Multiple sequence alignment - TraesCS5A01G016000

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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 TraesCS5A01G016000 chr5A 100.000 4322 0 0 1 4322 11522484 11518163 0.000000e+00 7982.0
1 TraesCS5A01G016000 chr5A 90.698 86 8 0 1988 2073 11520412 11520497 9.820000e-22 115.0
2 TraesCS5A01G016000 chr5D 96.798 1624 29 6 2711 4322 14970133 14968521 0.000000e+00 2689.0
3 TraesCS5A01G016000 chr5D 90.093 1827 105 32 222 1990 14972491 14970683 0.000000e+00 2302.0
4 TraesCS5A01G016000 chr5D 97.838 555 12 0 2097 2651 14970687 14970133 0.000000e+00 959.0
5 TraesCS5A01G016000 chr5B 92.506 1628 79 19 2713 4322 13703833 13702231 0.000000e+00 2290.0
6 TraesCS5A01G016000 chr5B 93.683 839 45 6 1817 2651 13704666 13703832 0.000000e+00 1249.0
7 TraesCS5A01G016000 chr5B 85.327 886 65 18 784 1652 13705800 13704963 0.000000e+00 856.0
8 TraesCS5A01G016000 chr5B 80.721 555 43 24 222 751 13706437 13705922 1.470000e-99 374.0
9 TraesCS5A01G016000 chr5B 82.323 198 20 8 1642 1825 13704886 13704690 1.610000e-34 158.0
10 TraesCS5A01G016000 chr5B 93.151 73 1 2 2650 2719 693990399 693990328 2.130000e-18 104.0
11 TraesCS5A01G016000 chr7D 80.377 265 48 2 3059 3322 411021315 411021054 9.480000e-47 198.0
12 TraesCS5A01G016000 chr7D 89.888 89 8 1 1985 2073 195308269 195308356 3.530000e-21 113.0
13 TraesCS5A01G016000 chr7D 96.970 66 0 1 2649 2714 560284956 560285019 4.570000e-20 110.0
14 TraesCS5A01G016000 chrUn 85.185 162 22 2 5 165 344010269 344010109 9.620000e-37 165.0
15 TraesCS5A01G016000 chrUn 85.185 162 22 2 5 165 420086867 420086707 9.620000e-37 165.0
16 TraesCS5A01G016000 chrUn 95.385 65 1 2 2650 2714 255530374 255530312 7.650000e-18 102.0
17 TraesCS5A01G016000 chrUn 88.889 81 7 2 1992 2072 183985786 183985708 9.890000e-17 99.0
18 TraesCS5A01G016000 chr2B 82.738 168 25 4 1 165 154238362 154238196 3.480000e-31 147.0
19 TraesCS5A01G016000 chr2B 83.108 148 18 6 18 163 364727480 364727338 1.260000e-25 128.0
20 TraesCS5A01G016000 chr2B 88.235 85 3 5 2648 2727 161436096 161436178 1.280000e-15 95.3
21 TraesCS5A01G016000 chr1A 82.927 164 26 2 3 165 502827331 502827169 3.480000e-31 147.0
22 TraesCS5A01G016000 chr1A 88.636 88 9 1 1987 2074 545330884 545330970 5.910000e-19 106.0
23 TraesCS5A01G016000 chr4A 82.424 165 27 2 1 165 596580086 596580248 4.510000e-30 143.0
24 TraesCS5A01G016000 chr4A 77.844 167 32 5 2 165 629302299 629302463 9.890000e-17 99.0
25 TraesCS5A01G016000 chr4A 87.952 83 9 1 1990 2072 259769018 259769099 3.560000e-16 97.1
26 TraesCS5A01G016000 chr3B 81.143 175 20 6 3 165 576046898 576047071 1.260000e-25 128.0
27 TraesCS5A01G016000 chr2D 88.776 98 11 0 1 98 429081901 429081804 2.110000e-23 121.0
28 TraesCS5A01G016000 chr2D 95.455 66 2 1 2650 2715 342487781 342487845 2.130000e-18 104.0
29 TraesCS5A01G016000 chr2A 87.619 105 12 1 2 106 82341654 82341551 2.110000e-23 121.0
30 TraesCS5A01G016000 chr2A 87.143 70 7 2 97 165 739442938 739443006 1.290000e-10 78.7
31 TraesCS5A01G016000 chr7B 91.358 81 6 1 1993 2073 13801860 13801939 4.570000e-20 110.0
32 TraesCS5A01G016000 chr7B 90.000 80 7 1 1994 2073 159137585 159137663 7.650000e-18 102.0
33 TraesCS5A01G016000 chr3D 89.655 87 7 2 1993 2078 550194741 550194656 4.570000e-20 110.0
34 TraesCS5A01G016000 chr3D 90.000 80 4 2 2639 2714 3821260 3821339 2.750000e-17 100.0
35 TraesCS5A01G016000 chr1B 96.970 66 1 1 2650 2714 642043870 642043805 4.570000e-20 110.0
36 TraesCS5A01G016000 chr7A 85.577 104 11 4 2650 2751 20649250 20649351 5.910000e-19 106.0
37 TraesCS5A01G016000 chr6D 95.385 65 1 1 2650 2714 322457574 322457512 7.650000e-18 102.0


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 TraesCS5A01G016000 chr5A 11518163 11522484 4321 True 7982.000000 7982 100.000000 1 4322 1 chr5A.!!$R1 4321
1 TraesCS5A01G016000 chr5D 14968521 14972491 3970 True 1983.333333 2689 94.909667 222 4322 3 chr5D.!!$R1 4100
2 TraesCS5A01G016000 chr5B 13702231 13706437 4206 True 985.400000 2290 86.912000 222 4322 5 chr5B.!!$R2 4100

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
178 179 0.103572 GTTTGACCGCGGATAGCCTA 59.896 55.0 35.9 9.07 44.76 3.93 F
179 180 0.103572 TTTGACCGCGGATAGCCTAC 59.896 55.0 35.9 12.06 44.76 3.18 F
180 181 0.754217 TTGACCGCGGATAGCCTACT 60.754 55.0 35.9 5.18 44.76 2.57 F
1063 1230 0.856982 TGTGGTCCCCAATGGTCTTT 59.143 50.0 0.0 0.00 34.18 2.52 F
2029 2337 1.388547 AGACGCTTTGGCAGTTCAAA 58.611 45.0 0.0 0.00 38.60 2.69 F
2577 2885 0.108585 GTTGGGAGCAGAACAGGTCA 59.891 55.0 0.0 0.00 37.74 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 2037 0.692476 TTCCATACCAGCACAGCACT 59.308 50.000 0.0 0.0 0.0 4.40 R
1775 2038 1.533625 TTTCCATACCAGCACAGCAC 58.466 50.000 0.0 0.0 0.0 4.40 R
1776 2039 1.885887 GTTTTCCATACCAGCACAGCA 59.114 47.619 0.0 0.0 0.0 4.41 R
2208 2516 0.798776 CATTCAGGAACCGCTGTCAC 59.201 55.000 0.0 0.0 0.0 3.67 R
3164 3479 0.605589 GAACCCGCCAAAGTAGCTGT 60.606 55.000 0.0 0.0 0.0 4.40 R
