Multiple sequence alignment - TraesCS2A01G413000

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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 TraesCS2A01G413000 chr2A 100.000 1859 0 0 1555 3413 670250304 670248446 0.000000e+00 3434
1 TraesCS2A01G413000 chr2A 100.000 1064 0 0 1 1064 670251858 670250795 0.000000e+00 1965
2 TraesCS2A01G413000 chr2A 91.570 605 46 4 224 824 12142673 12142070 0.000000e+00 830
3 TraesCS2A01G413000 chr2A 91.191 613 43 7 225 827 123569643 123570254 0.000000e+00 822
4 TraesCS2A01G413000 chr2A 91.156 147 13 0 2401 2547 670238283 670238137 2.080000e-47 200
5 TraesCS2A01G413000 chr2D 91.485 1832 122 18 1557 3358 524584529 524582702 0.000000e+00 2488
6 TraesCS2A01G413000 chr2D 96.653 239 7 1 827 1064 524584873 524584635 2.470000e-106 396
7 TraesCS2A01G413000 chr2B 94.663 1218 63 2 1557 2774 620593759 620594974 0.000000e+00 1888
8 TraesCS2A01G413000 chr2B 95.745 235 9 1 827 1060 620593415 620593649 8.940000e-101 377
9 TraesCS2A01G413000 chr5D 91.803 610 41 7 225 827 437472473 437471866 0.000000e+00 841
10 TraesCS2A01G413000 chr4A 91.297 609 43 6 221 821 313643328 313643934 0.000000e+00 822
11 TraesCS2A01G413000 chr4B 90.446 628 49 6 217 834 46564558 46565184 0.000000e+00 817
12 TraesCS2A01G413000 chr6D 90.998 611 45 8 225 827 397666747 397666139 0.000000e+00 815
13 TraesCS2A01G413000 chr7D 90.835 611 47 8 224 827 156208167 156208775 0.000000e+00 809
14 TraesCS2A01G413000 chr3D 90.939 607 47 6 221 821 31603951 31604555 0.000000e+00 809
15 TraesCS2A01G413000 chr3B 90.865 613 43 9 225 827 147163013 147162404 0.000000e+00 809


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 TraesCS2A01G413000 chr2A 670248446 670251858 3412 True 2699.5 3434 100.000 1 3413 2 chr2A.!!$R3 3412
1 TraesCS2A01G413000 chr2A 12142070 12142673 603 True 830.0 830 91.570 224 824 1 chr2A.!!$R1 600
2 TraesCS2A01G413000 chr2A 123569643 123570254 611 False 822.0 822 91.191 225 827 1 chr2A.!!$F1 602
3 TraesCS2A01G413000 chr2D 524582702 524584873 2171 True 1442.0 2488 94.069 827 3358 2 chr2D.!!$R1 2531
4 TraesCS2A01G413000 chr2B 620593415 620594974 1559 False 1132.5 1888 95.204 827 2774 2 chr2B.!!$F1 1947
5 TraesCS2A01G413000 chr5D 437471866 437472473 607 True 841.0 841 91.803 225 827 1 chr5D.!!$R1 602
6 TraesCS2A01G413000 chr4A 313643328 313643934 606 False 822.0 822 91.297 221 821 1 chr4A.!!$F1 600
7 TraesCS2A01G413000 chr4B 46564558 46565184 626 False 817.0 817 90.446 217 834 1 chr4B.!!$F1 617
8 TraesCS2A01G413000 chr6D 397666139 397666747 608 True 815.0 815 90.998 225 827 1 chr6D.!!$R1 602
9 TraesCS2A01G413000 chr7D 156208167 156208775 608 False 809.0 809 90.835 224 827 1 chr7D.!!$F1 603
10 TraesCS2A01G413000 chr3D 31603951 31604555 604 False 809.0 809 90.939 221 821 1 chr3D.!!$F1 600
11 TraesCS2A01G413000 chr3B 147162404 147163013 609 True 809.0 809 90.865 225 827 1 chr3B.!!$R1 602

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
62 63 0.240945 CCCAGCCAAACATGTCGTTC 59.759 55.0 0.00 0.0 36.59 3.95 F
88 89 0.253044 TAGCTTACAGGCCAGCTTGG 59.747 55.0 19.41 0.0 44.28 3.61 F
106 107 0.391661 GGCGAGATTGTGAGCCTCAA 60.392 55.0 0.00 0.0 45.67 3.02 F
452 461 0.546122 AGGCGAATATGCTGGGAACA 59.454 50.0 0.00 0.0 39.59 3.18 F
821 836 0.593128 GGCTCGAGCTTTTCTTGCAA 59.407 50.0 34.46 0.0 41.70 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1636 1.003718 GGGGTCCAGTTGGAGAACG 60.004 63.158 0.00 0.00 46.49 3.95 R
2034 2051 3.365265 CAAGCAAGGACACGGGGC 61.365 66.667 0.00 0.00 0.00 5.80 R
2223 2240 1.817520 CACCGCGATAATGGCACCA 60.818 57.895 8.23 0.00 0.00 4.17 R
2394 2411 0.096976 CTTAACCCATCGCGTGCTTG 59.903 55.000 5.77 0.00 0.00 4.01 R
2502 2519 1.517694 GCCGATGTTGCAATGCTGG 60.518 57.895 6.82 4.35 0.00 4.85 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
35 36 3.461946 GAGAATCTCGCCACTTTGTTG 57.538 47.619 0.00 0.00 0.00 3.33
36 37 2.154462 AGAATCTCGCCACTTTGTTGG 58.846 47.619 0.00 0.00 39.98 3.77
37 38 1.200020 GAATCTCGCCACTTTGTTGGG 59.800 52.381 0.00 0.00 37.10 4.12
41 42 4.599036 GCCACTTTGTTGGGGACT 57.401 55.556 0.00 0.00 37.10 3.85
42 43 3.737702 GCCACTTTGTTGGGGACTA 57.262 52.632 0.00 0.00 37.10 2.59
43 44 1.244816 GCCACTTTGTTGGGGACTAC 58.755 55.000 0.00 0.00 37.10 2.73
44 45 1.905637 CCACTTTGTTGGGGACTACC 58.094 55.000 0.00 0.00 35.03 3.18
55 56 3.978876 GGACTACCCAGCCAAACAT 57.021 52.632 0.00 0.00 34.14 2.71
56 57 1.463674 GGACTACCCAGCCAAACATG 58.536 55.000 0.00 0.00 34.14 3.21
57 58 1.271926 GGACTACCCAGCCAAACATGT 60.272 52.381 0.00 0.00 34.14 3.21
58 59 2.084546 GACTACCCAGCCAAACATGTC 58.915 52.381 0.00 0.00 0.00 3.06
59 60 1.086696 CTACCCAGCCAAACATGTCG 58.913 55.000 0.00 0.00 0.00 4.35
60 61 0.398696 TACCCAGCCAAACATGTCGT 59.601 50.000 0.00 0.00 0.00 4.34
61 62 0.467290 ACCCAGCCAAACATGTCGTT 60.467 50.000 0.00 0.00 40.50 3.85
