Multiple sequence alignment - TraesCS5A01G264000

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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 TraesCS5A01G264000 chr5A 100.000 5114 0 0 1 5114 476606515 476601402 0.000000e+00 9444
1 TraesCS5A01G264000 chr5A 93.033 689 43 2 4429 5114 502385952 502386638 0.000000e+00 1002
2 TraesCS5A01G264000 chr5A 92.450 702 43 3 4423 5114 651992891 651993592 0.000000e+00 994
3 TraesCS5A01G264000 chr5A 86.161 224 31 0 1424 1647 476605062 476604839 5.120000e-60 243
4 TraesCS5A01G264000 chr5A 86.161 224 31 0 1454 1677 476605092 476604869 5.120000e-60 243
5 TraesCS5A01G264000 chr5B 93.462 3319 165 20 147 3436 447844304 447841009 0.000000e+00 4879
6 TraesCS5A01G264000 chr5B 87.538 995 73 20 3467 4430 447841011 447840037 0.000000e+00 1103
7 TraesCS5A01G264000 chr5B 78.605 215 40 4 1424 1635 447842987 447842776 2.480000e-28 137
8 TraesCS5A01G264000 chr5D 93.151 3037 133 21 1454 4430 375194327 375191306 0.000000e+00 4386
9 TraesCS5A01G264000 chr5D 90.773 1539 95 27 147 1665 375195597 375194086 0.000000e+00 2012
10 TraesCS5A01G264000 chr5D 83.568 213 33 2 1424 1635 375194297 375194086 1.120000e-46 198
11 TraesCS5A01G264000 chr4A 93.208 692 40 2 4429 5114 191111514 191112204 0.000000e+00 1011
12 TraesCS5A01G264000 chr6A 92.561 699 39 3 4429 5114 422320824 422320126 0.000000e+00 990
13 TraesCS5A01G264000 chr6A 91.751 691 54 1 4427 5114 59958460 59959150 0.000000e+00 957
14 TraesCS5A01G264000 chr2A 92.253 697 44 3 4427 5114 617663439 617664134 0.000000e+00 979
15 TraesCS5A01G264000 chr2A 91.822 697 47 3 4427 5114 758424329 758423634 0.000000e+00 963
16 TraesCS5A01G264000 chr7D 92.086 695 46 4 4427 5114 422346607 422347299 0.000000e+00 970
17 TraesCS5A01G264000 chr3A 91.738 702 48 3 4422 5114 170656238 170656938 0.000000e+00 966
18 TraesCS5A01G264000 chr7A 76.411 496 105 10 2581 3068 222499208 222499699 1.830000e-64 257
19 TraesCS5A01G264000 chr7B 76.423 492 102 11 2583 3068 191777117 191776634 2.360000e-63 254


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 TraesCS5A01G264000 chr5A 476601402 476606515 5113 True 3310.000000 9444 90.774 1 5114 3 chr5A.!!$R1 5113
1 TraesCS5A01G264000 chr5A 502385952 502386638 686 False 1002.000000 1002 93.033 4429 5114 1 chr5A.!!$F1 685
2 TraesCS5A01G264000 chr5A 651992891 651993592 701 False 994.000000 994 92.450 4423 5114 1 chr5A.!!$F2 691
3 TraesCS5A01G264000 chr5B 447840037 447844304 4267 True 2039.666667 4879 86.535 147 4430 3 chr5B.!!$R1 4283
4 TraesCS5A01G264000 chr5D 375191306 375195597 4291 True 2198.666667 4386 89.164 147 4430 3 chr5D.!!$R1 4283
5 TraesCS5A01G264000 chr4A 191111514 191112204 690 False 1011.000000 1011 93.208 4429 5114 1 chr4A.!!$F1 685
6 TraesCS5A01G264000 chr6A 422320126 422320824 698 True 990.000000 990 92.561 4429 5114 1 chr6A.!!$R1 685
7 TraesCS5A01G264000 chr6A 59958460 59959150 690 False 957.000000 957 91.751 4427 5114 1 chr6A.!!$F1 687
8 TraesCS5A01G264000 chr2A 617663439 617664134 695 False 979.000000 979 92.253 4427 5114 1 chr2A.!!$F1 687
9 TraesCS5A01G264000 chr2A 758423634 758424329 695 True 963.000000 963 91.822 4427 5114 1 chr2A.!!$R1 687
10 TraesCS5A01G264000 chr7D 422346607 422347299 692 False 970.000000 970 92.086 4427 5114 1 chr7D.!!$F1 687
11 TraesCS5A01G264000 chr3A 170656238 170656938 700 False 966.000000 966 91.738 4422 5114 1 chr3A.!!$F1 692

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
606 621 0.103937 CTCGAGGCTTGATGGAGGAC 59.896 60.0 4.57 0.0 0.0 3.85 F
1540 1560 0.250209 AGCTGCTGATGATAAGGCCG 60.250 55.0 0.00 0.0 0.0 6.13 F
2771 2845 0.107643 TTCGTGCTGGTGGACATGAA 59.892 50.0 0.00 0.0 39.0 2.57 F
3271 3345 0.741326 ATGGACGGTGATGACTCTCG 59.259 55.0 0.00 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2443 0.037975 GTGCCAGTTTCCTGCCAATG 60.038 55.0 0.00 0.00 37.38 2.82 R
2979 3053 0.460284 CCGTGGAGTCGAGAATTGGG 60.460 60.0 0.00 0.00 0.00 4.12 R
3872 3949 0.458716 GCCACTCTTCTCCGCTACAC 60.459 60.0 0.00 0.00 0.00 2.90 R
4548 4652 0.620700 ACATTTAGGTCGGCCTCCCT 60.621 55.0 14.54 13.94 45.64 4.20 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
28 29 3.524606 TCGCGGATCGAGGGAACC 61.525 66.667 6.13 0.00 43.16 3.62
48 49 2.047179 GCCGTCCGCTTCTTTCCT 60.047 61.111 0.00 0.00 0.00 3.36
49 50 2.391389 GCCGTCCGCTTCTTTCCTG 61.391 63.158 0.00 0.00 0.00 3.86
50 51 1.004918 CCGTCCGCTTCTTTCCTGT 60.005 57.895 0.00 0.00 0.00 4.00
