Multiple sequence alignment - TraesCS3A01G251700

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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 TraesCS3A01G251700 chr3A 100.000 7250 0 0 1 7250 471371717 471364468 0.000000e+00 13389.0
1 TraesCS3A01G251700 chr3B 93.195 3512 143 38 150 3600 451879531 451876055 0.000000e+00 5073.0
2 TraesCS3A01G251700 chr3B 90.331 755 58 9 3588 4338 451876038 451875295 0.000000e+00 976.0
3 TraesCS3A01G251700 chr3B 87.281 857 62 20 5786 6604 451873698 451872851 0.000000e+00 935.0
4 TraesCS3A01G251700 chr3B 89.700 466 18 9 6813 7250 451855231 451854768 1.060000e-157 568.0
5 TraesCS3A01G251700 chr3B 89.665 358 24 4 4520 4873 451875078 451874730 1.860000e-120 444.0
6 TraesCS3A01G251700 chr3B 82.222 360 39 14 5181 5519 451874424 451874069 3.310000e-73 287.0
7 TraesCS3A01G251700 chr3B 91.270 126 8 3 4391 4515 451875272 451875149 1.250000e-37 169.0
8 TraesCS3A01G251700 chr3B 88.000 50 6 0 101 150 755574747 755574698 7.850000e-05 60.2
9 TraesCS3A01G251700 chr3B 90.476 42 4 0 4919 4960 710917308 710917267 1.000000e-03 56.5
10 TraesCS3A01G251700 chr3B 100.000 30 0 0 4931 4960 711049258 711049229 1.000000e-03 56.5
11 TraesCS3A01G251700 chr3B 90.476 42 4 0 4919 4960 711181799 711181758 1.000000e-03 56.5
12 TraesCS3A01G251700 chr3D 96.080 1709 35 10 3588 5284 352796776 352795088 0.000000e+00 2756.0
13 TraesCS3A01G251700 chr3D 97.791 1539 28 4 5283 6817 352795051 352793515 0.000000e+00 2649.0
14 TraesCS3A01G251700 chr3D 96.667 1530 44 7 2076 3600 352798320 352796793 0.000000e+00 2536.0
15 TraesCS3A01G251700 chr3D 90.392 1988 92 42 150 2081 352802688 352800744 0.000000e+00 2521.0
16 TraesCS3A01G251700 chr3D 91.183 465 14 7 6809 7248 352793489 352793027 2.240000e-169 606.0
17 TraesCS3A01G251700 chr3D 90.909 44 2 2 4931 4973 578734871 578734829 2.830000e-04 58.4
18 TraesCS3A01G251700 chrUn 76.944 360 51 13 170 512 93650966 93651310 7.480000e-40 176.0
19 TraesCS3A01G251700 chrUn 95.000 40 2 0 101 140 41396548 41396509 6.070000e-06 63.9
20 TraesCS3A01G251700 chrUn 91.304 46 4 0 101 146 327154412 327154457 6.070000e-06 63.9
21 TraesCS3A01G251700 chr6D 81.308 107 10 4 4865 4962 383747813 383747918 2.170000e-10 78.7
22 TraesCS3A01G251700 chr6D 95.238 42 2 0 101 142 457677752 457677711 4.690000e-07 67.6
23 TraesCS3A01G251700 chr6D 89.362 47 5 0 100 146 430139624 430139670 7.850000e-05 60.2
24 TraesCS3A01G251700 chr4B 91.228 57 3 2 4902 4958 668813784 668813838 7.800000e-10 76.8
25 TraesCS3A01G251700 chr7B 97.500 40 1 0 101 140 580948897 580948858 1.310000e-07 69.4
26 TraesCS3A01G251700 chr7B 100.000 32 0 0 4929 4960 639231742 639231773 7.850000e-05 60.2
27 TraesCS3A01G251700 chr2A 93.478 46 1 2 101 145 3277572 3277528 4.690000e-07 67.6
28 TraesCS3A01G251700 chr2A 91.304 46 4 0 101 146 750324543 750324498 6.070000e-06 63.9
29 TraesCS3A01G251700 chr2A 100.000 29 0 0 1 29 753672328 753672300 4.000000e-03 54.7
