Multiple sequence alignment - TraesCS4D01G126100

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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 TraesCS4D01G126100 chr4D 100.000 3146 0 0 1 3146 110109558 110112703 0.000000e+00 5810.0
1 TraesCS4D01G126100 chr4D 85.204 196 12 3 1 179 110094874 110095069 5.360000e-43 185.0
2 TraesCS4D01G126100 chr4A 94.723 1137 43 8 2019 3146 466575985 466574857 0.000000e+00 1751.0
3 TraesCS4D01G126100 chr4A 91.933 1128 34 23 687 1783 466579481 466578380 0.000000e+00 1526.0
4 TraesCS4D01G126100 chr4A 87.684 544 45 9 172 699 466629886 466629349 5.770000e-172 614.0
5 TraesCS4D01G126100 chr4A 92.339 248 4 7 1772 2019 466576181 466575949 3.890000e-89 339.0
6 TraesCS4D01G126100 chr4B 94.818 1100 42 5 2019 3109 171613735 171612642 0.000000e+00 1701.0
7 TraesCS4D01G126100 chr4B 88.992 1299 54 36 634 1885 171615237 171613981 0.000000e+00 1524.0
8 TraesCS4D01G126100 chr4B 87.006 354 22 7 264 597 171616265 171615916 8.240000e-101 377.0
9 TraesCS4D01G126100 chr4B 92.157 102 4 2 1916 2017 171613798 171613701 1.180000e-29 141.0
10 TraesCS4D01G126100 chr4B 95.349 43 2 0 1872 1914 171613962 171613920 5.630000e-08 69.4
11 TraesCS4D01G126100 chr5D 92.398 171 13 0 1 171 466349645 466349475 8.720000e-61 244.0
12 TraesCS4D01G126100 chr5D 91.954 174 12 2 1 173 17780813 17780985 3.130000e-60 243.0
13 TraesCS4D01G126100 chr2D 90.503 179 16 1 1 178 436741018 436740840 5.250000e-58 235.0
14 TraesCS4D01G126100 chr2D 91.935 124 10 0 55 178 425548666 425548543 1.160000e-39 174.0
15 TraesCS4D01G126100 chr7D 91.228 171 13 2 1 170 245423245 245423076 6.790000e-57 231.0
16 TraesCS4D01G126100 chr6D 85.052 194 11 7 1 177 369360319 369360127 6.930000e-42 182.0
17 TraesCS4D01G126100 chr6D 84.536 194 12 5 1 176 285817112 285816919 3.220000e-40 176.0
18 TraesCS4D01G126100 chr6D 83.978 181 21 8 3 178 428289140 428288963 1.940000e-37 167.0
19 TraesCS4D01G126100 chr6D 83.221 149 8 2 1 132 81514451 81514599 1.530000e-23 121.0
20 TraesCS4D01G126100 chr1D 84.694 196 12 6 1 178 429693670 429693475 2.490000e-41 180.0
21 TraesCS4D01G126100 chr3D 85.106 188 10 5 1 170 578352691 578352878 3.220000e-40 176.0
22 TraesCS4D01G126100 chr3D 84.574 188 10 6 1 170 128594975 128594789 5.400000e-38 169.0
23 TraesCS4D01G126100 chr3B 85.211 142 15 5 171 309 558082724 558082586 1.180000e-29 141.0
24 TraesCS4D01G126100 chr3B 88.750 80 8 1 171 249 767564423 767564344 2.580000e-16 97.1
25 TraesCS4D01G126100 chr3A 83.750 80 11 2 171 249 711450374 711450452 1.210000e-09 75.0


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 TraesCS4D01G126100 chr4D 110109558 110112703 3145 False 5810.000000 5810 100.000000 1 3146 1 chr4D.!!$F2 3145
1 TraesCS4D01G126100 chr4A 466574857 466579481 4624 True 1205.333333 1751 92.998333 687 3146 3 chr4A.!!$R2 2459
2 TraesCS4D01G126100 chr4A 466629349 466629886 537 True 614.000000 614 87.684000 172 699 1 chr4A.!!$R1 527
3 TraesCS4D01G126100 chr4B 171612642 171616265 3623 True 762.480000 1701 91.664400 264 3109 5 chr4B.!!$R1 2845

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
87 88 0.036858 GAGGCGGCTCTTGACTCTTT 60.037 55.0 30.02 0.0 0.00 2.52 F
632 654 0.037139 TCGATGTTGGGTTGGTACCG 60.037 55.0 7.57 0.0 46.04 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 4826 0.250124 TGCTCATCGTGGTTTCGGTT 60.250 50.0 0.0 0.0 0.0 4.44 R
2261 5372 0.026285 GCCGGTCATCATTTCGTTCG 59.974 55.0 1.9 0.0 0.0 3.95 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
42 43 3.688159 GCCACCTGCTGGGCTTTG 61.688 66.667 14.82 2.86 46.74 2.77
43 44 3.688159 CCACCTGCTGGGCTTTGC 61.688 66.667 14.82 0.00 39.10 3.68
53 54 4.522971 GGCTTTGCCGTCTCCTAG 57.477 61.111 0.00 0.00 39.62 3.02
54 55 1.815840 GGCTTTGCCGTCTCCTAGC 60.816 63.158 0.00 0.00 39.62 3.42
55 56 1.079127 GCTTTGCCGTCTCCTAGCA 60.079 57.895 0.00 0.00 33.97 3.49
56 57 1.086634 GCTTTGCCGTCTCCTAGCAG 61.087 60.000 0.00 0.00 37.89 4.24
57 58 1.079127 TTTGCCGTCTCCTAGCAGC 60.079 57.895 0.00 0.00 37.89 5.25
58 59 2.521958 TTTGCCGTCTCCTAGCAGCC 62.522 60.000 0.00 0.00 37.89 4.85
59 60 4.577246 GCCGTCTCCTAGCAGCCG 62.577 72.222 0.00 0.00 0.00 5.52
60 61 3.905678 CCGTCTCCTAGCAGCCGG 61.906 72.222 0.00 0.00 0.00 6.13