51 52 0.602905 CCGTCCGCTTCTTTCCTGTT 60.603 55.000 0.00 0.00 0.00 3.16
52 53 0.790814 CGTCCGCTTCTTTCCTGTTC 59.209 55.000 0.00 0.00 0.00 3.18
53 54 1.605712 CGTCCGCTTCTTTCCTGTTCT 60.606 52.381 0.00 0.00 0.00 3.01
54 55 1.801178 GTCCGCTTCTTTCCTGTTCTG 59.199 52.381 0.00 0.00 0.00 3.02
55 56 1.416401 TCCGCTTCTTTCCTGTTCTGT 59.584 47.619 0.00 0.00 0.00 3.41
56 57 2.158813 TCCGCTTCTTTCCTGTTCTGTT 60.159 45.455 0.00 0.00 0.00 3.16
57 58 2.224314 CCGCTTCTTTCCTGTTCTGTTC 59.776 50.000 0.00 0.00 0.00 3.18
58 59 3.134458 CGCTTCTTTCCTGTTCTGTTCT 58.866 45.455 0.00 0.00 0.00 3.01
59 60 3.561725 CGCTTCTTTCCTGTTCTGTTCTT 59.438 43.478 0.00 0.00 0.00 2.52
60 61 4.553547 CGCTTCTTTCCTGTTCTGTTCTTG 60.554 45.833 0.00 0.00 0.00 3.02
61 62 4.576463 GCTTCTTTCCTGTTCTGTTCTTGA 59.424 41.667 0.00 0.00 0.00 3.02
62 63 5.066505 GCTTCTTTCCTGTTCTGTTCTTGAA 59.933 40.000 0.00 0.00 0.00 2.69
63 64 6.238869 GCTTCTTTCCTGTTCTGTTCTTGAAT 60.239 38.462 0.00 0.00 0.00 2.57
64 65 7.041098 GCTTCTTTCCTGTTCTGTTCTTGAATA 60.041 37.037 0.00 0.00 0.00 1.75
65 66 7.730364 TCTTTCCTGTTCTGTTCTTGAATAC 57.270 36.000 0.00 0.00 0.00 1.89
66 67 6.423905 TCTTTCCTGTTCTGTTCTTGAATACG 59.576 38.462 0.00 0.00 0.00 3.06
67 68 3.994392 TCCTGTTCTGTTCTTGAATACGC 59.006 43.478 0.00 0.00 0.00 4.42
68 69 3.745975 CCTGTTCTGTTCTTGAATACGCA 59.254 43.478 0.00 0.00 0.00 5.24
69 70 4.393062 CCTGTTCTGTTCTTGAATACGCAT 59.607 41.667 0.00 0.00 0.00 4.73
70 71 5.106555 CCTGTTCTGTTCTTGAATACGCATT 60.107 40.000 0.00 0.00 0.00 3.56
71 72 6.312399 TGTTCTGTTCTTGAATACGCATTT 57.688 33.333 0.00 0.00 0.00 2.32
72 73 6.142139 TGTTCTGTTCTTGAATACGCATTTG 58.858 36.000 0.00 0.00 0.00 2.32
73 74 5.295431 TCTGTTCTTGAATACGCATTTGG 57.705 39.130 0.00 0.00 0.00 3.28
74 75 4.155826 TCTGTTCTTGAATACGCATTTGGG 59.844 41.667 0.00 0.00 0.00 4.12
75 76 3.823873 TGTTCTTGAATACGCATTTGGGT 59.176 39.130 5.56 5.56 43.82 4.51
76 77 4.279671 TGTTCTTGAATACGCATTTGGGTT 59.720 37.500 5.55 0.00 41.61 4.11
77 78 4.695217 TCTTGAATACGCATTTGGGTTC 57.305 40.909 5.55 0.00 41.61 3.62
78 79 4.331968 TCTTGAATACGCATTTGGGTTCT 58.668 39.130 5.55 0.00 41.61 3.01
79 80 4.155826 TCTTGAATACGCATTTGGGTTCTG 59.844 41.667 5.55 0.00 41.61 3.02
80 81 2.752354 TGAATACGCATTTGGGTTCTGG 59.248 45.455 5.55 0.00 41.61 3.86
81 82 2.507407 ATACGCATTTGGGTTCTGGT 57.493 45.000 5.55 0.00 41.61 4.00
82 83 1.529226 TACGCATTTGGGTTCTGGTG 58.471 50.000 5.55 0.00 41.61 4.17
83 84 1.080569 CGCATTTGGGTTCTGGTGC 60.081 57.895 0.00 0.00 0.00 5.01
84 85 1.293179 GCATTTGGGTTCTGGTGCC 59.707 57.895 0.00 0.00 0.00 5.01
85 86 1.586028 CATTTGGGTTCTGGTGCCG 59.414 57.895 0.00 0.00 0.00 5.69
86 87 2.275380 ATTTGGGTTCTGGTGCCGC 61.275 57.895 0.00 0.00 0.00 6.53
87 88 2.992817 ATTTGGGTTCTGGTGCCGCA 62.993 55.000 0.00 0.00 0.00 5.69
88 89 2.992817 TTTGGGTTCTGGTGCCGCAT 62.993 55.000 0.00 0.00 0.00 4.73
89 90 2.676471 GGGTTCTGGTGCCGCATT 60.676 61.111 0.00 0.00 0.00 3.56
90 91 2.700773 GGGTTCTGGTGCCGCATTC 61.701 63.158 0.00 0.00 0.00 2.67
91 92 1.675641 GGTTCTGGTGCCGCATTCT 60.676 57.895 0.00 0.00 0.00 2.40
92 93 1.503542 GTTCTGGTGCCGCATTCTG 59.496 57.895 0.00 0.00 0.00 3.02
93 94 1.073025 TTCTGGTGCCGCATTCTGT 59.927 52.632 0.00 0.00 0.00 3.41
94 95 0.955428 TTCTGGTGCCGCATTCTGTC 60.955 55.000 0.00 0.00 0.00 3.51
95 96 1.672030 CTGGTGCCGCATTCTGTCA 60.672 57.895 0.00 0.00 0.00 3.58
96 97 1.002257 TGGTGCCGCATTCTGTCAT 60.002 52.632 0.00 0.00 0.00 3.06
97 98 1.026182 TGGTGCCGCATTCTGTCATC 61.026 55.000 0.00 0.00 0.00 2.92
98 99 1.718757 GGTGCCGCATTCTGTCATCC 61.719 60.000 0.00 0.00 0.00 3.51
99 100 1.815003 TGCCGCATTCTGTCATCCG 60.815 57.895 0.00 0.00 0.00 4.18
100 101 3.017323 CCGCATTCTGTCATCCGC 58.983 61.111 0.00 0.00 0.00 5.54
101 102 1.815003 CCGCATTCTGTCATCCGCA 60.815 57.895 0.00 0.00 0.00 5.69
102 103 1.162181 CCGCATTCTGTCATCCGCAT 61.162 55.000 0.00 0.00 0.00 4.73
103 104 0.659427 CGCATTCTGTCATCCGCATT 59.341 50.000 0.00 0.00 0.00 3.56
104 105 1.064505 CGCATTCTGTCATCCGCATTT 59.935 47.619 0.00 0.00 0.00 2.32
105 106 2.724349 GCATTCTGTCATCCGCATTTC 58.276 47.619 0.00 0.00 0.00 2.17
106 107 2.357009 GCATTCTGTCATCCGCATTTCT 59.643 45.455 0.00 0.00 0.00 2.52
107 108 3.791122 GCATTCTGTCATCCGCATTTCTG 60.791 47.826 0.00 0.00 0.00 3.02
108 109 2.028420 TCTGTCATCCGCATTTCTGG 57.972 50.000 0.00 0.00 0.00 3.86
109 110 1.554617 TCTGTCATCCGCATTTCTGGA 59.445 47.619 0.00 0.00 38.95 3.86
110 111 2.027285 TCTGTCATCCGCATTTCTGGAA 60.027 45.455 0.00 0.00 37.90 3.53