30 TraesCS3A01G251700 chr1A 91.111 45 4 0 101 145 544043346 544043390 2.180000e-05 62.1
31 TraesCS3A01G251700 chr1D 90.698 43 3 1 4915 4957 394845773 394845732 1.000000e-03 56.5


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 TraesCS3A01G251700 chr3A 471364468 471371717 7249 True 13389.0 13389 100.0000 1 7250 1 chr3A.!!$R1 7249
1 TraesCS3A01G251700 chr3B 451872851 451879531 6680 True 1314.0 5073 88.9940 150 6604 6 chr3B.!!$R6 6454
2 TraesCS3A01G251700 chr3D 352793027 352802688 9661 True 2213.6 2756 94.4226 150 7248 5 chr3D.!!$R2 7098

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
930 950 0.169230 CACTCGTGGTCTTCTCCTCG 59.831 60.000 0.00 0.0 43.12 4.63 F
954 974 0.469144 TCCCACACCCAAAAAGCTCC 60.469 55.000 0.00 0.0 0.00 4.70 F
1059 1079 1.210931 CAACAGCATCGGCAAGGTG 59.789 57.895 0.00 0.0 44.61 4.00 F
2947 5474 1.065551 GATTTTACCTGCCATCGGTGC 59.934 52.381 0.00 0.0 35.98 5.01 F
3371 5910 0.033601 TGGTGGCAGGTGAACAGTTT 60.034 50.000 0.00 0.0 0.00 2.66 F
4150 6722 2.092212 CCATATGGGAGCAAAGTGGAGT 60.092 50.000 14.52 0.0 40.01 3.85 F
5487 8301 0.395312 GACGTTGGGGAGGAAGACAA 59.605 55.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2778 5304 1.977854 TGATGCACACAAGTAGGGAGT 59.022 47.619 0.0 0.0 0.00 3.85 R
2930 5457 0.676466 CAGCACCGATGGCAGGTAAA 60.676 55.000 0.0 0.0 40.59 2.01 R
2984 5511 4.508124 GTGCAATAGTCTCAATAGTTCCCG 59.492 45.833 0.0 0.0 0.00 5.14 R
4286 6858 1.069049 GGCAGCAAAAAGGAAGAAGCA 59.931 47.619 0.0 0.0 0.00 3.91 R
4290 6862 1.202758 TCTCGGCAGCAAAAAGGAAGA 60.203 47.619 0.0 0.0 0.00 2.87 R
5962 9051 0.541530 AGCAGAGGTCAGAGAGCACA 60.542 55.000 0.0 0.0 31.89 4.57 R
6898 10046 0.247185 ATTTGGCAGCATGGGAAACG 59.753 50.000 0.0 0.0 35.86 3.60 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
29 30 9.852091 ATATTCATTTGAGAGACAAGCTTTTTC 57.148 29.630 0.00 0.00 39.77 2.29
30 31 5.751680 TCATTTGAGAGACAAGCTTTTTCG 58.248 37.500 0.00 0.00 39.77 3.46
31 32 5.527214 TCATTTGAGAGACAAGCTTTTTCGA 59.473 36.000 0.00 0.00 39.77 3.71
32 33 5.811399 TTTGAGAGACAAGCTTTTTCGAA 57.189 34.783 0.00 0.00 39.77 3.71
33 34 6.377327 TTTGAGAGACAAGCTTTTTCGAAT 57.623 33.333 0.00 0.00 39.77 3.34
34 35 5.348418 TGAGAGACAAGCTTTTTCGAATG 57.652 39.130 0.00 0.00 0.00 2.67
35 36 5.056480 TGAGAGACAAGCTTTTTCGAATGA 58.944 37.500 0.00 0.00 0.00 2.57
36 37 5.527214 TGAGAGACAAGCTTTTTCGAATGAA 59.473 36.000 0.00 0.00 0.00 2.57
37 38 5.995055 AGAGACAAGCTTTTTCGAATGAAG 58.005 37.500 14.24 14.24 35.06 3.02
38 39 5.049129 AGAGACAAGCTTTTTCGAATGAAGG 60.049 40.000 18.05 5.84 35.06 3.46
39 40 4.022849 AGACAAGCTTTTTCGAATGAAGGG 60.023 41.667 18.05 2.92 35.06 3.95
40 41 3.888930 ACAAGCTTTTTCGAATGAAGGGA 59.111 39.130 18.05 0.00 35.06 4.20
41 42 4.340950 ACAAGCTTTTTCGAATGAAGGGAA 59.659 37.500 18.05 0.00 35.06 3.97
42 43 5.011023 ACAAGCTTTTTCGAATGAAGGGAAT 59.989 36.000 18.05 0.00 35.06 3.01