61 62 4.577246 CGTCTCCTAGCAGCCGGC 62.577 72.222 21.89 21.89 45.30 6.13
62 63 4.228567 GTCTCCTAGCAGCCGGCC 62.229 72.222 26.15 9.10 46.50 6.13
80 81 3.191539 GCGAAGAGGCGGCTCTTG 61.192 66.667 46.61 36.87 43.03 3.02
81 82 2.573869 CGAAGAGGCGGCTCTTGA 59.426 61.111 46.61 0.00 43.03 3.02
82 83 1.807573 CGAAGAGGCGGCTCTTGAC 60.808 63.158 46.61 34.19 43.03 3.18
83 84 1.594310 GAAGAGGCGGCTCTTGACT 59.406 57.895 46.61 30.40 43.03 3.41
84 85 0.459411 GAAGAGGCGGCTCTTGACTC 60.459 60.000 46.61 32.83 43.03 3.36
85 86 0.902516 AAGAGGCGGCTCTTGACTCT 60.903 55.000 42.76 24.91 41.61 3.24
86 87 0.902516 AGAGGCGGCTCTTGACTCTT 60.903 55.000 33.75 11.45 35.10 2.85
87 88 0.036858 GAGGCGGCTCTTGACTCTTT 60.037 55.000 30.02 0.00 0.00 2.52
88 89 0.321122 AGGCGGCTCTTGACTCTTTG 60.321 55.000 5.25 0.00 0.00 2.77
89 90 0.320771 GGCGGCTCTTGACTCTTTGA 60.321 55.000 0.00 0.00 0.00 2.69
90 91 1.512926 GCGGCTCTTGACTCTTTGAA 58.487 50.000 0.00 0.00 0.00 2.69
91 92 2.079925 GCGGCTCTTGACTCTTTGAAT 58.920 47.619 0.00 0.00 0.00 2.57
92 93 2.095053 GCGGCTCTTGACTCTTTGAATC 59.905 50.000 0.00 0.00 0.00 2.52
93 94 3.594134 CGGCTCTTGACTCTTTGAATCT 58.406 45.455 0.00 0.00 0.00 2.40
94 95 3.999663 CGGCTCTTGACTCTTTGAATCTT 59.000 43.478 0.00 0.00 0.00 2.40
95 96 4.142945 CGGCTCTTGACTCTTTGAATCTTG 60.143 45.833 0.00 0.00 0.00 3.02
96 97 4.999950 GGCTCTTGACTCTTTGAATCTTGA 59.000 41.667 0.00 0.00 0.00 3.02
97 98 5.122082 GGCTCTTGACTCTTTGAATCTTGAG 59.878 44.000 0.00 0.00 0.00 3.02
98 99 5.122082 GCTCTTGACTCTTTGAATCTTGAGG 59.878 44.000 0.00 0.00 0.00 3.86
99 100 6.425210 TCTTGACTCTTTGAATCTTGAGGA 57.575 37.500 0.00 0.00 0.00 3.71
100 101 6.830912 TCTTGACTCTTTGAATCTTGAGGAA 58.169 36.000 0.00 0.00 0.00 3.36
101 102 6.933521 TCTTGACTCTTTGAATCTTGAGGAAG 59.066 38.462 0.00 0.00 0.00 3.46
102 103 4.999950 TGACTCTTTGAATCTTGAGGAAGC 59.000 41.667 0.00 0.00 0.00 3.86
103 104 4.978099 ACTCTTTGAATCTTGAGGAAGCA 58.022 39.130 0.00 0.00 0.00 3.91
104 105 5.002516 ACTCTTTGAATCTTGAGGAAGCAG 58.997 41.667 0.00 0.00 0.00 4.24
105 106 3.755378 TCTTTGAATCTTGAGGAAGCAGC 59.245 43.478 0.00 0.00 0.00 5.25
106 107 2.119801 TGAATCTTGAGGAAGCAGCC 57.880 50.000 0.00 0.00 0.00 4.85
107 108 1.012841 GAATCTTGAGGAAGCAGCCG 58.987 55.000 0.00 0.00 0.00 5.52
108 109 0.393537 AATCTTGAGGAAGCAGCCGG 60.394 55.000 0.00 0.00 0.00 6.13
109 110 2.883267 ATCTTGAGGAAGCAGCCGGC 62.883 60.000 21.89 21.89 45.30 6.13
110 111 4.722700 TTGAGGAAGCAGCCGGCC 62.723 66.667 26.15 9.10 46.50 6.13
119 120 3.314331 CAGCCGGCCCCGATATCT 61.314 66.667 26.15 0.00 42.83 1.98
120 121 2.526873 AGCCGGCCCCGATATCTT 60.527 61.111 26.15 0.00 42.83 2.40
121 122 2.358737 GCCGGCCCCGATATCTTG 60.359 66.667 18.11 0.00 42.83 3.02
122 123 2.879233 GCCGGCCCCGATATCTTGA 61.879 63.158 18.11 0.00 42.83 3.02
123 124 1.752198 CCGGCCCCGATATCTTGAA 59.248 57.895 8.54 0.00 42.83 2.69
124 125 0.320771 CCGGCCCCGATATCTTGAAG 60.321 60.000 8.54 0.00 42.83 3.02
125 126 0.951040 CGGCCCCGATATCTTGAAGC 60.951 60.000 0.00 0.00 42.83 3.86
126 127 0.951040 GGCCCCGATATCTTGAAGCG 60.951 60.000 0.34 0.00 0.00 4.68
127 128 1.569479 GCCCCGATATCTTGAAGCGC 61.569 60.000 0.00 0.00 0.00 5.92
128 129 0.951040 CCCCGATATCTTGAAGCGCC 60.951 60.000 2.29 0.00 0.00 6.53
129 130 0.249868 CCCGATATCTTGAAGCGCCA 60.250 55.000 2.29 0.00 0.00 5.69
130 131 1.609061 CCCGATATCTTGAAGCGCCAT 60.609 52.381 2.29 0.00 0.00 4.40
131 132 1.462283 CCGATATCTTGAAGCGCCATG 59.538 52.381 2.29 0.00 0.00 3.66
132 133 1.462283 CGATATCTTGAAGCGCCATGG 59.538 52.381 7.63 7.63 0.00 3.66
133 134 1.808945 GATATCTTGAAGCGCCATGGG 59.191 52.381 15.13 4.77 0.00 4.00
134 135 0.179020 TATCTTGAAGCGCCATGGGG 60.179 55.000 23.98 23.98 37.18 4.96
135 136 2.916527 ATCTTGAAGCGCCATGGGGG 62.917 60.000 28.30 11.95 38.76 5.40
144 145 2.123164 CCATGGGGGCCAATGAGG 60.123 66.667 17.45 3.76 36.95 3.86
153 154 4.540153 CCAATGAGGCTACCCGTG 57.460 61.111 0.00 0.00 35.76 4.94
154 155 1.153168 CCAATGAGGCTACCCGTGG 60.153 63.158 0.00 0.00 35.76 4.94
155 156 1.819632 CAATGAGGCTACCCGTGGC 60.820 63.158 0.00 0.00 35.76 5.01
161 162 4.968370 GCTACCCGTGGCCAATTA 57.032 55.556 7.24 0.00 0.00 1.40
162 163 2.400911 GCTACCCGTGGCCAATTAC 58.599 57.895 7.24 0.00 0.00 1.89
163 164 0.107361 GCTACCCGTGGCCAATTACT 60.107 55.000 7.24 0.00 0.00 2.24
