.00 0.00 2.32
4 5 6.505344 TGATGGAGAGTATATGCCCCTAATTT 59.495 38.462 0.00 0.00 0.00 1.82
6 7 5.426833 GTGATGGAGAGTATATGCCCCTAAT 59.573 44.000 0.00 0.00 0.00 1.73
7 8 4.777896 GTGATGGAGAGTATATGCCCCTAA 59.222 45.833 0.00 0.00 0.00 2.69
8 9 4.202781 TGTGATGGAGAGTATATGCCCCTA 60.203 45.833 0.00 0.00 0.00 3.53
9 10 3.177228 GTGATGGAGAGTATATGCCCCT 58.823 50.000 0.00 0.00 0.00 4.79
10 11 2.906389 TGTGATGGAGAGTATATGCCCC 59.094 50.000 0.00 0.00 0.00 5.80
11 12 4.833478 ATGTGATGGAGAGTATATGCCC 57.167 45.455 0.00 0.00 0.00 5.36
12 13 7.334090 ACATAATGTGATGGAGAGTATATGCC 58.666 38.462 0.00 0.00 0.00 4.40
13 14 9.526713 CTACATAATGTGATGGAGAGTATATGC 57.473 37.037 0.00 0.00 39.82 3.14
14 15 9.526713 GCTACATAATGTGATGGAGAGTATATG 57.473 37.037 0.00 0.00 39.82 1.78
15 16 9.486123 AGCTACATAATGTGATGGAGAGTATAT 57.514 33.333 0.00 0.00 39.82 0.86
16 17 8.743714 CAGCTACATAATGTGATGGAGAGTATA 58.256 37.037 0.00 0.00 39.82 1.47
17 18 7.452813 TCAGCTACATAATGTGATGGAGAGTAT 59.547 37.037 0.00 0.00 39.82 2.12
18 19 6.777580 TCAGCTACATAATGTGATGGAGAGTA 59.222 38.462 0.00 0.00 39.82 2.59
19 20 5.600069 TCAGCTACATAATGTGATGGAGAGT 59.400 40.000 0.00 0.00 39.82 3.24
20 21 6.094193 TCAGCTACATAATGTGATGGAGAG 57.906 41.667 0.00 0.00 39.82 3.20
21 22 6.484364 TTCAGCTACATAATGTGATGGAGA 57.516 37.500 0.00 0.00 39.82 3.71
22 23 7.558161 TTTTCAGCTACATAATGTGATGGAG 57.442 36.000 0.00 0.00 40.33 3.86
23 24 7.936496 TTTTTCAGCTACATAATGTGATGGA 57.064 32.000 0.00 0.00 0.00 3.41
24 25 9.590451 AAATTTTTCAGCTACATAATGTGATGG 57.410 29.630 0.00 0.00 0.00 3.51
26 27 9.807649 GGAAATTTTTCAGCTACATAATGTGAT 57.192 29.630 5.48 0.00 38.92 3.06
27 28 8.801299 TGGAAATTTTTCAGCTACATAATGTGA 58.199 29.630 5.48 0.00 38.92 3.58
28 29 8.984891 TGGAAATTTTTCAGCTACATAATGTG 57.015 30.769 5.48 0.00 38.92 3.21
29 30 9.023962 TCTGGAAATTTTTCAGCTACATAATGT 57.976 29.630 11.93 0.00 38.92 2.71
30 31 9.859427 TTCTGGAAATTTTTCAGCTACATAATG 57.141 29.630 11.93 0.00 38.92 1.90
34 35 9.264719 CTTTTTCTGGAAATTTTTCAGCTACAT 57.735 29.630 11.93 0.00 38.92 2.29
35 36 8.474025 TCTTTTTCTGGAAATTTTTCAGCTACA 58.526 29.630 11.93 0.00 38.92 2.74
36 37 8.871686 TCTTTTTCTGGAAATTTTTCAGCTAC 57.128 30.769 11.93 0.00 38.92 3.58
38 39 8.969260 ATTCTTTTTCTGGAAATTTTTCAGCT 57.031 26.923 11.93 0.00 38.92 4.24
48 49 9.520515 AGAGCTACATAATTCTTTTTCTGGAAA 57.479 29.630 0.00 0.00 0.00 3.13