4046 4381 2.621055 TCGAAAATTGGTTGACACTGGG 59.379 45.455 0.0 0.0 0.0 4.45 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
18 19 4.093291 CTCCAGGGCGCTGCTTCT 62.093 66.667 24.51 0.00 0.00 2.85
19 20 3.618780 CTCCAGGGCGCTGCTTCTT 62.619 63.158 24.51 0.00 0.00 2.52
20 21 2.244117 CTCCAGGGCGCTGCTTCTTA 62.244 60.000 24.51 4.92 0.00 2.10
21 22 1.817099 CCAGGGCGCTGCTTCTTAG 60.817 63.158 24.51 5.93 0.00 2.18
22 23 1.817099 CAGGGCGCTGCTTCTTAGG 60.817 63.158 18.62 0.00 0.00 2.69
23 24 2.514824 GGGCGCTGCTTCTTAGGG 60.515 66.667 7.64 0.00 0.00 3.53
24 25 2.514824 GGCGCTGCTTCTTAGGGG 60.515 66.667 7.64 0.00 0.00 4.79
25 26 3.205536 GCGCTGCTTCTTAGGGGC 61.206 66.667 0.00 0.00 0.00 5.80
26 27 2.268920 CGCTGCTTCTTAGGGGCA 59.731 61.111 0.00 0.00 34.66 5.36
27 28 2.109126 CGCTGCTTCTTAGGGGCAC 61.109 63.158 0.00 0.00 32.33 5.01
28 29 2.109126 GCTGCTTCTTAGGGGCACG 61.109 63.158 0.00 0.00 32.33 5.34
29 30 1.296715 CTGCTTCTTAGGGGCACGT 59.703 57.895 0.00 0.00 32.33 4.49
30 31 1.003839 TGCTTCTTAGGGGCACGTG 60.004 57.895 12.28 12.28 0.00 4.49
31 32 2.399356 GCTTCTTAGGGGCACGTGC 61.399 63.158 32.15 32.15 41.14 5.34
32 33 1.003839 CTTCTTAGGGGCACGTGCA 60.004 57.895 38.60 18.47 44.36 4.57
33 34 1.298859 CTTCTTAGGGGCACGTGCAC 61.299 60.000 38.60 36.67 45.53 4.57
39 40 3.712881 GGGCACGTGCACGAAGAC 61.713 66.667 42.94 33.69 44.36 3.01
40 41 2.661866 GGCACGTGCACGAAGACT 60.662 61.111 42.94 19.98 44.36 3.24
41 42 2.244651 GGCACGTGCACGAAGACTT 61.245 57.895 42.94 19.18 44.36 3.01
42 43 1.201825 GCACGTGCACGAAGACTTC 59.798 57.895 42.94 19.21 43.02 3.01
43 44 1.215655 GCACGTGCACGAAGACTTCT 61.216 55.000 42.94 17.58 43.02 2.85
44 45 0.778815 CACGTGCACGAAGACTTCTC 59.221 55.000 42.94 0.00 43.02 2.87
45 46 0.660595 ACGTGCACGAAGACTTCTCG 60.661 55.000 42.94 14.73 43.02 4.04
46 47 1.337817 CGTGCACGAAGACTTCTCGG 61.338 60.000 34.93 0.00 43.02 4.63
47 48 1.372997 TGCACGAAGACTTCTCGGC 60.373 57.895 13.22 12.99 0.00 5.54
48 49 1.080434 GCACGAAGACTTCTCGGCT 60.080 57.895 13.22 0.00 0.00 5.52
49 50 1.347817 GCACGAAGACTTCTCGGCTG 61.348 60.000 13.22 0.00 0.00 4.85
50 51 1.080434 ACGAAGACTTCTCGGCTGC 60.080 57.895 13.22 0.00 0.00 5.25
51 52 1.807573 CGAAGACTTCTCGGCTGCC 60.808 63.158 9.11 9.11 0.00 4.85
52 53 1.293498 GAAGACTTCTCGGCTGCCA 59.707 57.895 20.29 5.07 0.00 4.92
53 54 0.107945 GAAGACTTCTCGGCTGCCAT 60.108 55.000 20.29 0.00 0.00 4.40
54 55 0.326264 AAGACTTCTCGGCTGCCATT 59.674 50.000 20.29 0.00 0.00 3.16
55 56 0.392193 AGACTTCTCGGCTGCCATTG 60.392 55.000 20.29 7.83 0.00 2.82
56 57 0.391661 GACTTCTCGGCTGCCATTGA 60.392 55.000 20.29 10.16 0.00 2.57
57 58 0.674895 ACTTCTCGGCTGCCATTGAC 60.675 55.000 20.29 0.00 0.00 3.18
58 59 0.674581 CTTCTCGGCTGCCATTGACA 60.675 55.000 20.29 0.00 0.00 3.58
59 60 0.250684 TTCTCGGCTGCCATTGACAA 60.251 50.000 20.29 0.00 0.00 3.18
60 61 0.674581 TCTCGGCTGCCATTGACAAG 60.675 55.000 20.29 0.00 0.00 3.16
61 62 1.651240 CTCGGCTGCCATTGACAAGG 61.651 60.000 20.29 0.00 0.00 3.61
62 63 1.973281 CGGCTGCCATTGACAAGGT 60.973 57.895 20.29 0.00 0.00 3.50
63 64 1.885871 GGCTGCCATTGACAAGGTC 59.114 57.895 15.17 0.00 0.00 3.85
64 65 0.895100 GGCTGCCATTGACAAGGTCA 60.895 55.000 15.17 0.00 41.09 4.02
70 71 4.473643 TTGACAAGGTCAAGCCGG 57.526 55.556 7.66 0.00 45.88 6.13
71 72 1.896660 TTGACAAGGTCAAGCCGGC 60.897 57.895 21.89 21.89 45.88 6.13
72 73 2.032681 GACAAGGTCAAGCCGGCT 59.967 61.111 27.08 27.08 43.70 5.52
73 74 2.032681 ACAAGGTCAAGCCGGCTC 59.967 61.111 32.93 18.07 43.70 4.70
74 75 2.747855 CAAGGTCAAGCCGGCTCC 60.748 66.667 32.93 26.75 43.70 4.70
75 76 4.394712 AAGGTCAAGCCGGCTCCG 62.395 66.667 32.93 24.15 43.70 4.63
91 92 2.202756 CGGTAGAGGAGCGGCAAC 60.203 66.667 1.45 0.00 45.37 4.17
92 93 2.978824 GGTAGAGGAGCGGCAACA 59.021 61.111 1.45 0.00 0.00 3.33
93 94 1.295423 GGTAGAGGAGCGGCAACAA 59.705 57.895 1.45 0.00 0.00 2.83
94 95 1.019805 GGTAGAGGAGCGGCAACAAC 61.020 60.000 1.45 0.00 0.00 3.32
95 96 1.080093 TAGAGGAGCGGCAACAACG 60.080 57.895 1.45 0.00 0.00 4.10
96 97 2.501223 TAGAGGAGCGGCAACAACGG 62.501 60.000 1.45 0.00 0.00 4.44
99 100 3.660111 GAGCGGCAACAACGGCTT 61.660 61.111 1.45 0.00 45.13 4.35
100 101 3.879351 GAGCGGCAACAACGGCTTG 62.879 63.158 1.45 0.00 45.13 4.01
101 102 4.264638 GCGGCAACAACGGCTTGT 62.265 61.111 0.00 0.00 42.81 3.16
103 104 1.657181 CGGCAACAACGGCTTGTTC 60.657 57.895 10.70 7.36 45.81 3.18
104 105 1.657181 GGCAACAACGGCTTGTTCG 60.657 57.895 10.70 8.67 45.81 3.95
105 106 1.657181 GCAACAACGGCTTGTTCGG 60.657 57.895 10.70 4.66 45.81 4.30
106 107 1.657181 CAACAACGGCTTGTTCGGC 60.657 57.895 10.70 0.00 45.81 5.54
107 108 2.115911 AACAACGGCTTGTTCGGCA 61.116 52.632 8.59 0.00 45.81 5.69
108 109 2.058829 AACAACGGCTTGTTCGGCAG 62.059 55.000 8.59 0.00 45.81 4.85
109 110 3.660111 AACGGCTTGTTCGGCAGC 61.660 61.111 0.00 0.00 35.27 5.25
110 111 4.927782 ACGGCTTGTTCGGCAGCA 62.928 61.111 0.00 0.00 0.00 4.41
111 112 4.093952 CGGCTTGTTCGGCAGCAG 62.094 66.667 0.00 0.00 0.00 4.24
