Multiple sequence alignment - TraesCS2A01G280900

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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 TraesCS2A01G280900 chr2A 100.000 3252 0 0 1 3252 469195228 469191977 0.000000e+00 6006
1 TraesCS2A01G280900 chr2A 97.667 986 21 2 2268 3252 75593668 75594652 0.000000e+00 1692
2 TraesCS2A01G280900 chr2D 95.184 1578 71 4 691 2265 351382525 351380950 0.000000e+00 2488
3 TraesCS2A01G280900 chr2D 86.164 318 23 5 342 654 351382834 351382533 1.130000e-84 324
4 TraesCS2A01G280900 chr1A 98.271 983 17 0 2270 3252 20564195 20563213 0.000000e+00 1722
5 TraesCS2A01G280900 chr1A 95.312 960 42 3 2296 3252 574293077 574294036 0.000000e+00 1520
6 TraesCS2A01G280900 chr7A 98.077 988 19 0 2265 3252 287018449 287017462 0.000000e+00 1720
7 TraesCS2A01G280900 chr7A 97.245 980 26 1 2268 3247 583866678 583867656 0.000000e+00 1659
8 TraesCS2A01G280900 chr5B 98.065 982 19 0 2266 3247 508772549 508771568 0.000000e+00 1709
9 TraesCS2A01G280900 chr2B 91.667 1224 84 9 333 1549 417773686 417772474 0.000000e+00 1679
10 TraesCS2A01G280900 chr2B 95.406 653 30 0 1613 2265 417772333 417771681 0.000000e+00 1040
11 TraesCS2A01G280900 chr6A 97.163 987 25 3 2268 3252 615684026 615683041 0.000000e+00 1664
12 TraesCS2A01G280900 chr3B 97.531 972 22 2 2282 3252 770217263 770216293 0.000000e+00 1661
13 TraesCS2A01G280900 chr5A 95.758 990 39 2 2266 3252 10922193 10923182 0.000000e+00 1592


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 TraesCS2A01G280900 chr2A 469191977 469195228 3251 True 6006.0 6006 100.0000 1 3252 1 chr2A.!!$R1 3251
1 TraesCS2A01G280900 chr2A 75593668 75594652 984 False 1692.0 1692 97.6670 2268 3252 1 chr2A.!!$F1 984
2 TraesCS2A01G280900 chr2D 351380950 351382834 1884 True 1406.0 2488 90.6740 342 2265 2 chr2D.!!$R1 1923
3 TraesCS2A01G280900 chr1A 20563213 20564195 982 True 1722.0 1722 98.2710 2270 3252 1 chr1A.!!$R1 982
4 TraesCS2A01G280900 chr1A 574293077 574294036 959 False 1520.0 1520 95.3120 2296 3252 1 chr1A.!!$F1 956
5 TraesCS2A01G280900 chr7A 287017462 287018449 987 True 1720.0 1720 98.0770 2265 3252 1 chr7A.!!$R1 987
6 TraesCS2A01G280900 chr7A 583866678 583867656 978 False 1659.0 1659 97.2450 2268 3247 1 chr7A.!!$F1 979
7 TraesCS2A01G280900 chr5B 508771568 508772549 981 True 1709.0 1709 98.0650 2266 3247 1 chr5B.!!$R1 981
8 TraesCS2A01G280900 chr2B 417771681 417773686 2005 True 1359.5 1679 93.5365 333 2265 2 chr2B.!!$R1 1932
9 TraesCS2A01G280900 chr6A 615683041 615684026 985 True 1664.0 1664 97.1630 2268 3252 1 chr6A.!!$R1 984
10 TraesCS2A01G280900 chr3B 770216293 770217263 970 True 1661.0 1661 97.5310 2282 3252 1 chr3B.!!$R1 970
11 TraesCS2A01G280900 chr5A 10922193 10923182 989 False 1592.0 1592 95.7580 2266 3252 1 chr5A.!!$F1 986

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
53 54 0.037590 ATGTAGGCCGAGCACCAAAA 59.962 50.0 0.00 0.0 0.00 2.44 F
467 468 0.174162 ATTGCATCCTTTTCCGCTGC 59.826 50.0 0.00 0.0 0.00 5.25 F
1476 1488 0.260816 ATGCTGCTGTCCATGGGAAT 59.739 50.0 13.02 0.0 31.38 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1926 0.036388 ATCGGCCGCCCATTATGTAG 60.036 55.0 23.51 0.0 0.00 2.74 R
2074 2163 1.093159 CAAGGCAGAATCTGGTGCTC 58.907 55.0 12.66 0.0 39.76 4.26 R
3208 3304 0.667993 CTCGCTCTCCTCAGTCCATC 59.332 60.0 0.00 0.0 0.00 3.51 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.879342 ACACATTTTCGGAATGTTTCAAATAA 57.121 26.923 13.17 0.00 38.69 1.40
26 27 9.319143 ACACATTTTCGGAATGTTTCAAATAAA 57.681 25.926 13.17 0.00 38.69 1.40
27 28 9.796062 CACATTTTCGGAATGTTTCAAATAAAG 57.204 29.630 13.17 0.00 38.69 1.85
28 29 8.987890 ACATTTTCGGAATGTTTCAAATAAAGG 58.012 29.630 10.88 0.00 37.58 3.11
29 30 7.954788 TTTTCGGAATGTTTCAAATAAAGGG 57.045 32.000 0.00 0.00 0.00 3.95
30 31 5.066968 TCGGAATGTTTCAAATAAAGGGC 57.933 39.130 0.00 0.00 0.00 5.19
31 32 4.770010 TCGGAATGTTTCAAATAAAGGGCT 59.230 37.500 0.00 0.00 0.00 5.19
32 33 5.102313 CGGAATGTTTCAAATAAAGGGCTC 58.898 41.667 0.00 0.00 0.00 4.70
33 34 5.105756 CGGAATGTTTCAAATAAAGGGCTCT 60.106 40.000 0.00 0.00 0.00 4.09
34 35 6.094881 CGGAATGTTTCAAATAAAGGGCTCTA 59.905 38.462 0.00 0.00 0.00 2.43
35 36 7.201821 CGGAATGTTTCAAATAAAGGGCTCTAT 60.202 37.037 0.00 0.00 0.00 1.98
36 37 7.922811 GGAATGTTTCAAATAAAGGGCTCTATG 59.077 37.037 0.00 0.00 0.00 2.23
37 38 7.961326 ATGTTTCAAATAAAGGGCTCTATGT 57.039 32.000 0.00 0.00 0.00 2.29