49 50 9.167311 GAGAGCTACATAATTCTTTTTCTGGAA 57.833 33.333 0.00 0.00 0.00 3.53
50 51 8.543774 AGAGAGCTACATAATTCTTTTTCTGGA 58.456 33.333 0.00 0.00 0.00 3.86
51 52 8.610896 CAGAGAGCTACATAATTCTTTTTCTGG 58.389 37.037 0.00 0.00 0.00 3.86
52 53 8.610896 CCAGAGAGCTACATAATTCTTTTTCTG 58.389 37.037 0.00 0.00 0.00 3.02
53 54 8.325046 ACCAGAGAGCTACATAATTCTTTTTCT 58.675 33.333 0.00 0.00 0.00 2.52
54 55 8.499403 ACCAGAGAGCTACATAATTCTTTTTC 57.501 34.615 0.00 0.00 0.00 2.29
55 56 8.734386 CAACCAGAGAGCTACATAATTCTTTTT 58.266 33.333 0.00 0.00 0.00 1.94
56 57 7.885399 ACAACCAGAGAGCTACATAATTCTTTT 59.115 33.333 0.00 0.00 0.00 2.27
57 58 7.398024 ACAACCAGAGAGCTACATAATTCTTT 58.602 34.615 0.00 0.00 0.00 2.52
58 59 6.951971 ACAACCAGAGAGCTACATAATTCTT 58.048 36.000 0.00 0.00 0.00 2.52
59 60 6.552445 ACAACCAGAGAGCTACATAATTCT 57.448 37.500 0.00 0.00 0.00 2.40
60 61 7.044798 AGAACAACCAGAGAGCTACATAATTC 58.955 38.462 0.00 0.00 0.00 2.17
61 62 6.951971 AGAACAACCAGAGAGCTACATAATT 58.048 36.000 0.00 0.00 0.00 1.40
62 63 6.552445 AGAACAACCAGAGAGCTACATAAT 57.448 37.500 0.00 0.00 0.00 1.28
63 64 7.661536 ATAGAACAACCAGAGAGCTACATAA 57.338 36.000 0.00 0.00 0.00 1.90
64 65 7.778382 TGTATAGAACAACCAGAGAGCTACATA 59.222 37.037 0.00 0.00 34.29 2.29
65 66 6.607600 TGTATAGAACAACCAGAGAGCTACAT 59.392 38.462 0.00 0.00 34.29 2.29
66 67 5.949952 TGTATAGAACAACCAGAGAGCTACA 59.050 40.000 0.00 0.00 34.29 2.74
67 68 6.095720 ACTGTATAGAACAACCAGAGAGCTAC 59.904 42.308 0.00 0.00 37.74 3.58
68 69 6.188407 ACTGTATAGAACAACCAGAGAGCTA 58.812 40.000 0.00 0.00 37.74 3.32
69 70 5.020132 ACTGTATAGAACAACCAGAGAGCT 58.980 41.667 0.00 0.00 37.74 4.09
70 71 5.331876 ACTGTATAGAACAACCAGAGAGC 57.668 43.478 0.00 0.00 37.74 4.09
71 72 7.607250 AGAAACTGTATAGAACAACCAGAGAG 58.393 38.462 0.00 0.00 37.74 3.20
72 73 7.540474 AGAAACTGTATAGAACAACCAGAGA 57.460 36.000 0.00 0.00 37.74 3.10
73 74 8.608844 AAAGAAACTGTATAGAACAACCAGAG 57.391 34.615 0.00 0.00 37.74 3.35
74 75 8.974060 AAAAGAAACTGTATAGAACAACCAGA 57.026 30.769 0.00 0.00 37.74 3.86
77 78 9.556030 GCATAAAAGAAACTGTATAGAACAACC 57.444 33.333 0.00 0.00 37.74 3.77
101 102 9.781425 ACCCCATCCAAAATTTATATATATGCA 57.219 29.630 5.44 0.00 0.00 3.96
106 107 9.533831 GTCTGACCCCATCCAAAATTTATATAT 57.466 33.333 0.00 0.00 0.00 0.86
107 108 8.732854 AGTCTGACCCCATCCAAAATTTATATA 58.267 33.333 3.76 0.00 0.00 0.86