62 63 0.240945 CCCAGCCAAACATGTCGTTC 59.759 55.000 0.00 0.00 36.59 3.95
63 64 1.238439 CCAGCCAAACATGTCGTTCT 58.762 50.000 0.00 0.00 36.59 3.01
64 65 2.422597 CCAGCCAAACATGTCGTTCTA 58.577 47.619 0.00 0.00 36.59 2.10
65 66 2.811431 CCAGCCAAACATGTCGTTCTAA 59.189 45.455 0.00 0.00 36.59 2.10
66 67 3.252215 CCAGCCAAACATGTCGTTCTAAA 59.748 43.478 0.00 0.00 36.59 1.85
67 68 4.219033 CAGCCAAACATGTCGTTCTAAAC 58.781 43.478 0.00 0.00 36.59 2.01
68 69 3.252458 AGCCAAACATGTCGTTCTAAACC 59.748 43.478 0.00 0.00 36.59 3.27
69 70 3.252458 GCCAAACATGTCGTTCTAAACCT 59.748 43.478 0.00 0.00 36.59 3.50
70 71 4.453136 GCCAAACATGTCGTTCTAAACCTA 59.547 41.667 0.00 0.00 36.59 3.08
71 72 5.390567 GCCAAACATGTCGTTCTAAACCTAG 60.391 44.000 0.00 0.00 36.59 3.02
72 73 5.390567 CCAAACATGTCGTTCTAAACCTAGC 60.391 44.000 0.00 0.00 36.59 3.42
73 74 4.803098 ACATGTCGTTCTAAACCTAGCT 57.197 40.909 0.00 0.00 0.00 3.32
74 75 5.148651 ACATGTCGTTCTAAACCTAGCTT 57.851 39.130 0.00 0.00 0.00 3.74
75 76 6.276832 ACATGTCGTTCTAAACCTAGCTTA 57.723 37.500 0.00 0.00 0.00 3.09
76 77 6.098017 ACATGTCGTTCTAAACCTAGCTTAC 58.902 40.000 0.00 0.00 0.00 2.34
77 78 5.710513 TGTCGTTCTAAACCTAGCTTACA 57.289 39.130 0.00 0.00 0.00 2.41
78 79 5.706916 TGTCGTTCTAAACCTAGCTTACAG 58.293 41.667 0.00 0.00 0.00 2.74
79 80 5.100943 GTCGTTCTAAACCTAGCTTACAGG 58.899 45.833 0.00 0.00 39.25 4.00
80 81 3.864003 CGTTCTAAACCTAGCTTACAGGC 59.136 47.826 0.60 0.00 36.57 4.85
81 82 4.190001 GTTCTAAACCTAGCTTACAGGCC 58.810 47.826 0.00 0.00 36.57 5.19
82 83 3.446968 TCTAAACCTAGCTTACAGGCCA 58.553 45.455 5.01 0.00 36.57 5.36
83 84 2.789409 AAACCTAGCTTACAGGCCAG 57.211 50.000 5.01 0.00 36.57 4.85
84 85 0.253327 AACCTAGCTTACAGGCCAGC 59.747 55.000 5.01 4.79 36.57 4.85
86 87 0.543749 CCTAGCTTACAGGCCAGCTT 59.456 55.000 19.41 5.52 44.28 3.74
87 88 1.661341 CTAGCTTACAGGCCAGCTTG 58.339 55.000 19.41 14.06 44.28 4.01
88 89 0.253044 TAGCTTACAGGCCAGCTTGG 59.747 55.000 19.41 0.00 44.28 3.61
97 98 4.308526 CCAGCTTGGCGAGATTGT 57.691 55.556 5.76 0.00 0.00 2.71
98 99 1.798735 CCAGCTTGGCGAGATTGTG 59.201 57.895 5.76 0.00 0.00 3.33
99 100 0.674581 CCAGCTTGGCGAGATTGTGA 60.675 55.000 5.76 0.00 0.00 3.58
100 101 0.725686 CAGCTTGGCGAGATTGTGAG 59.274 55.000 5.76 0.00 0.00 3.51
101 102 1.023513 AGCTTGGCGAGATTGTGAGC 61.024 55.000 5.76 0.00 0.00 4.26
104 105 4.116878 GGCGAGATTGTGAGCCTC 57.883 61.111 0.00 0.00 45.67 4.70
105 106 1.219124 GGCGAGATTGTGAGCCTCA 59.781 57.895 0.00 0.00 45.67 3.86
106 107 0.391661 GGCGAGATTGTGAGCCTCAA 60.392 55.000 0.00 0.00 45.67 3.02
107 108 1.442769 GCGAGATTGTGAGCCTCAAA 58.557 50.000 0.00 0.00 0.00 2.69
108 109 1.396301 GCGAGATTGTGAGCCTCAAAG 59.604 52.381 0.00 0.00 0.00 2.77
109 110 2.693069 CGAGATTGTGAGCCTCAAAGT 58.307 47.619 0.00 0.00 0.00 2.66
110 111 3.070018 CGAGATTGTGAGCCTCAAAGTT 58.930 45.455 0.00 0.00 0.00 2.66
111 112 4.245660 CGAGATTGTGAGCCTCAAAGTTA 58.754 43.478 0.00 0.00 0.00 2.24
112 113 4.872691 CGAGATTGTGAGCCTCAAAGTTAT 59.127 41.667 0.00 0.00 0.00 1.89
113 114 5.220548 CGAGATTGTGAGCCTCAAAGTTATG 60.221 44.000 0.00 0.00 0.00 1.90
114 115 5.809001 AGATTGTGAGCCTCAAAGTTATGA 58.191 37.500 0.00 0.00 0.00 2.15
115 116 6.421485 AGATTGTGAGCCTCAAAGTTATGAT 58.579 36.000 0.00 0.00 0.00 2.45
116 117 6.888632 AGATTGTGAGCCTCAAAGTTATGATT 59.111 34.615 0.00 0.00 0.00 2.57
117 118 6.500684 TTGTGAGCCTCAAAGTTATGATTC 57.499 37.500 0.00 0.00 0.00 2.52
118 119 4.943705 TGTGAGCCTCAAAGTTATGATTCC 59.056 41.667 0.00 0.00 0.00 3.01
119 120 5.189180 GTGAGCCTCAAAGTTATGATTCCT 58.811 41.667 0.00 0.00 0.00 3.36
120 121 6.070251 TGTGAGCCTCAAAGTTATGATTCCTA 60.070 38.462 0.00 0.00 0.00 2.94
121 122 6.823689 GTGAGCCTCAAAGTTATGATTCCTAA 59.176 38.462 0.00 0.00 0.00 2.69
122 123 7.336931 GTGAGCCTCAAAGTTATGATTCCTAAA 59.663 37.037 0.00 0.00 0.00 1.85
123 124 7.336931 TGAGCCTCAAAGTTATGATTCCTAAAC 59.663 37.037 0.00 0.00 0.00 2.01
124 125 7.406104 AGCCTCAAAGTTATGATTCCTAAACT 58.594 34.615 0.00 0.00 33.72 2.66
125 126 7.554476 AGCCTCAAAGTTATGATTCCTAAACTC 59.446 37.037 0.00 0.00 31.15 3.01
126 127 7.336931 GCCTCAAAGTTATGATTCCTAAACTCA 59.663 37.037 0.00 0.00 31.15 3.41
127 128 8.669243 CCTCAAAGTTATGATTCCTAAACTCAC 58.331 37.037 0.00 0.00 31.15 3.51
128 129 8.251750 TCAAAGTTATGATTCCTAAACTCACG 57.748 34.615 0.00 0.00 31.15 4.35
129 130 8.092068 TCAAAGTTATGATTCCTAAACTCACGA 58.908 33.333 0.00 0.00 31.15 4.35
130 131 8.717821 CAAAGTTATGATTCCTAAACTCACGAA 58.282 33.333 0.00 0.00 31.15 3.85
131 132 7.829378 AGTTATGATTCCTAAACTCACGAAC 57.171 36.000 0.00 0.00 0.00 3.95
132 133 7.383687 AGTTATGATTCCTAAACTCACGAACA 58.616 34.615 0.00 0.00 0.00 3.18
133 134 7.876068 AGTTATGATTCCTAAACTCACGAACAA 59.124 33.333 0.00 0.00 0.00 2.83
134 135 8.500773 GTTATGATTCCTAAACTCACGAACAAA 58.499 33.333 0.00 0.00 0.00 2.83