164 165 1.949465 CTACCCGTGGCCAATTACTC 58.051 55.000 7.24 0.00 0.00 2.59
165 166 0.542805 TACCCGTGGCCAATTACTCC 59.457 55.000 7.24 0.00 0.00 3.85
166 167 1.817941 CCCGTGGCCAATTACTCCG 60.818 63.158 7.24 4.51 0.00 4.63
167 168 1.219664 CCGTGGCCAATTACTCCGA 59.780 57.895 7.24 0.00 0.00 4.55
168 169 1.087771 CCGTGGCCAATTACTCCGAC 61.088 60.000 7.24 0.00 0.00 4.79
169 170 0.390603 CGTGGCCAATTACTCCGACA 60.391 55.000 7.24 0.00 0.00 4.35
170 171 1.369625 GTGGCCAATTACTCCGACAG 58.630 55.000 7.24 0.00 0.00 3.51
171 172 0.981183 TGGCCAATTACTCCGACAGT 59.019 50.000 0.61 0.00 39.41 3.55
172 173 1.066430 TGGCCAATTACTCCGACAGTC 60.066 52.381 0.61 0.00 36.43 3.51
173 174 1.278238 GCCAATTACTCCGACAGTCG 58.722 55.000 16.50 16.50 40.07 4.18
174 175 1.403780 GCCAATTACTCCGACAGTCGT 60.404 52.381 21.34 6.01 38.40 4.34
175 176 2.929592 GCCAATTACTCCGACAGTCGTT 60.930 50.000 21.34 5.36 38.40 3.85
176 177 2.921754 CCAATTACTCCGACAGTCGTTC 59.078 50.000 21.34 0.00 38.40 3.95
177 178 2.921754 CAATTACTCCGACAGTCGTTCC 59.078 50.000 21.34 0.00 38.40 3.62
178 179 1.901591 TTACTCCGACAGTCGTTCCT 58.098 50.000 21.34 3.86 38.40 3.36
179 180 1.446907 TACTCCGACAGTCGTTCCTC 58.553 55.000 21.34 0.00 38.40 3.71
180 181 0.250814 ACTCCGACAGTCGTTCCTCT 60.251 55.000 21.34 0.00 38.40 3.69
181 182 0.448593 CTCCGACAGTCGTTCCTCTC 59.551 60.000 21.34 0.00 38.40 3.20
182 183 1.134901 CCGACAGTCGTTCCTCTCG 59.865 63.158 21.34 0.00 38.40 4.04
187 188 4.144703 GTCGTTCCTCTCGGGGGC 62.145 72.222 0.00 0.00 35.33 5.80
201 202 3.292159 GGGCGTTGTTGTGGGTCC 61.292 66.667 0.00 0.00 0.00 4.46
210 211 1.465188 TTGTGGGTCCCCTCATGGT 60.465 57.895 5.13 0.00 39.04 3.55
232 233 1.340114 CCTAGGCTCCAGGGTGAAAAC 60.340 57.143 0.00 0.00 0.00 2.43
248 249 1.849977 AAACCCTAGTCCGTCCTCTC 58.150 55.000 0.00 0.00 0.00 3.20
311 317 2.525629 TTGTCGTGGAGCCCCAGA 60.526 61.111 0.00 0.00 44.55 3.86
472 487 1.243902 GCGAGGGGACAATTTCAACA 58.756 50.000 0.00 0.00 0.00 3.33
498 520 3.103742 GACTTGTCCTCCTCCAGAGATT 58.896 50.000 0.00 0.00 46.50 2.40
510 532 1.808945 CCAGAGATTGCTTGGTGTGTC 59.191 52.381 0.00 0.00 0.00 3.67
513 535 0.606401 AGATTGCTTGGTGTGTCCGG 60.606 55.000 0.00 0.00 39.52 5.14
547 569 1.148273 TGGTTTCTCAAGGCTGCGT 59.852 52.632 0.00 0.00 0.00 5.24
548 570 0.394938 TGGTTTCTCAAGGCTGCGTA 59.605 50.000 0.00 0.00 0.00 4.42
553 575 2.543777 TCTCAAGGCTGCGTAGTTTT 57.456 45.000 1.53 0.00 0.00 2.43
563 585 3.550030 GCTGCGTAGTTTTGGTCATGTTT 60.550 43.478 1.53 0.00 0.00 2.83
572 594 6.569780 AGTTTTGGTCATGTTTGGTAGTTTC 58.430 36.000 0.00 0.00 0.00 2.78
588 610 6.422701 TGGTAGTTTCGTTTGTCTCATGTTAG 59.577 38.462 0.00 0.00 0.00 2.34
595 617 4.084537 CGTTTGTCTCATGTTAGGTGTGAC 60.085 45.833 0.00 0.00 39.36 3.67
632 654 0.037139 TCGATGTTGGGTTGGTACCG 60.037 55.000 7.57 0.00 46.04 4.02
707 1390 3.839293 ACGAGGATTTTCTCAGTTCGAG 58.161 45.455 0.00 0.00 43.80 4.04
749 1432 3.117046 TGAAACATTTCGGCCGTTTTTC 58.883 40.909 27.15 23.49 40.01 2.29
753 1436 2.058057 CATTTCGGCCGTTTTTCAAGG 58.942 47.619 27.15 7.53 0.00 3.61
817 1504 3.514417 GGCCTTCCGATGAAAGGC 58.486 61.111 16.64 16.64 40.81 4.35
864 1558 0.461339 GCGCGTCCTTCCTTTATCCA 60.461 55.000 8.43 0.00 0.00 3.41
865 1559 1.810412 GCGCGTCCTTCCTTTATCCAT 60.810 52.381 8.43 0.00 0.00 3.41
866 1560 2.561569 CGCGTCCTTCCTTTATCCATT 58.438 47.619 0.00 0.00 0.00 3.16
867 1561 2.544267 CGCGTCCTTCCTTTATCCATTC 59.456 50.000 0.00 0.00 0.00 2.67
868 1562 2.879026 GCGTCCTTCCTTTATCCATTCC 59.121 50.000 0.00 0.00 0.00 3.01
894 1591 0.663153 ACGCAAGAACCAAGAACAGC 59.337 50.000 0.00 0.00 43.62 4.40
895 1592 0.384725 CGCAAGAACCAAGAACAGCG 60.385 55.000 0.00 0.00 43.02 5.18
896 1593 0.661483 GCAAGAACCAAGAACAGCGC 60.661 55.000 0.00 0.00 0.00 5.92
897 1594 0.947244 CAAGAACCAAGAACAGCGCT 59.053 50.000 2.64 2.64 0.00 5.92
954 1651 2.622629 CGCGCGAGTTCATCCATG 59.377 61.111 28.94 0.00 0.00 3.66
958 1655 0.460109 CGCGAGTTCATCCATGTCCA 60.460 55.000 0.00 0.00 0.00 4.02
961 1658 1.208052 CGAGTTCATCCATGTCCACCT 59.792 52.381 0.00 0.00 0.00 4.00
963 1660 1.561542 AGTTCATCCATGTCCACCTCC 59.438 52.381 0.00 0.00 0.00 4.30
964 1661 1.281867 GTTCATCCATGTCCACCTCCA 59.718 52.381 0.00 0.00 0.00 3.86
976 1673 1.241165 CACCTCCACCCCGTAAAAAC 58.759 55.000 0.00 0.00 0.00 2.43
1078 1775 3.605749 AAGGATGGCGACGGTGTGG 62.606 63.158 0.00 0.00 0.00 4.17