111 112 2.947652 CTGTCATCCGCATTTCTGGAAT 59.052 45.455 0.00 0.00 37.90 3.01
112 113 3.355378 TGTCATCCGCATTTCTGGAATT 58.645 40.909 0.00 0.00 37.90 2.17
113 114 3.378112 TGTCATCCGCATTTCTGGAATTC 59.622 43.478 0.00 0.00 37.90 2.17
114 115 3.378112 GTCATCCGCATTTCTGGAATTCA 59.622 43.478 7.93 0.00 37.90 2.57
115 116 3.628942 TCATCCGCATTTCTGGAATTCAG 59.371 43.478 7.93 3.37 44.68 3.02
116 117 3.071874 TCCGCATTTCTGGAATTCAGT 57.928 42.857 7.93 0.00 43.76 3.41
117 118 3.420893 TCCGCATTTCTGGAATTCAGTT 58.579 40.909 7.93 0.00 43.76 3.16
118 119 4.584874 TCCGCATTTCTGGAATTCAGTTA 58.415 39.130 7.93 0.00 43.76 2.24
119 120 4.635765 TCCGCATTTCTGGAATTCAGTTAG 59.364 41.667 7.93 0.25 43.76 2.34
120 121 4.396166 CCGCATTTCTGGAATTCAGTTAGT 59.604 41.667 7.93 0.00 43.76 2.24
121 122 5.447818 CCGCATTTCTGGAATTCAGTTAGTC 60.448 44.000 7.93 0.00 43.76 2.59
122 123 5.352569 CGCATTTCTGGAATTCAGTTAGTCT 59.647 40.000 7.93 0.00 43.76 3.24
123 124 6.549952 GCATTTCTGGAATTCAGTTAGTCTG 58.450 40.000 7.93 0.00 43.76 3.51
124 125 6.404074 GCATTTCTGGAATTCAGTTAGTCTGG 60.404 42.308 7.93 0.00 43.76 3.86
125 126 4.207891 TCTGGAATTCAGTTAGTCTGGC 57.792 45.455 7.93 0.00 43.76 4.85
126 127 3.055094 TCTGGAATTCAGTTAGTCTGGCC 60.055 47.826 7.93 0.00 43.76 5.36
127 128 2.642311 TGGAATTCAGTTAGTCTGGCCA 59.358 45.455 4.71 4.71 43.76 5.36
128 129 3.073798 TGGAATTCAGTTAGTCTGGCCAA 59.926 43.478 7.01 0.00 43.76 4.52
129 130 4.263905 TGGAATTCAGTTAGTCTGGCCAAT 60.264 41.667 7.01 0.00 43.76 3.16
130 131 4.706962 GGAATTCAGTTAGTCTGGCCAATT 59.293 41.667 7.01 0.00 43.76 2.32
131 132 5.185828 GGAATTCAGTTAGTCTGGCCAATTT 59.814 40.000 7.01 0.00 43.76 1.82
132 133 6.295292 GGAATTCAGTTAGTCTGGCCAATTTT 60.295 38.462 7.01 0.00 43.76 1.82
133 134 5.452078 TTCAGTTAGTCTGGCCAATTTTG 57.548 39.130 7.01 0.00 43.76 2.44
134 135 4.724399 TCAGTTAGTCTGGCCAATTTTGA 58.276 39.130 7.01 0.00 43.76 2.69
135 136 5.136828 TCAGTTAGTCTGGCCAATTTTGAA 58.863 37.500 7.01 0.00 43.76 2.69
136 137 5.009610 TCAGTTAGTCTGGCCAATTTTGAAC 59.990 40.000 7.01 6.84 43.76 3.18
137 138 5.010012 CAGTTAGTCTGGCCAATTTTGAACT 59.990 40.000 7.01 9.10 40.23 3.01
138 139 5.598417 AGTTAGTCTGGCCAATTTTGAACTT 59.402 36.000 7.01 0.00 0.00 2.66
139 140 4.590850 AGTCTGGCCAATTTTGAACTTC 57.409 40.909 7.01 0.00 0.00 3.01
140 141 4.218312 AGTCTGGCCAATTTTGAACTTCT 58.782 39.130 7.01 0.00 0.00 2.85
141 142 4.279420 AGTCTGGCCAATTTTGAACTTCTC 59.721 41.667 7.01 0.00 0.00 2.87
142 143 3.573967 TCTGGCCAATTTTGAACTTCTCC 59.426 43.478 7.01 0.00 0.00 3.71
143 144 2.295909 TGGCCAATTTTGAACTTCTCCG 59.704 45.455 0.61 0.00 0.00 4.63
144 145 2.328473 GCCAATTTTGAACTTCTCCGC 58.672 47.619 0.00 0.00 0.00 5.54
145 146 2.584791 CCAATTTTGAACTTCTCCGCG 58.415 47.619 0.00 0.00 0.00 6.46
179 180 1.160137 GCAACCATATGGATCGGAGC 58.840 55.000 28.77 16.52 38.94 4.70
188 193 0.970427 TGGATCGGAGCACTGCACTA 60.970 55.000 3.30 0.00 0.00 2.74
221 226 1.545582 TGCATAGTTTCTTGCTTGGCC 59.454 47.619 0.00 0.00 39.60 5.36
222 227 1.821136 GCATAGTTTCTTGCTTGGCCT 59.179 47.619 3.32 0.00 35.95 5.19
223 228 2.416431 GCATAGTTTCTTGCTTGGCCTG 60.416 50.000 3.32 0.00 35.95 4.85
224 229 2.949177 TAGTTTCTTGCTTGGCCTGA 57.051 45.000 3.32 0.00 0.00 3.86
236 241 4.489771 GCCTGACCGGTGATGGGG 62.490 72.222 14.63 1.60 34.25 4.96
274 279 3.657537 GACGCGTCCATTGTTCTTG 57.342 52.632 28.61 0.00 0.00 3.02
281 286 2.480419 CGTCCATTGTTCTTGGAGTCAC 59.520 50.000 0.00 0.00 43.78 3.67
332 337 1.949799 ACAGCTTGTCAGATCTCCCT 58.050 50.000 0.00 0.00 0.00 4.20
334 339 0.540923 AGCTTGTCAGATCTCCCTGC 59.459 55.000 0.00 0.00 34.28 4.85
497 512 4.696877 TGAATTGCACTAGGAGACACATTG 59.303 41.667 0.00 0.00 0.00 2.82
500 515 2.014068 GCACTAGGAGACACATTGCCC 61.014 57.143 0.00 0.00 0.00 5.36
517 532 1.379527 CCCGTACCCAATTCTCTTGC 58.620 55.000 0.00 0.00 0.00 4.01
600 615 1.685517 TCCAGATCTCGAGGCTTGATG 59.314 52.381 13.56 0.37 0.00 3.07
606 621 0.103937 CTCGAGGCTTGATGGAGGAC 59.896 60.000 4.57 0.00 0.00 3.85
667 684 5.163764 CGGCATGAACATTTGCTTCTTACTA 60.164 40.000 0.00 0.00 38.88 1.82
673 690 9.956720 ATGAACATTTGCTTCTTACTATTATGC 57.043 29.630 0.00 0.00 0.00 3.14
697 714 7.064134 TGCTAGTCGGTAACAAATTAATCAGTG 59.936 37.037 0.00 0.00 0.00 3.66
701 718 6.741358 GTCGGTAACAAATTAATCAGTGAAGC 59.259 38.462 0.00 0.00 0.00 3.86
726 743 4.970662 TGCCTTACTGAAATCTGCATTC 57.029 40.909 0.00 0.00 0.00 2.67
746 763 6.628175 GCATTCTATGTTGAGTACAGTGGAGA 60.628 42.308 0.00 0.00 40.83 3.71
765 782 5.470098 TGGAGATTACTTGTTTGCTCTGAAC 59.530 40.000 0.00 0.00 0.00 3.18