135 136 6.928979 TGATTCCTAAACTCACGAACAAAA 57.071 33.333 0.00 0.00 0.00 2.44
136 137 7.504924 TGATTCCTAAACTCACGAACAAAAT 57.495 32.000 0.00 0.00 0.00 1.82
137 138 7.936584 TGATTCCTAAACTCACGAACAAAATT 58.063 30.769 0.00 0.00 0.00 1.82
138 139 9.058174 TGATTCCTAAACTCACGAACAAAATTA 57.942 29.630 0.00 0.00 0.00 1.40
162 163 3.923017 AAAAGGAAATTGTCTCTGCGG 57.077 42.857 0.00 0.00 0.00 5.69
163 164 1.826385 AAGGAAATTGTCTCTGCGGG 58.174 50.000 0.00 0.00 0.00 6.13
164 165 0.693049 AGGAAATTGTCTCTGCGGGT 59.307 50.000 0.00 0.00 0.00 5.28
165 166 1.073923 AGGAAATTGTCTCTGCGGGTT 59.926 47.619 0.00 0.00 0.00 4.11
166 167 1.886542 GGAAATTGTCTCTGCGGGTTT 59.113 47.619 0.00 0.00 0.00 3.27
167 168 2.296190 GGAAATTGTCTCTGCGGGTTTT 59.704 45.455 0.00 0.00 0.00 2.43
168 169 3.243737 GGAAATTGTCTCTGCGGGTTTTT 60.244 43.478 0.00 0.00 0.00 1.94
194 195 8.635765 TTTTTAGTGGCAATCTCTGTAATCTT 57.364 30.769 0.00 0.00 0.00 2.40
195 196 7.615582 TTTAGTGGCAATCTCTGTAATCTTG 57.384 36.000 0.00 0.00 0.00 3.02
196 197 5.171339 AGTGGCAATCTCTGTAATCTTGT 57.829 39.130 0.00 0.00 0.00 3.16
197 198 6.299805 AGTGGCAATCTCTGTAATCTTGTA 57.700 37.500 0.00 0.00 0.00 2.41
198 199 6.344500 AGTGGCAATCTCTGTAATCTTGTAG 58.656 40.000 0.00 0.00 0.00 2.74
199 200 5.525378 GTGGCAATCTCTGTAATCTTGTAGG 59.475 44.000 0.00 0.00 0.00 3.18
200 201 5.059833 GGCAATCTCTGTAATCTTGTAGGG 58.940 45.833 0.00 0.00 0.00 3.53
201 202 5.059833 GCAATCTCTGTAATCTTGTAGGGG 58.940 45.833 0.00 0.00 0.00 4.79
202 203 5.615289 CAATCTCTGTAATCTTGTAGGGGG 58.385 45.833 0.00 0.00 0.00 5.40
203 204 4.348020 TCTCTGTAATCTTGTAGGGGGT 57.652 45.455 0.00 0.00 0.00 4.95
204 205 4.695606 TCTCTGTAATCTTGTAGGGGGTT 58.304 43.478 0.00 0.00 0.00 4.11
205 206 4.469945 TCTCTGTAATCTTGTAGGGGGTTG 59.530 45.833 0.00 0.00 0.00 3.77
206 207 4.431378 TCTGTAATCTTGTAGGGGGTTGA 58.569 43.478 0.00 0.00 0.00 3.18
207 208 5.036916 TCTGTAATCTTGTAGGGGGTTGAT 58.963 41.667 0.00 0.00 0.00 2.57
208 209 5.491078 TCTGTAATCTTGTAGGGGGTTGATT 59.509 40.000 0.00 0.00 0.00 2.57
209 210 6.011981 TCTGTAATCTTGTAGGGGGTTGATTT 60.012 38.462 0.00 0.00 0.00 2.17
210 211 7.183112 TCTGTAATCTTGTAGGGGGTTGATTTA 59.817 37.037 0.00 0.00 0.00 1.40
211 212 7.700846 TGTAATCTTGTAGGGGGTTGATTTAA 58.299 34.615 0.00 0.00 0.00 1.52
212 213 7.612633 TGTAATCTTGTAGGGGGTTGATTTAAC 59.387 37.037 0.00 0.00 38.60 2.01
231 232 1.146263 CGGGTTGGATGTAGGGCTC 59.854 63.158 0.00 0.00 0.00 4.70
282 283 4.406972 AGTTGGCTCAGCTCAACTCATATA 59.593 41.667 21.33 0.00 42.04 0.86
325 326 2.757314 TCAGTGAAGCTCATGATCGAGT 59.243 45.455 0.00 0.00 35.33 4.18
452 461 0.546122 AGGCGAATATGCTGGGAACA 59.454 50.000 0.00 0.00 39.59 3.18
457 466 3.181487 GCGAATATGCTGGGAACATTTGT 60.181 43.478 0.00 0.00 41.51 2.83
468 478 8.370940 TGCTGGGAACATTTGTCAAAAATATAA 58.629 29.630 1.31 0.00 41.51 0.98
508 518 3.737047 CGACCACGTGTCATAATTAGGCT 60.737 47.826 15.65 0.00 44.71 4.58
685 699 4.782019 AAATTAAGCGAGCCAACATTGA 57.218 36.364 0.00 0.00 0.00 2.57
694 708 4.183865 CGAGCCAACATTGACTCAAGATA 58.816 43.478 8.41 0.00 37.51 1.98
728 742 7.704271 TCTCGATCGATCTACATAAAGTGTTT 58.296 34.615 19.78 0.00 42.29 2.83
821 836 0.593128 GGCTCGAGCTTTTCTTGCAA 59.407 50.000 34.46 0.00 41.70 4.08
897 914 0.901124 CCACCAGAGACTCCTTCCTG 59.099 60.000 0.00 0.00 0.00 3.86
1060 1077 4.052229 CCTCCGCCACGACGAACT 62.052 66.667 0.00 0.00 34.06 3.01
1591 1608 3.075005 CTTCGCCTTCCCCTCCGA 61.075 66.667 0.00 0.00 0.00 4.55
1872 1889 3.934391 CTCCGTTGGTGGCGTCCTC 62.934 68.421 0.00 0.00 0.00 3.71
2046 2063 4.265056 GTGGTGCCCCGTGTCCTT 62.265 66.667 0.00 0.00 0.00 3.36
2223 2240 5.106157 CGCCTTGATAAAATCTCAGGTGTTT 60.106 40.000 9.42 0.00 36.75 2.83
2298 2315 3.626924 AAGGGCGTTGGCGAGTCT 61.627 61.111 0.00 0.00 41.24 3.24
2352 2369 4.479619 GAATTTTCATTGCAGACTTCGCT 58.520 39.130 0.00 0.00 0.00 4.93
2394 2411 1.364626 CTGGTGCTGGTGATTCGCTC 61.365 60.000 0.00 0.00 0.00 5.03
2433 2450 0.674895 GCAAGACCACGGCAGAGAAT 60.675 55.000 0.00 0.00 0.00 2.40
2502 2519 3.451178 TGTAGTAGTGGATTCAAGGAGGC 59.549 47.826 0.00 0.00 0.00 4.70
2518 2535 1.517694 GGCCAGCATTGCAACATCG 60.518 57.895 11.91 0.00 0.00 3.84
2556 2573 8.702438 GGTGAATGAGTTATTTTTGTTGTGATG 58.298 33.333 0.00 0.00 0.00 3.07
2574 2591 5.530915 TGTGATGTCCTTTGGAAGTAAACTG 59.469 40.000 0.00 0.00 31.38 3.16
2585 2602 9.341899 CTTTGGAAGTAAACTGTTATGCATTAC 57.658 33.333 3.54 6.72 0.00 1.89
2620 2637 7.769719 CAAATTATTGCTCAATTGTTTGCAC 57.230 32.000 17.80 0.95 35.01 4.57
2622 2639 2.237393 TTGCTCAATTGTTTGCACCC 57.763 45.000 17.80 0.00 35.01 4.61
2633 2650 2.688446 TGTTTGCACCCGATTTGTGTAA 59.312 40.909 0.00 0.00 36.69 2.41
2650 2668 7.255801 ATTTGTGTAAATCTTACCACCACTTGG 60.256 37.037 0.00 0.00 40.80 3.61
2681 2700 8.784043 AGAAATAAAACTACATGTGTCCAAGTC 58.216 33.333 9.11 0.00 0.00 3.01
2682 2701 8.458573 AAATAAAACTACATGTGTCCAAGTCA 57.541 30.769 9.11 0.00 0.00 3.41