43 44 6.208599 ACAAGCTTTTTCGAATGAAGGGAATA 59.791 34.615 18.05 0.00 35.06 1.75
44 45 6.196079 AGCTTTTTCGAATGAAGGGAATAC 57.804 37.500 18.05 5.75 35.06 1.89
45 46 5.946377 AGCTTTTTCGAATGAAGGGAATACT 59.054 36.000 18.05 7.35 35.06 2.12
46 47 6.030228 GCTTTTTCGAATGAAGGGAATACTG 58.970 40.000 18.05 0.00 35.06 2.74
47 48 6.349363 GCTTTTTCGAATGAAGGGAATACTGT 60.349 38.462 18.05 0.00 35.06 3.55
48 49 7.519032 TTTTTCGAATGAAGGGAATACTGTT 57.481 32.000 0.00 0.00 35.06 3.16
49 50 7.519032 TTTTCGAATGAAGGGAATACTGTTT 57.481 32.000 0.00 0.00 35.06 2.83
50 51 7.519032 TTTCGAATGAAGGGAATACTGTTTT 57.481 32.000 0.00 0.00 35.06 2.43
51 52 8.624367 TTTCGAATGAAGGGAATACTGTTTTA 57.376 30.769 0.00 0.00 35.06 1.52
52 53 8.624367 TTCGAATGAAGGGAATACTGTTTTAA 57.376 30.769 0.00 0.00 0.00 1.52
53 54 8.624367 TCGAATGAAGGGAATACTGTTTTAAA 57.376 30.769 0.00 0.00 0.00 1.52
54 55 8.508875 TCGAATGAAGGGAATACTGTTTTAAAC 58.491 33.333 0.20 0.20 0.00 2.01
55 56 8.293867 CGAATGAAGGGAATACTGTTTTAAACA 58.706 33.333 10.26 10.26 39.52 2.83
76 77 8.603242 AAACAGTATCTGAATGTCTAAAACGT 57.397 30.769 3.70 0.00 35.18 3.99
77 78 7.813852 ACAGTATCTGAATGTCTAAAACGTC 57.186 36.000 3.70 0.00 35.18 4.34
78 79 7.603651 ACAGTATCTGAATGTCTAAAACGTCT 58.396 34.615 3.70 0.00 35.18 4.18
79 80 7.755822 ACAGTATCTGAATGTCTAAAACGTCTC 59.244 37.037 3.70 0.00 35.18 3.36
80 81 7.755373 CAGTATCTGAATGTCTAAAACGTCTCA 59.245 37.037 0.00 0.00 32.44 3.27
81 82 8.470805 AGTATCTGAATGTCTAAAACGTCTCAT 58.529 33.333 0.00 0.00 0.00 2.90
82 83 9.731819 GTATCTGAATGTCTAAAACGTCTCATA 57.268 33.333 0.00 0.00 0.00 2.15
84 85 9.653287 ATCTGAATGTCTAAAACGTCTCATAAA 57.347 29.630 0.00 0.00 0.00 1.40
85 86 9.483916 TCTGAATGTCTAAAACGTCTCATAAAA 57.516 29.630 0.00 0.00 0.00 1.52
88 89 9.543018 GAATGTCTAAAACGTCTCATAAAAAGG 57.457 33.333 0.00 0.00 0.00 3.11
89 90 8.842358 ATGTCTAAAACGTCTCATAAAAAGGA 57.158 30.769 0.00 0.00 0.00 3.36
90 91 8.665643 TGTCTAAAACGTCTCATAAAAAGGAA 57.334 30.769 0.00 0.00 0.00 3.36
91 92 8.553696 TGTCTAAAACGTCTCATAAAAAGGAAC 58.446 33.333 0.00 0.00 0.00 3.62
92 93 8.553696 GTCTAAAACGTCTCATAAAAAGGAACA 58.446 33.333 0.00 0.00 0.00 3.18
93 94 8.770828 TCTAAAACGTCTCATAAAAAGGAACAG 58.229 33.333 0.00 0.00 0.00 3.16
94 95 7.562454 AAAACGTCTCATAAAAAGGAACAGA 57.438 32.000 0.00 0.00 0.00 3.41
95 96 6.787085 AACGTCTCATAAAAAGGAACAGAG 57.213 37.500 0.00 0.00 0.00 3.35
96 97 5.238583 ACGTCTCATAAAAAGGAACAGAGG 58.761 41.667 0.00 0.00 0.00 3.69
97 98 4.093556 CGTCTCATAAAAAGGAACAGAGGC 59.906 45.833 0.00 0.00 0.00 4.70
98 99 5.003804 GTCTCATAAAAAGGAACAGAGGCA 58.996 41.667 0.00 0.00 0.00 4.75
99 100 5.003804 TCTCATAAAAAGGAACAGAGGCAC 58.996 41.667 0.00 0.00 0.00 5.01
101 102 5.385198 TCATAAAAAGGAACAGAGGCACTT 58.615 37.500 0.00 0.00 41.55 3.16
102 103 5.241506 TCATAAAAAGGAACAGAGGCACTTG 59.758 40.000 0.00 0.00 41.55 3.16
103 104 3.297134 AAAAGGAACAGAGGCACTTGA 57.703 42.857 0.00 0.00 41.55 3.02