38 39 9.474313 AATGTTTCAAATAAAGGGCTCTATGTA 57.526 29.630 0.00 0.00 0.00 2.29
39 40 8.506168 TGTTTCAAATAAAGGGCTCTATGTAG 57.494 34.615 0.00 0.00 0.00 2.74
40 41 7.556275 TGTTTCAAATAAAGGGCTCTATGTAGG 59.444 37.037 0.00 0.00 0.00 3.18
41 42 5.621193 TCAAATAAAGGGCTCTATGTAGGC 58.379 41.667 0.00 0.00 41.17 3.93
46 47 1.290639 GGCTCTATGTAGGCCGAGC 59.709 63.158 17.01 17.01 46.06 5.03
47 48 2.041976 GCTCTATGTAGGCCGAGCA 58.958 57.895 19.47 10.61 46.06 4.26
48 49 0.319125 GCTCTATGTAGGCCGAGCAC 60.319 60.000 19.47 7.81 46.06 4.40
49 50 0.315568 CTCTATGTAGGCCGAGCACC 59.684 60.000 0.00 0.00 0.00 5.01
50 51 0.396556 TCTATGTAGGCCGAGCACCA 60.397 55.000 0.00 0.00 0.00 4.17
51 52 0.464036 CTATGTAGGCCGAGCACCAA 59.536 55.000 0.00 0.00 0.00 3.67
52 53 0.906066 TATGTAGGCCGAGCACCAAA 59.094 50.000 0.00 0.00 0.00 3.28
53 54 0.037590 ATGTAGGCCGAGCACCAAAA 59.962 50.000 0.00 0.00 0.00 2.44
54 55 0.887387 TGTAGGCCGAGCACCAAAAC 60.887 55.000 0.00 0.00 0.00 2.43
55 56 1.669760 TAGGCCGAGCACCAAAACG 60.670 57.895 0.00 0.00 0.00 3.60
56 57 4.700365 GGCCGAGCACCAAAACGC 62.700 66.667 0.00 0.00 0.00 4.84
57 58 3.660111 GCCGAGCACCAAAACGCT 61.660 61.111 0.00 0.00 42.42 5.07
58 59 2.252260 CCGAGCACCAAAACGCTG 59.748 61.111 0.00 0.00 38.99 5.18
59 60 2.427410 CGAGCACCAAAACGCTGC 60.427 61.111 0.00 0.00 38.99 5.25
60 61 2.721231 GAGCACCAAAACGCTGCA 59.279 55.556 0.00 0.00 38.99 4.41
61 62 1.286880 GAGCACCAAAACGCTGCAT 59.713 52.632 0.00 0.00 38.99 3.96
62 63 0.318955 GAGCACCAAAACGCTGCATT 60.319 50.000 0.00 0.00 38.99 3.56
63 64 0.318955 AGCACCAAAACGCTGCATTC 60.319 50.000 0.00 0.00 37.02 2.67
64 65 0.597118 GCACCAAAACGCTGCATTCA 60.597 50.000 0.00 0.00 0.00 2.57
65 66 1.936203 GCACCAAAACGCTGCATTCAT 60.936 47.619 0.00 0.00 0.00 2.57
66 67 2.406130 CACCAAAACGCTGCATTCATT 58.594 42.857 0.00 0.00 0.00 2.57
67 68 3.573598 CACCAAAACGCTGCATTCATTA 58.426 40.909 0.00 0.00 0.00 1.90
68 69 3.609373 CACCAAAACGCTGCATTCATTAG 59.391 43.478 0.00 0.00 0.00 1.73
69 70 3.505680 ACCAAAACGCTGCATTCATTAGA 59.494 39.130 0.00 0.00 0.00 2.10
70 71 4.158394 ACCAAAACGCTGCATTCATTAGAT 59.842 37.500 0.00 0.00 0.00 1.98
71 72 5.356751 ACCAAAACGCTGCATTCATTAGATA 59.643 36.000 0.00 0.00 0.00 1.98
72 73 5.682862 CCAAAACGCTGCATTCATTAGATAC 59.317 40.000 0.00 0.00 0.00 2.24
73 74 6.257423 CAAAACGCTGCATTCATTAGATACA 58.743 36.000 0.00 0.00 0.00 2.29
74 75 6.624352 AAACGCTGCATTCATTAGATACAT 57.376 33.333 0.00 0.00 0.00 2.29
75 76 6.624352 AACGCTGCATTCATTAGATACATT 57.376 33.333 0.00 0.00 0.00 2.71
76 77 6.233430 ACGCTGCATTCATTAGATACATTC 57.767 37.500 0.00 0.00 0.00 2.67
77 78 5.107337 ACGCTGCATTCATTAGATACATTCG 60.107 40.000 0.00 0.00 0.00 3.34
78 79 5.119125 CGCTGCATTCATTAGATACATTCGA 59.881 40.000 0.00 0.00 0.00 3.71
79 80 6.346838 CGCTGCATTCATTAGATACATTCGAA 60.347 38.462 0.00 0.00 0.00 3.71
80 81 7.014115 GCTGCATTCATTAGATACATTCGAAG 58.986 38.462 3.35 0.00 0.00 3.79
81 82 7.095481 GCTGCATTCATTAGATACATTCGAAGA 60.095 37.037 3.35 0.00 0.00 2.87
82 83 8.076714 TGCATTCATTAGATACATTCGAAGAC 57.923 34.615 3.35 0.00 34.32 3.01
83 84 7.710475 TGCATTCATTAGATACATTCGAAGACA 59.290 33.333 3.35 0.00 34.32 3.41
84 85 8.551205 GCATTCATTAGATACATTCGAAGACAA 58.449 33.333 3.35 0.00 34.32 3.18
86 87 9.823647 ATTCATTAGATACATTCGAAGACAAGT 57.176 29.630 3.35 0.00 34.32 3.16
93 94 8.808529 AGATACATTCGAAGACAAGTAATTTCG 58.191 33.333 3.35 0.00 42.61 3.46
94 95 6.165659 ACATTCGAAGACAAGTAATTTCGG 57.834 37.500 3.35 0.00 41.82 4.30
95 96 5.929992 ACATTCGAAGACAAGTAATTTCGGA 59.070 36.000 3.35 0.00 41.82 4.55
96 97 5.834239 TTCGAAGACAAGTAATTTCGGAC 57.166 39.130 0.00 0.00 41.82 4.79
97 98 3.916172 TCGAAGACAAGTAATTTCGGACG 59.084 43.478 5.76 0.00 41.82 4.79
98 99 3.060363 CGAAGACAAGTAATTTCGGACGG 59.940 47.826 0.00 0.00 38.87 4.79
99 100 3.947910 AGACAAGTAATTTCGGACGGA 57.052 42.857 0.00 0.00 0.00 4.69
100 101 3.846360 AGACAAGTAATTTCGGACGGAG 58.154 45.455 0.00 0.00 0.00 4.63
101 102 2.928116 GACAAGTAATTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
102 103 2.301009 ACAAGTAATTTCGGACGGAGGT 59.699 45.455 0.00 0.00 0.00 3.85
103 104 3.511146 ACAAGTAATTTCGGACGGAGGTA 59.489 43.478 0.00 0.00 0.00 3.08
104 105 4.021192 ACAAGTAATTTCGGACGGAGGTAA 60.021 41.667 0.00 0.00 0.00 2.85
105 106 5.114081 CAAGTAATTTCGGACGGAGGTAAT 58.886 41.667 0.00 0.00 0.00 1.89
106 107 6.127366 ACAAGTAATTTCGGACGGAGGTAATA 60.127 38.462 0.00 0.00 0.00 0.98
107 108 6.661304 AGTAATTTCGGACGGAGGTAATAT 57.339 37.500 0.00 0.00 0.00 1.28