2705 2724 4.689345 ACACTTGCTAACGGAGATGTAAAC 59.311 41.667 0.00 0.00 0.00 2.01
2735 2754 1.900245 TCAGCTCAAGCATTCAAGCA 58.100 45.000 4.59 0.00 45.16 3.91
2761 2780 9.054922 AGCACTGCAAAATACAATTGTTTTTAT 57.945 25.926 22.08 12.59 30.88 1.40
2798 2844 8.839343 TGATCGATATTGTTTATCAGTTGCAAT 58.161 29.630 0.59 0.00 34.62 3.56
2804 2850 6.825284 TTGTTTATCAGTTGCAATGTTGTG 57.175 33.333 0.59 0.00 0.00 3.33
2813 2859 0.524862 GCAATGTTGTGCTCCAGGAG 59.475 55.000 12.81 12.81 41.51 3.69
2815 2861 2.082231 CAATGTTGTGCTCCAGGAGAG 58.918 52.381 21.89 0.00 46.29 3.20
2829 2875 3.389329 CCAGGAGAGCACATACATTAGGT 59.611 47.826 0.00 0.00 0.00 3.08
2896 2942 4.356405 TGGATGAGAAGAACTGCAGAAA 57.644 40.909 23.35 0.00 0.00 2.52
2903 2949 6.866480 TGAGAAGAACTGCAGAAATTTTGTT 58.134 32.000 23.35 8.46 0.00 2.83
2906 2952 6.976925 AGAAGAACTGCAGAAATTTTGTTGAG 59.023 34.615 23.35 0.00 0.00 3.02
2908 2954 6.268566 AGAACTGCAGAAATTTTGTTGAGAC 58.731 36.000 23.35 0.00 0.00 3.36
2909 2955 4.936891 ACTGCAGAAATTTTGTTGAGACC 58.063 39.130 23.35 0.00 0.00 3.85
2922 2968 3.118261 TGTTGAGACCTCTGGGAATATGC 60.118 47.826 0.00 0.00 36.25 3.14
2931 2977 2.705658 TCTGGGAATATGCGAGTTGGAT 59.294 45.455 0.00 0.00 0.00 3.41
2956 3002 4.376340 AGTCTTTGTCAAGGCAAACAAG 57.624 40.909 0.00 0.00 37.05 3.16
2957 3003 3.763897 AGTCTTTGTCAAGGCAAACAAGT 59.236 39.130 0.00 0.00 37.05 3.16
2959 3005 3.509575 TCTTTGTCAAGGCAAACAAGTGT 59.490 39.130 0.00 0.00 36.78 3.55
2967 3013 2.831526 AGGCAAACAAGTGTTCCTTTGT 59.168 40.909 0.00 0.00 37.25 2.83
2974 3020 4.340617 ACAAGTGTTCCTTTGTCTTCCAA 58.659 39.130 0.00 0.00 0.00 3.53
2984 3030 3.953712 TTGTCTTCCAATACGAGCTGA 57.046 42.857 0.00 0.00 0.00 4.26
2991 3037 3.096852 TCCAATACGAGCTGAAAGGAGA 58.903 45.455 0.00 0.00 0.00 3.71
2992 3038 3.513912 TCCAATACGAGCTGAAAGGAGAA 59.486 43.478 0.00 0.00 0.00 2.87
2993 3039 4.162320 TCCAATACGAGCTGAAAGGAGAAT 59.838 41.667 0.00 0.00 0.00 2.40
3005 3051 6.093357 GCTGAAAGGAGAATAAAAGGTGAGAG 59.907 42.308 0.00 0.00 0.00 3.20
3013 3059 7.172361 GGAGAATAAAAGGTGAGAGATACATGC 59.828 40.741 0.00 0.00 0.00 4.06
3021 3067 4.274459 GGTGAGAGATACATGCCAATGTTC 59.726 45.833 0.00 0.00 44.94 3.18
3030 3076 8.573885 AGATACATGCCAATGTTCAGAAATATG 58.426 33.333 0.00 0.00 44.94 1.78
3031 3077 6.778834 ACATGCCAATGTTCAGAAATATGA 57.221 33.333 0.00 0.00 44.94 2.15
3032 3078 7.172868 ACATGCCAATGTTCAGAAATATGAA 57.827 32.000 0.00 0.00 44.94 2.57
3052 3098 9.730705 ATATGAATAGTTGATAACAGACCATGG 57.269 33.333 11.19 11.19 0.00 3.66
3056 3102 8.682936 AATAGTTGATAACAGACCATGGATTC 57.317 34.615 21.47 6.48 0.00 2.52
3066 3112 4.341235 CAGACCATGGATTCGAGTACCTTA 59.659 45.833 21.47 0.00 0.00 2.69
3069 3115 3.997021 CCATGGATTCGAGTACCTTATGC 59.003 47.826 5.56 0.00 0.00 3.14
3080 3126 5.242795 AGTACCTTATGCTGGAACACTTT 57.757 39.130 0.00 0.00 0.00 2.66
3084 3130 3.194116 CCTTATGCTGGAACACTTTGCAT 59.806 43.478 0.00 0.00 44.93 3.96
3085 3131 2.736144 ATGCTGGAACACTTTGCATG 57.264 45.000 0.00 0.00 41.93 4.06
3104 3150 5.745514 GCATGTGCACAAGATTGATAGTAG 58.254 41.667 25.72 0.00 41.59 2.57
3143 3190 1.605710 GCAGTGTCTCAATTGTGTGCT 59.394 47.619 5.13 1.18 0.00 4.40
3147 3194 3.562973 AGTGTCTCAATTGTGTGCTCAAG 59.437 43.478 5.13 0.00 0.00 3.02
3153 3200 3.754850 TCAATTGTGTGCTCAAGGATCAG 59.245 43.478 5.13 0.00 0.00 2.90
3174 3221 3.826729 AGTCTTACACCTTTGATTTGCCC 59.173 43.478 0.00 0.00 0.00 5.36
3189 3236 2.035442 GCCCGAGCTTCACCTTGAC 61.035 63.158 0.00 0.00 35.50 3.18
3199 3246 3.724374 CTTCACCTTGACGACAAACCTA 58.276 45.455 1.35 0.00 35.49 3.08
3215 3262 2.200081 ACCTATCACCACTCTGGCAAT 58.800 47.619 0.00 0.00 42.67 3.56
3216 3263 2.092753 ACCTATCACCACTCTGGCAATG 60.093 50.000 0.00 0.00 42.67 2.82
3217 3264 1.945394 CTATCACCACTCTGGCAATGC 59.055 52.381 0.00 0.00 42.67 3.56
3220 3267 1.089920 CACCACTCTGGCAATGCTAC 58.910 55.000 4.82 0.00 42.67 3.58
3258 3305 9.877178 GAGTTTCCCTTGTATGATATGGTATAG 57.123 37.037 0.00 0.00 0.00 1.31
3274 3321 6.156748 TGGTATAGCTGACGTACATGAATT 57.843 37.500 0.00 0.00 0.00 2.17
3276 3323 7.045416 TGGTATAGCTGACGTACATGAATTTT 58.955 34.615 0.00 0.00 0.00 1.82
3280 3327 8.718102 ATAGCTGACGTACATGAATTTTACTT 57.282 30.769 0.00 0.00 0.00 2.24
3281 3328 6.831769 AGCTGACGTACATGAATTTTACTTG 58.168 36.000 0.00 0.00 0.00 3.16
3294 3341 8.830201 TGAATTTTACTTGGAAAATCATGTGG 57.170 30.769 4.26 0.00 37.91 4.17
3296 3343 9.271828 GAATTTTACTTGGAAAATCATGTGGTT 57.728 29.630 4.26 0.00 37.91 3.67
3299 3346 5.612725 ACTTGGAAAATCATGTGGTTGTT 57.387 34.783 0.00 0.00 0.00 2.83
3302 3349 7.560368 ACTTGGAAAATCATGTGGTTGTTAAA 58.440 30.769 0.00 0.00 0.00 1.52
3303 3350 7.494298 ACTTGGAAAATCATGTGGTTGTTAAAC 59.506 33.333 0.00 0.00 35.40 2.01
3304 3351 7.118496 TGGAAAATCATGTGGTTGTTAAACT 57.882 32.000 0.00 0.00 36.48 2.66