108 109 7.595488 AGTCTGACCCCATCCAAAATTTATAT 58.405 34.615 3.76 0.00 0.00 0.86
109 110 6.980577 AGTCTGACCCCATCCAAAATTTATA 58.019 36.000 3.76 0.00 0.00 0.98
110 111 5.842339 AGTCTGACCCCATCCAAAATTTAT 58.158 37.500 3.76 0.00 0.00 1.40
111 112 5.269554 AGTCTGACCCCATCCAAAATTTA 57.730 39.130 3.76 0.00 0.00 1.40
112 113 4.132122 AGTCTGACCCCATCCAAAATTT 57.868 40.909 3.76 0.00 0.00 1.82
113 114 3.833559 AGTCTGACCCCATCCAAAATT 57.166 42.857 3.76 0.00 0.00 1.82
114 115 3.075882 TGAAGTCTGACCCCATCCAAAAT 59.924 43.478 3.76 0.00 0.00 1.82
115 116 2.445145 TGAAGTCTGACCCCATCCAAAA 59.555 45.455 3.76 0.00 0.00 2.44
116 117 2.061848 TGAAGTCTGACCCCATCCAAA 58.938 47.619 3.76 0.00 0.00 3.28
117 118 1.741028 TGAAGTCTGACCCCATCCAA 58.259 50.000 3.76 0.00 0.00 3.53
118 119 1.351017 GTTGAAGTCTGACCCCATCCA 59.649 52.381 3.76 0.00 0.00 3.41
119 120 1.340114 GGTTGAAGTCTGACCCCATCC 60.340 57.143 3.76 7.60 0.00 3.51
120 121 1.340114 GGGTTGAAGTCTGACCCCATC 60.340 57.143 12.50 6.80 45.94 3.51
121 122 0.698818 GGGTTGAAGTCTGACCCCAT 59.301 55.000 12.50 0.00 45.94 4.00
122 123 2.151369 GGGTTGAAGTCTGACCCCA 58.849 57.895 12.50 5.20 45.94 4.96
125 126 2.368875 TCTTCTGGGTTGAAGTCTGACC 59.631 50.000 3.76 0.00 42.76 4.02
126 127 3.658709 CTCTTCTGGGTTGAAGTCTGAC 58.341 50.000 0.00 0.00 42.76 3.51
127 128 2.037772 GCTCTTCTGGGTTGAAGTCTGA 59.962 50.000 0.00 0.00 42.76 3.27
128 129 2.224378 TGCTCTTCTGGGTTGAAGTCTG 60.224 50.000 0.00 0.00 42.76 3.51
129 130 2.038295 CTGCTCTTCTGGGTTGAAGTCT 59.962 50.000 0.00 0.00 42.76 3.24
130 131 2.421619 CTGCTCTTCTGGGTTGAAGTC 58.578 52.381 0.00 0.00 42.76 3.01
131 132 1.544314 GCTGCTCTTCTGGGTTGAAGT 60.544 52.381 0.00 0.00 42.76 3.01
132 133 1.163554 GCTGCTCTTCTGGGTTGAAG 58.836 55.000 0.00 0.00 43.36 3.02
133 134 0.767375 AGCTGCTCTTCTGGGTTGAA 59.233 50.000 0.00 0.00 0.00 2.69
134 135 0.322975 GAGCTGCTCTTCTGGGTTGA 59.677 55.000 21.93 0.00 0.00 3.18
135 136 0.324285 AGAGCTGCTCTTCTGGGTTG 59.676 55.000 25.80 0.00 37.60 3.77
136 137 1.830477 CTAGAGCTGCTCTTCTGGGTT 59.170 52.381 34.42 12.71 41.50 4.11
137 138 1.006519 TCTAGAGCTGCTCTTCTGGGT 59.993 52.381 34.42 13.43 41.50 4.51
138 139 1.774110 TCTAGAGCTGCTCTTCTGGG 58.226 55.000 34.42 19.36 41.50 4.45
139 140 4.405116 AATTCTAGAGCTGCTCTTCTGG 57.595 45.455 34.42 21.46 41.50 3.86
140 141 4.810491 GGAAATTCTAGAGCTGCTCTTCTG 59.190 45.833 34.42 23.70 41.50 3.02