112 113 2.980233 GGCTTGTTCGGCAGCAGT 60.980 61.111 0.00 0.00 0.00 4.40
113 114 1.671054 GGCTTGTTCGGCAGCAGTA 60.671 57.895 0.00 0.00 0.00 2.74
114 115 1.639298 GGCTTGTTCGGCAGCAGTAG 61.639 60.000 0.00 0.00 0.00 2.57
115 116 0.951040 GCTTGTTCGGCAGCAGTAGT 60.951 55.000 0.00 0.00 0.00 2.73
116 117 0.792640 CTTGTTCGGCAGCAGTAGTG 59.207 55.000 0.00 0.00 0.00 2.74
117 118 0.602638 TTGTTCGGCAGCAGTAGTGG 60.603 55.000 0.00 0.00 0.00 4.00
118 119 1.004918 GTTCGGCAGCAGTAGTGGT 60.005 57.895 0.00 0.00 33.53 4.16
119 120 1.014564 GTTCGGCAGCAGTAGTGGTC 61.015 60.000 0.00 0.00 29.64 4.02
120 121 2.486636 TTCGGCAGCAGTAGTGGTCG 62.487 60.000 0.00 1.94 29.64 4.79
121 122 2.657237 GGCAGCAGTAGTGGTCGT 59.343 61.111 0.00 0.00 29.64 4.34
122 123 1.004918 GGCAGCAGTAGTGGTCGTT 60.005 57.895 0.00 0.00 29.64 3.85
123 124 0.602905 GGCAGCAGTAGTGGTCGTTT 60.603 55.000 0.00 0.00 29.64 3.60
124 125 0.512952 GCAGCAGTAGTGGTCGTTTG 59.487 55.000 0.00 0.00 29.64 2.93
125 126 1.148310 CAGCAGTAGTGGTCGTTTGG 58.852 55.000 0.00 0.00 29.64 3.28
126 127 0.756903 AGCAGTAGTGGTCGTTTGGT 59.243 50.000 0.00 0.00 0.00 3.67
127 128 0.865769 GCAGTAGTGGTCGTTTGGTG 59.134 55.000 0.00 0.00 0.00 4.17
128 129 1.508632 CAGTAGTGGTCGTTTGGTGG 58.491 55.000 0.00 0.00 0.00 4.61
129 130 0.250166 AGTAGTGGTCGTTTGGTGGC 60.250 55.000 0.00 0.00 0.00 5.01
130 131 1.071814 TAGTGGTCGTTTGGTGGCC 59.928 57.895 0.00 0.00 0.00 5.36
131 132 1.697082 TAGTGGTCGTTTGGTGGCCA 61.697 55.000 0.00 0.00 0.00 5.36
132 133 2.517402 TGGTCGTTTGGTGGCCAC 60.517 61.111 28.57 28.57 30.78 5.01
133 134 3.656045 GGTCGTTTGGTGGCCACG 61.656 66.667 29.08 17.78 30.78 4.94
134 135 3.656045 GTCGTTTGGTGGCCACGG 61.656 66.667 29.08 15.22 30.78 4.94
135 136 4.939368 TCGTTTGGTGGCCACGGG 62.939 66.667 29.08 15.55 30.78 5.28
136 137 4.939368 CGTTTGGTGGCCACGGGA 62.939 66.667 29.08 14.63 30.78 5.14
137 138 2.519780 GTTTGGTGGCCACGGGAA 60.520 61.111 29.08 19.49 30.78 3.97
138 139 1.906333 GTTTGGTGGCCACGGGAAT 60.906 57.895 29.08 0.00 30.78 3.01
139 140 1.605165 TTTGGTGGCCACGGGAATC 60.605 57.895 29.08 14.79 30.78 2.52
140 141 2.075355 TTTGGTGGCCACGGGAATCT 62.075 55.000 29.08 0.00 30.78 2.40
141 142 2.124695 GGTGGCCACGGGAATCTC 60.125 66.667 29.08 9.28 0.00 2.75
142 143 2.511600 GTGGCCACGGGAATCTCG 60.512 66.667 22.49 0.00 0.00 4.04
143 144 2.682136 TGGCCACGGGAATCTCGA 60.682 61.111 10.46 0.00 0.00 4.04
144 145 2.063979 TGGCCACGGGAATCTCGAT 61.064 57.895 10.46 0.00 0.00 3.59
145 146 1.595382 GGCCACGGGAATCTCGATG 60.595 63.158 10.46 3.75 0.00 3.84
146 147 1.144057 GCCACGGGAATCTCGATGT 59.856 57.895 10.46 0.00 0.00 3.06
147 148 0.387929 GCCACGGGAATCTCGATGTA 59.612 55.000 10.46 0.00 0.00 2.29
148 149 1.202486 GCCACGGGAATCTCGATGTAA 60.202 52.381 10.46 0.00 0.00 2.41
149 150 2.548067 GCCACGGGAATCTCGATGTAAT 60.548 50.000 10.46 0.00 0.00 1.89
150 151 3.728845 CCACGGGAATCTCGATGTAATT 58.271 45.455 10.46 0.00 0.00 1.40
151 152 4.127171 CCACGGGAATCTCGATGTAATTT 58.873 43.478 10.46 0.00 0.00 1.82
152 153 4.574828 CCACGGGAATCTCGATGTAATTTT 59.425 41.667 10.46 0.00 0.00 1.82
153 154 5.065988 CCACGGGAATCTCGATGTAATTTTT 59.934 40.000 10.46 0.00 0.00 1.94
154 155 6.259167 CCACGGGAATCTCGATGTAATTTTTA 59.741 38.462 10.46 0.00 0.00 1.52
155 156 7.041372 CCACGGGAATCTCGATGTAATTTTTAT 60.041 37.037 10.46 0.00 0.00 1.40
156 157 8.342634 CACGGGAATCTCGATGTAATTTTTATT 58.657 33.333 10.46 0.00 0.00 1.40
157 158 9.550406 ACGGGAATCTCGATGTAATTTTTATTA 57.450 29.630 10.46 0.00 0.00 0.98
169 170 8.383264 TGTAATTTTTATTATGTTTGACCGCG 57.617 30.769 0.00 0.00 0.00 6.46
170 171 6.879188 AATTTTTATTATGTTTGACCGCGG 57.121 33.333 26.86 26.86 0.00 6.46
171 172 5.624344 TTTTTATTATGTTTGACCGCGGA 57.376 34.783 35.90 7.50 0.00 5.54
172 173 5.821516 TTTTATTATGTTTGACCGCGGAT 57.178 34.783 35.90 16.95 0.00 4.18
173 174 6.922247 TTTTATTATGTTTGACCGCGGATA 57.078 33.333 35.90 17.68 0.00 2.59
174 175 6.533819 TTTATTATGTTTGACCGCGGATAG 57.466 37.500 35.90 5.06 0.00 2.08
175 176 1.860676 TATGTTTGACCGCGGATAGC 58.139 50.000 35.90 17.99 43.95 2.97
176 177 0.814010 ATGTTTGACCGCGGATAGCC 60.814 55.000 35.90 16.64 44.76 3.93
177 178 1.153429 GTTTGACCGCGGATAGCCT 60.153 57.895 35.90 8.10 44.76 4.58
178 179 0.103572 GTTTGACCGCGGATAGCCTA 59.896 55.000 35.90 9.07 44.76 3.93
179 180 0.103572 TTTGACCGCGGATAGCCTAC 59.896 55.000 35.90 12.06 44.76 3.18
180 181 0.754217 TTGACCGCGGATAGCCTACT 60.754 55.000 35.90 5.18 44.76 2.57
181 182 1.286260 GACCGCGGATAGCCTACTG 59.714 63.158 35.90 0.00 44.76 2.74
182 183 2.143594 GACCGCGGATAGCCTACTGG 62.144 65.000 35.90 0.00 44.76 4.00
183 184 2.651361 CGCGGATAGCCTACTGGG 59.349 66.667 0.00 0.00 44.76 4.45
224 225 2.982130 CGTAGCTGGGCCTCAGTT 59.018 61.111 18.80 16.17 45.08 3.16
225 226 1.448540 CGTAGCTGGGCCTCAGTTG 60.449 63.158 18.80 6.48 45.08 3.16
226 227 1.679898 GTAGCTGGGCCTCAGTTGT 59.320 57.895 18.80 9.41 45.08 3.32
276 281 3.954740 TAACCGAGGTGGGGCCCAT 62.955 63.158 31.48 14.84 44.64 4.00
361 371 3.012560 CGAAGCAATCCATCCCTCC 57.987 57.895 0.00 0.00 0.00 4.30