108 109 6.453092 AGTAATTTCGGACGGAGGTAATATG 58.547 40.000 0.00 0.00 0.00 1.78
109 110 4.950205 ATTTCGGACGGAGGTAATATGT 57.050 40.909 0.00 0.00 0.00 2.29
110 111 3.720949 TTCGGACGGAGGTAATATGTG 57.279 47.619 0.00 0.00 0.00 3.21
111 112 2.934887 TCGGACGGAGGTAATATGTGA 58.065 47.619 0.00 0.00 0.00 3.58
112 113 3.493334 TCGGACGGAGGTAATATGTGAT 58.507 45.455 0.00 0.00 0.00 3.06
113 114 4.654915 TCGGACGGAGGTAATATGTGATA 58.345 43.478 0.00 0.00 0.00 2.15
114 115 5.258841 TCGGACGGAGGTAATATGTGATAT 58.741 41.667 0.00 0.00 0.00 1.63
115 116 5.124936 TCGGACGGAGGTAATATGTGATATG 59.875 44.000 0.00 0.00 0.00 1.78
116 117 5.105877 CGGACGGAGGTAATATGTGATATGT 60.106 44.000 0.00 0.00 0.00 2.29
117 118 6.571731 CGGACGGAGGTAATATGTGATATGTT 60.572 42.308 0.00 0.00 0.00 2.71
118 119 7.159372 GGACGGAGGTAATATGTGATATGTTT 58.841 38.462 0.00 0.00 0.00 2.83
119 120 7.660208 GGACGGAGGTAATATGTGATATGTTTT 59.340 37.037 0.00 0.00 0.00 2.43
120 121 8.378172 ACGGAGGTAATATGTGATATGTTTTG 57.622 34.615 0.00 0.00 0.00 2.44
121 122 7.990886 ACGGAGGTAATATGTGATATGTTTTGT 59.009 33.333 0.00 0.00 0.00 2.83
122 123 8.836413 CGGAGGTAATATGTGATATGTTTTGTT 58.164 33.333 0.00 0.00 0.00 2.83
127 128 9.872757 GTAATATGTGATATGTTTTGTTACCCG 57.127 33.333 0.00 0.00 0.00 5.28
128 129 8.514330 AATATGTGATATGTTTTGTTACCCGT 57.486 30.769 0.00 0.00 0.00 5.28
129 130 5.614923 TGTGATATGTTTTGTTACCCGTG 57.385 39.130 0.00 0.00 0.00 4.94
130 131 5.306394 TGTGATATGTTTTGTTACCCGTGA 58.694 37.500 0.00 0.00 0.00 4.35
131 132 5.941058 TGTGATATGTTTTGTTACCCGTGAT 59.059 36.000 0.00 0.00 0.00 3.06
132 133 7.104290 TGTGATATGTTTTGTTACCCGTGATA 58.896 34.615 0.00 0.00 0.00 2.15
133 134 7.771361 TGTGATATGTTTTGTTACCCGTGATAT 59.229 33.333 0.00 0.00 0.00 1.63
134 135 8.617809 GTGATATGTTTTGTTACCCGTGATATT 58.382 33.333 0.00 0.00 0.00 1.28
135 136 8.832521 TGATATGTTTTGTTACCCGTGATATTC 58.167 33.333 0.00 0.00 0.00 1.75
136 137 8.740123 ATATGTTTTGTTACCCGTGATATTCA 57.260 30.769 0.00 0.00 0.00 2.57
137 138 6.879276 TGTTTTGTTACCCGTGATATTCAA 57.121 33.333 0.00 0.00 0.00 2.69
138 139 6.670233 TGTTTTGTTACCCGTGATATTCAAC 58.330 36.000 0.00 0.00 0.00 3.18
139 140 6.487331 TGTTTTGTTACCCGTGATATTCAACT 59.513 34.615 0.00 0.00 0.00 3.16
140 141 7.013464 TGTTTTGTTACCCGTGATATTCAACTT 59.987 33.333 0.00 0.00 0.00 2.66
141 142 7.513371 TTTGTTACCCGTGATATTCAACTTT 57.487 32.000 0.00 0.00 0.00 2.66
142 143 6.730960 TGTTACCCGTGATATTCAACTTTC 57.269 37.500 0.00 0.00 0.00 2.62
143 144 6.231951 TGTTACCCGTGATATTCAACTTTCA 58.768 36.000 0.00 0.00 0.00 2.69
144 145 6.711194 TGTTACCCGTGATATTCAACTTTCAA 59.289 34.615 0.00 0.00 0.00 2.69
145 146 7.392113 TGTTACCCGTGATATTCAACTTTCAAT 59.608 33.333 0.00 0.00 0.00 2.57
146 147 6.834168 ACCCGTGATATTCAACTTTCAATT 57.166 33.333 0.00 0.00 0.00 2.32
147 148 7.227049 ACCCGTGATATTCAACTTTCAATTT 57.773 32.000 0.00 0.00 0.00 1.82
148 149 7.666623 ACCCGTGATATTCAACTTTCAATTTT 58.333 30.769 0.00 0.00 0.00 1.82
149 150 8.798402 ACCCGTGATATTCAACTTTCAATTTTA 58.202 29.630 0.00 0.00 0.00 1.52
150 151 9.632807 CCCGTGATATTCAACTTTCAATTTTAA 57.367 29.630 0.00 0.00 0.00 1.52
178 179 9.921637 TTTATTGAAAAGACAAACTTTCTGTGT 57.078 25.926 0.00 0.00 46.55 3.72
209 210 9.090692 AGAATCATCTGTTTCTGTTTGTTTTTG 57.909 29.630 3.34 0.00 34.01 2.44
210 211 9.086336 GAATCATCTGTTTCTGTTTGTTTTTGA 57.914 29.630 0.00 0.00 0.00 2.69
211 212 9.603921 AATCATCTGTTTCTGTTTGTTTTTGAT 57.396 25.926 0.00 0.00 0.00 2.57
212 213 9.603921 ATCATCTGTTTCTGTTTGTTTTTGATT 57.396 25.926 0.00 0.00 0.00 2.57
213 214 9.434420 TCATCTGTTTCTGTTTGTTTTTGATTT 57.566 25.926 0.00 0.00 0.00 2.17
217 218 9.833894 CTGTTTCTGTTTGTTTTTGATTTATCG 57.166 29.630 0.00 0.00 0.00 2.92
218 219 9.360093 TGTTTCTGTTTGTTTTTGATTTATCGT 57.640 25.926 0.00 0.00 0.00 3.73
280 281 9.770097 AGTTGATACTTTATATGACATGAGGTG 57.230 33.333 0.00 0.00 0.00 4.00
281 282 8.993121 GTTGATACTTTATATGACATGAGGTGG 58.007 37.037 0.00 0.00 0.00 4.61
282 283 8.262601 TGATACTTTATATGACATGAGGTGGT 57.737 34.615 0.00 0.00 0.00 4.16
283 284 9.374711 TGATACTTTATATGACATGAGGTGGTA 57.625 33.333 0.00 0.00 0.00 3.25
287 288 9.154632 ACTTTATATGACATGAGGTGGTATACA 57.845 33.333 5.01 0.00 0.00 2.29
304 305 7.881142 TGGTATACACAATCAGTTTCCTTTTG 58.119 34.615 5.01 0.00 0.00 2.44
305 306 7.504238 TGGTATACACAATCAGTTTCCTTTTGT 59.496 33.333 5.01 0.00 0.00 2.83
306 307 9.005777 GGTATACACAATCAGTTTCCTTTTGTA 57.994 33.333 5.01 0.00 0.00 2.41
312 313 9.573133 CACAATCAGTTTCCTTTTGTATTATCC 57.427 33.333 0.00 0.00 0.00 2.59