141 142 4.716287 AGGAAATTCTAGAGCTGCTCTTCT 59.284 41.667 34.42 15.60 41.50 2.85
142 143 5.022282 AGGAAATTCTAGAGCTGCTCTTC 57.978 43.478 34.42 23.83 41.50 2.87
143 144 5.046014 TGAAGGAAATTCTAGAGCTGCTCTT 60.046 40.000 34.42 17.49 36.82 2.85
144 145 4.469227 TGAAGGAAATTCTAGAGCTGCTCT 59.531 41.667 32.31 32.31 38.88 4.09
145 146 4.764172 TGAAGGAAATTCTAGAGCTGCTC 58.236 43.478 21.72 21.72 38.83 4.26
146 147 4.833478 TGAAGGAAATTCTAGAGCTGCT 57.167 40.909 0.00 0.00 38.83 4.24
147 148 6.094603 TGAAATGAAGGAAATTCTAGAGCTGC 59.905 38.462 0.00 0.00 38.83 5.25
148 149 7.621428 TGAAATGAAGGAAATTCTAGAGCTG 57.379 36.000 0.00 0.00 38.83 4.24
149 150 8.820153 AATGAAATGAAGGAAATTCTAGAGCT 57.180 30.769 0.00 0.00 38.83 4.09
150 151 9.513727 GAAATGAAATGAAGGAAATTCTAGAGC 57.486 33.333 0.00 0.00 38.83 4.09
155 156 8.863086 TGTCTGAAATGAAATGAAGGAAATTCT 58.137 29.630 0.00 0.00 38.83 2.40
156 157 9.136952 CTGTCTGAAATGAAATGAAGGAAATTC 57.863 33.333 0.00 0.00 38.50 2.17
157 158 8.092687 CCTGTCTGAAATGAAATGAAGGAAATT 58.907 33.333 0.00 0.00 0.00 1.82
158 159 7.452501 TCCTGTCTGAAATGAAATGAAGGAAAT 59.547 33.333 0.00 0.00 0.00 2.17
159 160 6.777091 TCCTGTCTGAAATGAAATGAAGGAAA 59.223 34.615 0.00 0.00 0.00 3.13
160 161 6.207417 GTCCTGTCTGAAATGAAATGAAGGAA 59.793 38.462 0.00 0.00 32.20 3.36
161 162 5.707298 GTCCTGTCTGAAATGAAATGAAGGA 59.293 40.000 0.00 0.00 0.00 3.36
162 163 5.709164 AGTCCTGTCTGAAATGAAATGAAGG 59.291 40.000 0.00 0.00 0.00 3.46
163 164 6.814506 AGTCCTGTCTGAAATGAAATGAAG 57.185 37.500 0.00 0.00 0.00 3.02
172 173 2.180276 ACGGCTAGTCCTGTCTGAAAT 58.820 47.619 0.00 0.00 0.00 2.17
182 183 1.529865 GTGTGTTTCAACGGCTAGTCC 59.470 52.381 0.00 0.00 0.00 3.85
240 241 0.617935 GAAAGGGGAAGCTGAGCTCT 59.382 55.000 16.19 0.00 38.25 4.09
282 283 2.125106 GGCTCCGGCGAGTCAAAT 60.125 61.111 9.30 0.00 40.69 2.32
348 349 0.609681 GGGAATTTACGGGTGTGCCA 60.610 55.000 0.00 0.00 36.17 4.92
372 374 4.653888 CGGGGAAGGGCGTGGTTT 62.654 66.667 0.00 0.00 0.00 3.27
433 599 3.619729 TGTTTGGCTTTACGCGTTTAAG 58.380 40.909 20.78 21.73 40.44 1.85
635 812 1.693627 GGGAGAGGAGAGCGTGATAA 58.306 55.000 0.00 0.00 0.00 1.75
784 977 1.135333 TCCCAGGAACAAAACGCAAAC 59.865 47.619 0.00 0.00 0.00 2.93
789 982 3.380142 CACAAATCCCAGGAACAAAACG 58.620 45.455 0.00 0.00 0.00 3.60
790 983 3.386402 TCCACAAATCCCAGGAACAAAAC 59.614 43.478 0.00 0.00 0.00 2.43