549 590 1.603739 GGCGTCCCCTTTCTTTGCT 60.604 57.895 0.00 0.00 0.00 3.91
575 628 2.012673 CTGTTCTGGCTGGCACTAATC 58.987 52.381 0.00 0.00 0.00 1.75
616 669 3.826157 GTCCATGGTTTGGTTCTTGATGA 59.174 43.478 12.58 0.00 46.52 2.92
617 670 4.463891 GTCCATGGTTTGGTTCTTGATGAT 59.536 41.667 12.58 0.00 46.52 2.45
618 671 5.047092 GTCCATGGTTTGGTTCTTGATGATT 60.047 40.000 12.58 0.00 46.52 2.57
619 672 5.543405 TCCATGGTTTGGTTCTTGATGATTT 59.457 36.000 12.58 0.00 46.52 2.17
620 673 5.640357 CCATGGTTTGGTTCTTGATGATTTG 59.360 40.000 2.57 0.00 40.99 2.32
654 711 8.186178 ACATATCACAAGTTCTGTAAATCGAC 57.814 34.615 0.00 0.00 36.10 4.20
673 732 2.534903 GCGGAGGAAATAGCACGGC 61.535 63.158 0.00 0.00 0.00 5.68
675 734 1.527370 GGAGGAAATAGCACGGCCT 59.473 57.895 0.00 0.00 0.00 5.19
689 748 2.343758 GCCTGACGGAGCTGAACA 59.656 61.111 0.00 0.00 0.00 3.18
711 770 5.105635 ACAAAGACATCACATTTATGCCCTG 60.106 40.000 0.00 0.00 0.00 4.45
713 772 5.372343 AGACATCACATTTATGCCCTGTA 57.628 39.130 0.00 0.00 0.00 2.74
714 773 5.945310 AGACATCACATTTATGCCCTGTAT 58.055 37.500 0.00 0.00 0.00 2.29
786 934 2.711547 AGCCTGTAGGATGGGAAATACC 59.288 50.000 1.17 0.00 37.39 2.73
803 951 6.096423 GGAAATACCCCATTACTCTTTTGGAC 59.904 42.308 0.00 0.00 31.94 4.02
830 978 4.441079 GGAGTGCCAAATCATCATTTCCTG 60.441 45.833 0.00 0.00 28.97 3.86
832 980 2.159212 TGCCAAATCATCATTTCCTGCG 60.159 45.455 0.00 0.00 28.97 5.18
854 1002 7.095910 TGCGGACAAATTTGATAAACATCATT 58.904 30.769 24.64 0.00 0.00 2.57
856 1004 7.275341 GCGGACAAATTTGATAAACATCATTCA 59.725 33.333 24.64 0.00 0.00 2.57
880 1028 2.016318 CGCCAAATCCTCTGTTATGCA 58.984 47.619 0.00 0.00 0.00 3.96
898 1046 3.911868 TGCAATCTCCATTTTCCGTTTG 58.088 40.909 0.00 0.00 0.00 2.93
1063 1230 0.856982 TGTGGTCCCCAATGGTCTTT 59.143 50.000 0.00 0.00 34.18 2.52
1097 1264 8.661352 AGGTTTCAAGGTAATGAATTGTTTTG 57.339 30.769 0.00 0.00 38.98 2.44
1160 1327 5.087397 GGTTGCGTACTCATATCTATCGTC 58.913 45.833 0.00 0.00 0.00 4.20
1249 1416 8.851145 ACTGAATCTTATGAGACACGTACATAT 58.149 33.333 0.00 0.00 33.99 1.78
1258 1425 5.048713 TGAGACACGTACATATCAGCCATAG 60.049 44.000 0.00 0.00 0.00 2.23
1259 1426 4.218635 AGACACGTACATATCAGCCATAGG 59.781 45.833 0.00 0.00 0.00 2.57
1295 1462 9.599866 TTGATAACAAATATGACCTGTACTGAG 57.400 33.333 0.60 0.00 32.73 3.35
1320 1487 7.039270 GGAAACTTTGTGTCACCTTACAAATT 58.961 34.615 0.00 0.00 43.44 1.82
1334 1501 7.274250 CACCTTACAAATTCTTAGCTCATTTGC 59.726 37.037 15.40 0.00 40.23 3.68
1345 1512 6.886459 TCTTAGCTCATTTGCTACTTTCCATT 59.114 34.615 0.00 0.00 44.15 3.16
1405 1573 5.120830 GGTTCAGCTCATGTTGTTAGTGTAG 59.879 44.000 0.00 0.00 0.00 2.74
1425 1593 5.827797 TGTAGAAGTTTTGACTTGGCTCATT 59.172 36.000 0.00 0.00 0.00 2.57
1443 1611 6.040166 GGCTCATTGTCATCCAGTATGAAATT 59.960 38.462 0.00 0.00 46.17 1.82
1444 1612 6.916387 GCTCATTGTCATCCAGTATGAAATTG 59.084 38.462 0.00 0.00 46.17 2.32
1588 1756 6.371271 CCCTTTTCTTTTCTTTGCAAAGTTCA 59.629 34.615 32.46 18.42 37.31 3.18
1590 1758 8.453320 CCTTTTCTTTTCTTTGCAAAGTTCATT 58.547 29.630 32.46 0.00 37.31 2.57
1714 1975 6.564328 ACTCCTTGTTGATTTGTTCTTGTTC 58.436 36.000 0.00 0.00 0.00 3.18
1778 2041 9.893305 ACTCAAAATAGTTGTAATTTGTAGTGC 57.107 29.630 0.00 0.00 32.77 4.40
1815 2088 6.801862 GGAAAACAATTACAGATGTTTCGAGG 59.198 38.462 4.56 0.00 46.09 4.63
1904 2209 4.735369 TGTCCTGTATTGGTGGTGATTTT 58.265 39.130 0.00 0.00 0.00 1.82
1990 2298 4.082787 GCAGTACCGTGTTACCTTACTACA 60.083 45.833 0.00 0.00 0.00 2.74
1991 2299 5.393962 CAGTACCGTGTTACCTTACTACAC 58.606 45.833 0.00 0.00 38.96 2.90
2001 2309 4.618920 ACCTTACTACACCCTCTGTTTG 57.381 45.455 0.00 0.00 33.91 2.93
2029 2337 1.388547 AGACGCTTTGGCAGTTCAAA 58.611 45.000 0.00 0.00 38.60 2.69
2064 2372 7.419204 CCAAAACGTCTTACATTTAGGAACAA 58.581 34.615 0.00 0.00 0.00 2.83
2208 2516 8.839947 TGAGCAATTACAATTTCATAATCACG 57.160 30.769 0.00 0.00 0.00 4.35
2350 2658 8.527810 ACAATTTCAGAAAACTCAAGTTAACCA 58.472 29.630 0.88 0.00 37.25 3.67
2577 2885 0.108585 GTTGGGAGCAGAACAGGTCA 59.891 55.000 0.00 0.00 37.74 4.02
2654 2962 9.000486 ACTTTAGTGCTCAATAAAAACTACTCC 58.000 33.333 4.45 0.00 31.64 3.85
2655 2963 7.916914 TTAGTGCTCAATAAAAACTACTCCC 57.083 36.000 0.00 0.00 0.00 4.30
2656 2964 6.128138 AGTGCTCAATAAAAACTACTCCCT 57.872 37.500 0.00 0.00 0.00 4.20
2657 2965 6.174049 AGTGCTCAATAAAAACTACTCCCTC 58.826 40.000 0.00 0.00 0.00 4.30
2658 2966 6.013293 AGTGCTCAATAAAAACTACTCCCTCT 60.013 38.462 0.00 0.00 0.00 3.69
2659 2967 6.092807 GTGCTCAATAAAAACTACTCCCTCTG 59.907 42.308 0.00 0.00 0.00 3.35
2660 2968 6.174049 GCTCAATAAAAACTACTCCCTCTGT 58.826 40.000 0.00 0.00 0.00 3.41
2661 2969 7.038587 TGCTCAATAAAAACTACTCCCTCTGTA 60.039 37.037 0.00 0.00 0.00 2.74
2662 2970 7.822822 GCTCAATAAAAACTACTCCCTCTGTAA 59.177 37.037 0.00 0.00 0.00 2.41
2663 2971 9.720769 CTCAATAAAAACTACTCCCTCTGTAAA 57.279 33.333 0.00 0.00 0.00 2.01
2664 2972 9.498176 TCAATAAAAACTACTCCCTCTGTAAAC 57.502 33.333 0.00 0.00 0.00 2.01
2665 2973 9.503399 CAATAAAAACTACTCCCTCTGTAAACT 57.497 33.333 0.00 0.00 0.00 2.66