1128 1855 3.451828 CGCACGCACGCAACAATG 61.452 61.111 0.00 0.00 0.00 2.82
1268 1995 4.129737 ATCGCGGAGGTGGACACG 62.130 66.667 6.13 0.00 0.00 4.49
1380 2113 0.596577 CGTCTTCGACCAGGACAAGA 59.403 55.000 0.00 0.00 39.71 3.02
1397 2130 0.459237 AGAACGGCTTCATCTCGCTG 60.459 55.000 0.00 0.00 38.46 5.18
1528 2261 0.741221 GAGTTCGCCAGGGTCATGAC 60.741 60.000 17.91 17.91 0.00 3.06
1556 2295 1.012086 CAGTGCCATTCCGTCTCATG 58.988 55.000 0.00 0.00 0.00 3.07
1557 2296 0.745845 AGTGCCATTCCGTCTCATGC 60.746 55.000 0.00 0.00 0.00 4.06
1558 2297 1.026182 GTGCCATTCCGTCTCATGCA 61.026 55.000 0.00 0.00 0.00 3.96
1559 2298 0.107066 TGCCATTCCGTCTCATGCAT 60.107 50.000 0.00 0.00 0.00 3.96
1569 2308 1.592081 GTCTCATGCATCTTCTCACGC 59.408 52.381 0.00 0.00 0.00 5.34
1641 2380 7.582667 ATCAATGAATCAATCAATCTGCAGA 57.417 32.000 20.79 20.79 42.54 4.26
1649 2388 4.880120 TCAATCAATCTGCAGAATGGACTC 59.120 41.667 27.35 0.00 35.86 3.36
1650 2389 2.897436 TCAATCTGCAGAATGGACTCG 58.103 47.619 27.35 5.20 35.86 4.18
1651 2390 2.497273 TCAATCTGCAGAATGGACTCGA 59.503 45.455 27.35 8.04 35.86 4.04
1652 2391 2.593346 ATCTGCAGAATGGACTCGAC 57.407 50.000 22.50 0.00 35.86 4.20
1653 2392 0.171231 TCTGCAGAATGGACTCGACG 59.829 55.000 15.67 0.00 35.86 5.12
1654 2393 0.803768 CTGCAGAATGGACTCGACGG 60.804 60.000 8.42 0.00 35.86 4.79
1754 2493 1.399744 ATGCAGATCGGCCGGAGTAA 61.400 55.000 27.83 5.39 0.00 2.24
1799 4748 4.727235 GCAACTTGCGTTAACTAGTCTT 57.273 40.909 3.71 0.00 31.71 3.01
1800 4749 4.699303 GCAACTTGCGTTAACTAGTCTTC 58.301 43.478 3.71 0.00 31.71 2.87
1801 4750 4.210537 GCAACTTGCGTTAACTAGTCTTCA 59.789 41.667 3.71 0.00 31.71 3.02
1802 4751 5.667175 CAACTTGCGTTAACTAGTCTTCAC 58.333 41.667 3.71 0.00 0.00 3.18
1803 4752 5.197682 ACTTGCGTTAACTAGTCTTCACT 57.802 39.130 3.71 0.00 36.55 3.41
1804 4753 5.221130 ACTTGCGTTAACTAGTCTTCACTC 58.779 41.667 3.71 0.00 33.62 3.51
1805 4754 5.009811 ACTTGCGTTAACTAGTCTTCACTCT 59.990 40.000 3.71 0.00 33.62 3.24
1862 4818 1.736645 GCACTTGCAAGGCAGCATG 60.737 57.895 29.18 17.96 45.19 4.06
1932 5036 9.920133 ATGATACTACTAGAATGCTATGTGTTG 57.080 33.333 0.00 0.00 0.00 3.33
1933 5037 7.867909 TGATACTACTAGAATGCTATGTGTTGC 59.132 37.037 0.00 0.00 0.00 4.17
1934 5038 6.227298 ACTACTAGAATGCTATGTGTTGCT 57.773 37.500 0.00 0.00 0.00 3.91
1935 5039 7.348080 ACTACTAGAATGCTATGTGTTGCTA 57.652 36.000 0.00 0.00 0.00 3.49
1936 5040 7.429633 ACTACTAGAATGCTATGTGTTGCTAG 58.570 38.462 0.00 0.00 0.00 3.42
2017 5121 2.386661 AAACAGCCGTGAGATGGTAG 57.613 50.000 0.00 0.00 0.00 3.18
2018 5122 0.537188 AACAGCCGTGAGATGGTAGG 59.463 55.000 0.00 0.00 0.00 3.18
2019 5123 1.330655 ACAGCCGTGAGATGGTAGGG 61.331 60.000 0.00 0.00 0.00 3.53
2020 5124 2.109181 GCCGTGAGATGGTAGGGC 59.891 66.667 0.00 0.00 40.17 5.19
2021 5125 2.417516 CCGTGAGATGGTAGGGCG 59.582 66.667 0.00 0.00 0.00 6.13
2022 5126 2.417516 CGTGAGATGGTAGGGCGG 59.582 66.667 0.00 0.00 0.00 6.13
2023 5127 2.125326 CGTGAGATGGTAGGGCGGA 61.125 63.158 0.00 0.00 0.00 5.54
2024 5128 1.672854 CGTGAGATGGTAGGGCGGAA 61.673 60.000 0.00 0.00 0.00 4.30
2025 5129 0.105039 GTGAGATGGTAGGGCGGAAG 59.895 60.000 0.00 0.00 0.00 3.46
2026 5130 0.325296 TGAGATGGTAGGGCGGAAGT 60.325 55.000 0.00 0.00 0.00 3.01
2027 5131 0.389757 GAGATGGTAGGGCGGAAGTC 59.610 60.000 0.00 0.00 0.00 3.01
2028 5132 0.325296 AGATGGTAGGGCGGAAGTCA 60.325 55.000 0.00 0.00 37.54 3.41
2029 5133 0.179081 GATGGTAGGGCGGAAGTCAC 60.179 60.000 0.00 0.00 37.54 3.67
2030 5134 0.907704 ATGGTAGGGCGGAAGTCACA 60.908 55.000 0.00 0.00 37.54 3.58
2031 5135 1.218316 GGTAGGGCGGAAGTCACAG 59.782 63.158 0.00 0.00 37.54 3.66
2032 5136 1.448013 GTAGGGCGGAAGTCACAGC 60.448 63.158 0.00 0.00 37.54 4.40
2033 5137 1.911269 TAGGGCGGAAGTCACAGCA 60.911 57.895 0.00 0.00 37.54 4.41
2034 5138 1.476845 TAGGGCGGAAGTCACAGCAA 61.477 55.000 0.00 0.00 37.54 3.91
2035 5139 1.896660 GGGCGGAAGTCACAGCAAA 60.897 57.895 0.00 0.00 37.54 3.68
2036 5140 1.452145 GGGCGGAAGTCACAGCAAAA 61.452 55.000 0.00 0.00 37.54 2.44
2037 5141 0.317854 GGCGGAAGTCACAGCAAAAC 60.318 55.000 0.00 0.00 34.40 2.43
2038 5142 0.380378 GCGGAAGTCACAGCAAAACA 59.620 50.000 0.00 0.00 0.00 2.83
2039 5143 1.597937 GCGGAAGTCACAGCAAAACAG 60.598 52.381 0.00 0.00 0.00 3.16
2040 5144 1.670811 CGGAAGTCACAGCAAAACAGT 59.329 47.619 0.00 0.00 0.00 3.55