878 898 4.775253 TGCCATGGCATAATCATCATGATT 59.225 37.500 35.59 17.12 46.18 2.57
1045 1065 6.093357 GGAAGAGAGAAATGACCATTCAACTC 59.907 42.308 12.23 12.23 34.61 3.01
1063 1083 2.069273 CTCATGTGGAAGTGGAACGAC 58.931 52.381 0.00 0.00 45.86 4.34
1110 1130 4.870123 ATCAGAGTATGAAGCAGCTAGG 57.130 45.455 0.00 0.00 42.53 3.02
1143 1163 5.080337 TCATCTCAAGGTGAGTCTAACAGT 58.920 41.667 5.23 0.00 44.58 3.55
1249 1269 3.118884 GGCCAGAACTAATTCCACTCGTA 60.119 47.826 0.00 0.00 35.18 3.43
1540 1560 0.250209 AGCTGCTGATGATAAGGCCG 60.250 55.000 0.00 0.00 0.00 6.13
1553 1573 2.436115 GGCCGTTGAGGGTGTAGC 60.436 66.667 0.00 0.00 41.48 3.58
1607 1627 3.461085 ACTGATGATAAGGCCATTGAGGT 59.539 43.478 5.01 0.00 40.61 3.85
1608 1628 3.819337 CTGATGATAAGGCCATTGAGGTG 59.181 47.826 5.01 0.00 40.61 4.00
1609 1629 3.459227 TGATGATAAGGCCATTGAGGTGA 59.541 43.478 5.01 0.00 40.61 4.02
1683 1703 2.096248 GAGGGTGTAGAGACCAGTGAG 58.904 57.143 0.00 0.00 37.80 3.51
1685 1705 2.313342 AGGGTGTAGAGACCAGTGAGAT 59.687 50.000 0.00 0.00 37.80 2.75
1835 1855 9.058174 AGCATATGAAAAGAATGATGAGAAGAG 57.942 33.333 6.97 0.00 0.00 2.85
1896 1916 0.884704 TTCGTGAAGTTGCTGCCCTC 60.885 55.000 0.00 0.00 0.00 4.30
1918 1938 6.017440 CCTCGAGGTTTCTCTCTACTCTATTG 60.017 46.154 24.04 0.00 37.86 1.90
1956 1976 7.628769 ATGTTCATCACATAAACTGCATACA 57.371 32.000 0.00 0.00 45.00 2.29
1974 1994 4.803426 CCAGCTCGGCGTCTGTCC 62.803 72.222 22.51 3.19 0.00 4.02
2086 2106 4.510038 AAGTCTTGTGGCAATGATGTTC 57.490 40.909 0.00 0.00 0.00 3.18
2105 2125 5.139001 TGTTCCAAGGTAAATAAACGGGTT 58.861 37.500 0.00 0.00 0.00 4.11
2186 2250 6.367374 TGTAGGTTGACATTCTGGTTATCA 57.633 37.500 0.00 0.00 0.00 2.15
2204 2268 6.311723 GTTATCAAACACAATTGTCCTACGG 58.688 40.000 8.48 0.00 33.55 4.02
2270 2334 5.163864 TGCAGTTATGAATGCTTTCACTACG 60.164 40.000 16.45 13.21 44.36 3.51
2276 2340 4.377021 TGAATGCTTTCACTACGAACAGT 58.623 39.130 10.76 0.00 36.94 3.55
2279 2343 6.145534 TGAATGCTTTCACTACGAACAGTAAG 59.854 38.462 10.76 0.00 36.94 2.34
2285 2349 7.148999 GCTTTCACTACGAACAGTAAGAGTAAC 60.149 40.741 0.00 0.00 34.45 2.50
2290 2354 5.149273 TACGAACAGTAAGAGTAACGCAAG 58.851 41.667 0.00 0.00 36.23 4.01
2294 2358 6.128902 CGAACAGTAAGAGTAACGCAAGAAAT 60.129 38.462 0.00 0.00 43.62 2.17
2311 2375 7.575720 CGCAAGAAATCTTTACAAGAATTCCCT 60.576 37.037 0.65 0.00 44.69 4.20
2375 2439 2.167900 ACCTACTATCACGCAGTTTCCC 59.832 50.000 0.00 0.00 41.61 3.97
2376 2440 2.167693 CCTACTATCACGCAGTTTCCCA 59.832 50.000 0.00 0.00 41.61 4.37
2379 2443 3.270877 ACTATCACGCAGTTTCCCAATC 58.729 45.455 0.00 0.00 41.61 2.67
2450 2514 4.937620 TCTTGGATCTTTTCTCGGATTGTG 59.062 41.667 0.00 0.00 0.00 3.33
2551 2617 8.905702 GCTAGTTGTAAAACATGACTGAAAATG 58.094 33.333 0.00 0.00 0.00 2.32
2581 2655 7.350467 CAATTCAGTCAATATTCTGATCGGTG 58.650 38.462 7.48 0.00 39.85 4.94
2592 2666 2.233922 TCTGATCGGTGTTTCTCTTCCC 59.766 50.000 0.42 0.00 0.00 3.97
2622 2696 3.450904 ACTCCCTGTATGCAAACTCCTA 58.549 45.455 0.00 0.00 0.00 2.94
2649 2723 3.938963 GGATTCATCAACTCCAAGCGTTA 59.061 43.478 0.00 0.00 0.00 3.18
2698 2772 4.986034 TGATCAGCATCAAAGCACTTTTTG 59.014 37.500 0.00 0.00 35.99 2.44
2715 2789 7.116805 GCACTTTTTGTATTGATCTTTGGAAGG 59.883 37.037 0.00 0.00 0.00 3.46
2726 2800 1.802365 CTTTGGAAGGCTGCATTTTGC 59.198 47.619 0.00 0.00 45.29 3.68
2739 2813 1.591158 CATTTTGCGATGCATTCAGCC 59.409 47.619 16.47 0.00 44.83 4.85
2747 2821 2.481568 CGATGCATTCAGCCGAATATGT 59.518 45.455 0.00 0.00 44.83 2.29
2771 2845 0.107643 TTCGTGCTGGTGGACATGAA 59.892 50.000 0.00 0.00 39.00 2.57
2786 2860 1.406539 CATGAATGTGGCTGCTTACCC 59.593 52.381 0.00 0.00 0.00 3.69
2792 2866 1.832366 TGTGGCTGCTTACCCGTATTA 59.168 47.619 0.00 0.00 0.00 0.98
2874 2948 4.691860 ATGTGTTTATGAGCTGTTCTGC 57.308 40.909 0.00 0.00 0.00 4.26
2976 3050 8.857374 ATGAGATACCATCTGATCCAATATCT 57.143 34.615 8.26 8.26 40.38 1.98
2979 3053 8.076910 AGATACCATCTGATCCAATATCTGAC 57.923 38.462 7.93 0.00 38.44 3.51
2982 3056 4.287845 CCATCTGATCCAATATCTGACCCA 59.712 45.833 0.00 0.00 0.00 4.51
2988 3062 6.537355 TGATCCAATATCTGACCCAATTCTC 58.463 40.000 0.00 0.00 0.00 2.87
2996 3070 1.275291 TGACCCAATTCTCGACTCCAC 59.725 52.381 0.00 0.00 0.00 4.02
3132 3206 8.327941 TCAATTCCATGAAGAACAAACTAGAG 57.672 34.615 0.00 0.00 0.00 2.43
3271 3345 0.741326 ATGGACGGTGATGACTCTCG 59.259 55.000 0.00 0.00 0.00 4.04
3292 3366 1.792757 AAGGATGGCCAAGGTGCAGA 61.793 55.000 10.96 0.00 36.29 4.26
3447 3521 2.860735 GCATAACTCCTTGCTACACTCG 59.139 50.000 0.00 0.00 35.95 4.18