313 314 9.533831 ACAATCAGTTTCCTTTTGTATTATCCT 57.466 29.630 0.00 0.00 0.00 3.24
322 323 9.983024 TTCCTTTTGTATTATCCTATTTGTGGA 57.017 29.630 0.00 0.00 38.06 4.02
327 328 8.690203 TTGTATTATCCTATTTGTGGATGTGG 57.310 34.615 5.61 0.00 43.48 4.17
328 329 7.230747 TGTATTATCCTATTTGTGGATGTGGG 58.769 38.462 5.61 0.00 43.48 4.61
329 330 3.600448 ATCCTATTTGTGGATGTGGGG 57.400 47.619 0.00 0.00 42.22 4.96
330 331 2.283834 TCCTATTTGTGGATGTGGGGT 58.716 47.619 0.00 0.00 0.00 4.95
331 332 2.652348 TCCTATTTGTGGATGTGGGGTT 59.348 45.455 0.00 0.00 0.00 4.11
332 333 3.076785 TCCTATTTGTGGATGTGGGGTTT 59.923 43.478 0.00 0.00 0.00 3.27
333 334 3.195396 CCTATTTGTGGATGTGGGGTTTG 59.805 47.826 0.00 0.00 0.00 2.93
334 335 2.166907 TTTGTGGATGTGGGGTTTGT 57.833 45.000 0.00 0.00 0.00 2.83
335 336 3.314307 TTTGTGGATGTGGGGTTTGTA 57.686 42.857 0.00 0.00 0.00 2.41
336 337 3.534357 TTGTGGATGTGGGGTTTGTAT 57.466 42.857 0.00 0.00 0.00 2.29
337 338 4.659529 TTGTGGATGTGGGGTTTGTATA 57.340 40.909 0.00 0.00 0.00 1.47
431 432 2.639347 TCTCTGCCAACTTTCCTGATCA 59.361 45.455 0.00 0.00 0.00 2.92
467 468 0.174162 ATTGCATCCTTTTCCGCTGC 59.826 50.000 0.00 0.00 0.00 5.25
475 476 1.405463 CCTTTTCCGCTGCCTATTTCC 59.595 52.381 0.00 0.00 0.00 3.13
496 497 0.671781 CAGGGCTAGCGTATCATGGC 60.672 60.000 9.00 0.00 0.00 4.40
500 501 1.423395 GCTAGCGTATCATGGCACTC 58.577 55.000 0.00 0.00 0.00 3.51
501 502 1.937108 GCTAGCGTATCATGGCACTCC 60.937 57.143 0.00 0.00 0.00 3.85
502 503 1.615883 CTAGCGTATCATGGCACTCCT 59.384 52.381 0.00 0.00 0.00 3.69
503 504 1.704641 AGCGTATCATGGCACTCCTA 58.295 50.000 0.00 0.00 0.00 2.94
504 505 2.251818 AGCGTATCATGGCACTCCTAT 58.748 47.619 0.00 0.00 0.00 2.57
520 522 8.739972 GGCACTCCTATTTTCTTAATTCTTCAA 58.260 33.333 0.00 0.00 0.00 2.69
540 542 7.337689 TCTTCAATGACAGGGATGAGTTAATTG 59.662 37.037 0.00 0.00 0.00 2.32
541 543 5.357878 TCAATGACAGGGATGAGTTAATTGC 59.642 40.000 0.00 0.00 0.00 3.56
545 547 3.016736 CAGGGATGAGTTAATTGCGGTT 58.983 45.455 0.00 0.00 0.00 4.44
556 558 3.592898 AATTGCGGTTTTCCCTTGATC 57.407 42.857 0.00 0.00 36.42 2.92
702 708 8.686334 CATGTACTATAATTTTTCCTGCCAACT 58.314 33.333 0.00 0.00 0.00 3.16
703 709 9.914834 ATGTACTATAATTTTTCCTGCCAACTA 57.085 29.630 0.00 0.00 0.00 2.24
704 710 9.742144 TGTACTATAATTTTTCCTGCCAACTAA 57.258 29.630 0.00 0.00 0.00 2.24
721 727 9.646427 TGCCAACTAAAACATTTTATTATGGAC 57.354 29.630 18.05 12.90 34.67 4.02
836 842 2.972713 AGGCTGTCTGTTCTTGTAGGAA 59.027 45.455 0.00 0.00 0.00 3.36
968 976 3.695556 CCATCAAGCACCATCACACATTA 59.304 43.478 0.00 0.00 0.00 1.90
982 990 8.533965 CCATCACACATTAAAAATAATCAAGCG 58.466 33.333 0.00 0.00 0.00 4.68
1045 1057 1.283793 CCGCTTGTTCAAGCACAGG 59.716 57.895 28.69 20.65 45.75 4.00
1101 1113 2.042831 CAGGCCAAGGCTTTCTCCG 61.043 63.158 5.01 0.00 41.60 4.63
1122 1134 4.414999 GGTTACCATGACCGAAAAAGAC 57.585 45.455 0.00 0.00 0.00 3.01
1124 1136 4.276431 GGTTACCATGACCGAAAAAGACAA 59.724 41.667 0.00 0.00 0.00 3.18
1343 1355 1.425066 AGCTGGAGAAAATGGGTGTCA 59.575 47.619 0.00 0.00 0.00 3.58
1476 1488 0.260816 ATGCTGCTGTCCATGGGAAT 59.739 50.000 13.02 0.00 31.38 3.01
1506 1518 4.510038 TTCTGACGAGGTTTACCAGTAC 57.490 45.455 1.13 0.00 38.89 2.73
1507 1519 2.821969 TCTGACGAGGTTTACCAGTACC 59.178 50.000 1.13 0.00 38.89 3.34
1560 1639 9.852091 GATCTTCCATAATAATTCAAATGCTCC 57.148 33.333 0.00 0.00 0.00 4.70
1730 1819 2.980233 GCTCCAGCGGCAACAGTT 60.980 61.111 1.45 0.00 0.00 3.16
1758 1847 0.600255 GTGGAAGCATACGATCCCCG 60.600 60.000 0.00 0.00 45.44 5.73
1826 1915 3.497031 GCTTCGCCAGCGGGTTAC 61.497 66.667 12.71 0.00 39.29 2.50
1837 1926 1.912371 GCGGGTTACACAGCAAGCTC 61.912 60.000 0.00 0.00 0.00 4.09
1855 1944 1.116536 TCTACATAATGGGCGGCCGA 61.117 55.000 33.48 8.89 0.00 5.54
2083 2172 2.343758 GGCAGTTCGAGCACCAGA 59.656 61.111 1.01 0.00 0.00 3.86
2140 2229 3.077556 TCGCAGGAGGAAGAGGGC 61.078 66.667 0.00 0.00 0.00 5.19
2452 2541 1.592400 GCCCCAACTAGGCCGAAAAC 61.592 60.000 0.00 0.00 45.16 2.43
2539 2628 1.164041 CCCACCTTTTCGCGTGAACT 61.164 55.000 11.68 0.00 32.71 3.01
2792 2887 4.653888 CCCGTTTCCCGCCAACCT 62.654 66.667 0.00 0.00 34.38 3.50
2927 3022 3.011119 GTCCAGTGTAGTCGAGATGTCT 58.989 50.000 0.00 0.00 0.00 3.41
3159 3255 3.971305 TGAAAGGTGGAAGAAGGTAGTGA 59.029 43.478 0.00 0.00 0.00 3.41
3208 3304 7.381323 AGGACTTTAGAAAAGCATCCATTTTG 58.619 34.615 10.12 0.00 30.22 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.879342 TTATTTGAAACATTCCGAAAATGTGT 57.121 26.923 14.35 10.36 40.43 3.72