104 105 3.297134 AAAGGAACAGAGGCACTTGAA 57.703 42.857 0.00 0.00 41.55 2.69
105 106 2.262423 AGGAACAGAGGCACTTGAAC 57.738 50.000 0.00 0.00 41.55 3.18
106 107 1.771255 AGGAACAGAGGCACTTGAACT 59.229 47.619 0.00 0.00 41.55 3.01
107 108 2.972713 AGGAACAGAGGCACTTGAACTA 59.027 45.455 0.00 0.00 41.55 2.24
108 109 3.391296 AGGAACAGAGGCACTTGAACTAA 59.609 43.478 0.00 0.00 41.55 2.24
109 110 4.134563 GGAACAGAGGCACTTGAACTAAA 58.865 43.478 0.00 0.00 41.55 1.85
110 111 4.578928 GGAACAGAGGCACTTGAACTAAAA 59.421 41.667 0.00 0.00 41.55 1.52
111 112 5.500645 AACAGAGGCACTTGAACTAAAAC 57.499 39.130 0.00 0.00 41.55 2.43
112 113 3.883489 ACAGAGGCACTTGAACTAAAACC 59.117 43.478 0.00 0.00 41.55 3.27
113 114 3.882888 CAGAGGCACTTGAACTAAAACCA 59.117 43.478 0.00 0.00 41.55 3.67
114 115 3.883489 AGAGGCACTTGAACTAAAACCAC 59.117 43.478 0.00 0.00 41.55 4.16
115 116 2.616842 AGGCACTTGAACTAAAACCACG 59.383 45.455 0.00 0.00 27.25 4.94
116 117 2.614983 GGCACTTGAACTAAAACCACGA 59.385 45.455 0.00 0.00 0.00 4.35
117 118 3.547413 GGCACTTGAACTAAAACCACGAC 60.547 47.826 0.00 0.00 0.00 4.34
118 119 3.843510 GCACTTGAACTAAAACCACGACG 60.844 47.826 0.00 0.00 0.00 5.12
119 120 3.552699 CACTTGAACTAAAACCACGACGA 59.447 43.478 0.00 0.00 0.00 4.20
120 121 3.800506 ACTTGAACTAAAACCACGACGAG 59.199 43.478 0.00 0.00 0.00 4.18
121 122 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
122 123 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
123 124 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
124 125 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
125 126 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
126 127 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
127 128 7.651304 TGAACTAAAACCACGACGAGTAATTTA 59.349 33.333 0.00 1.47 0.00 1.40
128 129 7.945033 ACTAAAACCACGACGAGTAATTTAA 57.055 32.000 0.00 0.00 0.00 1.52
129 130 8.364129 ACTAAAACCACGACGAGTAATTTAAA 57.636 30.769 0.00 0.00 0.00 1.52
130 131 8.825745 ACTAAAACCACGACGAGTAATTTAAAA 58.174 29.630 0.00 0.00 0.00 1.52
131 132 7.897153 AAAACCACGACGAGTAATTTAAAAC 57.103 32.000 0.00 0.00 0.00 2.43
132 133 5.254669 ACCACGACGAGTAATTTAAAACG 57.745 39.130 0.00 0.00 0.00 3.60
133 134 4.150451 ACCACGACGAGTAATTTAAAACGG 59.850 41.667 0.00 0.00 0.00 4.44
134 135 4.385447 CCACGACGAGTAATTTAAAACGGA 59.615 41.667 0.00 0.00 0.00 4.69
135 136 5.107530 CCACGACGAGTAATTTAAAACGGAA 60.108 40.000 0.00 0.00 0.00 4.30
136 137 6.005289 CACGACGAGTAATTTAAAACGGAAG 58.995 40.000 0.00 0.00 0.00 3.46
137 138 5.920273 ACGACGAGTAATTTAAAACGGAAGA 59.080 36.000 0.00 0.00 0.00 2.87
138 139 6.420604 ACGACGAGTAATTTAAAACGGAAGAA 59.579 34.615 0.00 0.00 0.00 2.52
139 140 6.946584 CGACGAGTAATTTAAAACGGAAGAAG 59.053 38.462 0.00 0.00 0.00 2.85
140 141 6.596703 ACGAGTAATTTAAAACGGAAGAAGC 58.403 36.000 0.00 0.00 0.00 3.86
141 142 6.203338 ACGAGTAATTTAAAACGGAAGAAGCA 59.797 34.615 0.00 0.00 0.00 3.91
142 143 6.736853 CGAGTAATTTAAAACGGAAGAAGCAG 59.263 38.462 0.00 0.00 0.00 4.24