794 987 3.541242 AATCCACAAATCCCAGGAACA 57.459 42.857 0.00 0.00 33.17 3.18
875 1070 1.381076 CTCCTTAAAACCCGCCCCA 59.619 57.895 0.00 0.00 0.00 4.96
898 1093 2.680352 ATCTCGCACCACCTCCGT 60.680 61.111 0.00 0.00 0.00 4.69
1282 1477 4.806339 CTTCCTCGGCCTCCCCCT 62.806 72.222 0.00 0.00 0.00 4.79
1558 1756 1.432023 TTTGGGGGTGGGGAAGAGAC 61.432 60.000 0.00 0.00 0.00 3.36
1598 1796 5.812127 GGGGCAAAAGATTAAAAGTGCTATG 59.188 40.000 0.00 0.00 32.61 2.23
1600 1798 4.835615 TGGGGCAAAAGATTAAAAGTGCTA 59.164 37.500 0.00 0.00 32.61 3.49
1601 1799 3.645687 TGGGGCAAAAGATTAAAAGTGCT 59.354 39.130 0.00 0.00 32.61 4.40
1602 1800 4.001618 TGGGGCAAAAGATTAAAAGTGC 57.998 40.909 0.00 0.00 0.00 4.40
1603 1801 5.643348 GGATTGGGGCAAAAGATTAAAAGTG 59.357 40.000 0.00 0.00 0.00 3.16
1604 1802 5.309282 TGGATTGGGGCAAAAGATTAAAAGT 59.691 36.000 0.00 0.00 0.00 2.66
1605 1803 5.643348 GTGGATTGGGGCAAAAGATTAAAAG 59.357 40.000 0.00 0.00 0.00 2.27
1606 1804 5.072329 TGTGGATTGGGGCAAAAGATTAAAA 59.928 36.000 0.00 0.00 0.00 1.52
1607 1805 4.594920 TGTGGATTGGGGCAAAAGATTAAA 59.405 37.500 0.00 0.00 0.00 1.52
1608 1806 4.163427 TGTGGATTGGGGCAAAAGATTAA 58.837 39.130 0.00 0.00 0.00 1.40
1665 2032 6.097981 AGACCTAATCTACGGAAACTTTAGGG 59.902 42.308 10.37 0.00 39.86 3.53
1672 2039 5.831702 TCTGAGACCTAATCTACGGAAAC 57.168 43.478 0.00 0.00 38.00 2.78
1754 2135 1.271656 ACAAGGAACGAACTACCGAGG 59.728 52.381 0.00 0.00 0.00 4.63
1758 2139 3.000727 CCATGACAAGGAACGAACTACC 58.999 50.000 0.00 0.00 0.00 3.18
1856 2237 1.064654 GCTTCGAATCTTGCATGACCC 59.935 52.381 4.14 0.00 0.00 4.46
1879 2260 3.810188 GGCCCCTACTTGCTCCCC 61.810 72.222 0.00 0.00 0.00 4.81
1946 2327 3.319122 CAGAACCCCACCAAAGAAAAGAG 59.681 47.826 0.00 0.00 0.00 2.85
1955 2336 4.966787 GCGGCAGAACCCCACCAA 62.967 66.667 0.00 0.00 33.26 3.67
2110 2501 2.050533 GTTGCGCGTTGCCATCAA 60.051 55.556 8.43 0.00 45.60 2.57
2157 2548 0.393077 CTCACAAACCGGGTCTGTCT 59.607 55.000 2.41 0.00 0.00 3.41
2158 2549 0.106149 ACTCACAAACCGGGTCTGTC 59.894 55.000 2.41 0.00 0.00 3.51
2159 2550 0.179056 CACTCACAAACCGGGTCTGT 60.179 55.000 6.32 0.00 0.00 3.41
2160 2551 0.179056 ACACTCACAAACCGGGTCTG 60.179 55.000 6.32 0.00 0.00 3.51
2161 2552 0.106149 GACACTCACAAACCGGGTCT 59.894 55.000 6.32 0.00 0.00 3.85
2166 2557 1.013596 TGCTTGACACTCACAAACCG 58.986 50.000 0.00 0.00 0.00 4.44
2477 2909 6.607689 TGAAAAACATCCAATGTAAGCTACG 58.392 36.000 0.00 0.00 44.07 3.51