2676 2984 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2678 2986 9.931698 TCCCTCTGTAAACTAATATAAGAGTGA 57.068 33.333 0.00 0.00 0.00 3.41
2705 3013 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2706 3014 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2707 3015 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2708 3016 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2709 3017 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2710 3018 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3164 3479 4.986774 AGGCGGTGGGGGTGGTAA 62.987 66.667 0.00 0.00 0.00 2.85
3213 3528 0.249238 CTATCGTGCTGCTCCTGGAC 60.249 60.000 0.00 0.00 0.00 4.02
3597 3915 4.277672 TGGATATTACTGTCGAGTGGCTAC 59.722 45.833 0.00 0.00 33.21 3.58
3606 3924 0.738975 CGAGTGGCTACCGAAGATCA 59.261 55.000 0.00 0.00 0.00 2.92
3610 3928 0.829990 TGGCTACCGAAGATCATGCA 59.170 50.000 0.00 0.00 0.00 3.96
3631 3949 5.124457 TGCACATTATTTCTTCTCTCTTGCC 59.876 40.000 0.00 0.00 0.00 4.52
3720 4038 7.928908 TTGCTTTTGTCTACTTTTATGCTTG 57.071 32.000 0.00 0.00 0.00 4.01
3800 4118 1.561643 TGTTGGGGTTGCTTTTGTCA 58.438 45.000 0.00 0.00 0.00 3.58
3830 4152 9.638239 TTTATGCCTTACTTTTCACATCAAATC 57.362 29.630 0.00 0.00 0.00 2.17
3831 4153 5.698832 TGCCTTACTTTTCACATCAAATCG 58.301 37.500 0.00 0.00 0.00 3.34
3832 4154 5.471797 TGCCTTACTTTTCACATCAAATCGA 59.528 36.000 0.00 0.00 0.00 3.59
3833 4155 6.016693 TGCCTTACTTTTCACATCAAATCGAA 60.017 34.615 0.00 0.00 0.00 3.71
3834 4156 7.029563 GCCTTACTTTTCACATCAAATCGAAT 58.970 34.615 0.00 0.00 0.00 3.34
3998 4324 6.041296 CCAAAAGAGAATGAATAATGGAGGGG 59.959 42.308 0.00 0.00 0.00 4.79
4046 4381 8.764287 CAAAGGTGGAAGTATCATTTTGTTTTC 58.236 33.333 0.00 0.00 0.00 2.29
4292 4628 1.392853 GTGTCGACGATGTACGAGTCT 59.607 52.381 11.62 0.00 45.77 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.244117 TAAGAAGCAGCGCCCTGGAG 62.244 60.000 2.29 0.00 39.54 3.86
3 4 1.817099 CTAAGAAGCAGCGCCCTGG 60.817 63.158 2.29 0.00 39.54 4.45
4 5 1.817099 CCTAAGAAGCAGCGCCCTG 60.817 63.158 2.29 0.00 42.13 4.45
5 6 2.586792 CCTAAGAAGCAGCGCCCT 59.413 61.111 2.29 0.00 0.00 5.19
6 7 2.514824 CCCTAAGAAGCAGCGCCC 60.515 66.667 2.29 0.00 0.00 6.13
7 8 2.514824 CCCCTAAGAAGCAGCGCC 60.515 66.667 2.29 0.00 0.00 6.53
8 9 3.205536 GCCCCTAAGAAGCAGCGC 61.206 66.667 0.00 0.00 0.00 5.92
9 10 2.109126 GTGCCCCTAAGAAGCAGCG 61.109 63.158 0.00 0.00 37.15 5.18
10 11 2.109126 CGTGCCCCTAAGAAGCAGC 61.109 63.158 0.00 0.00 37.15 5.25
11 12 1.021390 CACGTGCCCCTAAGAAGCAG 61.021 60.000 0.82 0.00 37.15 4.24
12 13 1.003839 CACGTGCCCCTAAGAAGCA 60.004 57.895 0.82 0.00 0.00 3.91
13 14 2.399356 GCACGTGCCCCTAAGAAGC 61.399 63.158 30.12 0.00 34.31 3.86
14 15 1.003839 TGCACGTGCCCCTAAGAAG 60.004 57.895 35.72 0.00 41.18 2.85
15 16 1.302192 GTGCACGTGCCCCTAAGAA 60.302 57.895 35.72 13.53 41.18 2.52
16 17 2.345991 GTGCACGTGCCCCTAAGA 59.654 61.111 35.72 14.34 41.18 2.10
17 18 3.118454 CGTGCACGTGCCCCTAAG 61.118 66.667 35.72 16.82 41.18 2.18
18 19 3.166490 TTCGTGCACGTGCCCCTAA 62.166 57.895 35.72 21.18 41.18 2.69
19 20 3.583276 CTTCGTGCACGTGCCCCTA 62.583 63.158 35.72 16.34 41.18 3.53
20 21 4.988598 CTTCGTGCACGTGCCCCT 62.989 66.667 35.72 0.00 41.18 4.79
21 22 4.980805 TCTTCGTGCACGTGCCCC 62.981 66.667 35.72 24.77 41.18 5.80
22 23 3.712881 GTCTTCGTGCACGTGCCC 61.713 66.667 35.72 25.39 41.18 5.36
23 24 2.159272 GAAGTCTTCGTGCACGTGCC 62.159 60.000 35.72 25.12 41.18 5.01
24 25 1.201825 GAAGTCTTCGTGCACGTGC 59.798 57.895 35.74 33.11 40.80 5.34
25 26 0.778815 GAGAAGTCTTCGTGCACGTG 59.221 55.000 35.74 28.05 40.80 4.49
26 27 0.660595 CGAGAAGTCTTCGTGCACGT 60.661 55.000 35.74 18.16 40.80 4.49
27 28 1.337817 CCGAGAAGTCTTCGTGCACG 61.338 60.000 32.76 32.76 41.45 5.34
28 29 1.618640 GCCGAGAAGTCTTCGTGCAC 61.619 60.000 6.82 6.82 34.02 4.57
29 30 1.372997 GCCGAGAAGTCTTCGTGCA 60.373 57.895 14.99 0.00 34.02 4.57
30 31 1.080434 AGCCGAGAAGTCTTCGTGC 60.080 57.895 6.94 10.57 34.02 5.34
31 32 1.347817 GCAGCCGAGAAGTCTTCGTG 61.348 60.000 6.94 3.86 34.02 4.35
32 33 1.080434 GCAGCCGAGAAGTCTTCGT 60.080 57.895 6.94 0.00 34.02 3.85
33 34 1.807573 GGCAGCCGAGAAGTCTTCG 60.808 63.158 6.94 0.00 34.02 3.79
34 35 0.107945 ATGGCAGCCGAGAAGTCTTC 60.108 55.000 7.03 4.26 0.00 2.87
35 36 0.326264 AATGGCAGCCGAGAAGTCTT 59.674 50.000 7.03 0.00 0.00 3.01
36 37 0.392193 CAATGGCAGCCGAGAAGTCT 60.392 55.000 7.03 0.00 0.00 3.24
37 38 0.391661 TCAATGGCAGCCGAGAAGTC 60.392 55.000 7.03 0.00 0.00 3.01
38 39 0.674895 GTCAATGGCAGCCGAGAAGT 60.675 55.000 7.03 0.00 0.00 3.01
39 40 0.674581 TGTCAATGGCAGCCGAGAAG 60.675 55.000 7.03 0.00 0.00 2.85
40 41 0.250684 TTGTCAATGGCAGCCGAGAA 60.251 50.000 7.03 0.00 0.00 2.87
41 42 0.674581 CTTGTCAATGGCAGCCGAGA 60.675 55.000 7.03 1.11 0.00 4.04
42 43 1.651240 CCTTGTCAATGGCAGCCGAG 61.651 60.000 7.03 0.00 0.00 4.63
43 44 1.675310 CCTTGTCAATGGCAGCCGA 60.675 57.895 7.03 0.00 0.00 5.54
44 45 1.926511 GACCTTGTCAATGGCAGCCG 61.927 60.000 7.03 0.00 32.09 5.52