143 144 7.506328 AGTAATTTAAAACGGAAGAAGCAGT 57.494 32.000 0.00 0.00 0.00 4.40
144 145 8.611654 AGTAATTTAAAACGGAAGAAGCAGTA 57.388 30.769 0.00 0.00 0.00 2.74
145 146 9.059260 AGTAATTTAAAACGGAAGAAGCAGTAA 57.941 29.630 0.00 0.00 0.00 2.24
146 147 9.110617 GTAATTTAAAACGGAAGAAGCAGTAAC 57.889 33.333 0.00 0.00 0.00 2.50
147 148 3.872560 AAAACGGAAGAAGCAGTAACG 57.127 42.857 0.00 0.00 0.00 3.18
148 149 2.806608 AACGGAAGAAGCAGTAACGA 57.193 45.000 0.00 0.00 0.00 3.85
161 162 9.378551 AGAAGCAGTAACGAAAATATGATGTAA 57.621 29.630 0.00 0.00 0.00 2.41
162 163 9.422196 GAAGCAGTAACGAAAATATGATGTAAC 57.578 33.333 0.00 0.00 0.00 2.50
250 251 2.888863 CTCCTCCTCGCAGACCAC 59.111 66.667 0.00 0.00 0.00 4.16
592 602 1.177401 GATTTCCTTGCCAGGGTGAC 58.823 55.000 3.59 0.00 41.25 3.67
632 642 2.203195 TGCCCAGTGTCAGTGTGC 60.203 61.111 8.07 8.07 0.00 4.57
651 664 0.304705 CGATGCGAAATGTGGGTAGC 59.695 55.000 0.00 0.00 0.00 3.58
657 670 1.369625 GAAATGTGGGTAGCGTGAGG 58.630 55.000 0.00 0.00 0.00 3.86
826 846 3.114616 CAGGCACCAACGAGAGCG 61.115 66.667 0.00 0.00 44.79 5.03
912 932 4.465446 CCTCCTCGGCTCCTCCCA 62.465 72.222 0.00 0.00 0.00 4.37
930 950 0.169230 CACTCGTGGTCTTCTCCTCG 59.831 60.000 0.00 0.00 43.12 4.63
954 974 0.469144 TCCCACACCCAAAAAGCTCC 60.469 55.000 0.00 0.00 0.00 4.70
962 982 1.344438 CCCAAAAAGCTCCAGGGAAAC 59.656 52.381 7.52 0.00 42.25 2.78
1059 1079 1.210931 CAACAGCATCGGCAAGGTG 59.789 57.895 0.00 0.00 44.61 4.00
1120 1140 1.849823 AAGCTCAAGGCACCCCTCT 60.850 57.895 0.00 0.00 41.90 3.69
1123 1143 2.610859 TCAAGGCACCCCTCTCCC 60.611 66.667 0.00 0.00 41.90 4.30
1125 1145 3.960313 AAGGCACCCCTCTCCCCT 61.960 66.667 0.00 0.00 41.90 4.79
1129 1149 3.700350 CACCCCTCTCCCCTCCCT 61.700 72.222 0.00 0.00 0.00 4.20
1130 1150 3.700350 ACCCCTCTCCCCTCCCTG 61.700 72.222 0.00 0.00 0.00 4.45
1153 1182 1.435256 CCTTATCCATCCCTTCCGGT 58.565 55.000 0.00 0.00 0.00 5.28
1181 1215 2.283617 CGCTGCTGCTTACTGTTAGATG 59.716 50.000 14.03 0.00 36.97 2.90
1329 1363 4.577677 TGCGTTGCCTGCTTCCCA 62.578 61.111 0.00 0.00 0.00 4.37
1361 1395 3.117046 GTTTCTCTTCTCGCCCGATTAG 58.883 50.000 0.00 0.00 0.00 1.73
1376 1432 2.352715 CGATTAGTAGGATGCCGCATGA 60.353 50.000 11.49 0.00 0.00 3.07
1556 1613 4.036971 CCATAGGTGAGCTACAGTACAGTC 59.963 50.000 0.00 0.00 0.00 3.51
1831 1920 7.480542 CGTAAGTATGCATTCTACCAAAACAAC 59.519 37.037 3.54 0.00 0.00 3.32
1863 1952 4.854399 TCTTGCACAAACTATTTTGACCG 58.146 39.130 12.06 2.32 44.38 4.79
1881 1970 7.724305 TTGACCGTTCTTGCTATAATATTCC 57.276 36.000 0.00 0.00 0.00 3.01
2421 4946 7.817418 TCACTTTGTTTACAGCCTTTTCTAT 57.183 32.000 0.00 0.00 0.00 1.98
2424 4949 9.313118 CACTTTGTTTACAGCCTTTTCTATTTT 57.687 29.630 0.00 0.00 0.00 1.82
2778 5304 4.014406 TGTCTAGTTTACTGGAGATGCGA 58.986 43.478 0.00 0.00 34.04 5.10
2865 5392 7.004555 TGGAGATGTACTTCTCTGCTTTTTA 57.995 36.000 28.20 10.09 41.58 1.52