2041 5145 2.286418 CGGAAGTCACAGCAAAACAGTC 60.286 50.000 0.00 0.00 0.00 3.51
2042 5146 2.286418 GGAAGTCACAGCAAAACAGTCG 60.286 50.000 0.00 0.00 0.00 4.18
2043 5147 2.024176 AGTCACAGCAAAACAGTCGT 57.976 45.000 0.00 0.00 0.00 4.34
2044 5148 1.665679 AGTCACAGCAAAACAGTCGTG 59.334 47.619 0.00 0.00 0.00 4.35
2045 5149 1.663643 GTCACAGCAAAACAGTCGTGA 59.336 47.619 0.00 0.00 0.00 4.35
2046 5150 1.933181 TCACAGCAAAACAGTCGTGAG 59.067 47.619 0.00 0.00 0.00 3.51
2047 5151 1.933181 CACAGCAAAACAGTCGTGAGA 59.067 47.619 0.00 0.00 38.16 3.27
2048 5152 2.545526 CACAGCAAAACAGTCGTGAGAT 59.454 45.455 0.00 0.00 45.19 2.75
2049 5153 2.545526 ACAGCAAAACAGTCGTGAGATG 59.454 45.455 0.00 0.00 45.19 2.90
2050 5154 2.096069 CAGCAAAACAGTCGTGAGATGG 60.096 50.000 0.00 0.00 45.19 3.51
2051 5155 1.873591 GCAAAACAGTCGTGAGATGGT 59.126 47.619 0.00 0.00 45.19 3.55
2052 5156 3.064207 GCAAAACAGTCGTGAGATGGTA 58.936 45.455 0.00 0.00 45.19 3.25
2148 5258 5.303971 CCCTCATGTATCATCCTCTGAAAC 58.696 45.833 0.00 0.00 37.44 2.78
2190 5300 4.633565 CCCTTCAGTTCTGATTTACAGCTC 59.366 45.833 3.28 0.00 45.38 4.09
2234 5344 8.196802 ACAAGGCAAAAACAAGAAATTAACTC 57.803 30.769 0.00 0.00 0.00 3.01
2258 5369 5.394443 CCATGGTCTCACAATTTACAATGGG 60.394 44.000 2.57 0.00 39.03 4.00
2259 5370 4.991776 TGGTCTCACAATTTACAATGGGA 58.008 39.130 0.00 0.00 0.00 4.37
2260 5371 5.389520 TGGTCTCACAATTTACAATGGGAA 58.610 37.500 0.00 0.00 0.00 3.97
2261 5372 5.242838 TGGTCTCACAATTTACAATGGGAAC 59.757 40.000 0.00 0.00 0.00 3.62
2497 5611 1.133976 GCTGACAACAGGGCTATCCAT 60.134 52.381 0.00 0.00 43.62 3.41
2527 5641 6.536941 ACTTACAAAATGCGGTGAACAATTTT 59.463 30.769 0.00 0.00 0.00 1.82
2528 5642 5.809719 ACAAAATGCGGTGAACAATTTTT 57.190 30.435 0.00 0.00 0.00 1.94
2565 5679 4.695396 CTGAGAATGGATCAACTCAGGAG 58.305 47.826 20.03 0.00 46.93 3.69
2843 5958 1.606737 GCACCTCTCAGTTGACAGACC 60.607 57.143 0.00 0.00 0.00 3.85
2863 5978 6.095440 CAGACCCTACTTCCAAACCATAATTG 59.905 42.308 0.00 0.00 0.00 2.32
2899 6014 6.174720 ACCTTGTGAAATTCTAGAGTGTCA 57.825 37.500 4.05 4.05 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.688159 CAAAGCCCAGCAGGTGGC 61.688 66.667 13.73 8.90 46.45 5.01
27 28 3.688159 GGCAAAGCCCAGCAGGTG 61.688 66.667 0.00 0.00 44.06 4.00
36 37 1.815840 GCTAGGAGACGGCAAAGCC 60.816 63.158 0.00 0.00 46.75 4.35
37 38 1.079127 TGCTAGGAGACGGCAAAGC 60.079 57.895 0.00 0.00 39.98 3.51
38 39 1.086634 GCTGCTAGGAGACGGCAAAG 61.087 60.000 16.44 0.00 41.66 2.77
39 40 1.079127 GCTGCTAGGAGACGGCAAA 60.079 57.895 16.44 0.00 41.66 3.68
40 41 2.579201 GCTGCTAGGAGACGGCAA 59.421 61.111 16.44 0.00 41.66 4.52
41 42 3.461773 GGCTGCTAGGAGACGGCA 61.462 66.667 16.44 0.00 40.04 5.69
42 43 4.577246 CGGCTGCTAGGAGACGGC 62.577 72.222 30.09 10.79 41.08 5.68
44 45 4.577246 GCCGGCTGCTAGGAGACG 62.577 72.222 30.69 30.69 44.64 4.18
45 46 4.228567 GGCCGGCTGCTAGGAGAC 62.229 72.222 28.56 11.95 40.92 3.36
68 69 0.036858 AAAGAGTCAAGAGCCGCCTC 60.037 55.000 0.00 0.00 38.42 4.70
69 70 0.321122 CAAAGAGTCAAGAGCCGCCT 60.321 55.000 0.00 0.00 0.00 5.52
70 71 0.320771 TCAAAGAGTCAAGAGCCGCC 60.321 55.000 0.00 0.00 0.00 6.13
71 72 1.512926 TTCAAAGAGTCAAGAGCCGC 58.487 50.000 0.00 0.00 0.00 6.53
72 73 3.594134 AGATTCAAAGAGTCAAGAGCCG 58.406 45.455 0.00 0.00 0.00 5.52
73 74 4.999950 TCAAGATTCAAAGAGTCAAGAGCC 59.000 41.667 0.00 0.00 0.00 4.70
74 75 5.122082 CCTCAAGATTCAAAGAGTCAAGAGC 59.878 44.000 0.00 0.00 0.00 4.09
75 76 6.462500 TCCTCAAGATTCAAAGAGTCAAGAG 58.538 40.000 0.00 0.00 0.00 2.85
76 77 6.425210 TCCTCAAGATTCAAAGAGTCAAGA 57.575 37.500 0.00 0.00 0.00 3.02
77 78 6.348376 GCTTCCTCAAGATTCAAAGAGTCAAG 60.348 42.308 0.00 0.00 0.00 3.02
78 79 5.471456 GCTTCCTCAAGATTCAAAGAGTCAA 59.529 40.000 0.00 0.00 0.00 3.18
79 80 4.999950 GCTTCCTCAAGATTCAAAGAGTCA 59.000 41.667 0.00 0.00 0.00 3.41
80 81 4.999950 TGCTTCCTCAAGATTCAAAGAGTC 59.000 41.667 0.00 0.00 0.00 3.36
81 82 4.978099 TGCTTCCTCAAGATTCAAAGAGT 58.022 39.130 0.00 0.00 0.00 3.24
82 83 4.142643 GCTGCTTCCTCAAGATTCAAAGAG 60.143 45.833 0.00 0.00 0.00 2.85
83 84 3.755378 GCTGCTTCCTCAAGATTCAAAGA 59.245 43.478 0.00 0.00 0.00 2.52
84 85 3.119566 GGCTGCTTCCTCAAGATTCAAAG 60.120 47.826 0.00 0.00 0.00 2.77
85 86 2.821969 GGCTGCTTCCTCAAGATTCAAA 59.178 45.455 0.00 0.00 0.00 2.69