3872 3949 2.124151 CGCCCCTTCATTGGAGGG 60.124 66.667 21.96 21.96 42.94 4.30
3945 4034 1.085715 AGAGGAGAGGGTACACCAGT 58.914 55.000 0.00 0.00 43.89 4.00
4018 4107 4.124351 CTCCGCCGTCGCCTTGTA 62.124 66.667 0.00 0.00 0.00 2.41
4029 4118 2.442188 GCCTTGTAACGGAGTCGCG 61.442 63.158 0.00 0.00 45.00 5.87
4039 4128 1.421485 GGAGTCGCGCATTTCAGTG 59.579 57.895 8.75 0.00 0.00 3.66
4044 4133 3.168271 GCGCATTTCAGTGCTCGA 58.832 55.556 0.30 0.00 42.88 4.04
4140 4229 0.468029 ACCTGCAGGACTTGTTTGGG 60.468 55.000 39.19 9.37 38.94 4.12
4158 4247 4.348863 TGGGTGTTGCTTTGCATAAAAT 57.651 36.364 0.00 0.00 38.76 1.82
4251 4340 0.588252 CTCCTCGCTGGTGTTGTTTG 59.412 55.000 0.00 0.00 37.07 2.93
4278 4382 2.026262 TCCACTGCAGAATTTCTACCCC 60.026 50.000 23.35 0.00 0.00 4.95
4279 4383 2.369394 CACTGCAGAATTTCTACCCCC 58.631 52.381 23.35 0.00 0.00 5.40
4289 4393 5.427481 AGAATTTCTACCCCCTCATTCGTTA 59.573 40.000 0.00 0.00 0.00 3.18
4315 4419 1.000607 TGAGCTCGTTCGTTAGTTGCT 60.001 47.619 9.64 0.00 0.00 3.91
4316 4420 1.649662 GAGCTCGTTCGTTAGTTGCTC 59.350 52.381 0.00 0.00 38.58 4.26
4317 4421 1.269998 AGCTCGTTCGTTAGTTGCTCT 59.730 47.619 0.00 0.00 0.00 4.09
4318 4422 2.059541 GCTCGTTCGTTAGTTGCTCTT 58.940 47.619 0.00 0.00 0.00 2.85
4319 4423 2.475487 GCTCGTTCGTTAGTTGCTCTTT 59.525 45.455 0.00 0.00 0.00 2.52
4351 4455 9.619316 CTTCTTCTCATGTACTAGCATACATAC 57.381 37.037 5.86 0.00 42.63 2.39
4441 4545 3.788227 TGGTGTAAGAGCAACTCCAAT 57.212 42.857 0.00 0.00 37.51 3.16
4499 4603 4.323477 CCGTTTGGGTCGGCCAGA 62.323 66.667 9.07 0.00 41.48 3.86
4526 4630 2.321263 CCGGTGTCCGCATTTTAAAAC 58.679 47.619 1.97 0.00 46.86 2.43
4758 4884 2.597510 GCCCTTGCCCTTGACGTT 60.598 61.111 0.00 0.00 0.00 3.99
4760 4886 1.528309 CCCTTGCCCTTGACGTTGT 60.528 57.895 0.00 0.00 0.00 3.32
4781 4907 2.579787 CGTCGGTGAGGTCGATGC 60.580 66.667 0.00 0.00 38.93 3.91
4948 5083 1.521450 GCATGGCCTCATAGCGCATT 61.521 55.000 11.47 0.00 31.33 3.56
4959 5094 0.391130 TAGCGCATTTGCTCCTCGTT 60.391 50.000 11.47 0.00 45.87 3.85
5048 5183 2.879907 CGGCGAAGTAGACGGGAA 59.120 61.111 0.00 0.00 39.34 3.97
5063 5198 3.567797 GAAGCGCGCTCACCCATC 61.568 66.667 36.57 23.18 0.00 3.51
5097 5232 0.971447 GTCCACGAGTAGGCCTCCTT 60.971 60.000 9.68 0.00 36.82 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.925576 CGGTTCCCTCGATCCGCG 62.926 72.222 0.00 0.00 42.71 6.46
13 14 3.486252 CTCGGTTCCCTCGATCCGC 62.486 68.421 5.03 0.00 46.57 5.54
15 16 2.417936 GCTCGGTTCCCTCGATCC 59.582 66.667 0.00 0.00 36.01 3.36
16 17 2.417936 GGCTCGGTTCCCTCGATC 59.582 66.667 0.00 0.00 36.01 3.69
17 18 3.528370 CGGCTCGGTTCCCTCGAT 61.528 66.667 0.00 0.00 36.01 3.59
19 20 4.493747 GACGGCTCGGTTCCCTCG 62.494 72.222 0.00 0.00 0.00 4.63
20 21 4.144703 GGACGGCTCGGTTCCCTC 62.145 72.222 0.00 0.00 0.00 4.30
31 32 2.047179 AGGAAAGAAGCGGACGGC 60.047 61.111 0.00 0.00 44.05 5.68
32 33 0.602905 AACAGGAAAGAAGCGGACGG 60.603 55.000 0.00 0.00 0.00 4.79
33 34 0.790814 GAACAGGAAAGAAGCGGACG 59.209 55.000 0.00 0.00 0.00 4.79
34 35 1.801178 CAGAACAGGAAAGAAGCGGAC 59.199 52.381 0.00 0.00 0.00 4.79
35 36 1.416401 ACAGAACAGGAAAGAAGCGGA 59.584 47.619 0.00 0.00 0.00 5.54
36 37 1.884235 ACAGAACAGGAAAGAAGCGG 58.116 50.000 0.00 0.00 0.00 5.52
37 38 3.134458 AGAACAGAACAGGAAAGAAGCG 58.866 45.455 0.00 0.00 0.00 4.68
38 39 4.576463 TCAAGAACAGAACAGGAAAGAAGC 59.424 41.667 0.00 0.00 0.00 3.86
39 40 6.683974 TTCAAGAACAGAACAGGAAAGAAG 57.316 37.500 0.00 0.00 0.00 2.85
40 41 7.042051 CGTATTCAAGAACAGAACAGGAAAGAA 60.042 37.037 0.00 0.00 0.00 2.52
41 42 6.423905 CGTATTCAAGAACAGAACAGGAAAGA 59.576 38.462 0.00 0.00 0.00 2.52
42 43 6.593978 CGTATTCAAGAACAGAACAGGAAAG 58.406 40.000 0.00 0.00 0.00 2.62
43 44 5.049680 GCGTATTCAAGAACAGAACAGGAAA 60.050 40.000 0.00 0.00 0.00 3.13
44 45 4.451096 GCGTATTCAAGAACAGAACAGGAA 59.549 41.667 0.00 0.00 0.00 3.36
45 46 3.994392 GCGTATTCAAGAACAGAACAGGA 59.006 43.478 0.00 0.00 0.00 3.86
46 47 3.745975 TGCGTATTCAAGAACAGAACAGG 59.254 43.478 0.00 0.00 0.00 4.00
47 48 4.990543 TGCGTATTCAAGAACAGAACAG 57.009 40.909 0.00 0.00 0.00 3.16
48 49 5.940192 AATGCGTATTCAAGAACAGAACA 57.060 34.783 0.00 0.00 0.00 3.18
49 50 5.569059 CCAAATGCGTATTCAAGAACAGAAC 59.431 40.000 0.00 0.00 0.00 3.01
50 51 5.335583 CCCAAATGCGTATTCAAGAACAGAA 60.336 40.000 0.00 0.00 0.00 3.02
51 52 4.155826 CCCAAATGCGTATTCAAGAACAGA 59.844 41.667 0.00 0.00 0.00 3.41
52 53 4.082787 ACCCAAATGCGTATTCAAGAACAG 60.083 41.667 0.00 0.00 0.00 3.16