2904 5431 4.142609 AGGGATGTATACAGTGCTTGTG 57.857 45.455 11.91 0.00 41.10 3.33
2922 5449 5.969435 GCTTGTGTAGTGTTTGTAGAAAACC 59.031 40.000 0.00 0.00 0.00 3.27
2930 5457 9.708092 GTAGTGTTTGTAGAAAACCTAGAGATT 57.292 33.333 0.00 0.00 0.00 2.40
2947 5474 1.065551 GATTTTACCTGCCATCGGTGC 59.934 52.381 0.00 0.00 35.98 5.01
3068 5595 7.411804 GCATTTATTGTTTGGCTGTCATACAAC 60.412 37.037 18.08 4.61 45.29 3.32
3077 5604 4.019771 TGGCTGTCATACAACCTATGTCAA 60.020 41.667 1.57 0.00 42.70 3.18
3166 5693 5.431420 TTGCGAAGACATTTAAAGCAGAA 57.569 34.783 0.00 0.00 34.52 3.02
3298 5836 5.163426 TGTGTCATCTTTTTCCATGTTTGCT 60.163 36.000 0.00 0.00 0.00 3.91
3316 5854 1.868498 GCTACAACTGTTGCGTTACCA 59.132 47.619 19.82 0.00 37.09 3.25
3371 5910 0.033601 TGGTGGCAGGTGAACAGTTT 60.034 50.000 0.00 0.00 0.00 2.66
3557 6096 3.199946 TGGAGACTCCACTTGTTGAGTTT 59.800 43.478 20.74 3.87 42.67 2.66
3664 6233 3.827817 TCTTTAGAGAGACTCACCCCA 57.172 47.619 5.02 0.00 32.06 4.96
3795 6364 8.947115 GGTAGTCAATTTAACTAGTGAAGCATT 58.053 33.333 0.00 0.00 30.11 3.56
4024 6595 3.451178 ACCGAGGTGCATTAGTTCATACT 59.549 43.478 0.00 0.00 38.44 2.12
4076 6647 7.801716 TTTTGAGAACATGTACTTGCTAGTT 57.198 32.000 6.03 0.00 35.78 2.24
4150 6722 2.092212 CCATATGGGAGCAAAGTGGAGT 60.092 50.000 14.52 0.00 40.01 3.85
4581 7220 0.595095 CTTCTGCTCTGGTTTGTGGC 59.405 55.000 0.00 0.00 0.00 5.01
4584 7223 1.035139 CTGCTCTGGTTTGTGGCTTT 58.965 50.000 0.00 0.00 0.00 3.51
4779 7418 5.902613 TTTCTCTTGCTTGGATGGTAATG 57.097 39.130 0.00 0.00 0.00 1.90
4907 7550 6.700081 CCATACTAATTGTCGCTGCTTTAGTA 59.300 38.462 0.00 7.93 38.80 1.82
4908 7551 7.306632 CCATACTAATTGTCGCTGCTTTAGTAC 60.307 40.741 13.23 0.00 37.87 2.73
4947 7601 5.292765 AGCTGTGACAAGTAATATGGATCG 58.707 41.667 0.00 0.00 0.00 3.69
5011 7666 7.133334 ACCTTTAAGGCTATTGCATTGGCAG 62.133 44.000 17.14 6.73 45.60 4.85
5077 7733 0.544357 TTGTGATCACGAGGGGAGGT 60.544 55.000 20.54 0.00 0.00 3.85
5103 7759 2.043941 GGGGTAGGGGGTGATGGT 59.956 66.667 0.00 0.00 0.00 3.55
5132 7788 5.856126 ACACTTAACATACATTGTGGACG 57.144 39.130 0.00 0.00 38.99 4.79
5133 7789 4.153475 ACACTTAACATACATTGTGGACGC 59.847 41.667 0.00 0.00 38.99 5.19
5375 8189 1.344065 TGGAGACGAAAGGTTAGCCA 58.656 50.000 0.00 0.00 37.19 4.75
5487 8301 0.395312 GACGTTGGGGAGGAAGACAA 59.605 55.000 0.00 0.00 0.00 3.18
5568 8388 1.133823 TGCAGTTGTTGGGATGTCTGT 60.134 47.619 0.00 0.00 0.00 3.41
5569 8389 1.267806 GCAGTTGTTGGGATGTCTGTG 59.732 52.381 0.00 0.00 0.00 3.66
5639 8716 5.127682 TCTCTTGTAATCATGCAGCTACAGA 59.872 40.000 0.00 0.00 0.00 3.41
5641 8718 3.447742 TGTAATCATGCAGCTACAGACG 58.552 45.455 0.00 0.00 0.00 4.18
5703 8780 3.157087 CTCACTAAATTGCAAGTGGGGT 58.843 45.455 14.64 5.38 42.72 4.95
5712 8789 1.903404 CAAGTGGGGTGGGTGCTTC 60.903 63.158 0.00 0.00 0.00 3.86
6384 9492 6.373759 TGACTGCCCTTATAGATCTAACAGA 58.626 40.000 6.52 0.00 0.00 3.41
6480 9588 9.327628 GGTATATTAGTTTGTTCTCTTCCCTTC 57.672 37.037 0.00 0.00 0.00 3.46