3305 3352 8.239038 TGGAAAATCATGTGGTTGTTAAACTA 57.761 30.769 0.00 0.00 36.48 2.24
3306 3353 8.865090 TGGAAAATCATGTGGTTGTTAAACTAT 58.135 29.630 0.00 0.00 36.48 2.12
3331 3378 5.728637 TTATGGTGTCTCTATCGCATGAT 57.271 39.130 0.00 0.00 38.67 2.45
3358 3405 8.288208 CAGCATGTCTATCTGAATTGATAAACC 58.712 37.037 0.00 0.00 0.00 3.27
3359 3406 8.216423 AGCATGTCTATCTGAATTGATAAACCT 58.784 33.333 0.00 0.00 0.00 3.50
3360 3407 8.844244 GCATGTCTATCTGAATTGATAAACCTT 58.156 33.333 0.00 0.00 0.00 3.50
3399 3446 9.807921 TCCTTAAGGAACATTATTTGAGTTTCT 57.192 29.630 22.27 0.00 42.18 2.52
3404 3451 9.449719 AAGGAACATTATTTGAGTTTCTATCGT 57.550 29.630 0.00 0.00 31.08 3.73
3409 3456 9.547753 ACATTATTTGAGTTTCTATCGTATGCT 57.452 29.630 0.00 0.00 0.00 3.79
3410 3457 9.803130 CATTATTTGAGTTTCTATCGTATGCTG 57.197 33.333 0.00 0.00 0.00 4.41
3411 3458 8.942338 TTATTTGAGTTTCTATCGTATGCTGT 57.058 30.769 0.00 0.00 0.00 4.40
3412 3459 6.647212 TTTGAGTTTCTATCGTATGCTGTG 57.353 37.500 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.404073 ACAAAGTGGCGAGATTCTCTATCT 59.596 41.667 11.75 0.00 46.41 1.98
11 12 4.688021 ACAAAGTGGCGAGATTCTCTATC 58.312 43.478 11.75 2.29 0.00 2.08
12 13 4.744795 ACAAAGTGGCGAGATTCTCTAT 57.255 40.909 11.75 0.00 0.00 1.98
13 14 4.245660 CAACAAAGTGGCGAGATTCTCTA 58.754 43.478 11.75 0.00 0.00 2.43
14 15 3.070018 CAACAAAGTGGCGAGATTCTCT 58.930 45.455 11.75 0.00 0.00 3.10
15 16 2.160417 CCAACAAAGTGGCGAGATTCTC 59.840 50.000 3.43 3.43 0.00 2.87
16 17 2.154462 CCAACAAAGTGGCGAGATTCT 58.846 47.619 0.00 0.00 0.00 2.40
17 18 1.200020 CCCAACAAAGTGGCGAGATTC 59.800 52.381 0.00 0.00 37.34 2.52
18 19 1.247567 CCCAACAAAGTGGCGAGATT 58.752 50.000 0.00 0.00 37.34 2.40
19 20 0.609131 CCCCAACAAAGTGGCGAGAT 60.609 55.000 0.00 0.00 37.34 2.75
20 21 1.228124 CCCCAACAAAGTGGCGAGA 60.228 57.895 0.00 0.00 37.34 4.04
21 22 1.228124 TCCCCAACAAAGTGGCGAG 60.228 57.895 0.00 0.00 37.34 5.03
22 23 1.527380 GTCCCCAACAAAGTGGCGA 60.527 57.895 0.00 0.00 37.34 5.54
23 24 0.250553 TAGTCCCCAACAAAGTGGCG 60.251 55.000 0.00 0.00 37.34 5.69
24 25 1.244816 GTAGTCCCCAACAAAGTGGC 58.755 55.000 0.00 0.00 37.34 5.01
25 26 1.905637 GGTAGTCCCCAACAAAGTGG 58.094 55.000 0.00 0.00 38.51 4.00
37 38 1.271926 ACATGTTTGGCTGGGTAGTCC 60.272 52.381 0.00 0.00 0.00 3.85
38 39 2.084546 GACATGTTTGGCTGGGTAGTC 58.915 52.381 0.00 0.00 0.00 2.59
39 40 1.610624 CGACATGTTTGGCTGGGTAGT 60.611 52.381 0.00 0.00 0.00 2.73
40 41 1.086696 CGACATGTTTGGCTGGGTAG 58.913 55.000 0.00 0.00 0.00 3.18
41 42 0.398696 ACGACATGTTTGGCTGGGTA 59.601 50.000 0.00 0.00 0.00 3.69
42 43 0.467290 AACGACATGTTTGGCTGGGT 60.467 50.000 0.00 0.00 37.59 4.51
43 44 0.240945 GAACGACATGTTTGGCTGGG 59.759 55.000 0.00 0.00 42.09 4.45
44 45 1.238439 AGAACGACATGTTTGGCTGG 58.762 50.000 0.00 0.00 42.09 4.85
45 46 4.219033 GTTTAGAACGACATGTTTGGCTG 58.781 43.478 0.00 0.00 42.09 4.85
46 47 3.252458 GGTTTAGAACGACATGTTTGGCT 59.748 43.478 0.00 0.00 42.09 4.75
47 48 3.252458 AGGTTTAGAACGACATGTTTGGC 59.748 43.478 0.00 0.00 42.09 4.52
48 49 5.390567 GCTAGGTTTAGAACGACATGTTTGG 60.391 44.000 0.00 0.00 42.09 3.28
49 50 5.408604 AGCTAGGTTTAGAACGACATGTTTG 59.591 40.000 0.00 0.00 42.09 2.93
50 51 5.548406 AGCTAGGTTTAGAACGACATGTTT 58.452 37.500 0.00 0.00 42.09 2.83
51 52 5.148651 AGCTAGGTTTAGAACGACATGTT 57.851 39.130 0.00 0.00 45.61 2.71
52 53 4.803098 AGCTAGGTTTAGAACGACATGT 57.197 40.909 0.00 0.00 0.00 3.21
53 54 6.097356 TGTAAGCTAGGTTTAGAACGACATG 58.903 40.000 13.21 0.00 0.00 3.21
54 55 6.276832 TGTAAGCTAGGTTTAGAACGACAT 57.723 37.500 13.21 0.00 0.00 3.06
55 56 5.336213 CCTGTAAGCTAGGTTTAGAACGACA 60.336 44.000 13.21 8.11 0.00 4.35
56 57 5.100943 CCTGTAAGCTAGGTTTAGAACGAC 58.899 45.833 13.21 3.61 0.00 4.34
57 58 4.381292 GCCTGTAAGCTAGGTTTAGAACGA 60.381 45.833 13.21 0.00 37.64 3.85
58 59 3.864003 GCCTGTAAGCTAGGTTTAGAACG 59.136 47.826 13.21 2.18 37.64 3.95
59 60 4.190001 GGCCTGTAAGCTAGGTTTAGAAC 58.810 47.826 13.21 5.45 37.64 3.01
60 61 3.841845 TGGCCTGTAAGCTAGGTTTAGAA 59.158 43.478 13.21 0.00 37.64 2.10
61 62 3.446968 TGGCCTGTAAGCTAGGTTTAGA 58.553 45.455 13.21 0.00 37.64 2.10
62 63 3.798202 CTGGCCTGTAAGCTAGGTTTAG 58.202 50.000 13.21 11.33 37.68 1.85
63 64 2.093128 GCTGGCCTGTAAGCTAGGTTTA 60.093 50.000 13.21 1.99 41.34 2.01
64 65 1.340114 GCTGGCCTGTAAGCTAGGTTT 60.340 52.381 13.21 0.00 41.34 3.27
65 66 0.253327 GCTGGCCTGTAAGCTAGGTT 59.747 55.000 12.54 12.54 41.34 3.50
66 67 1.908483 GCTGGCCTGTAAGCTAGGT 59.092 57.895 11.69 0.00 41.34 3.08
67 68 4.865865 GCTGGCCTGTAAGCTAGG 57.134 61.111 11.69 0.00 41.34 3.02
71 72 3.595819 CCAAGCTGGCCTGTAAGC 58.404 61.111 11.69 8.14 39.82 3.09
80 81 0.674581 TCACAATCTCGCCAAGCTGG 60.675 55.000 0.00 0.00 41.55 4.85
81 82 0.725686 CTCACAATCTCGCCAAGCTG 59.274 55.000 0.00 0.00 0.00 4.24
82 83 1.023513 GCTCACAATCTCGCCAAGCT 61.024 55.000 0.00 0.00 0.00 3.74