86 87 2.440409 GGCTGCTTCCTCAAGATTCAA 58.560 47.619 0.00 0.00 0.00 2.69
87 88 1.676916 CGGCTGCTTCCTCAAGATTCA 60.677 52.381 0.00 0.00 0.00 2.57
88 89 1.012841 CGGCTGCTTCCTCAAGATTC 58.987 55.000 0.00 0.00 0.00 2.52
89 90 0.393537 CCGGCTGCTTCCTCAAGATT 60.394 55.000 0.00 0.00 0.00 2.40
90 91 1.222936 CCGGCTGCTTCCTCAAGAT 59.777 57.895 0.00 0.00 0.00 2.40
91 92 2.665000 CCGGCTGCTTCCTCAAGA 59.335 61.111 0.00 0.00 0.00 3.02
92 93 3.130160 GCCGGCTGCTTCCTCAAG 61.130 66.667 22.15 0.00 36.87 3.02
93 94 4.722700 GGCCGGCTGCTTCCTCAA 62.723 66.667 28.56 0.00 40.92 3.02
102 103 2.883828 AAGATATCGGGGCCGGCTG 61.884 63.158 28.56 16.81 40.25 4.85
103 104 2.526873 AAGATATCGGGGCCGGCT 60.527 61.111 28.56 8.66 40.25 5.52
104 105 2.358737 CAAGATATCGGGGCCGGC 60.359 66.667 21.18 21.18 40.25 6.13
105 106 0.320771 CTTCAAGATATCGGGGCCGG 60.321 60.000 4.42 4.42 40.25 6.13
106 107 0.951040 GCTTCAAGATATCGGGGCCG 60.951 60.000 0.00 0.00 41.35 6.13
107 108 0.951040 CGCTTCAAGATATCGGGGCC 60.951 60.000 0.00 0.00 0.00 5.80
108 109 1.569479 GCGCTTCAAGATATCGGGGC 61.569 60.000 0.00 3.61 0.00 5.80
109 110 0.951040 GGCGCTTCAAGATATCGGGG 60.951 60.000 7.64 0.00 0.00 5.73
110 111 0.249868 TGGCGCTTCAAGATATCGGG 60.250 55.000 7.64 0.00 0.00 5.14
111 112 1.462283 CATGGCGCTTCAAGATATCGG 59.538 52.381 7.64 0.00 0.00 4.18
112 113 1.462283 CCATGGCGCTTCAAGATATCG 59.538 52.381 7.64 0.00 0.00 2.92
113 114 1.808945 CCCATGGCGCTTCAAGATATC 59.191 52.381 6.09 0.00 0.00 1.63
114 115 1.546323 CCCCATGGCGCTTCAAGATAT 60.546 52.381 6.09 0.00 0.00 1.63
115 116 0.179020 CCCCATGGCGCTTCAAGATA 60.179 55.000 6.09 0.00 0.00 1.98
116 117 1.454479 CCCCATGGCGCTTCAAGAT 60.454 57.895 6.09 0.00 0.00 2.40
117 118 2.045045 CCCCATGGCGCTTCAAGA 60.045 61.111 6.09 0.00 0.00 3.02
118 119 3.142838 CCCCCATGGCGCTTCAAG 61.143 66.667 6.09 0.00 0.00 3.02
127 128 2.123164 CCTCATTGGCCCCCATGG 60.123 66.667 4.14 4.14 31.53 3.66
136 137 1.153168 CCACGGGTAGCCTCATTGG 60.153 63.158 9.73 6.40 39.35 3.16
137 138 1.819632 GCCACGGGTAGCCTCATTG 60.820 63.158 9.73 0.88 0.00 2.82
138 139 2.590092 GCCACGGGTAGCCTCATT 59.410 61.111 9.73 0.00 0.00 2.57
139 140 3.480133 GGCCACGGGTAGCCTCAT 61.480 66.667 9.73 0.00 46.14 2.90
144 145 0.107361 AGTAATTGGCCACGGGTAGC 60.107 55.000 3.88 0.00 0.00 3.58
145 146 1.474498 GGAGTAATTGGCCACGGGTAG 60.474 57.143 3.88 0.00 0.00 3.18
146 147 0.542805 GGAGTAATTGGCCACGGGTA 59.457 55.000 3.88 0.00 0.00 3.69
147 148 1.301954 GGAGTAATTGGCCACGGGT 59.698 57.895 3.88 0.00 0.00 5.28
148 149 1.817941 CGGAGTAATTGGCCACGGG 60.818 63.158 3.88 0.00 0.00 5.28
149 150 1.087771 GTCGGAGTAATTGGCCACGG 61.088 60.000 3.88 0.00 0.00 4.94
150 151 0.390603 TGTCGGAGTAATTGGCCACG 60.391 55.000 3.88 3.59 0.00 4.94
151 152 1.338769 ACTGTCGGAGTAATTGGCCAC 60.339 52.381 3.88 0.00 30.86 5.01
152 153 0.981183 ACTGTCGGAGTAATTGGCCA 59.019 50.000 0.00 0.00 30.86 5.36
153 154 1.653151 GACTGTCGGAGTAATTGGCC 58.347 55.000 0.00 0.00 33.83 5.36
154 155 1.278238 CGACTGTCGGAGTAATTGGC 58.722 55.000 21.78 0.00 36.00 4.52
155 156 2.649331 ACGACTGTCGGAGTAATTGG 57.351 50.000 30.81 3.07 45.59 3.16
156 157 2.921754 GGAACGACTGTCGGAGTAATTG 59.078 50.000 30.81 3.78 45.59 2.32
157 158 2.824341 AGGAACGACTGTCGGAGTAATT 59.176 45.455 30.81 16.62 45.59 1.40
158 159 2.422832 GAGGAACGACTGTCGGAGTAAT 59.577 50.000 30.81 13.57 45.59 1.89
159 160 1.808945 GAGGAACGACTGTCGGAGTAA 59.191 52.381 30.81 0.00 45.59 2.24
160 161 1.002888 AGAGGAACGACTGTCGGAGTA 59.997 52.381 30.81 0.00 45.59 2.59
161 162 0.250814 AGAGGAACGACTGTCGGAGT 60.251 55.000 30.81 17.33 45.59 3.85
162 163 0.448593 GAGAGGAACGACTGTCGGAG 59.551 60.000 30.81 7.35 45.59 4.63
163 164 1.296755 CGAGAGGAACGACTGTCGGA 61.297 60.000 30.81 0.00 46.63 4.55
164 165 1.134901 CGAGAGGAACGACTGTCGG 59.865 63.158 30.81 15.05 46.63 4.79
165 166 4.747543 CGAGAGGAACGACTGTCG 57.252 61.111 26.94 26.94 45.60 4.35
177 178 2.742372 CAACAACGCCCCCGAGAG 60.742 66.667 0.00 0.00 38.29 3.20
178 179 3.552384 ACAACAACGCCCCCGAGA 61.552 61.111 0.00 0.00 38.29 4.04
179 180 3.353836 CACAACAACGCCCCCGAG 61.354 66.667 0.00 0.00 38.29 4.63
180 181 4.939368 CCACAACAACGCCCCCGA 62.939 66.667 0.00 0.00 38.29 5.14
182 183 4.906537 ACCCACAACAACGCCCCC 62.907 66.667 0.00 0.00 0.00 5.40