1 2 9.796062 CTTTATTTGAAACATTCCGAAAATGTG 57.204 29.630 14.35 0.00 40.43 3.21
2 3 8.987890 CCTTTATTTGAAACATTCCGAAAATGT 58.012 29.630 9.50 9.50 42.19 2.71
3 4 8.442384 CCCTTTATTTGAAACATTCCGAAAATG 58.558 33.333 8.42 8.42 0.00 2.32
5 6 6.425417 GCCCTTTATTTGAAACATTCCGAAAA 59.575 34.615 0.00 0.00 0.00 2.29
6 7 5.929415 GCCCTTTATTTGAAACATTCCGAAA 59.071 36.000 0.00 0.00 0.00 3.46
7 8 5.245075 AGCCCTTTATTTGAAACATTCCGAA 59.755 36.000 0.00 0.00 0.00 4.30
8 9 4.770010 AGCCCTTTATTTGAAACATTCCGA 59.230 37.500 0.00 0.00 0.00 4.55
9 10 5.072040 AGCCCTTTATTTGAAACATTCCG 57.928 39.130 0.00 0.00 0.00 4.30
10 11 6.286240 AGAGCCCTTTATTTGAAACATTCC 57.714 37.500 0.00 0.00 0.00 3.01
11 12 8.470002 ACATAGAGCCCTTTATTTGAAACATTC 58.530 33.333 0.00 0.00 0.00 2.67
12 13 8.366359 ACATAGAGCCCTTTATTTGAAACATT 57.634 30.769 0.00 0.00 0.00 2.71
13 14 7.961326 ACATAGAGCCCTTTATTTGAAACAT 57.039 32.000 0.00 0.00 0.00 2.71
14 15 7.556275 CCTACATAGAGCCCTTTATTTGAAACA 59.444 37.037 0.00 0.00 0.00 2.83
15 16 7.468768 GCCTACATAGAGCCCTTTATTTGAAAC 60.469 40.741 0.00 0.00 0.00 2.78
16 17 6.546034 GCCTACATAGAGCCCTTTATTTGAAA 59.454 38.462 0.00 0.00 0.00 2.69
17 18 6.062095 GCCTACATAGAGCCCTTTATTTGAA 58.938 40.000 0.00 0.00 0.00 2.69
18 19 5.456186 GGCCTACATAGAGCCCTTTATTTGA 60.456 44.000 0.00 0.00 41.00 2.69
19 20 4.762251 GGCCTACATAGAGCCCTTTATTTG 59.238 45.833 0.00 0.00 41.00 2.32
20 21 4.505039 CGGCCTACATAGAGCCCTTTATTT 60.505 45.833 0.00 0.00 44.13 1.40
21 22 3.008049 CGGCCTACATAGAGCCCTTTATT 59.992 47.826 0.00 0.00 44.13 1.40
22 23 2.567615 CGGCCTACATAGAGCCCTTTAT 59.432 50.000 0.00 0.00 44.13 1.40
23 24 1.968493 CGGCCTACATAGAGCCCTTTA 59.032 52.381 0.00 0.00 44.13 1.85
24 25 0.759346 CGGCCTACATAGAGCCCTTT 59.241 55.000 0.00 0.00 44.13 3.11
25 26 0.105658 TCGGCCTACATAGAGCCCTT 60.106 55.000 0.00 0.00 44.13 3.95
26 27 0.540830 CTCGGCCTACATAGAGCCCT 60.541 60.000 0.00 0.00 44.13 5.19
27 28 1.968310 CTCGGCCTACATAGAGCCC 59.032 63.158 0.00 0.00 44.13 5.19
30 31 0.315568 GGTGCTCGGCCTACATAGAG 59.684 60.000 0.00 0.00 0.00 2.43
31 32 0.396556 TGGTGCTCGGCCTACATAGA 60.397 55.000 0.00 0.00 0.00 1.98
32 33 0.464036 TTGGTGCTCGGCCTACATAG 59.536 55.000 0.00 0.00 0.00 2.23
33 34 0.906066 TTTGGTGCTCGGCCTACATA 59.094 50.000 0.00 0.00 0.00 2.29
34 35 0.037590 TTTTGGTGCTCGGCCTACAT 59.962 50.000 0.00 0.00 0.00 2.29
35 36 0.887387 GTTTTGGTGCTCGGCCTACA 60.887 55.000 0.00 0.00 0.00 2.74
36 37 1.873863 GTTTTGGTGCTCGGCCTAC 59.126 57.895 0.00 0.00 0.00 3.18
37 38 1.669760 CGTTTTGGTGCTCGGCCTA 60.670 57.895 0.00 0.00 0.00 3.93
38 39 2.978010 CGTTTTGGTGCTCGGCCT 60.978 61.111 0.00 0.00 0.00 5.19
39 40 4.700365 GCGTTTTGGTGCTCGGCC 62.700 66.667 0.00 0.00 0.00 6.13
40 41 3.660111 AGCGTTTTGGTGCTCGGC 61.660 61.111 0.00 0.00 36.53 5.54
41 42 2.252260 CAGCGTTTTGGTGCTCGG 59.748 61.111 0.00 0.00 40.03 4.63
47 48 2.818130 AATGAATGCAGCGTTTTGGT 57.182 40.000 0.16 0.00 0.00 3.67
48 49 4.095410 TCTAATGAATGCAGCGTTTTGG 57.905 40.909 0.16 0.00 0.00 3.28
49 50 6.257423 TGTATCTAATGAATGCAGCGTTTTG 58.743 36.000 0.16 0.00 0.00 2.44
50 51 6.435430 TGTATCTAATGAATGCAGCGTTTT 57.565 33.333 0.16 0.00 0.00 2.43
51 52 6.624352 ATGTATCTAATGAATGCAGCGTTT 57.376 33.333 0.16 0.00 0.00 3.60
52 53 6.564686 CGAATGTATCTAATGAATGCAGCGTT 60.565 38.462 0.00 0.00 0.00 4.84
53 54 5.107337 CGAATGTATCTAATGAATGCAGCGT 60.107 40.000 0.00 0.00 0.00 5.07
54 55 5.119125 TCGAATGTATCTAATGAATGCAGCG 59.881 40.000 0.00 0.00 0.00 5.18
55 56 6.471976 TCGAATGTATCTAATGAATGCAGC 57.528 37.500 0.00 0.00 0.00 5.25
56 57 8.219769 GTCTTCGAATGTATCTAATGAATGCAG 58.780 37.037 0.00 0.00 0.00 4.41
57 58 7.710475 TGTCTTCGAATGTATCTAATGAATGCA 59.290 33.333 0.00 0.00 0.00 3.96
58 59 8.076714 TGTCTTCGAATGTATCTAATGAATGC 57.923 34.615 0.00 0.00 0.00 3.56
60 61 9.823647 ACTTGTCTTCGAATGTATCTAATGAAT 57.176 29.630 0.00 0.00 0.00 2.57
67 68 8.808529 CGAAATTACTTGTCTTCGAATGTATCT 58.191 33.333 0.00 0.00 42.44 1.98
68 69 8.056571 CCGAAATTACTTGTCTTCGAATGTATC 58.943 37.037 0.00 0.00 42.44 2.24
69 70 7.762615 TCCGAAATTACTTGTCTTCGAATGTAT 59.237 33.333 0.00 0.00 42.44 2.29
70 71 7.062605 GTCCGAAATTACTTGTCTTCGAATGTA 59.937 37.037 0.00 0.00 42.44 2.29
71 72 5.929992 TCCGAAATTACTTGTCTTCGAATGT 59.070 36.000 0.00 0.00 42.44 2.71
72 73 6.241385 GTCCGAAATTACTTGTCTTCGAATG 58.759 40.000 0.00 0.00 42.44 2.67
73 74 5.061808 CGTCCGAAATTACTTGTCTTCGAAT 59.938 40.000 0.00 0.00 42.44 3.34
74 75 4.383649 CGTCCGAAATTACTTGTCTTCGAA 59.616 41.667 0.00 0.00 42.44 3.71