83 84 1.427020 GCTCACAATCTCGCCAAGC 59.573 57.895 0.00 0.00 0.00 4.01
84 85 0.392193 AGGCTCACAATCTCGCCAAG 60.392 55.000 0.00 0.00 44.85 3.61
85 86 0.391661 GAGGCTCACAATCTCGCCAA 60.392 55.000 10.25 0.00 44.85 4.52
86 87 1.219124 GAGGCTCACAATCTCGCCA 59.781 57.895 10.25 0.00 44.85 5.69
87 88 0.391661 TTGAGGCTCACAATCTCGCC 60.392 55.000 18.55 0.00 42.79 5.54
88 89 1.396301 CTTTGAGGCTCACAATCTCGC 59.604 52.381 18.55 0.00 0.00 5.03
89 90 2.693069 ACTTTGAGGCTCACAATCTCG 58.307 47.619 18.55 0.75 0.00 4.04
90 91 5.877012 TCATAACTTTGAGGCTCACAATCTC 59.123 40.000 18.55 0.00 0.00 2.75
91 92 5.809001 TCATAACTTTGAGGCTCACAATCT 58.191 37.500 18.55 3.68 0.00 2.40
92 93 6.690194 ATCATAACTTTGAGGCTCACAATC 57.310 37.500 18.55 0.00 0.00 2.67
93 94 6.096001 GGAATCATAACTTTGAGGCTCACAAT 59.904 38.462 18.55 0.00 0.00 2.71
94 95 5.415701 GGAATCATAACTTTGAGGCTCACAA 59.584 40.000 18.55 13.37 0.00 3.33
95 96 4.943705 GGAATCATAACTTTGAGGCTCACA 59.056 41.667 18.55 10.34 0.00 3.58
96 97 5.189180 AGGAATCATAACTTTGAGGCTCAC 58.811 41.667 18.55 0.41 0.00 3.51
97 98 5.441718 AGGAATCATAACTTTGAGGCTCA 57.558 39.130 14.43 14.43 0.00 4.26
98 99 7.554476 AGTTTAGGAATCATAACTTTGAGGCTC 59.446 37.037 7.79 7.79 0.00 4.70
99 100 7.406104 AGTTTAGGAATCATAACTTTGAGGCT 58.594 34.615 0.00 0.00 0.00 4.58
100 101 7.336931 TGAGTTTAGGAATCATAACTTTGAGGC 59.663 37.037 0.00 0.00 31.41 4.70
101 102 8.669243 GTGAGTTTAGGAATCATAACTTTGAGG 58.331 37.037 0.00 0.00 31.41 3.86
102 103 8.383619 CGTGAGTTTAGGAATCATAACTTTGAG 58.616 37.037 0.00 0.00 31.41 3.02
103 104 8.092068 TCGTGAGTTTAGGAATCATAACTTTGA 58.908 33.333 0.00 0.00 31.41 2.69
104 105 8.251750 TCGTGAGTTTAGGAATCATAACTTTG 57.748 34.615 0.00 0.00 31.41 2.77
105 106 8.718734 GTTCGTGAGTTTAGGAATCATAACTTT 58.281 33.333 0.00 0.00 31.41 2.66
106 107 7.876068 TGTTCGTGAGTTTAGGAATCATAACTT 59.124 33.333 0.00 0.00 31.41 2.66
107 108 7.383687 TGTTCGTGAGTTTAGGAATCATAACT 58.616 34.615 0.00 0.00 33.78 2.24
108 109 7.591006 TGTTCGTGAGTTTAGGAATCATAAC 57.409 36.000 0.00 0.00 0.00 1.89
109 110 8.610248 TTTGTTCGTGAGTTTAGGAATCATAA 57.390 30.769 0.00 0.00 0.00 1.90
110 111 8.610248 TTTTGTTCGTGAGTTTAGGAATCATA 57.390 30.769 0.00 0.00 0.00 2.15
111 112 7.504924 TTTTGTTCGTGAGTTTAGGAATCAT 57.495 32.000 0.00 0.00 0.00 2.45
112 113 6.928979 TTTTGTTCGTGAGTTTAGGAATCA 57.071 33.333 0.00 0.00 0.00 2.57
136 137 8.836413 CCGCAGAGACAATTTCCTTTTATATAA 58.164 33.333 0.00 0.00 0.00 0.98
137 138 7.444183 CCCGCAGAGACAATTTCCTTTTATATA 59.556 37.037 0.00 0.00 0.00 0.86
138 139 6.263168 CCCGCAGAGACAATTTCCTTTTATAT 59.737 38.462 0.00 0.00 0.00 0.86
139 140 5.588648 CCCGCAGAGACAATTTCCTTTTATA 59.411 40.000 0.00 0.00 0.00 0.98
140 141 4.399303 CCCGCAGAGACAATTTCCTTTTAT 59.601 41.667 0.00 0.00 0.00 1.40
141 142 3.756434 CCCGCAGAGACAATTTCCTTTTA 59.244 43.478 0.00 0.00 0.00 1.52
142 143 2.558359 CCCGCAGAGACAATTTCCTTTT 59.442 45.455 0.00 0.00 0.00 2.27
143 144 2.162681 CCCGCAGAGACAATTTCCTTT 58.837 47.619 0.00 0.00 0.00 3.11
144 145 1.073923 ACCCGCAGAGACAATTTCCTT 59.926 47.619 0.00 0.00 0.00 3.36
145 146 0.693049 ACCCGCAGAGACAATTTCCT 59.307 50.000 0.00 0.00 0.00 3.36
146 147 1.534729 AACCCGCAGAGACAATTTCC 58.465 50.000 0.00 0.00 0.00 3.13
147 148 3.643159 AAAACCCGCAGAGACAATTTC 57.357 42.857 0.00 0.00 0.00 2.17
169 170 8.514594 CAAGATTACAGAGATTGCCACTAAAAA 58.485 33.333 0.00 0.00 0.00 1.94
170 171 7.665559 ACAAGATTACAGAGATTGCCACTAAAA 59.334 33.333 0.00 0.00 0.00 1.52
171 172 7.168219 ACAAGATTACAGAGATTGCCACTAAA 58.832 34.615 0.00 0.00 0.00 1.85
172 173 6.711277 ACAAGATTACAGAGATTGCCACTAA 58.289 36.000 0.00 0.00 0.00 2.24
173 174 6.299805 ACAAGATTACAGAGATTGCCACTA 57.700 37.500 0.00 0.00 0.00 2.74
174 175 5.171339 ACAAGATTACAGAGATTGCCACT 57.829 39.130 0.00 0.00 0.00 4.00
175 176 5.525378 CCTACAAGATTACAGAGATTGCCAC 59.475 44.000 0.00 0.00 0.00 5.01
176 177 5.396772 CCCTACAAGATTACAGAGATTGCCA 60.397 44.000 0.00 0.00 0.00 4.92
177 178 5.059833 CCCTACAAGATTACAGAGATTGCC 58.940 45.833 0.00 0.00 0.00 4.52
178 179 5.059833 CCCCTACAAGATTACAGAGATTGC 58.940 45.833 0.00 0.00 0.00 3.56
179 180 5.131142 ACCCCCTACAAGATTACAGAGATTG 59.869 44.000 0.00 0.00 0.00 2.67
180 181 5.289510 ACCCCCTACAAGATTACAGAGATT 58.710 41.667 0.00 0.00 0.00 2.40
181 182 4.897051 ACCCCCTACAAGATTACAGAGAT 58.103 43.478 0.00 0.00 0.00 2.75
182 183 4.348020 ACCCCCTACAAGATTACAGAGA 57.652 45.455 0.00 0.00 0.00 3.10
183 184 4.469945 TCAACCCCCTACAAGATTACAGAG 59.530 45.833 0.00 0.00 0.00 3.35
184 185 4.431378 TCAACCCCCTACAAGATTACAGA 58.569 43.478 0.00 0.00 0.00 3.41
185 186 4.837093 TCAACCCCCTACAAGATTACAG 57.163 45.455 0.00 0.00 0.00 2.74
186 187 5.789574 AATCAACCCCCTACAAGATTACA 57.210 39.130 0.00 0.00 0.00 2.41
187 188 7.993101 GTTAAATCAACCCCCTACAAGATTAC 58.007 38.462 0.00 0.00 0.00 1.89
202 203 3.508402 ACATCCAACCCGGTTAAATCAAC 59.492 43.478 1.43 0.00 36.32 3.18