45 46 0.895100 TGACCTTGTCAATGGCAGCC 60.895 55.000 3.66 3.66 39.78 4.85
46 47 0.961019 TTGACCTTGTCAATGGCAGC 59.039 50.000 5.59 0.00 45.88 5.25
54 55 2.281484 GCCGGCTTGACCTTGTCA 60.281 61.111 22.15 0.00 41.09 3.58
55 56 2.032681 AGCCGGCTTGACCTTGTC 59.967 61.111 27.08 0.00 35.61 3.18
56 57 2.032681 GAGCCGGCTTGACCTTGT 59.967 61.111 33.34 4.05 35.61 3.16
57 58 2.747855 GGAGCCGGCTTGACCTTG 60.748 66.667 33.34 0.00 35.61 3.61
58 59 4.394712 CGGAGCCGGCTTGACCTT 62.395 66.667 33.34 5.97 35.61 3.50
72 73 3.949885 TTGCCGCTCCTCTACCGGA 62.950 63.158 9.46 0.00 44.55 5.14
73 74 3.458163 TTGCCGCTCCTCTACCGG 61.458 66.667 0.00 0.00 44.58 5.28
74 75 2.202756 GTTGCCGCTCCTCTACCG 60.203 66.667 0.00 0.00 0.00 4.02
75 76 1.019805 GTTGTTGCCGCTCCTCTACC 61.020 60.000 0.00 0.00 0.00 3.18
76 77 1.352156 CGTTGTTGCCGCTCCTCTAC 61.352 60.000 0.00 0.00 0.00 2.59
77 78 1.080093 CGTTGTTGCCGCTCCTCTA 60.080 57.895 0.00 0.00 0.00 2.43
78 79 2.357517 CGTTGTTGCCGCTCCTCT 60.358 61.111 0.00 0.00 0.00 3.69
79 80 3.423154 CCGTTGTTGCCGCTCCTC 61.423 66.667 0.00 0.00 0.00 3.71
82 83 3.660111 AAGCCGTTGTTGCCGCTC 61.660 61.111 0.00 0.00 0.00 5.03
83 84 3.964875 CAAGCCGTTGTTGCCGCT 61.965 61.111 0.00 0.00 0.00 5.52
84 85 4.264638 ACAAGCCGTTGTTGCCGC 62.265 61.111 0.00 0.00 45.00 6.53
91 92 2.252260 CTGCCGAACAAGCCGTTG 59.748 61.111 0.00 0.00 38.19 4.10
92 93 3.660111 GCTGCCGAACAAGCCGTT 61.660 61.111 0.00 0.00 41.86 4.44
93 94 4.927782 TGCTGCCGAACAAGCCGT 62.928 61.111 0.00 0.00 0.00 5.68
94 95 4.093952 CTGCTGCCGAACAAGCCG 62.094 66.667 0.00 0.00 0.00 5.52
95 96 1.639298 CTACTGCTGCCGAACAAGCC 61.639 60.000 0.00 0.00 0.00 4.35
96 97 0.951040 ACTACTGCTGCCGAACAAGC 60.951 55.000 0.00 0.00 0.00 4.01
97 98 0.792640 CACTACTGCTGCCGAACAAG 59.207 55.000 0.00 0.00 0.00 3.16
98 99 0.602638 CCACTACTGCTGCCGAACAA 60.603 55.000 0.00 0.00 0.00 2.83
99 100 1.005037 CCACTACTGCTGCCGAACA 60.005 57.895 0.00 0.00 0.00 3.18
100 101 1.004918 ACCACTACTGCTGCCGAAC 60.005 57.895 0.00 0.00 0.00 3.95
101 102 1.292223 GACCACTACTGCTGCCGAA 59.708 57.895 0.00 0.00 0.00 4.30
102 103 2.970639 GACCACTACTGCTGCCGA 59.029 61.111 0.00 0.00 0.00 5.54
103 104 2.507102 CGACCACTACTGCTGCCG 60.507 66.667 0.00 0.00 0.00 5.69
104 105 0.602905 AAACGACCACTACTGCTGCC 60.603 55.000 0.00 0.00 0.00 4.85
105 106 0.512952 CAAACGACCACTACTGCTGC 59.487 55.000 0.00 0.00 0.00 5.25
106 107 1.148310 CCAAACGACCACTACTGCTG 58.852 55.000 0.00 0.00 0.00 4.41
107 108 0.756903 ACCAAACGACCACTACTGCT 59.243 50.000 0.00 0.00 0.00 4.24
108 109 0.865769 CACCAAACGACCACTACTGC 59.134 55.000 0.00 0.00 0.00 4.40
109 110 1.508632 CCACCAAACGACCACTACTG 58.491 55.000 0.00 0.00 0.00 2.74
110 111 0.250166 GCCACCAAACGACCACTACT 60.250 55.000 0.00 0.00 0.00 2.57
111 112 1.232621 GGCCACCAAACGACCACTAC 61.233 60.000 0.00 0.00 0.00 2.73
112 113 1.071814 GGCCACCAAACGACCACTA 59.928 57.895 0.00 0.00 0.00 2.74
113 114 2.203294 GGCCACCAAACGACCACT 60.203 61.111 0.00 0.00 0.00 4.00
114 115 2.517402 TGGCCACCAAACGACCAC 60.517 61.111 0.00 0.00 0.00 4.16
115 116 2.517402 GTGGCCACCAAACGACCA 60.517 61.111 26.31 0.00 34.18 4.02
116 117 3.656045 CGTGGCCACCAAACGACC 61.656 66.667 29.95 1.81 34.18 4.79
117 118 3.656045 CCGTGGCCACCAAACGAC 61.656 66.667 29.95 2.63 34.18 4.34
118 119 4.939368 CCCGTGGCCACCAAACGA 62.939 66.667 29.95 0.00 34.18 3.85
119 120 4.939368 TCCCGTGGCCACCAAACG 62.939 66.667 29.95 17.73 34.18 3.60
120 121 1.873270 GATTCCCGTGGCCACCAAAC 61.873 60.000 29.95 14.61 34.18 2.93
121 122 1.605165 GATTCCCGTGGCCACCAAA 60.605 57.895 29.95 20.48 34.18 3.28
122 123 2.034999 GATTCCCGTGGCCACCAA 59.965 61.111 29.95 19.60 34.18 3.67
123 124 2.933287 AGATTCCCGTGGCCACCA 60.933 61.111 29.95 11.56 0.00 4.17
124 125 2.124695 GAGATTCCCGTGGCCACC 60.125 66.667 29.95 14.67 0.00 4.61
125 126 2.311688 ATCGAGATTCCCGTGGCCAC 62.312 60.000 26.78 26.78 0.00 5.01
126 127 2.063979 ATCGAGATTCCCGTGGCCA 61.064 57.895 0.00 0.00 0.00 5.36
127 128 1.595382 CATCGAGATTCCCGTGGCC 60.595 63.158 0.00 0.00 0.00 5.36
128 129 0.387929 TACATCGAGATTCCCGTGGC 59.612 55.000 0.00 0.00 0.00 5.01
129 130 2.882927 TTACATCGAGATTCCCGTGG 57.117 50.000 0.00 0.00 0.00 4.94
130 131 5.734855 AAAATTACATCGAGATTCCCGTG 57.265 39.130 0.00 0.00 0.00 4.94
131 132 8.446599 AATAAAAATTACATCGAGATTCCCGT 57.553 30.769 0.00 0.00 0.00 5.28
143 144 9.015577 CGCGGTCAAACATAATAAAAATTACAT 57.984 29.630 0.00 0.00 0.00 2.29
144 145 7.485277 CCGCGGTCAAACATAATAAAAATTACA 59.515 33.333 19.50 0.00 0.00 2.41
145 146 7.697291 TCCGCGGTCAAACATAATAAAAATTAC 59.303 33.333 27.15 0.00 0.00 1.89
146 147 7.759465 TCCGCGGTCAAACATAATAAAAATTA 58.241 30.769 27.15 0.00 0.00 1.40
147 148 6.622549 TCCGCGGTCAAACATAATAAAAATT 58.377 32.000 27.15 0.00 0.00 1.82
148 149 6.197364 TCCGCGGTCAAACATAATAAAAAT 57.803 33.333 27.15 0.00 0.00 1.82
149 150 5.624344 TCCGCGGTCAAACATAATAAAAA 57.376 34.783 27.15 0.00 0.00 1.94
150 151 5.821516 ATCCGCGGTCAAACATAATAAAA 57.178 34.783 27.15 0.00 0.00 1.52