53 54 3.823873 ACCCAAATGCGTATTCAAGAACA 59.176 39.130 0.00 0.00 0.00 3.18
54 55 4.434713 ACCCAAATGCGTATTCAAGAAC 57.565 40.909 0.00 0.00 0.00 3.01
55 56 4.764823 AGAACCCAAATGCGTATTCAAGAA 59.235 37.500 0.00 0.00 0.00 2.52
56 57 4.155826 CAGAACCCAAATGCGTATTCAAGA 59.844 41.667 0.00 0.00 0.00 3.02
57 58 4.414852 CAGAACCCAAATGCGTATTCAAG 58.585 43.478 0.00 0.00 0.00 3.02
58 59 3.192422 CCAGAACCCAAATGCGTATTCAA 59.808 43.478 0.00 0.00 0.00 2.69
59 60 2.752354 CCAGAACCCAAATGCGTATTCA 59.248 45.455 0.00 0.00 0.00 2.57
60 61 2.752903 ACCAGAACCCAAATGCGTATTC 59.247 45.455 0.00 0.00 0.00 1.75
61 62 2.491693 CACCAGAACCCAAATGCGTATT 59.508 45.455 0.00 0.00 0.00 1.89
62 63 2.091541 CACCAGAACCCAAATGCGTAT 58.908 47.619 0.00 0.00 0.00 3.06
63 64 1.529226 CACCAGAACCCAAATGCGTA 58.471 50.000 0.00 0.00 0.00 4.42
64 65 1.805428 GCACCAGAACCCAAATGCGT 61.805 55.000 0.00 0.00 0.00 5.24
65 66 1.080569 GCACCAGAACCCAAATGCG 60.081 57.895 0.00 0.00 0.00 4.73
66 67 1.293179 GGCACCAGAACCCAAATGC 59.707 57.895 0.00 0.00 0.00 3.56
67 68 1.586028 CGGCACCAGAACCCAAATG 59.414 57.895 0.00 0.00 0.00 2.32
68 69 2.275380 GCGGCACCAGAACCCAAAT 61.275 57.895 0.00 0.00 0.00 2.32
69 70 2.909965 GCGGCACCAGAACCCAAA 60.910 61.111 0.00 0.00 0.00 3.28
70 71 2.992817 AATGCGGCACCAGAACCCAA 62.993 55.000 4.03 0.00 0.00 4.12
71 72 3.505790 AATGCGGCACCAGAACCCA 62.506 57.895 4.03 0.00 0.00 4.51
72 73 2.676471 AATGCGGCACCAGAACCC 60.676 61.111 4.03 0.00 0.00 4.11
73 74 1.675641 AGAATGCGGCACCAGAACC 60.676 57.895 4.03 0.00 0.00 3.62
74 75 1.237285 ACAGAATGCGGCACCAGAAC 61.237 55.000 4.03 0.00 42.53 3.01
75 76 0.955428 GACAGAATGCGGCACCAGAA 60.955 55.000 4.03 0.00 42.53 3.02
76 77 1.375908 GACAGAATGCGGCACCAGA 60.376 57.895 4.03 0.00 42.53 3.86
77 78 1.028330 ATGACAGAATGCGGCACCAG 61.028 55.000 4.03 0.00 42.53 4.00
78 79 1.002257 ATGACAGAATGCGGCACCA 60.002 52.632 4.03 0.00 42.53 4.17
79 80 1.718757 GGATGACAGAATGCGGCACC 61.719 60.000 4.03 0.00 42.53 5.01
80 81 1.723870 GGATGACAGAATGCGGCAC 59.276 57.895 4.03 0.00 42.53 5.01
81 82 1.815003 CGGATGACAGAATGCGGCA 60.815 57.895 4.58 4.58 42.53 5.69
82 83 3.017323 CGGATGACAGAATGCGGC 58.983 61.111 0.00 0.00 42.53 6.53
83 84 1.162181 ATGCGGATGACAGAATGCGG 61.162 55.000 0.00 0.00 42.53 5.69
84 85 0.659427 AATGCGGATGACAGAATGCG 59.341 50.000 0.00 0.00 42.53 4.73
85 86 2.357009 AGAAATGCGGATGACAGAATGC 59.643 45.455 0.00 0.00 42.53 3.56
86 87 3.242969 CCAGAAATGCGGATGACAGAATG 60.243 47.826 0.00 0.00 46.00 2.67
87 88 2.947652 CCAGAAATGCGGATGACAGAAT 59.052 45.455 0.00 0.00 0.00 2.40
88 89 2.027285 TCCAGAAATGCGGATGACAGAA 60.027 45.455 0.00 0.00 0.00 3.02
89 90 1.554617 TCCAGAAATGCGGATGACAGA 59.445 47.619 0.00 0.00 0.00 3.41
90 91 2.028420 TCCAGAAATGCGGATGACAG 57.972 50.000 0.00 0.00 0.00 3.51
91 92 2.488204 TTCCAGAAATGCGGATGACA 57.512 45.000 0.00 0.00 0.00 3.58
92 93 3.378112 TGAATTCCAGAAATGCGGATGAC 59.622 43.478 2.27 0.00 0.00 3.06
93 94 3.619419 TGAATTCCAGAAATGCGGATGA 58.381 40.909 2.27 0.00 0.00 2.92
94 95 3.379372 ACTGAATTCCAGAAATGCGGATG 59.621 43.478 2.27 0.00 45.78 3.51
95 96 3.624777 ACTGAATTCCAGAAATGCGGAT 58.375 40.909 2.27 0.00 45.78 4.18
96 97 3.071874 ACTGAATTCCAGAAATGCGGA 57.928 42.857 2.27 0.00 45.78 5.54
97 98 3.855689 AACTGAATTCCAGAAATGCGG 57.144 42.857 2.27 0.00 45.78 5.69
98 99 5.352569 AGACTAACTGAATTCCAGAAATGCG 59.647 40.000 2.27 0.00 45.78 4.73
99 100 6.749923 AGACTAACTGAATTCCAGAAATGC 57.250 37.500 2.27 0.00 45.78 3.56
113 114 5.010012 AGTTCAAAATTGGCCAGACTAACTG 59.990 40.000 5.11 0.00 45.36 3.16
114 115 5.140454 AGTTCAAAATTGGCCAGACTAACT 58.860 37.500 5.11 9.74 0.00 2.24
115 116 5.453567 AGTTCAAAATTGGCCAGACTAAC 57.546 39.130 5.11 7.54 0.00 2.34
116 117 5.833131 AGAAGTTCAAAATTGGCCAGACTAA 59.167 36.000 5.11 0.00 0.00 2.24
117 118 5.385198 AGAAGTTCAAAATTGGCCAGACTA 58.615 37.500 5.11 0.00 0.00 2.59
118 119 4.218312 AGAAGTTCAAAATTGGCCAGACT 58.782 39.130 5.11 0.04 0.00 3.24
119 120 4.550422 GAGAAGTTCAAAATTGGCCAGAC 58.450 43.478 5.11 0.00 0.00 3.51
120 121 3.573967 GGAGAAGTTCAAAATTGGCCAGA 59.426 43.478 5.11 0.00 0.00 3.86
121 122 3.612479 CGGAGAAGTTCAAAATTGGCCAG 60.612 47.826 5.11 0.00 0.00 4.85
122 123 2.295909 CGGAGAAGTTCAAAATTGGCCA 59.704 45.455 0.00 0.00 0.00 5.36
123 124 2.926586 GCGGAGAAGTTCAAAATTGGCC 60.927 50.000 5.50 0.00 0.00 5.36
124 125 2.328473 GCGGAGAAGTTCAAAATTGGC 58.672 47.619 5.50 0.00 0.00 4.52
125 126 2.584791 CGCGGAGAAGTTCAAAATTGG 58.415 47.619 5.50 0.00 0.00 3.16