2589 3030 1.225745 GTGCGTGCGTCTACATTGC 60.226 57.895 0.00 0.00 0.00 3.56
2630 3075 1.069204 CAGTAGGTGCTGTGTGAGTGT 59.931 52.381 0.00 0.00 0.00 3.55
2716 3161 7.963532 AGTTTCAAGATGAGAACCAACTAGTA 58.036 34.615 0.00 0.00 0.00 1.82
2889 3337 8.039603 TGGTTAAACATGCAGAAGTATAAGTG 57.960 34.615 0.00 0.00 0.00 3.16
2963 3411 7.016072 AGCACCACTGATAATTAAGCTCTCTAT 59.984 37.037 0.00 0.00 0.00 1.98
2966 3414 5.363939 AGCACCACTGATAATTAAGCTCTC 58.636 41.667 0.00 0.00 0.00 3.20
2992 3442 4.341806 TCCTGAATCAACATGCAACAACTT 59.658 37.500 0.00 0.00 0.00 2.66
3058 3508 6.144724 CGTTAGCAGAGAGAATACAAATAGCC 59.855 42.308 0.00 0.00 0.00 3.93
3378 3828 0.815734 GAACAGGACTAGCCGCTACA 59.184 55.000 0.00 0.00 43.43 2.74
3489 4064 4.165779 ACGCAAATCGAATGGTCAAAATC 58.834 39.130 0.00 0.00 41.67 2.17
3491 4066 3.634568 ACGCAAATCGAATGGTCAAAA 57.365 38.095 0.00 0.00 41.67 2.44
3493 4068 4.750952 TTTACGCAAATCGAATGGTCAA 57.249 36.364 0.00 0.00 41.67 3.18
3494 4069 4.750952 TTTTACGCAAATCGAATGGTCA 57.249 36.364 0.00 0.00 41.67 4.02
3495 4070 4.912766 TGTTTTTACGCAAATCGAATGGTC 59.087 37.500 0.00 0.00 41.67 4.02
3497 4072 4.915085 ACTGTTTTTACGCAAATCGAATGG 59.085 37.500 0.00 0.00 41.67 3.16
3498 4073 5.219587 CGACTGTTTTTACGCAAATCGAATG 60.220 40.000 0.00 0.00 41.67 2.67
3499 4074 4.843984 CGACTGTTTTTACGCAAATCGAAT 59.156 37.500 0.00 0.00 41.67 3.34
3500 4075 4.025896 TCGACTGTTTTTACGCAAATCGAA 60.026 37.500 2.20 0.00 41.67 3.71
3501 4076 3.490155 TCGACTGTTTTTACGCAAATCGA 59.510 39.130 0.81 0.81 41.67 3.59
3502 4077 3.790058 TCGACTGTTTTTACGCAAATCG 58.210 40.909 0.00 0.00 45.38 3.34
3509 4101 6.627690 ATGTGTAGATCGACTGTTTTTACG 57.372 37.500 7.51 0.00 0.00 3.18
3517 4109 4.330074 GGGTCAAAATGTGTAGATCGACTG 59.670 45.833 7.51 0.00 0.00 3.51
3518 4110 4.223032 AGGGTCAAAATGTGTAGATCGACT 59.777 41.667 7.51 0.00 0.00 4.18
3525 4117 5.880054 AATCGAAGGGTCAAAATGTGTAG 57.120 39.130 0.00 0.00 0.00 2.74
3540 4135 6.260377 TCTTGCTGATAAATGCAAATCGAAG 58.740 36.000 0.00 0.00 46.55 3.79
3587 4182 6.757010 CAGTTACGTTTTGCAGGAGATATACT 59.243 38.462 0.00 0.00 0.00 2.12
3828 4423 1.591703 CCAGTTCTGGTCTGCGCTA 59.408 57.895 9.73 0.00 0.00 4.26
3876 4471 2.362736 GATGTGCTTCTTGATGCCTCA 58.637 47.619 6.13 6.16 0.00 3.86
4037 4632 1.621814 CCGACAGAAAACCTAGTGGGA 59.378 52.381 0.00 0.00 38.76 4.37
4113 4708 6.816640 TGTAGCTACACAATATCCAACAAGAC 59.183 38.462 22.67 0.00 0.00 3.01