151 152 5.049954 GCTATCCGCGGTCAAACATAATAAA 60.050 40.000 27.15 0.00 0.00 1.40
152 153 4.449743 GCTATCCGCGGTCAAACATAATAA 59.550 41.667 27.15 0.00 0.00 1.40
153 154 3.991773 GCTATCCGCGGTCAAACATAATA 59.008 43.478 27.15 10.99 0.00 0.98
154 155 2.806244 GCTATCCGCGGTCAAACATAAT 59.194 45.455 27.15 10.34 0.00 1.28
155 156 2.206750 GCTATCCGCGGTCAAACATAA 58.793 47.619 27.15 1.58 0.00 1.90
156 157 1.539496 GGCTATCCGCGGTCAAACATA 60.539 52.381 27.15 13.25 40.44 2.29
157 158 0.814010 GGCTATCCGCGGTCAAACAT 60.814 55.000 27.15 12.75 40.44 2.71
158 159 1.448893 GGCTATCCGCGGTCAAACA 60.449 57.895 27.15 4.32 40.44 2.83
159 160 0.103572 TAGGCTATCCGCGGTCAAAC 59.896 55.000 27.15 14.07 40.44 2.93
160 161 0.103572 GTAGGCTATCCGCGGTCAAA 59.896 55.000 27.15 5.72 40.44 2.69
161 162 0.754217 AGTAGGCTATCCGCGGTCAA 60.754 55.000 27.15 6.18 40.44 3.18
162 163 1.152819 AGTAGGCTATCCGCGGTCA 60.153 57.895 27.15 13.23 40.44 4.02
163 164 1.286260 CAGTAGGCTATCCGCGGTC 59.714 63.158 27.15 12.62 40.44 4.79
164 165 2.201022 CCAGTAGGCTATCCGCGGT 61.201 63.158 27.15 15.22 40.44 5.68
165 166 2.651361 CCAGTAGGCTATCCGCGG 59.349 66.667 22.12 22.12 40.44 6.46
166 167 2.651361 CCCAGTAGGCTATCCGCG 59.349 66.667 0.00 0.00 40.44 6.46
203 204 4.874977 GAGGCCCAGCTACGCGTC 62.875 72.222 18.63 1.13 33.31 5.19
205 206 4.880537 CTGAGGCCCAGCTACGCG 62.881 72.222 3.53 3.53 35.89 6.01
206 207 3.316573 AACTGAGGCCCAGCTACGC 62.317 63.158 18.07 0.00 46.81 4.42
207 208 1.448540 CAACTGAGGCCCAGCTACG 60.449 63.158 18.07 4.08 46.81 3.51
208 209 0.674895 CACAACTGAGGCCCAGCTAC 60.675 60.000 18.07 0.00 46.81 3.58
209 210 1.679311 CACAACTGAGGCCCAGCTA 59.321 57.895 18.07 0.00 46.81 3.32
210 211 2.433446 CACAACTGAGGCCCAGCT 59.567 61.111 18.07 6.28 46.81 4.24
211 212 2.674380 CCACAACTGAGGCCCAGC 60.674 66.667 18.07 1.32 46.81 4.85
212 213 2.674380 GCCACAACTGAGGCCCAG 60.674 66.667 16.92 16.92 44.49 4.45
217 218 0.671781 CTTCGAGGCCACAACTGAGG 60.672 60.000 5.01 0.00 0.00 3.86
218 219 0.671781 CCTTCGAGGCCACAACTGAG 60.672 60.000 5.01 0.00 0.00 3.35
219 220 1.371183 CCTTCGAGGCCACAACTGA 59.629 57.895 5.01 0.00 0.00 3.41
220 221 1.071471 ACCTTCGAGGCCACAACTG 59.929 57.895 5.01 0.00 39.63 3.16
221 222 1.071471 CACCTTCGAGGCCACAACT 59.929 57.895 5.01 0.00 39.63 3.16
222 223 1.966451 CCACCTTCGAGGCCACAAC 60.966 63.158 5.01 0.00 39.63 3.32
223 224 2.429930 CCACCTTCGAGGCCACAA 59.570 61.111 5.01 0.00 39.63 3.33
224 225 4.329545 GCCACCTTCGAGGCCACA 62.330 66.667 5.01 0.00 45.18 4.17
243 244 2.370849 TCGGTTACTCTTGGGCTTTTCT 59.629 45.455 0.00 0.00 0.00 2.52
298 303 2.530497 CGGCCGAGAGAGAGAGACG 61.530 68.421 24.07 0.00 0.00 4.18
299 304 0.534203 ATCGGCCGAGAGAGAGAGAC 60.534 60.000 33.87 0.00 0.00 3.36
380 391 3.531207 TGGCCGGAGATCGCTCTG 61.531 66.667 5.05 0.00 45.36 3.35
407 418 2.758737 CCGAACCCTAGTCCCGCT 60.759 66.667 0.00 0.00 0.00 5.52
440 451 2.047179 GTCTCCGCGGCTTTCCTT 60.047 61.111 23.51 0.00 0.00 3.36
527 542 0.476771 AAAGAAAGGGGACGCCTCAA 59.523 50.000 12.13 0.00 0.00 3.02
549 590 2.061220 CCAGCCAGAACAGAGTCCA 58.939 57.895 0.00 0.00 0.00 4.02
583 636 0.405585 ACCATGGACCAGAACAAGGG 59.594 55.000 21.47 0.00 30.11 3.95
633 686 4.091509 GCGTCGATTTACAGAACTTGTGAT 59.908 41.667 0.00 0.00 41.10 3.06
654 711 2.237751 CCGTGCTATTTCCTCCGCG 61.238 63.158 0.00 0.00 0.00 6.46
673 732 1.151668 CTTTGTTCAGCTCCGTCAGG 58.848 55.000 0.00 0.00 39.46 3.86
675 734 1.138069 TGTCTTTGTTCAGCTCCGTCA 59.862 47.619 0.00 0.00 0.00 4.35
683 742 6.529125 GGCATAAATGTGATGTCTTTGTTCAG 59.471 38.462 0.00 0.00 0.00 3.02
689 748 5.018809 ACAGGGCATAAATGTGATGTCTTT 58.981 37.500 0.00 0.00 0.00 2.52
786 934 5.076873 TCCAAAGTCCAAAAGAGTAATGGG 58.923 41.667 0.00 0.00 36.41 4.00
830 978 7.275341 TGAATGATGTTTATCAAATTTGTCCGC 59.725 33.333 17.47 6.78 45.82 5.54
832 980 9.421806 TGTGAATGATGTTTATCAAATTTGTCC 57.578 29.630 17.47 3.81 45.82 4.02
854 1002 0.321564 CAGAGGATTTGGCGGTGTGA 60.322 55.000 0.00 0.00 0.00 3.58
856 1004 0.110486 AACAGAGGATTTGGCGGTGT 59.890 50.000 0.00 0.00 0.00 4.16
880 1028 7.090173 CACAATACAAACGGAAAATGGAGATT 58.910 34.615 0.00 0.00 0.00 2.40
1063 1230 7.291566 TCATTACCTTGAAACCTCCTTGTTAA 58.708 34.615 0.00 0.00 0.00 2.01
1097 1264 4.735338 GCGCATTAAACAGCCTAAATTCTC 59.265 41.667 0.30 0.00 0.00 2.87
1108 1275 3.871006 TCACCATAGAGCGCATTAAACAG 59.129 43.478 11.47 0.00 0.00 3.16
1249 1416 1.837439 ACATTCGAACCCTATGGCTGA 59.163 47.619 0.00 0.00 33.59 4.26
1258 1425 8.402472 TCATATTTGTTATCAACATTCGAACCC 58.598 33.333 0.00 0.00 41.79 4.11
1259 1426 9.221775 GTCATATTTGTTATCAACATTCGAACC 57.778 33.333 0.00 0.00 41.79 3.62
1295 1462 5.570234 TTGTAAGGTGACACAAAGTTTCC 57.430 39.130 8.08 0.00 31.93 3.13
1390 1557 8.612619 AGTCAAAACTTCTACACTAACAACATG 58.387 33.333 0.00 0.00 28.74 3.21
1405 1573 4.936891 ACAATGAGCCAAGTCAAAACTTC 58.063 39.130 0.00 0.00 43.99 3.01
1425 1593 9.056005 GCTAATACAATTTCATACTGGATGACA 57.944 33.333 1.02 0.00 44.53 3.58
1443 1611 8.836413 GCCATCACTTAAGTTTATGCTAATACA 58.164 33.333 17.05 0.00 0.00 2.29