6525 9635 4.946772 TGCTTTACTTGCAGCACCATTATA 59.053 37.500 0.00 0.00 41.20 0.98
6549 9659 1.543802 TGCTTTTAAGAATGCGTGGGG 59.456 47.619 0.00 0.00 38.41 4.96
6620 9733 8.255206 ACAACTCTTGTGATATACCGTCAATTA 58.745 33.333 0.00 0.00 43.48 1.40
6632 9745 2.331194 CGTCAATTACTTCGGTTCCGT 58.669 47.619 11.04 0.00 0.00 4.69
6677 9790 1.676967 CAGAAGCTTCCCCCAGTGC 60.677 63.158 22.81 0.00 0.00 4.40
6682 9795 2.839098 CTTCCCCCAGTGCACTGT 59.161 61.111 37.55 9.56 42.27 3.55
6700 9813 2.951642 CTGTCACAGTTGTGGGAAATGT 59.048 45.455 11.98 0.00 45.65 2.71
6898 10046 4.220382 CAGGATGATCTCATACCTGTCTCC 59.780 50.000 19.72 7.08 41.46 3.71
6899 10047 3.192422 GGATGATCTCATACCTGTCTCCG 59.808 52.174 0.00 0.00 36.57 4.63
6924 10072 1.274167 CCATGCTGCCAAATGAAGTGT 59.726 47.619 0.00 0.00 0.00 3.55
7074 10238 4.847990 ATTTTCCAACCCTACCGTGATA 57.152 40.909 0.00 0.00 0.00 2.15
7105 10270 2.831526 AGGTTTGCTTTCTGTGTGGTTT 59.168 40.909 0.00 0.00 0.00 3.27
7111 10276 2.099405 CTTTCTGTGTGGTTTGGTGGT 58.901 47.619 0.00 0.00 0.00 4.16
7113 10278 2.631160 TCTGTGTGGTTTGGTGGTAG 57.369 50.000 0.00 0.00 0.00 3.18
7131 10296 0.395586 AGGCACAGTTTTGTCCAGCA 60.396 50.000 0.00 0.00 34.62 4.41
7233 10406 1.003355 CACATCAGTCGCCTTGGGT 60.003 57.895 0.00 0.00 0.00 4.51
7235 10408 1.296392 CATCAGTCGCCTTGGGTCA 59.704 57.895 0.00 0.00 0.00 4.02
7245 10418 1.751927 CTTGGGTCAGGCAGCATCC 60.752 63.158 0.00 0.00 0.00 3.51
7248 10421 4.864334 GGTCAGGCAGCATCCGGG 62.864 72.222 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.852091 GAAAAAGCTTGTCTCTCAAATGAATAT 57.148 29.630 0.00 0.00 35.48 1.28
4 5 8.017373 CGAAAAAGCTTGTCTCTCAAATGAATA 58.983 33.333 0.00 0.00 35.48 1.75
5 6 6.860023 CGAAAAAGCTTGTCTCTCAAATGAAT 59.140 34.615 0.00 0.00 35.48 2.57
6 7 6.038161 TCGAAAAAGCTTGTCTCTCAAATGAA 59.962 34.615 0.00 0.00 35.48 2.57
7 8 5.527214 TCGAAAAAGCTTGTCTCTCAAATGA 59.473 36.000 0.00 0.00 35.48 2.57
8 9 5.751680 TCGAAAAAGCTTGTCTCTCAAATG 58.248 37.500 0.00 0.00 35.48 2.32
9 10 6.377327 TTCGAAAAAGCTTGTCTCTCAAAT 57.623 33.333 0.00 0.00 35.48 2.32
10 11 5.811399 TTCGAAAAAGCTTGTCTCTCAAA 57.189 34.783 0.00 0.00 35.48 2.69
11 12 5.527214 TCATTCGAAAAAGCTTGTCTCTCAA 59.473 36.000 0.00 0.00 34.61 3.02
12 13 5.056480 TCATTCGAAAAAGCTTGTCTCTCA 58.944 37.500 0.00 0.00 0.00 3.27
13 14 5.597813 TCATTCGAAAAAGCTTGTCTCTC 57.402 39.130 0.00 0.00 0.00 3.20
14 15 5.049129 CCTTCATTCGAAAAAGCTTGTCTCT 60.049 40.000 14.87 0.00 0.00 3.10
15 16 5.149977 CCTTCATTCGAAAAAGCTTGTCTC 58.850 41.667 14.87 0.00 0.00 3.36
16 17 4.022849 CCCTTCATTCGAAAAAGCTTGTCT 60.023 41.667 14.87 0.00 0.00 3.41
17 18 4.023193 TCCCTTCATTCGAAAAAGCTTGTC 60.023 41.667 14.87 0.00 0.00 3.18
18 19 3.888930 TCCCTTCATTCGAAAAAGCTTGT 59.111 39.130 14.87 0.00 0.00 3.16
19 20 4.503741 TCCCTTCATTCGAAAAAGCTTG 57.496 40.909 14.87 3.53 0.00 4.01
20 21 5.728637 ATTCCCTTCATTCGAAAAAGCTT 57.271 34.783 14.87 0.00 0.00 3.74