4173 4768 7.147724 CCAGGTAATCCAACAGATGAAGTAGTA 60.148 40.741 0.00 0.00 34.56 1.82
4174 4769 6.352222 CCAGGTAATCCAACAGATGAAGTAGT 60.352 42.308 0.00 0.00 34.56 2.73
4175 4770 6.051717 CCAGGTAATCCAACAGATGAAGTAG 58.948 44.000 0.00 0.00 34.56 2.57
4288 4883 7.848128 TGAAGCCTTAGTAGTAGTAAAGCAAT 58.152 34.615 16.95 8.14 0.00 3.56
4297 4892 8.880750 GTTTGGTAAATGAAGCCTTAGTAGTAG 58.119 37.037 0.00 0.00 0.00 2.57
4346 4941 5.242434 TCGCAAGGCTTTCTAAACATAAGA 58.758 37.500 0.00 0.00 38.47 2.10
4347 4942 5.351465 TCTCGCAAGGCTTTCTAAACATAAG 59.649 40.000 0.00 0.00 38.47 1.73
4350 4945 3.674997 TCTCGCAAGGCTTTCTAAACAT 58.325 40.909 0.00 0.00 38.47 2.71
4356 4951 1.967319 TGTTTCTCGCAAGGCTTTCT 58.033 45.000 0.00 0.00 38.47 2.52
4358 4953 2.229792 TGATGTTTCTCGCAAGGCTTT 58.770 42.857 0.00 0.00 38.47 3.51
4363 4958 4.153986 GTCAACATGATGTTTCTCGCAAG 58.846 43.478 8.30 0.00 38.77 4.01
4480 5075 8.297426 ACACGTACACATCACATCCTTATATAG 58.703 37.037 0.00 0.00 0.00 1.31
4481 5076 8.079809 CACACGTACACATCACATCCTTATATA 58.920 37.037 0.00 0.00 0.00 0.86
4502 5097 5.411361 TCCTCATCCTGAAATTTTACACACG 59.589 40.000 0.00 0.00 0.00 4.49
4503 5098 6.623767 GCTCCTCATCCTGAAATTTTACACAC 60.624 42.308 0.00 0.00 0.00 3.82
4509 5104 4.670765 AGTGCTCCTCATCCTGAAATTTT 58.329 39.130 0.00 0.00 0.00 1.82
4638 5885 1.202203 CGCCATCGATGCCAAAATTG 58.798 50.000 20.25 4.84 38.10 2.32
4641 5888 3.062500 GCCGCCATCGATGCCAAAA 62.063 57.895 20.25 0.00 38.10 2.44
4648 5895 3.792053 GAACTCGGCCGCCATCGAT 62.792 63.158 23.51 1.18 38.10 3.59
4651 5898 3.757248 ATGGAACTCGGCCGCCATC 62.757 63.158 24.26 18.82 36.43 3.51
4654 5901 3.202706 GAATGGAACTCGGCCGCC 61.203 66.667 23.51 17.02 0.00 6.13
4655 5902 3.564027 CGAATGGAACTCGGCCGC 61.564 66.667 23.51 6.01 0.00 6.53
4656 5903 2.890474 CCGAATGGAACTCGGCCG 60.890 66.667 22.12 22.12 40.25 6.13
4744 5991 1.954382 GAGGGTTTTGACCACACCTTC 59.046 52.381 0.00 0.00 0.00 3.46
4745 5992 1.286553 TGAGGGTTTTGACCACACCTT 59.713 47.619 0.00 0.00 0.00 3.50
4764 6013 1.466167 CTGCGACCATGACCTCTTTTG 59.534 52.381 0.00 0.00 0.00 2.44
4783 6032 1.513158 CTCTTGACCGCCATCGTCT 59.487 57.895 0.00 0.00 0.00 4.18
4891 6143 0.321564 CATGCACGGGAGGAAGTTCA 60.322 55.000 5.01 0.00 0.00 3.18
4895 6147 1.746615 CACCATGCACGGGAGGAAG 60.747 63.158 12.94 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.