1444 1612 9.057089 AGCCATCACTTAAGTTTATGCTAATAC 57.943 33.333 17.05 6.59 0.00 1.89
1448 1616 6.414732 ACAGCCATCACTTAAGTTTATGCTA 58.585 36.000 17.05 0.00 0.00 3.49
1462 1630 8.986477 AAAGATTGTAAAATTACAGCCATCAC 57.014 30.769 14.32 3.00 43.77 3.06
1479 1647 4.686191 TTCCATGGTTGCAAAAGATTGT 57.314 36.364 12.58 0.00 38.85 2.71
1588 1756 5.700402 ACTCAAGGTCAAGGCTACATAAT 57.300 39.130 0.00 0.00 0.00 1.28
1590 1758 5.720041 AGTAACTCAAGGTCAAGGCTACATA 59.280 40.000 0.00 0.00 0.00 2.29
1767 2030 2.586425 ACCAGCACAGCACTACAAATT 58.414 42.857 0.00 0.00 0.00 1.82
1768 2031 2.276732 ACCAGCACAGCACTACAAAT 57.723 45.000 0.00 0.00 0.00 2.32
1769 2032 2.920724 TACCAGCACAGCACTACAAA 57.079 45.000 0.00 0.00 0.00 2.83
1770 2033 2.615240 CCATACCAGCACAGCACTACAA 60.615 50.000 0.00 0.00 0.00 2.41
1771 2034 1.066215 CCATACCAGCACAGCACTACA 60.066 52.381 0.00 0.00 0.00 2.74
1772 2035 1.207089 TCCATACCAGCACAGCACTAC 59.793 52.381 0.00 0.00 0.00 2.73
1773 2036 1.567357 TCCATACCAGCACAGCACTA 58.433 50.000 0.00 0.00 0.00 2.74
1774 2037 0.692476 TTCCATACCAGCACAGCACT 59.308 50.000 0.00 0.00 0.00 4.40
1775 2038 1.533625 TTTCCATACCAGCACAGCAC 58.466 50.000 0.00 0.00 0.00 4.40
1776 2039 1.885887 GTTTTCCATACCAGCACAGCA 59.114 47.619 0.00 0.00 0.00 4.41
1777 2040 1.885887 TGTTTTCCATACCAGCACAGC 59.114 47.619 0.00 0.00 0.00 4.40
1778 2041 4.789012 ATTGTTTTCCATACCAGCACAG 57.211 40.909 0.00 0.00 0.00 3.66
1779 2042 5.536538 TGTAATTGTTTTCCATACCAGCACA 59.463 36.000 0.00 0.00 0.00 4.57
1826 2131 2.165437 CAGGAAGTAGTGGTCTGAGAGC 59.835 54.545 4.41 4.41 0.00 4.09
1904 2209 2.303022 AGAATTTTCCGACAGAGGAGCA 59.697 45.455 0.00 0.00 41.98 4.26
1990 2298 5.699458 CGTCTTACATTTACAAACAGAGGGT 59.301 40.000 0.00 0.00 0.00 4.34
1991 2299 5.390567 GCGTCTTACATTTACAAACAGAGGG 60.391 44.000 0.00 0.00 0.00 4.30
2001 2309 4.083484 ACTGCCAAAGCGTCTTACATTTAC 60.083 41.667 0.00 0.00 44.31 2.01
2029 2337 4.385358 AAGACGTTTTGGCAGTTCAAAT 57.615 36.364 0.00 0.00 36.63 2.32
2064 2372 6.547510 GGCAATAAGAAGAATGATACACCCTT 59.452 38.462 0.00 0.00 0.00 3.95
2208 2516 0.798776 CATTCAGGAACCGCTGTCAC 59.201 55.000 0.00 0.00 0.00 3.67
2335 2643 7.823745 AATGAGATGTGGTTAACTTGAGTTT 57.176 32.000 5.42 0.00 39.31 2.66
2350 2658 4.021102 ACTTCCCGTTCAAATGAGATGT 57.979 40.909 0.00 0.00 0.00 3.06
2577 2885 7.338703 ACAAGTTATGAATCATGTCAAGCTCAT 59.661 33.333 5.91 0.00 0.00 2.90
2652 2960 9.931698 TCACTCTTATATTAGTTTACAGAGGGA 57.068 33.333 0.00 0.00 37.07 4.20
2679 2987 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2680 2988 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2681 2989 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2682 2990 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2683 2991 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2684 2992 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2685 2993 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2686 2994 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2687 2995 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2688 2996 9.866655 TTACTCCCTCCGTAAACTAATATAAGA 57.133 33.333 0.00 0.00 0.00 2.10
2694 3002 9.819754 AGTATATTACTCCCTCCGTAAACTAAT 57.180 33.333 0.00 0.00 32.47 1.73
2702 3010 7.720515 GCAGATATAGTATATTACTCCCTCCGT 59.279 40.741 4.15 0.00 40.14 4.69
2703 3011 7.940137 AGCAGATATAGTATATTACTCCCTCCG 59.060 40.741 4.15 0.00 40.14 4.63
2704 3012 9.292195 GAGCAGATATAGTATATTACTCCCTCC 57.708 40.741 4.15 0.00 40.14 4.30
2705 3013 9.854668 TGAGCAGATATAGTATATTACTCCCTC 57.145 37.037 17.06 12.39 40.14 4.30
2706 3014 9.635404 GTGAGCAGATATAGTATATTACTCCCT 57.365 37.037 17.06 4.36 40.14 4.20
2707 3015 9.635404 AGTGAGCAGATATAGTATATTACTCCC 57.365 37.037 17.06 10.87 40.14 4.30
2956 3264 6.173339 AGAACAGAACAGAACAGAACAGAAA 58.827 36.000 0.00 0.00 0.00 2.52
2957 3265 5.734720 AGAACAGAACAGAACAGAACAGAA 58.265 37.500 0.00 0.00 0.00 3.02
2958 3266 5.105351 TGAGAACAGAACAGAACAGAACAGA 60.105 40.000 0.00 0.00 0.00 3.41
2959 3267 5.006165 GTGAGAACAGAACAGAACAGAACAG 59.994 44.000 0.00 0.00 0.00 3.16
2960 3268 4.870426 GTGAGAACAGAACAGAACAGAACA 59.130 41.667 0.00 0.00 0.00 3.18
2961 3269 4.870426 TGTGAGAACAGAACAGAACAGAAC 59.130 41.667 0.00 0.00 0.00 3.01
3164 3479 0.605589 GAACCCGCCAAAGTAGCTGT 60.606 55.000 0.00 0.00 0.00 4.40
3562 3880 4.593206 CAGTAATATCCAGACTTGGCCCTA 59.407 45.833 0.00 0.00 44.63 3.53
3597 3915 6.309712 AGAAATAATGTGCATGATCTTCGG 57.690 37.500 0.00 0.00 0.00 4.30
3606 3924 6.183360 GGCAAGAGAGAAGAAATAATGTGCAT 60.183 38.462 0.00 0.00 0.00 3.96
3610 3928 5.491982 ACGGCAAGAGAGAAGAAATAATGT 58.508 37.500 0.00 0.00 0.00 2.71
3800 4118 6.969993 TGTGAAAAGTAAGGCATAAAGGTT 57.030 33.333 0.00 0.00 0.00 3.50
3998 4324 3.820777 TTGTTTGTTTTGTTTGGCTGC 57.179 38.095 0.00 0.00 0.00 5.25
4046 4381 2.621055 TCGAAAATTGGTTGACACTGGG 59.379 45.455 0.00 0.00 0.00 4.45
4190 4526 3.119743 CCTACAACGACGACTACATCCAA 60.120 47.826 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.