201 202 2.049627 GAGCCTAGGCACCATGAGGG 62.050 65.000 34.70 0.00 44.88 4.30
210 211 2.688666 CACCCTGGAGCCTAGGCA 60.689 66.667 34.70 14.36 44.88 4.75
232 233 4.144418 CGAGAGGACGGACTAGGG 57.856 66.667 0.00 0.00 0.00 3.53
322 328 1.202371 TGAAGCCGTTGGATAGCTACG 60.202 52.381 0.00 0.00 35.30 3.51
324 330 1.412710 CCTGAAGCCGTTGGATAGCTA 59.587 52.381 0.00 0.00 35.30 3.32
373 379 1.451936 GCCACCCTGTGACAGAGTT 59.548 57.895 15.33 0.00 35.23 3.01
472 487 1.343069 GGAGGAGGACAAGTCACACT 58.657 55.000 2.29 0.00 0.00 3.55
498 520 1.070105 GTACCGGACACACCAAGCA 59.930 57.895 9.46 0.00 38.90 3.91
513 535 1.374252 CCACCTGACACCGCAGTAC 60.374 63.158 0.00 0.00 34.06 2.73
547 569 7.467539 CGAAACTACCAAACATGACCAAAACTA 60.468 37.037 0.00 0.00 0.00 2.24
548 570 6.538945 AAACTACCAAACATGACCAAAACT 57.461 33.333 0.00 0.00 0.00 2.66
553 575 3.811083 ACGAAACTACCAAACATGACCA 58.189 40.909 0.00 0.00 0.00 4.02
563 585 4.699637 ACATGAGACAAACGAAACTACCA 58.300 39.130 0.00 0.00 0.00 3.25
572 594 4.055360 TCACACCTAACATGAGACAAACG 58.945 43.478 0.00 0.00 0.00 3.60
588 610 3.849708 GTGAAAACAAAAGACGTCACACC 59.150 43.478 19.50 0.00 36.30 4.16
595 617 2.026990 CGAGCGTGAAAACAAAAGACG 58.973 47.619 0.00 0.00 0.00 4.18
707 1390 2.602257 AACCAAGAAACAGGCTTTGC 57.398 45.000 0.00 0.00 0.00 3.68
749 1432 3.602946 CGTATTATTTGTACGCCGCCTTG 60.603 47.826 0.00 0.00 38.51 3.61
753 1436 2.882876 CACGTATTATTTGTACGCCGC 58.117 47.619 5.69 0.00 46.46 6.53
811 1498 3.577313 GCCGAGATGCCGCCTTTC 61.577 66.667 0.00 0.00 0.00 2.62
812 1499 4.408821 TGCCGAGATGCCGCCTTT 62.409 61.111 0.00 0.00 0.00 3.11
817 1504 4.519437 TGCTCTGCCGAGATGCCG 62.519 66.667 9.60 0.00 39.74 5.69
864 1558 3.578456 CTTGCGTTGGCGAGGAAT 58.422 55.556 0.00 0.00 45.39 3.01
897 1594 4.918129 GCCTCGTAATCCGCGCGA 62.918 66.667 34.63 18.26 36.19 5.87
954 1651 1.482748 TTTACGGGGTGGAGGTGGAC 61.483 60.000 0.00 0.00 0.00 4.02
958 1655 0.845337 TGTTTTTACGGGGTGGAGGT 59.155 50.000 0.00 0.00 0.00 3.85
961 1658 3.958798 TGAATTTGTTTTTACGGGGTGGA 59.041 39.130 0.00 0.00 0.00 4.02
963 1660 4.303282 CCTGAATTTGTTTTTACGGGGTG 58.697 43.478 0.00 0.00 0.00 4.61
964 1661 3.322541 CCCTGAATTTGTTTTTACGGGGT 59.677 43.478 0.00 0.00 38.64 4.95
976 1673 4.706476 TCATCCAGCTTAACCCTGAATTTG 59.294 41.667 0.00 0.00 32.03 2.32
1078 1775 3.611766 TCGAATGGAGGAAGAAGGAAC 57.388 47.619 0.00 0.00 0.00 3.62
1128 1855 2.536928 CGGAATCAAAATCTCGAACCGC 60.537 50.000 0.00 0.00 31.95 5.68
1167 1894 2.202756 GGTCGTGATCGTCCCTGC 60.203 66.667 0.00 0.00 38.83 4.85
1380 2113 1.448540 CCAGCGAGATGAAGCCGTT 60.449 57.895 0.00 0.00 0.00 4.44
1397 2130 4.353437 ACGTGCCGGAACTCGTCC 62.353 66.667 11.82 0.00 43.90 4.79
1556 2295 2.012673 AGATTTGGCGTGAGAAGATGC 58.987 47.619 0.00 0.00 0.00 3.91
1557 2296 2.223203 GCAGATTTGGCGTGAGAAGATG 60.223 50.000 0.00 0.00 0.00 2.90
1558 2297 2.012673 GCAGATTTGGCGTGAGAAGAT 58.987 47.619 0.00 0.00 0.00 2.40
1559 2298 1.270785 TGCAGATTTGGCGTGAGAAGA 60.271 47.619 0.00 0.00 0.00 2.87
1569 2308 5.578005 AGAACATCTCATTGCAGATTTGG 57.422 39.130 0.00 0.00 30.07 3.28
1641 2380 2.181021 GTCGCCGTCGAGTCCATT 59.819 61.111 0.00 0.00 46.46 3.16
1649 2388 3.975083 TTTGATCCCGTCGCCGTCG 62.975 63.158 0.00 0.00 0.00 5.12
1650 2389 1.738830 TTTTGATCCCGTCGCCGTC 60.739 57.895 0.00 0.00 0.00 4.79
1651 2390 2.030958 GTTTTGATCCCGTCGCCGT 61.031 57.895 0.00 0.00 0.00 5.68
1652 2391 2.746803 GGTTTTGATCCCGTCGCCG 61.747 63.158 0.00 0.00 0.00 6.46
1653 2392 1.029947 ATGGTTTTGATCCCGTCGCC 61.030 55.000 0.00 0.00 0.00 5.54
1654 2393 0.377203 GATGGTTTTGATCCCGTCGC 59.623 55.000 0.00 0.00 0.00 5.19
1754 2493 2.498885 GGTGGAGTGTACCCTCGTTTAT 59.501 50.000 0.00 0.00 31.98 1.40
1862 4818 2.481185 TCGTGGTTTCGGTTAAAGATGC 59.519 45.455 0.00 0.00 0.00 3.91
1863 4819 4.390603 TCATCGTGGTTTCGGTTAAAGATG 59.609 41.667 0.00 0.00 31.82 2.90
1864 4820 4.571919 TCATCGTGGTTTCGGTTAAAGAT 58.428 39.130 0.00 0.00 0.00 2.40
1866 4822 3.424433 GCTCATCGTGGTTTCGGTTAAAG 60.424 47.826 0.00 0.00 0.00 1.85
1867 4823 2.481185 GCTCATCGTGGTTTCGGTTAAA 59.519 45.455 0.00 0.00 0.00 1.52
1868 4824 2.070783 GCTCATCGTGGTTTCGGTTAA 58.929 47.619 0.00 0.00 0.00 2.01
1869 4825 1.001068 TGCTCATCGTGGTTTCGGTTA 59.999 47.619 0.00 0.00 0.00 2.85
1870 4826 0.250124 TGCTCATCGTGGTTTCGGTT 60.250 50.000 0.00 0.00 0.00 4.44