75 76 3.916172 CGTCCGAAATTACTTGTCTTCGA 59.084 43.478 4.74 0.00 42.44 3.71
76 77 3.060363 CCGTCCGAAATTACTTGTCTTCG 59.940 47.826 0.00 0.00 40.18 3.79
77 78 4.240096 TCCGTCCGAAATTACTTGTCTTC 58.760 43.478 0.00 0.00 0.00 2.87
78 79 4.243270 CTCCGTCCGAAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
79 80 3.368116 CCTCCGTCCGAAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
80 81 2.928116 CCTCCGTCCGAAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
81 82 2.301009 ACCTCCGTCCGAAATTACTTGT 59.699 45.455 0.00 0.00 0.00 3.16
82 83 2.968675 ACCTCCGTCCGAAATTACTTG 58.031 47.619 0.00 0.00 0.00 3.16
83 84 4.806640 TTACCTCCGTCCGAAATTACTT 57.193 40.909 0.00 0.00 0.00 2.24
84 85 6.041296 ACATATTACCTCCGTCCGAAATTACT 59.959 38.462 0.00 0.00 0.00 2.24
85 86 6.145048 CACATATTACCTCCGTCCGAAATTAC 59.855 42.308 0.00 0.00 0.00 1.89
86 87 6.040729 TCACATATTACCTCCGTCCGAAATTA 59.959 38.462 0.00 0.00 0.00 1.40
87 88 5.054477 CACATATTACCTCCGTCCGAAATT 58.946 41.667 0.00 0.00 0.00 1.82
88 89 4.342951 TCACATATTACCTCCGTCCGAAAT 59.657 41.667 0.00 0.00 0.00 2.17
89 90 3.700539 TCACATATTACCTCCGTCCGAAA 59.299 43.478 0.00 0.00 0.00 3.46
90 91 3.289836 TCACATATTACCTCCGTCCGAA 58.710 45.455 0.00 0.00 0.00 4.30
91 92 2.934887 TCACATATTACCTCCGTCCGA 58.065 47.619 0.00 0.00 0.00 4.55
92 93 3.936372 ATCACATATTACCTCCGTCCG 57.064 47.619 0.00 0.00 0.00 4.79
93 94 6.282199 ACATATCACATATTACCTCCGTCC 57.718 41.667 0.00 0.00 0.00 4.79
94 95 8.495949 CAAAACATATCACATATTACCTCCGTC 58.504 37.037 0.00 0.00 0.00 4.79
95 96 7.990886 ACAAAACATATCACATATTACCTCCGT 59.009 33.333 0.00 0.00 0.00 4.69
96 97 8.378172 ACAAAACATATCACATATTACCTCCG 57.622 34.615 0.00 0.00 0.00 4.63
101 102 9.872757 CGGGTAACAAAACATATCACATATTAC 57.127 33.333 0.00 0.00 39.74 1.89
102 103 9.616156 ACGGGTAACAAAACATATCACATATTA 57.384 29.630 0.00 0.00 39.74 0.98
103 104 8.402472 CACGGGTAACAAAACATATCACATATT 58.598 33.333 0.00 0.00 39.74 1.28
104 105 7.771361 TCACGGGTAACAAAACATATCACATAT 59.229 33.333 0.00 0.00 39.74 1.78
105 106 7.104290 TCACGGGTAACAAAACATATCACATA 58.896 34.615 0.00 0.00 39.74 2.29
106 107 5.941058 TCACGGGTAACAAAACATATCACAT 59.059 36.000 0.00 0.00 39.74 3.21
107 108 5.306394 TCACGGGTAACAAAACATATCACA 58.694 37.500 0.00 0.00 39.74 3.58
108 109 5.866335 TCACGGGTAACAAAACATATCAC 57.134 39.130 0.00 0.00 39.74 3.06
109 110 8.740123 AATATCACGGGTAACAAAACATATCA 57.260 30.769 0.00 0.00 39.74 2.15
110 111 8.832521 TGAATATCACGGGTAACAAAACATATC 58.167 33.333 0.00 0.00 39.74 1.63
111 112 8.740123 TGAATATCACGGGTAACAAAACATAT 57.260 30.769 0.00 0.00 39.74 1.78
112 113 8.452534 GTTGAATATCACGGGTAACAAAACATA 58.547 33.333 0.00 0.00 39.74 2.29
113 114 7.175990 AGTTGAATATCACGGGTAACAAAACAT 59.824 33.333 0.00 0.00 39.74 2.71
114 115 6.487331 AGTTGAATATCACGGGTAACAAAACA 59.513 34.615 0.00 0.00 39.74 2.83
115 116 6.905578 AGTTGAATATCACGGGTAACAAAAC 58.094 36.000 0.00 0.00 39.74 2.43
116 117 7.513371 AAGTTGAATATCACGGGTAACAAAA 57.487 32.000 0.00 0.00 39.74 2.44
117 118 7.228906 TGAAAGTTGAATATCACGGGTAACAAA 59.771 33.333 0.00 0.00 39.74 2.83
118 119 6.711194 TGAAAGTTGAATATCACGGGTAACAA 59.289 34.615 0.00 0.00 39.74 2.83
119 120 6.231951 TGAAAGTTGAATATCACGGGTAACA 58.768 36.000 0.00 0.00 39.74 2.41
120 121 6.730960 TGAAAGTTGAATATCACGGGTAAC 57.269 37.500 0.00 0.00 0.00 2.50
121 122 7.931578 ATTGAAAGTTGAATATCACGGGTAA 57.068 32.000 0.00 0.00 0.00 2.85
122 123 7.931578 AATTGAAAGTTGAATATCACGGGTA 57.068 32.000 0.00 0.00 0.00 3.69
123 124 6.834168 AATTGAAAGTTGAATATCACGGGT 57.166 33.333 0.00 0.00 0.00 5.28
124 125 9.632807 TTAAAATTGAAAGTTGAATATCACGGG 57.367 29.630 0.00 0.00 0.00 5.28
152 153 9.921637 ACACAGAAAGTTTGTCTTTTCAATAAA 57.078 25.926 0.00 0.00 45.15 1.40
183 184 9.090692 CAAAAACAAACAGAAACAGATGATTCT 57.909 29.630 0.00 0.00 37.61 2.40
184 185 9.086336 TCAAAAACAAACAGAAACAGATGATTC 57.914 29.630 0.00 0.00 0.00 2.52
185 186 9.603921 ATCAAAAACAAACAGAAACAGATGATT 57.396 25.926 0.00 0.00 0.00 2.57
186 187 9.603921 AATCAAAAACAAACAGAAACAGATGAT 57.396 25.926 0.00 0.00 0.00 2.45
187 188 9.434420 AAATCAAAAACAAACAGAAACAGATGA 57.566 25.926 0.00 0.00 0.00 2.92
191 192 9.833894 CGATAAATCAAAAACAAACAGAAACAG 57.166 29.630 0.00 0.00 0.00 3.16
192 193 9.360093 ACGATAAATCAAAAACAAACAGAAACA 57.640 25.926 0.00 0.00 0.00 2.83
254 255 9.770097 CACCTCATGTCATATAAAGTATCAACT 57.230 33.333 0.00 0.00 37.65 3.16
255 256 8.993121 CCACCTCATGTCATATAAAGTATCAAC 58.007 37.037 0.00 0.00 0.00 3.18