126 127 2.031157 ACCGCGGAGAAGTTCAAAATTG 60.031 45.455 35.90 0.00 0.00 2.32
127 128 2.031157 CACCGCGGAGAAGTTCAAAATT 60.031 45.455 35.90 0.00 0.00 1.82
128 129 1.535462 CACCGCGGAGAAGTTCAAAAT 59.465 47.619 35.90 0.00 0.00 1.82
129 130 0.941542 CACCGCGGAGAAGTTCAAAA 59.058 50.000 35.90 0.00 0.00 2.44
130 131 0.882927 CCACCGCGGAGAAGTTCAAA 60.883 55.000 35.90 0.00 36.56 2.69
131 132 1.301401 CCACCGCGGAGAAGTTCAA 60.301 57.895 35.90 0.00 36.56 2.69
132 133 2.342279 CCACCGCGGAGAAGTTCA 59.658 61.111 35.90 0.00 36.56 3.18
133 134 3.119096 GCCACCGCGGAGAAGTTC 61.119 66.667 35.90 9.29 36.56 3.01
134 135 4.699522 GGCCACCGCGGAGAAGTT 62.700 66.667 35.90 4.54 36.56 2.66
136 137 3.976701 AATGGCCACCGCGGAGAAG 62.977 63.158 35.90 17.75 36.56 2.85
137 138 3.561120 AAATGGCCACCGCGGAGAA 62.561 57.895 35.90 13.66 36.56 2.87
138 139 4.028490 AAATGGCCACCGCGGAGA 62.028 61.111 35.90 8.83 36.56 3.71
139 140 3.814268 CAAATGGCCACCGCGGAG 61.814 66.667 35.90 25.83 36.56 4.63
142 143 4.054825 AAGCAAATGGCCACCGCG 62.055 61.111 8.16 0.00 46.50 6.46
143 144 2.432972 CAAGCAAATGGCCACCGC 60.433 61.111 8.16 11.71 46.50 5.68
144 145 2.432972 GCAAGCAAATGGCCACCG 60.433 61.111 8.16 0.00 46.50 4.94
145 146 1.071128 TTGCAAGCAAATGGCCACC 59.929 52.632 8.16 0.00 46.50 4.61
152 153 4.500205 CGATCCATATGGTTGCAAGCAAAT 60.500 41.667 32.60 20.72 40.14 2.32
218 223 4.489771 CCCATCACCGGTCAGGCC 62.490 72.222 2.59 0.00 46.52 5.19
221 226 0.255890 AATTCCCCATCACCGGTCAG 59.744 55.000 2.59 0.00 0.00 3.51
222 227 0.254747 GAATTCCCCATCACCGGTCA 59.745 55.000 2.59 0.00 0.00 4.02
223 228 0.465642 GGAATTCCCCATCACCGGTC 60.466 60.000 14.03 0.00 0.00 4.79
224 229 1.613061 GGAATTCCCCATCACCGGT 59.387 57.895 14.03 0.00 0.00 5.28
236 241 1.287425 CTAGTCGTTGCCCGGAATTC 58.713 55.000 0.73 0.00 37.11 2.17
274 279 1.513586 CGGCGAAGTACGTGACTCC 60.514 63.158 0.00 0.00 44.60 3.85
332 337 0.753867 TGTACCGAAACTGGACTGCA 59.246 50.000 0.00 0.00 0.00 4.41
334 339 1.000955 AGCTGTACCGAAACTGGACTG 59.999 52.381 0.00 0.00 0.00 3.51
497 512 1.379527 CAAGAGAATTGGGTACGGGC 58.620 55.000 0.00 0.00 0.00 6.13
500 515 1.398390 GCAGCAAGAGAATTGGGTACG 59.602 52.381 0.00 0.00 0.00 3.67
517 532 3.615224 AAATTAATGCCCCAACAGCAG 57.385 42.857 0.00 0.00 44.90 4.24
600 615 4.202172 GGATCAAACAGCTAGTAGTCCTCC 60.202 50.000 0.00 0.00 0.00 4.30
606 621 2.101582 AGCCGGATCAAACAGCTAGTAG 59.898 50.000 5.05 0.00 30.46 2.57
673 690 8.697846 TCACTGATTAATTTGTTACCGACTAG 57.302 34.615 0.00 0.00 0.00 2.57
689 706 3.266510 AGGCATTCGCTTCACTGATTA 57.733 42.857 0.00 0.00 38.60 1.75
691 708 2.119801 AAGGCATTCGCTTCACTGAT 57.880 45.000 0.00 0.00 38.60 2.90
693 710 2.094894 CAGTAAGGCATTCGCTTCACTG 59.905 50.000 0.00 0.00 38.60 3.66
697 714 4.333926 AGATTTCAGTAAGGCATTCGCTTC 59.666 41.667 0.00 0.00 38.60 3.86
701 718 3.374988 TGCAGATTTCAGTAAGGCATTCG 59.625 43.478 0.00 0.00 0.00 3.34
726 743 8.001881 AGTAATCTCCACTGTACTCAACATAG 57.998 38.462 0.00 0.00 37.50 2.23
746 763 7.934120 AGTAGAAGTTCAGAGCAAACAAGTAAT 59.066 33.333 5.50 0.00 0.00 1.89
810 827 7.786178 TGCATATAACGAGCTTTAACTGAAT 57.214 32.000 0.00 0.00 0.00 2.57
878 898 2.030027 AGTGACATCCAGGAAGGTCA 57.970 50.000 18.82 18.82 37.89 4.02
1045 1065 1.877637 TGTCGTTCCACTTCCACATG 58.122 50.000 0.00 0.00 0.00 3.21
1063 1083 3.879892 GCTTCCTTCCCTAGTTTAGCATG 59.120 47.826 0.00 0.00 0.00 4.06
1110 1130 4.006319 CACCTTGAGATGAAAAGGAGTCC 58.994 47.826 0.00 0.00 44.93 3.85
1160 1180 3.494398 CGGAACCCTTGAGACTCTTTTCA 60.494 47.826 3.68 0.00 0.00 2.69
1219 1239 1.334160 TTAGTTCTGGCCAGACGTGA 58.666 50.000 35.26 18.21 37.14 4.35
1249 1269 8.915057 ATATATTGCAGCTTCTTGTTGACTAT 57.085 30.769 0.00 0.00 0.00 2.12
1540 1560 0.601558 TCAGTCGCTACACCCTCAAC 59.398 55.000 0.00 0.00 0.00 3.18
1553 1573 3.732212 TCAATGGCCTTATCATCAGTCG 58.268 45.455 3.32 0.00 0.00 4.18
1607 1627 3.056536 GGCCTTATCATCAGTCGCTATCA 60.057 47.826 0.00 0.00 0.00 2.15
1608 1628 3.056536 TGGCCTTATCATCAGTCGCTATC 60.057 47.826 3.32 0.00 0.00 2.08
1609 1629 2.899900 TGGCCTTATCATCAGTCGCTAT 59.100 45.455 3.32 0.00 0.00 2.97
1683 1703 4.641989 TCCTTTGCTTCTTCAATGGCTATC 59.358 41.667 0.00 0.00 39.65 2.08
1685 1705 4.032960 TCCTTTGCTTCTTCAATGGCTA 57.967 40.909 0.00 0.00 39.65 3.93
1896 1916 6.491394 CACAATAGAGTAGAGAGAAACCTCG 58.509 44.000 0.00 0.00 38.19 4.63
1947 1967 1.219124 CCGAGCTGGTGTATGCAGT 59.781 57.895 0.00 0.00 0.00 4.40
1956 1976 4.057428 GACAGACGCCGAGCTGGT 62.057 66.667 14.08 2.93 41.21 4.00
1974 1994 8.571461 ACTTTGATGCATGGATATATAACCTG 57.429 34.615 2.46 7.18 0.00 4.00