1932 5036 2.879002 TGCACTGTGAGATAGCTAGC 57.121 50.000 12.86 6.62 0.00 3.42
1933 5037 4.319139 ACATGCACTGTGAGATAGCTAG 57.681 45.455 12.86 0.00 36.48 3.42
1934 5038 4.436332 CAACATGCACTGTGAGATAGCTA 58.564 43.478 12.86 0.00 38.39 3.32
1935 5039 3.268330 CAACATGCACTGTGAGATAGCT 58.732 45.455 12.86 0.00 38.39 3.32
1936 5040 2.223203 GCAACATGCACTGTGAGATAGC 60.223 50.000 12.86 4.04 44.26 2.97
2017 5121 1.452145 TTTTGCTGTGACTTCCGCCC 61.452 55.000 0.00 0.00 0.00 6.13
2018 5122 0.317854 GTTTTGCTGTGACTTCCGCC 60.318 55.000 0.00 0.00 0.00 6.13
2019 5123 0.380378 TGTTTTGCTGTGACTTCCGC 59.620 50.000 0.00 0.00 0.00 5.54
2020 5124 1.670811 ACTGTTTTGCTGTGACTTCCG 59.329 47.619 0.00 0.00 0.00 4.30
2021 5125 2.286418 CGACTGTTTTGCTGTGACTTCC 60.286 50.000 0.00 0.00 0.00 3.46
2022 5126 2.351726 ACGACTGTTTTGCTGTGACTTC 59.648 45.455 0.00 0.00 0.00 3.01
2023 5127 2.095853 CACGACTGTTTTGCTGTGACTT 59.904 45.455 0.00 0.00 0.00 3.01
2024 5128 1.665679 CACGACTGTTTTGCTGTGACT 59.334 47.619 0.00 0.00 0.00 3.41
2025 5129 1.663643 TCACGACTGTTTTGCTGTGAC 59.336 47.619 0.00 0.00 31.93 3.67
2026 5130 1.933181 CTCACGACTGTTTTGCTGTGA 59.067 47.619 0.00 0.00 35.31 3.58
2027 5131 1.933181 TCTCACGACTGTTTTGCTGTG 59.067 47.619 0.00 0.00 0.00 3.66
2028 5132 2.309528 TCTCACGACTGTTTTGCTGT 57.690 45.000 0.00 0.00 0.00 4.40
2029 5133 2.096069 CCATCTCACGACTGTTTTGCTG 60.096 50.000 0.00 0.00 0.00 4.41
2030 5134 2.146342 CCATCTCACGACTGTTTTGCT 58.854 47.619 0.00 0.00 0.00 3.91
2031 5135 1.873591 ACCATCTCACGACTGTTTTGC 59.126 47.619 0.00 0.00 0.00 3.68
2032 5136 3.679980 CCTACCATCTCACGACTGTTTTG 59.320 47.826 0.00 0.00 0.00 2.44
2033 5137 3.576982 TCCTACCATCTCACGACTGTTTT 59.423 43.478 0.00 0.00 0.00 2.43
2034 5138 3.162666 TCCTACCATCTCACGACTGTTT 58.837 45.455 0.00 0.00 0.00 2.83
2035 5139 2.755655 CTCCTACCATCTCACGACTGTT 59.244 50.000 0.00 0.00 0.00 3.16
2036 5140 2.026169 TCTCCTACCATCTCACGACTGT 60.026 50.000 0.00 0.00 0.00 3.55
2037 5141 2.616376 CTCTCCTACCATCTCACGACTG 59.384 54.545 0.00 0.00 0.00 3.51
2038 5142 2.506231 TCTCTCCTACCATCTCACGACT 59.494 50.000 0.00 0.00 0.00 4.18
2039 5143 2.920524 TCTCTCCTACCATCTCACGAC 58.079 52.381 0.00 0.00 0.00 4.34
2040 5144 3.200165 TCTTCTCTCCTACCATCTCACGA 59.800 47.826 0.00 0.00 0.00 4.35
2041 5145 3.314080 GTCTTCTCTCCTACCATCTCACG 59.686 52.174 0.00 0.00 0.00 4.35
2042 5146 3.634910 GGTCTTCTCTCCTACCATCTCAC 59.365 52.174 0.00 0.00 32.04 3.51
2043 5147 3.685835 CGGTCTTCTCTCCTACCATCTCA 60.686 52.174 0.00 0.00 32.04 3.27
2044 5148 2.882137 CGGTCTTCTCTCCTACCATCTC 59.118 54.545 0.00 0.00 32.04 2.75
2045 5149 2.423660 CCGGTCTTCTCTCCTACCATCT 60.424 54.545 0.00 0.00 32.04 2.90
2046 5150 1.957877 CCGGTCTTCTCTCCTACCATC 59.042 57.143 0.00 0.00 32.04 3.51
2047 5151 2.030045 GCCGGTCTTCTCTCCTACCAT 61.030 57.143 1.90 0.00 32.04 3.55
2048 5152 0.683504 GCCGGTCTTCTCTCCTACCA 60.684 60.000 1.90 0.00 32.04 3.25
2049 5153 1.726533 CGCCGGTCTTCTCTCCTACC 61.727 65.000 1.90 0.00 0.00 3.18
2050 5154 1.726533 CCGCCGGTCTTCTCTCCTAC 61.727 65.000 1.90 0.00 0.00 3.18
2051 5155 1.453379 CCGCCGGTCTTCTCTCCTA 60.453 63.158 1.90 0.00 0.00 2.94
2052 5156 2.756283 CCGCCGGTCTTCTCTCCT 60.756 66.667 1.90 0.00 0.00 3.69
2190 5300 6.668323 CCTTGTTACATACACTTGTTCCTTG 58.332 40.000 0.00 0.00 36.21 3.61
2234 5344 5.394443 CCCATTGTAAATTGTGAGACCATGG 60.394 44.000 11.19 11.19 35.74 3.66
2258 5369 2.222729 CCGGTCATCATTTCGTTCGTTC 60.223 50.000 0.00 0.00 0.00 3.95
2259 5370 1.730064 CCGGTCATCATTTCGTTCGTT 59.270 47.619 0.00 0.00 0.00 3.85
2260 5371 1.355971 CCGGTCATCATTTCGTTCGT 58.644 50.000 0.00 0.00 0.00 3.85
2261 5372 0.026285 GCCGGTCATCATTTCGTTCG 59.974 55.000 1.90 0.00 0.00 3.95
2497 5611 2.737783 CACCGCATTTTGTAAGTACCGA 59.262 45.455 0.00 0.00 0.00 4.69
2527 5641 3.176411 TCTCAGGAGCTGGATCAAGAAA 58.824 45.455 0.00 0.00 31.51 2.52
2528 5642 2.825223 TCTCAGGAGCTGGATCAAGAA 58.175 47.619 0.00 0.00 31.51 2.52
2565 5679 5.710567 GGGTAAACTATTAGCATCCCATTCC 59.289 44.000 0.00 0.00 40.49 3.01
2863 5978 8.947055 AATTTCACAAGGTAAATTATCATGCC 57.053 30.769 0.00 0.00 34.40 4.40
2899 6014 2.165437 TGAAGTTCGCAAAGCAAAAGGT 59.835 40.909 0.00 0.00 0.00 3.50
2998 6113 7.395489 AGAATATGCTGAACTGAATCCACTTTT 59.605 33.333 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.