256 257 8.713971 ACCACCTCATGTCATATAAAGTATCAA 58.286 33.333 0.00 0.00 0.00 2.57
257 258 8.262601 ACCACCTCATGTCATATAAAGTATCA 57.737 34.615 0.00 0.00 0.00 2.15
261 262 9.154632 TGTATACCACCTCATGTCATATAAAGT 57.845 33.333 0.00 0.00 0.00 2.66
262 263 9.424319 GTGTATACCACCTCATGTCATATAAAG 57.576 37.037 0.00 0.00 38.18 1.85
263 264 8.929487 TGTGTATACCACCTCATGTCATATAAA 58.071 33.333 0.00 0.00 43.85 1.40
264 265 8.485578 TGTGTATACCACCTCATGTCATATAA 57.514 34.615 0.00 0.00 43.85 0.98
265 266 8.485578 TTGTGTATACCACCTCATGTCATATA 57.514 34.615 0.00 0.00 43.85 0.86
266 267 6.994421 TGTGTATACCACCTCATGTCATAT 57.006 37.500 0.00 0.00 43.85 1.78
267 268 6.800072 TTGTGTATACCACCTCATGTCATA 57.200 37.500 0.00 0.00 43.85 2.15
268 269 5.692115 TTGTGTATACCACCTCATGTCAT 57.308 39.130 0.00 0.00 43.85 3.06
269 270 5.188751 TGATTGTGTATACCACCTCATGTCA 59.811 40.000 0.00 0.00 43.85 3.58
270 271 5.670485 TGATTGTGTATACCACCTCATGTC 58.330 41.667 0.00 0.00 43.85 3.06
271 272 5.189736 ACTGATTGTGTATACCACCTCATGT 59.810 40.000 0.00 3.07 43.85 3.21
272 273 5.674525 ACTGATTGTGTATACCACCTCATG 58.325 41.667 0.00 0.00 43.85 3.07
273 274 5.957771 ACTGATTGTGTATACCACCTCAT 57.042 39.130 0.00 0.00 43.85 2.90
274 275 5.755409 AACTGATTGTGTATACCACCTCA 57.245 39.130 0.00 3.82 43.85 3.86
275 276 5.585047 GGAAACTGATTGTGTATACCACCTC 59.415 44.000 0.00 0.00 43.85 3.85
276 277 5.250774 AGGAAACTGATTGTGTATACCACCT 59.749 40.000 0.00 0.00 41.03 4.00
277 278 5.497474 AGGAAACTGATTGTGTATACCACC 58.503 41.667 0.00 0.00 41.03 4.61
278 279 7.448748 AAAGGAAACTGATTGTGTATACCAC 57.551 36.000 0.00 0.00 42.68 4.16
279 280 7.504238 ACAAAAGGAAACTGATTGTGTATACCA 59.496 33.333 0.00 0.00 44.76 3.25
280 281 7.882179 ACAAAAGGAAACTGATTGTGTATACC 58.118 34.615 0.00 0.00 44.76 2.73
286 287 9.573133 GGATAATACAAAAGGAAACTGATTGTG 57.427 33.333 0.00 0.00 45.51 3.33
287 288 9.533831 AGGATAATACAAAAGGAAACTGATTGT 57.466 29.630 0.00 0.00 46.73 2.71
296 297 9.983024 TCCACAAATAGGATAATACAAAAGGAA 57.017 29.630 0.00 0.00 0.00 3.36
301 302 9.130661 CCACATCCACAAATAGGATAATACAAA 57.869 33.333 0.00 0.00 43.90 2.83
302 303 7.723616 CCCACATCCACAAATAGGATAATACAA 59.276 37.037 0.00 0.00 43.90 2.41
303 304 7.230747 CCCACATCCACAAATAGGATAATACA 58.769 38.462 0.00 0.00 43.90 2.29
304 305 6.659242 CCCCACATCCACAAATAGGATAATAC 59.341 42.308 0.00 0.00 43.90 1.89
305 306 6.334237 ACCCCACATCCACAAATAGGATAATA 59.666 38.462 0.00 0.00 43.90 0.98
306 307 5.136048 ACCCCACATCCACAAATAGGATAAT 59.864 40.000 0.00 0.00 43.90 1.28
307 308 4.480537 ACCCCACATCCACAAATAGGATAA 59.519 41.667 0.00 0.00 43.90 1.75
308 309 4.051478 ACCCCACATCCACAAATAGGATA 58.949 43.478 0.00 0.00 43.90 2.59
309 310 2.858768 ACCCCACATCCACAAATAGGAT 59.141 45.455 0.00 0.00 46.61 3.24
310 311 2.283834 ACCCCACATCCACAAATAGGA 58.716 47.619 0.00 0.00 39.97 2.94
311 312 2.826674 ACCCCACATCCACAAATAGG 57.173 50.000 0.00 0.00 0.00 2.57
312 313 3.831911 ACAAACCCCACATCCACAAATAG 59.168 43.478 0.00 0.00 0.00 1.73
313 314 3.850752 ACAAACCCCACATCCACAAATA 58.149 40.909 0.00 0.00 0.00 1.40
314 315 2.688477 ACAAACCCCACATCCACAAAT 58.312 42.857 0.00 0.00 0.00 2.32
315 316 2.166907 ACAAACCCCACATCCACAAA 57.833 45.000 0.00 0.00 0.00 2.83
316 317 3.534357 ATACAAACCCCACATCCACAA 57.466 42.857 0.00 0.00 0.00 3.33
317 318 4.228438 TCATATACAAACCCCACATCCACA 59.772 41.667 0.00 0.00 0.00 4.17
318 319 4.787551 TCATATACAAACCCCACATCCAC 58.212 43.478 0.00 0.00 0.00 4.02
319 320 5.044476 AGTTCATATACAAACCCCACATCCA 60.044 40.000 0.00 0.00 0.00 3.41
320 321 5.445964 AGTTCATATACAAACCCCACATCC 58.554 41.667 0.00 0.00 0.00 3.51
321 322 6.377146 ACAAGTTCATATACAAACCCCACATC 59.623 38.462 0.00 0.00 0.00 3.06
322 323 6.252995 ACAAGTTCATATACAAACCCCACAT 58.747 36.000 0.00 0.00 0.00 3.21
323 324 5.636123 ACAAGTTCATATACAAACCCCACA 58.364 37.500 0.00 0.00 0.00 4.17
324 325 5.708230 TGACAAGTTCATATACAAACCCCAC 59.292 40.000 0.00 0.00 0.00 4.61
325 326 5.882040 TGACAAGTTCATATACAAACCCCA 58.118 37.500 0.00 0.00 0.00 4.96
326 327 7.404671 AATGACAAGTTCATATACAAACCCC 57.595 36.000 0.00 0.00 44.86 4.95
327 328 7.416326 GGGAATGACAAGTTCATATACAAACCC 60.416 40.741 0.00 0.00 44.86 4.11
328 329 7.122055 TGGGAATGACAAGTTCATATACAAACC 59.878 37.037 0.00 0.00 44.86 3.27
329 330 8.050778 TGGGAATGACAAGTTCATATACAAAC 57.949 34.615 0.00 0.00 44.86 2.93
330 331 8.642935 TTGGGAATGACAAGTTCATATACAAA 57.357 30.769 0.00 0.00 44.86 2.83
331 332 8.685427 CATTGGGAATGACAAGTTCATATACAA 58.315 33.333 0.00 0.00 44.86 2.41