2086 2106 9.783081 ATACTATAACCCGTTTATTTACCTTGG 57.217 33.333 0.00 0.00 32.31 3.61
2204 2268 4.240096 CAAAGGTTTGTGCAATGATCTCC 58.760 43.478 0.00 0.00 33.59 3.71
2244 2308 4.763793 AGTGAAAGCATTCATAACTGCAGT 59.236 37.500 15.25 15.25 46.67 4.40
2270 2334 6.520792 TTTCTTGCGTTACTCTTACTGTTC 57.479 37.500 0.00 0.00 0.00 3.18
2276 2340 8.821147 TGTAAAGATTTCTTGCGTTACTCTTA 57.179 30.769 0.00 0.00 36.12 2.10
2294 2358 8.245446 GCATTGGCAGGGAATTCTTGTAAAGA 62.245 42.308 5.23 0.00 46.04 2.52
2311 2375 1.823610 TCATTTTCCATCGCATTGGCA 59.176 42.857 0.00 0.00 41.24 4.92
2375 2439 2.675889 GCCAGTTTCCTGCCAATGATTG 60.676 50.000 0.00 0.00 37.38 2.67
2376 2440 1.551883 GCCAGTTTCCTGCCAATGATT 59.448 47.619 0.00 0.00 37.38 2.57
2379 2443 0.037975 GTGCCAGTTTCCTGCCAATG 60.038 55.000 0.00 0.00 37.38 2.82
2450 2514 1.302033 CTGCCACCACACAGACTCC 60.302 63.158 0.00 0.00 35.90 3.85
2483 2547 5.363101 TGACAAAATTGCCAGCATAAAACA 58.637 33.333 0.00 0.00 0.00 2.83
2484 2548 5.695816 TCTGACAAAATTGCCAGCATAAAAC 59.304 36.000 4.77 0.00 38.37 2.43
2491 2555 1.670967 GGCTCTGACAAAATTGCCAGC 60.671 52.381 4.77 2.21 38.37 4.85
2509 2573 5.048013 ACAACTAGCAGGTCAAATTTAAGGC 60.048 40.000 0.00 0.00 0.00 4.35
2551 2617 9.727627 GATCAGAATATTGACTGAATTGGAAAC 57.272 33.333 10.05 0.00 44.47 2.78
2581 2655 1.072331 TCAGTGCCTGGGAAGAGAAAC 59.928 52.381 0.00 0.00 31.51 2.78
2603 2677 4.473196 TCAATAGGAGTTTGCATACAGGGA 59.527 41.667 10.02 0.00 0.00 4.20
2622 2696 4.643784 GCTTGGAGTTGATGAATCCTCAAT 59.356 41.667 4.38 0.00 35.26 2.57
2649 2723 1.633945 AGAATGCCCTAACGGTTTCCT 59.366 47.619 0.00 0.00 30.33 3.36
2698 2772 3.696051 TGCAGCCTTCCAAAGATCAATAC 59.304 43.478 0.00 0.00 0.00 1.89
2726 2800 2.481568 ACATATTCGGCTGAATGCATCG 59.518 45.455 27.59 14.41 44.46 3.84
2732 2806 4.636249 GAAGAGGACATATTCGGCTGAAT 58.364 43.478 23.72 23.72 46.41 2.57
2747 2821 1.533033 TCCACCAGCACGAAGAGGA 60.533 57.895 0.00 0.00 0.00 3.71
2771 2845 0.837272 ATACGGGTAAGCAGCCACAT 59.163 50.000 0.00 0.00 42.89 3.21
2786 2860 4.189231 AGCTTACCAGTTTGGCTAATACG 58.811 43.478 0.00 0.00 42.67 3.06
2792 2866 4.470602 ACTTAAAGCTTACCAGTTTGGCT 58.529 39.130 0.00 0.00 42.67 4.75
2976 3050 1.275291 GTGGAGTCGAGAATTGGGTCA 59.725 52.381 0.00 0.00 0.00 4.02
2979 3053 0.460284 CCGTGGAGTCGAGAATTGGG 60.460 60.000 0.00 0.00 0.00 4.12
2982 3056 1.893801 AGAACCGTGGAGTCGAGAATT 59.106 47.619 0.00 0.00 0.00 2.17
2988 3062 2.432628 GGCAGAACCGTGGAGTCG 60.433 66.667 0.00 0.00 0.00 4.18
2996 3070 0.962356 AGCTGGAATTGGCAGAACCG 60.962 55.000 0.00 0.00 43.94 4.44
3132 3206 5.542779 ACTAAGATCATCGAAATGCCCTAC 58.457 41.667 0.00 0.00 32.58 3.18
3271 3345 3.010413 GCACCTTGGCCATCCTTGC 62.010 63.158 6.09 9.95 0.00 4.01
3292 3366 1.811778 TCTGCTATTGCCATCTCCCT 58.188 50.000 0.00 0.00 38.71 4.20
3550 3624 0.681887 TCGACGGGCAGACCTATCAA 60.682 55.000 0.00 0.00 36.97 2.57
3553 3627 0.389391 CAATCGACGGGCAGACCTAT 59.611 55.000 0.00 0.00 36.97 2.57
3681 3755 4.219070 TGGATTCATTCAACTTCAGCAAGG 59.781 41.667 0.00 0.00 33.37 3.61
3872 3949 0.458716 GCCACTCTTCTCCGCTACAC 60.459 60.000 0.00 0.00 0.00 2.90
3945 4034 2.281002 TCGTCCAGGTCGTCGTCA 60.281 61.111 5.97 0.00 0.00 4.35
4018 4107 1.626654 CTGAAATGCGCGACTCCGTT 61.627 55.000 12.10 0.00 38.24 4.44
4023 4112 2.863153 GCACTGAAATGCGCGACT 59.137 55.556 12.10 0.00 35.50 4.18
4029 4118 1.800586 TCTTGTCGAGCACTGAAATGC 59.199 47.619 0.00 0.00 46.50 3.56
4039 4128 3.491652 GGCGCCTTCTTGTCGAGC 61.492 66.667 22.15 0.00 0.00 5.03
4140 4229 3.423384 CGCCATTTTATGCAAAGCAACAC 60.423 43.478 0.00 0.00 43.62 3.32
4206 4295 3.774766 TCATCCCTCTTTGATTCTTCGGA 59.225 43.478 0.00 0.00 0.00 4.55
4251 4340 3.005155 AGAAATTCTGCAGTGGACAAAGC 59.995 43.478 14.67 0.00 0.00 3.51
4289 4393 4.421479 CGAACGAGCTCACCGGCT 62.421 66.667 15.40 0.00 46.11 5.52
4351 4455 6.211384 ACCATCCTTTCCTTACAATTTTCCAG 59.789 38.462 0.00 0.00 0.00 3.86
4548 4652 0.620700 ACATTTAGGTCGGCCTCCCT 60.621 55.000 14.54 13.94 45.64 4.20
4640 4748 8.598916 TGTTTATTAGATGTAGGTGGACTTTGA 58.401 33.333 0.00 0.00 0.00 2.69
4758 4884 2.592574 ACCTCACCGACGACGACA 60.593 61.111 9.28 0.00 42.66 4.35
4760 4886 3.417224 CGACCTCACCGACGACGA 61.417 66.667 9.28 0.00 42.66 4.20
4927 5062 1.895707 GCGCTATGAGGCCATGCTT 60.896 57.895 5.01 0.00 34.31 3.91
4948 5083 2.357034 GGCGACAACGAGGAGCAA 60.357 61.111 0.00 0.00 42.66 3.91


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

AutoCloner maintained by Alex Coulton.