203 204 3.768878 ACATCCAACCCGGTTAAATCAA 58.231 40.909 1.43 0.00 35.57 2.57
204 205 3.443145 ACATCCAACCCGGTTAAATCA 57.557 42.857 1.43 0.00 35.57 2.57
205 206 3.881089 CCTACATCCAACCCGGTTAAATC 59.119 47.826 1.43 0.00 35.57 2.17
206 207 3.372241 CCCTACATCCAACCCGGTTAAAT 60.372 47.826 1.43 0.00 35.57 1.40
207 208 2.026075 CCCTACATCCAACCCGGTTAAA 60.026 50.000 1.43 0.00 35.57 1.52
208 209 1.560611 CCCTACATCCAACCCGGTTAA 59.439 52.381 1.43 0.00 35.57 2.01
209 210 1.205966 CCCTACATCCAACCCGGTTA 58.794 55.000 1.43 0.00 35.57 2.85
210 211 1.996086 CCCTACATCCAACCCGGTT 59.004 57.895 0.00 0.00 35.57 4.44
211 212 2.676265 GCCCTACATCCAACCCGGT 61.676 63.158 0.00 0.00 35.57 5.28
212 213 2.192175 GCCCTACATCCAACCCGG 59.808 66.667 0.00 0.00 0.00 5.73
213 214 1.146263 GAGCCCTACATCCAACCCG 59.854 63.158 0.00 0.00 0.00 5.28
214 215 1.279025 TGGAGCCCTACATCCAACCC 61.279 60.000 0.00 0.00 42.61 4.11
215 216 2.307153 TGGAGCCCTACATCCAACC 58.693 57.895 0.00 0.00 42.61 3.77
303 304 3.194329 ACTCGATCATGAGCTTCACTGAA 59.806 43.478 9.64 0.00 39.68 3.02
305 306 3.162202 ACTCGATCATGAGCTTCACTG 57.838 47.619 9.64 0.00 39.68 3.66
325 326 3.005367 TGAGCACGAGTCATGTTCTACAA 59.995 43.478 4.69 0.00 0.00 2.41
468 478 6.916387 CGTGGTCGACTATGTGTTAAATATCT 59.084 38.462 16.46 0.00 39.71 1.98
519 529 9.515020 CGTACATGGAAACTTAATTAAATGCAT 57.485 29.630 0.00 0.00 0.00 3.96
524 534 8.848182 ACCAACGTACATGGAAACTTAATTAAA 58.152 29.630 18.84 0.00 40.56 1.52
543 553 9.990360 ATTTTTCTCCATTTTATTTACCAACGT 57.010 25.926 0.00 0.00 0.00 3.99
669 683 3.329300 AGTCAATGTTGGCTCGCTT 57.671 47.368 0.00 0.00 39.25 4.68
685 699 3.181495 CGAGAAACGAGCCTATCTTGAGT 60.181 47.826 0.00 0.00 45.77 3.41
803 818 1.664302 GGTTGCAAGAAAAGCTCGAGC 60.664 52.381 30.01 30.01 42.49 5.03
821 836 3.810623 TCCCCTAAACATCCAACTAGGT 58.189 45.455 0.00 0.00 39.02 3.08
1554 1571 1.717937 CGCTGAATTGCTTCCGGAG 59.282 57.895 3.34 0.00 0.00 4.63
1555 1572 2.398554 GCGCTGAATTGCTTCCGGA 61.399 57.895 0.00 0.00 0.00 5.14
1560 1577 1.503542 CGAAGGCGCTGAATTGCTT 59.496 52.632 7.64 0.00 0.00 3.91
1619 1636 1.003718 GGGGTCCAGTTGGAGAACG 60.004 63.158 0.00 0.00 46.49 3.95
1842 1859 4.988716 ACGGAGCGGTGGAGACCA 62.989 66.667 0.00 0.00 43.33 4.02
2034 2051 3.365265 CAAGCAAGGACACGGGGC 61.365 66.667 0.00 0.00 0.00 5.80
2223 2240 1.817520 CACCGCGATAATGGCACCA 60.818 57.895 8.23 0.00 0.00 4.17
2298 2315 0.747852 TGACCACTGCAGACGTTGTA 59.252 50.000 23.35 3.92 0.00 2.41
2352 2369 1.140052 TGGAAGAACAGGCACGAAAGA 59.860 47.619 0.00 0.00 0.00 2.52
2394 2411 0.096976 CTTAACCCATCGCGTGCTTG 59.903 55.000 5.77 0.00 0.00 4.01
2442 2459 5.815740 ACAGAACTAAATTATGCTGGTACGG 59.184 40.000 0.00 0.00 32.40 4.02
2502 2519 1.517694 GCCGATGTTGCAATGCTGG 60.518 57.895 6.82 4.35 0.00 4.85
2556 2573 6.016610 TGCATAACAGTTTACTTCCAAAGGAC 60.017 38.462 0.00 0.00 0.00 3.85
2599 2616 4.937015 GGGTGCAAACAATTGAGCAATAAT 59.063 37.500 20.37 0.00 38.94 1.28
2602 2619 2.769893 GGGTGCAAACAATTGAGCAAT 58.230 42.857 20.37 0.00 38.94 3.56
2654 2672 9.787435 ACTTGGACACATGTAGTTTTATTTCTA 57.213 29.630 0.00 0.00 33.68 2.10
2681 2700 2.688507 ACATCTCCGTTAGCAAGTGTG 58.311 47.619 0.00 0.00 0.00 3.82
2682 2701 4.530710 TTACATCTCCGTTAGCAAGTGT 57.469 40.909 0.00 0.00 0.00 3.55
2694 2713 8.131731 GCTGATCTTAAAATGGTTTACATCTCC 58.868 37.037 0.00 0.00 39.40 3.71
2705 2724 5.571784 TGCTTGAGCTGATCTTAAAATGG 57.428 39.130 4.44 0.00 42.66 3.16
2735 2754 6.923928 AAAACAATTGTATTTTGCAGTGCT 57.076 29.167 17.60 0.00 0.00 4.40
2777 2823 9.357652 ACAACATTGCAACTGATAAACAATATC 57.642 29.630 0.00 0.00 30.16 1.63
2778 2824 9.142515 CACAACATTGCAACTGATAAACAATAT 57.857 29.630 0.00 0.00 30.16 1.28
2786 2832 3.191162 GGAGCACAACATTGCAACTGATA 59.809 43.478 0.00 0.00 45.62 2.15
2791 2837 1.603678 CCTGGAGCACAACATTGCAAC 60.604 52.381 0.00 0.00 45.62 4.17
2838 2884 7.394816 AGCTTTGAAAGGAATTGCTACTACTA 58.605 34.615 7.09 0.00 0.00 1.82
2840 2886 6.502136 AGCTTTGAAAGGAATTGCTACTAC 57.498 37.500 7.09 0.00 0.00 2.73
2845 2891 6.040842 TGACTAAAGCTTTGAAAGGAATTGCT 59.959 34.615 22.02 0.00 0.00 3.91
2853 2899 6.207417 TCCAAGGATGACTAAAGCTTTGAAAG 59.793 38.462 22.02 13.42 0.00 2.62
2896 2942 4.453480 TTCCCAGAGGTCTCAACAAAAT 57.547 40.909 0.55 0.00 0.00 1.82
2903 2949 1.688735 CGCATATTCCCAGAGGTCTCA 59.311 52.381 0.55 0.00 0.00 3.27
2906 2952 1.689273 ACTCGCATATTCCCAGAGGTC 59.311 52.381 0.00 0.00 33.58 3.85
2908 2954 2.487934 CAACTCGCATATTCCCAGAGG 58.512 52.381 0.00 0.00 33.58 3.69
2909 2955 2.103094 TCCAACTCGCATATTCCCAGAG 59.897 50.000 0.00 0.00 35.28 3.35
2922 2968 5.410924 TGACAAAGACTATCATCCAACTCG 58.589 41.667 0.00 0.00 0.00 4.18
2931 2977 5.129634 TGTTTGCCTTGACAAAGACTATCA 58.870 37.500 0.00 0.00 40.07 2.15
2956 3002 4.753107 TCGTATTGGAAGACAAAGGAACAC 59.247 41.667 0.00 0.00 43.46 3.32