332 333 8.052141 TCATTGGGAATGACAAGTTCATATACA 58.948 33.333 0.00 0.00 44.86 2.29
333 334 8.450578 TCATTGGGAATGACAAGTTCATATAC 57.549 34.615 0.00 0.00 44.86 1.47
334 335 9.473007 TTTCATTGGGAATGACAAGTTCATATA 57.527 29.630 0.00 0.00 46.90 0.86
335 336 7.959658 TTCATTGGGAATGACAAGTTCATAT 57.040 32.000 0.00 0.00 46.90 1.78
336 337 7.773489 TTTCATTGGGAATGACAAGTTCATA 57.227 32.000 0.00 0.00 46.90 2.15
337 338 6.669125 TTTCATTGGGAATGACAAGTTCAT 57.331 33.333 0.00 0.00 46.90 2.57
376 377 4.450082 AGTTTCCAACAACCAACAGAAC 57.550 40.909 0.00 0.00 0.00 3.01
385 386 8.926715 AAAATGAGTTCTAAGTTTCCAACAAC 57.073 30.769 0.00 0.00 0.00 3.32
386 387 8.966868 AGAAAATGAGTTCTAAGTTTCCAACAA 58.033 29.630 6.51 0.00 36.06 2.83
431 432 3.770388 TGCAATTTGGTGTCATCCATCAT 59.230 39.130 0.00 0.00 33.15 2.45
467 468 1.541233 CGCTAGCCCTGTGGAAATAGG 60.541 57.143 9.66 0.00 0.00 2.57
475 476 1.606480 CCATGATACGCTAGCCCTGTG 60.606 57.143 9.66 0.00 0.00 3.66
503 504 9.312904 TCCCTGTCATTGAAGAATTAAGAAAAT 57.687 29.630 0.00 0.00 0.00 1.82
504 505 8.704849 TCCCTGTCATTGAAGAATTAAGAAAA 57.295 30.769 0.00 0.00 0.00 2.29
520 522 3.879295 CGCAATTAACTCATCCCTGTCAT 59.121 43.478 0.00 0.00 0.00 3.06
524 526 2.643551 ACCGCAATTAACTCATCCCTG 58.356 47.619 0.00 0.00 0.00 4.45
540 542 1.474330 ATGGATCAAGGGAAAACCGC 58.526 50.000 0.00 0.00 46.96 5.68
541 543 3.088532 TGAATGGATCAAGGGAAAACCG 58.911 45.455 0.00 0.00 37.47 4.44
583 586 7.085116 ACACTAGAATGAGTTCGAGTACAAAG 58.915 38.462 0.00 0.00 44.97 2.77
694 700 9.868277 TCCATAATAAAATGTTTTAGTTGGCAG 57.132 29.630 14.68 0.00 36.22 4.85
702 708 8.754080 CACCCAGGTCCATAATAAAATGTTTTA 58.246 33.333 0.87 0.87 37.08 1.52
703 709 7.456269 TCACCCAGGTCCATAATAAAATGTTTT 59.544 33.333 0.00 0.00 0.00 2.43
704 710 6.957020 TCACCCAGGTCCATAATAAAATGTTT 59.043 34.615 0.00 0.00 0.00 2.83
721 727 8.924511 ATCAAACTATATTAATGTCACCCAGG 57.075 34.615 0.00 0.00 0.00 4.45
836 842 3.641436 GTGGAAGTCCTTGGAATGGTTTT 59.359 43.478 0.00 0.00 36.82 2.43
904 910 1.079503 GGTGAATGAGGCTCGTCAAC 58.920 55.000 18.88 18.02 0.00 3.18
968 976 5.010617 ACCTGTGGAACGCTTGATTATTTTT 59.989 36.000 0.00 0.00 42.39 1.94
982 990 3.256631 AGCATTGAAATCACCTGTGGAAC 59.743 43.478 0.00 0.00 37.35 3.62
1045 1057 4.973055 TGTACCACGGTGGCACGC 62.973 66.667 26.62 14.15 42.67 5.34
1101 1113 3.816523 TGTCTTTTTCGGTCATGGTAACC 59.183 43.478 0.00 0.00 0.00 2.85
1122 1134 2.400399 AGACCGTCGTGTGTATTGTTG 58.600 47.619 0.00 0.00 0.00 3.33
1124 1136 3.921119 TTAGACCGTCGTGTGTATTGT 57.079 42.857 0.00 0.00 0.00 2.71
1242 1254 0.108424 ACTCTCTGCTGCCGATGAAC 60.108 55.000 0.00 0.00 0.00 3.18
1335 1347 1.841556 GACCTCCCAGTGACACCCA 60.842 63.158 0.84 0.00 0.00 4.51
1343 1355 2.204151 CCCCCAAGACCTCCCAGT 60.204 66.667 0.00 0.00 0.00 4.00
1476 1488 2.307768 ACCTCGTCAGAAACAGAGTCA 58.692 47.619 0.00 0.00 31.05 3.41
1506 1518 2.110967 CCTGTTGAGCCGAGCATGG 61.111 63.158 0.00 0.00 0.00 3.66
1507 1519 0.108186 TACCTGTTGAGCCGAGCATG 60.108 55.000 0.00 0.00 0.00 4.06
1758 1847 0.529378 CAGCCTCCATCTGTTTTGCC 59.471 55.000 0.00 0.00 0.00 4.52
1826 1915 3.562973 CCCATTATGTAGAGCTTGCTGTG 59.437 47.826 0.00 0.00 0.00 3.66
1837 1926 0.036388 ATCGGCCGCCCATTATGTAG 60.036 55.000 23.51 0.00 0.00 2.74
2074 2163 1.093159 CAAGGCAGAATCTGGTGCTC 58.907 55.000 12.66 0.00 39.76 4.26
2122 2211 3.087666 GCCCTCTTCCTCCTGCGAG 62.088 68.421 0.00 0.00 35.72 5.03
2140 2229 3.456663 CGTCATCGTCTGATACCCG 57.543 57.895 0.00 0.00 35.97 5.28
2182 2271 3.450115 GACGTCCCCCACTCCGAG 61.450 72.222 3.51 0.00 0.00 4.63
2452 2541 2.223923 CCTATGGGAAGCTGAAGAGTCG 60.224 54.545 0.00 0.00 33.58 4.18
2518 2607 0.882927 TTCACGCGAAAAGGTGGGAG 60.883 55.000 15.93 0.00 34.93 4.30
2519 2608 1.146485 TTCACGCGAAAAGGTGGGA 59.854 52.632 15.93 0.00 34.93 4.37
2539 2628 0.888736 CCATGCAACTTCGGTCACCA 60.889 55.000 0.00 0.00 0.00 4.17
2573 2662 1.277273 ACCCTTTTCGGCCTACAGTAC 59.723 52.381 0.00 0.00 0.00 2.73
2615 2708 7.798596 TTTCATTGCAAAATGGTTACACAAT 57.201 28.000 1.71 0.00 0.00 2.71
2792 2887 1.770294 GGGAACATATGGCGGGAAAA 58.230 50.000 7.80 0.00 0.00 2.29
2904 2999 4.081031 AGACATCTCGACTACACTGGACTA 60.081 45.833 0.00 0.00 0.00 2.59
2927 3022 9.443323 TGAAAACTACGATCAAAAGGATAATGA 57.557 29.630 0.00 0.00 36.00 2.57
3159 3255 5.365619 TCTAAAAGTTTCACTCTTCGGCTT 58.634 37.500 0.00 0.00 0.00 4.35
3208 3304 0.667993 CTCGCTCTCCTCAGTCCATC 59.332 60.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.