2957 3003 4.963373 TCGTATTGGAAGACAAAGGAACA 58.037 39.130 0.00 0.00 43.46 3.18
2959 3005 4.000988 GCTCGTATTGGAAGACAAAGGAA 58.999 43.478 0.00 0.00 43.46 3.36
2967 3013 3.513912 TCCTTTCAGCTCGTATTGGAAGA 59.486 43.478 5.72 0.00 32.67 2.87
2974 3020 6.763610 CCTTTTATTCTCCTTTCAGCTCGTAT 59.236 38.462 0.00 0.00 0.00 3.06
2984 3030 8.826765 TGTATCTCTCACCTTTTATTCTCCTTT 58.173 33.333 0.00 0.00 0.00 3.11
2991 3037 6.662755 TGGCATGTATCTCTCACCTTTTATT 58.337 36.000 0.00 0.00 0.00 1.40
2992 3038 6.252599 TGGCATGTATCTCTCACCTTTTAT 57.747 37.500 0.00 0.00 0.00 1.40
2993 3039 5.692115 TGGCATGTATCTCTCACCTTTTA 57.308 39.130 0.00 0.00 0.00 1.52
3005 3051 8.570488 TCATATTTCTGAACATTGGCATGTATC 58.430 33.333 0.00 0.00 43.34 2.24
3030 3076 8.682936 AATCCATGGTCTGTTATCAACTATTC 57.317 34.615 12.58 0.00 0.00 1.75
3031 3077 7.442364 CGAATCCATGGTCTGTTATCAACTATT 59.558 37.037 12.58 0.00 0.00 1.73
3032 3078 6.931281 CGAATCCATGGTCTGTTATCAACTAT 59.069 38.462 12.58 0.00 0.00 2.12
3043 3089 2.695666 AGGTACTCGAATCCATGGTCTG 59.304 50.000 12.58 0.57 0.00 3.51
3050 3096 3.069586 CCAGCATAAGGTACTCGAATCCA 59.930 47.826 0.00 0.00 38.49 3.41
3052 3098 4.585955 TCCAGCATAAGGTACTCGAATC 57.414 45.455 0.00 0.00 38.49 2.52
3056 3102 3.119101 AGTGTTCCAGCATAAGGTACTCG 60.119 47.826 0.00 0.00 38.49 4.18
3066 3112 1.965643 ACATGCAAAGTGTTCCAGCAT 59.034 42.857 0.00 0.00 45.92 3.79
3069 3115 1.774639 GCACATGCAAAGTGTTCCAG 58.225 50.000 19.75 0.00 41.59 3.86
3084 3130 5.111989 GCTCTACTATCAATCTTGTGCACA 58.888 41.667 17.42 17.42 0.00 4.57
3085 3131 5.111989 TGCTCTACTATCAATCTTGTGCAC 58.888 41.667 10.75 10.75 0.00 4.57
3104 3150 4.252073 CTGCCAGATCATAAGGTATGCTC 58.748 47.826 0.00 0.00 36.14 4.26
3122 3169 1.335324 GCACACAATTGAGACACTGCC 60.335 52.381 13.59 0.00 0.00 4.85
3143 3190 5.306937 TCAAAGGTGTAAGACTGATCCTTGA 59.693 40.000 0.00 0.00 35.78 3.02
3147 3194 6.623767 GCAAATCAAAGGTGTAAGACTGATCC 60.624 42.308 0.00 0.00 0.00 3.36
3153 3200 3.365969 CGGGCAAATCAAAGGTGTAAGAC 60.366 47.826 0.00 0.00 0.00 3.01
3174 3221 0.318699 TGTCGTCAAGGTGAAGCTCG 60.319 55.000 0.00 0.00 0.00 5.03
3189 3236 3.254060 CAGAGTGGTGATAGGTTTGTCG 58.746 50.000 0.00 0.00 0.00 4.35
3199 3246 0.330604 AGCATTGCCAGAGTGGTGAT 59.669 50.000 4.70 0.00 40.46 3.06
3238 3285 7.268586 GTCAGCTATACCATATCATACAAGGG 58.731 42.308 0.00 0.00 0.00 3.95
3239 3286 6.975197 CGTCAGCTATACCATATCATACAAGG 59.025 42.308 0.00 0.00 0.00 3.61
3258 3305 6.021596 CCAAGTAAAATTCATGTACGTCAGC 58.978 40.000 0.00 0.00 0.00 4.26
3274 3321 7.118496 ACAACCACATGATTTTCCAAGTAAA 57.882 32.000 0.00 0.00 0.00 2.01
3276 3323 6.723298 AACAACCACATGATTTTCCAAGTA 57.277 33.333 0.00 0.00 0.00 2.24
3280 3327 7.118496 AGTTTAACAACCACATGATTTTCCA 57.882 32.000 0.00 0.00 32.70 3.53
3302 3349 8.349568 TGCGATAGAGACACCATAATTATAGT 57.650 34.615 0.00 0.00 39.76 2.12
3303 3350 9.242477 CATGCGATAGAGACACCATAATTATAG 57.758 37.037 0.00 0.00 39.76 1.31
3304 3351 8.966868 TCATGCGATAGAGACACCATAATTATA 58.033 33.333 0.00 0.00 39.76 0.98
3305 3352 7.840931 TCATGCGATAGAGACACCATAATTAT 58.159 34.615 0.00 0.00 39.76 1.28
3306 3353 7.227049 TCATGCGATAGAGACACCATAATTA 57.773 36.000 0.00 0.00 39.76 1.40
3307 3354 6.101650 TCATGCGATAGAGACACCATAATT 57.898 37.500 0.00 0.00 39.76 1.40
3308 3355 5.728637 TCATGCGATAGAGACACCATAAT 57.271 39.130 0.00 0.00 39.76 1.28
3309 3356 5.243730 TGATCATGCGATAGAGACACCATAA 59.756 40.000 0.00 0.00 39.76 1.90
3311 3358 3.575687 TGATCATGCGATAGAGACACCAT 59.424 43.478 0.00 0.00 39.76 3.55
3312 3359 2.958355 TGATCATGCGATAGAGACACCA 59.042 45.455 0.00 0.00 39.76 4.17
3313 3360 3.573598 CTGATCATGCGATAGAGACACC 58.426 50.000 0.00 0.00 39.76 4.16
3314 3361 2.985809 GCTGATCATGCGATAGAGACAC 59.014 50.000 0.00 0.00 39.76 3.67
3315 3362 2.624838 TGCTGATCATGCGATAGAGACA 59.375 45.455 0.00 0.00 39.76 3.41
3316 3363 3.294816 TGCTGATCATGCGATAGAGAC 57.705 47.619 0.00 0.00 39.76 3.36
3331 3378 9.049523 GTTTATCAATTCAGATAGACATGCTGA 57.950 33.333 0.00 0.00 36.28 4.26
3373 3420 9.807921 AGAAACTCAAATAATGTTCCTTAAGGA 57.192 29.630 20.72 20.72 43.73 3.36
3378 3425 9.449719 ACGATAGAAACTCAAATAATGTTCCTT 57.550 29.630 0.00 0.00 41.38 3.36
3383 3430 9.547753 AGCATACGATAGAAACTCAAATAATGT 57.452 29.630 0.00 0.00 41.38 2.71
3384 3431 9.803130 CAGCATACGATAGAAACTCAAATAATG 57.197 33.333 0.00 0.00 41.38 1.90
3385 3432 9.547753 ACAGCATACGATAGAAACTCAAATAAT 57.452 29.630 0.00 0.00 41.38 1.28
3386 3433 8.817100 CACAGCATACGATAGAAACTCAAATAA 58.183 33.333 0.00 0.00 41.38 1.40
3387 3434 8.352752 CACAGCATACGATAGAAACTCAAATA 57.647 34.615 0.00 0.00 41.38 1.40
3388 3435 7.239166 CACAGCATACGATAGAAACTCAAAT 57.761 36.000 0.00 0.00 41.38 2.32
3389 3436 6.647212 CACAGCATACGATAGAAACTCAAA 57.353 37.500 0.00 0.00 41.38 2.69


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

AutoCloner maintained by Alex Coulton.