21 22 5.946377 AGTATTCCCTTCATTCGAAAAAGCT 59.054 36.000 14.87 6.03 0.00 3.74
22 23 6.030228 CAGTATTCCCTTCATTCGAAAAAGC 58.970 40.000 14.87 4.34 0.00 3.51
23 24 7.145932 ACAGTATTCCCTTCATTCGAAAAAG 57.854 36.000 0.00 9.19 0.00 2.27
24 25 7.519032 AACAGTATTCCCTTCATTCGAAAAA 57.481 32.000 0.00 0.00 0.00 1.94
25 26 7.519032 AAACAGTATTCCCTTCATTCGAAAA 57.481 32.000 0.00 0.00 0.00 2.29
26 27 7.519032 AAAACAGTATTCCCTTCATTCGAAA 57.481 32.000 0.00 0.00 0.00 3.46
27 28 8.624367 TTAAAACAGTATTCCCTTCATTCGAA 57.376 30.769 0.00 0.00 0.00 3.71
28 29 8.508875 GTTTAAAACAGTATTCCCTTCATTCGA 58.491 33.333 0.00 0.00 0.00 3.71
29 30 8.293867 TGTTTAAAACAGTATTCCCTTCATTCG 58.706 33.333 0.00 0.00 36.25 3.34
50 51 9.701098 ACGTTTTAGACATTCAGATACTGTTTA 57.299 29.630 0.00 0.00 32.61 2.01
51 52 8.603242 ACGTTTTAGACATTCAGATACTGTTT 57.397 30.769 0.00 0.00 32.61 2.83
52 53 8.088981 AGACGTTTTAGACATTCAGATACTGTT 58.911 33.333 0.00 0.00 32.61 3.16
53 54 7.603651 AGACGTTTTAGACATTCAGATACTGT 58.396 34.615 0.00 0.00 32.61 3.55
54 55 7.755373 TGAGACGTTTTAGACATTCAGATACTG 59.245 37.037 0.00 0.00 0.00 2.74
55 56 7.827701 TGAGACGTTTTAGACATTCAGATACT 58.172 34.615 0.00 0.00 0.00 2.12
56 57 8.635877 ATGAGACGTTTTAGACATTCAGATAC 57.364 34.615 0.00 0.00 0.00 2.24
58 59 9.653287 TTTATGAGACGTTTTAGACATTCAGAT 57.347 29.630 0.00 0.00 0.00 2.90
59 60 9.483916 TTTTATGAGACGTTTTAGACATTCAGA 57.516 29.630 0.00 0.00 0.00 3.27
62 63 9.543018 CCTTTTTATGAGACGTTTTAGACATTC 57.457 33.333 0.00 0.00 0.00 2.67
63 64 9.280174 TCCTTTTTATGAGACGTTTTAGACATT 57.720 29.630 0.00 0.00 0.00 2.71
64 65 8.842358 TCCTTTTTATGAGACGTTTTAGACAT 57.158 30.769 0.00 0.00 0.00 3.06
65 66 8.553696 GTTCCTTTTTATGAGACGTTTTAGACA 58.446 33.333 0.00 0.00 0.00 3.41
66 67 8.553696 TGTTCCTTTTTATGAGACGTTTTAGAC 58.446 33.333 0.00 0.00 0.00 2.59
67 68 8.665643 TGTTCCTTTTTATGAGACGTTTTAGA 57.334 30.769 0.00 0.00 0.00 2.10
68 69 8.770828 TCTGTTCCTTTTTATGAGACGTTTTAG 58.229 33.333 0.00 0.00 0.00 1.85
69 70 8.665643 TCTGTTCCTTTTTATGAGACGTTTTA 57.334 30.769 0.00 0.00 0.00 1.52
70 71 7.255139 CCTCTGTTCCTTTTTATGAGACGTTTT 60.255 37.037 0.00 0.00 0.00 2.43
71 72 6.204882 CCTCTGTTCCTTTTTATGAGACGTTT 59.795 38.462 0.00 0.00 0.00 3.60
72 73 5.701290 CCTCTGTTCCTTTTTATGAGACGTT 59.299 40.000 0.00 0.00 0.00 3.99
73 74 5.238583 CCTCTGTTCCTTTTTATGAGACGT 58.761 41.667 0.00 0.00 0.00 4.34
74 75 4.093556 GCCTCTGTTCCTTTTTATGAGACG 59.906 45.833 0.00 0.00 0.00 4.18
75 76 5.003804 TGCCTCTGTTCCTTTTTATGAGAC 58.996 41.667 0.00 0.00 0.00 3.36
76 77 5.003804 GTGCCTCTGTTCCTTTTTATGAGA 58.996 41.667 0.00 0.00 0.00 3.27
77 78 5.006386 AGTGCCTCTGTTCCTTTTTATGAG 58.994 41.667 0.00 0.00 0.00 2.90
78 79 4.985538 AGTGCCTCTGTTCCTTTTTATGA 58.014 39.130 0.00 0.00 0.00 2.15
79 80 5.241506 TCAAGTGCCTCTGTTCCTTTTTATG 59.758 40.000 0.00 0.00 0.00 1.90
80 81 5.385198 TCAAGTGCCTCTGTTCCTTTTTAT 58.615 37.500 0.00 0.00 0.00 1.40
81 82 4.787551 TCAAGTGCCTCTGTTCCTTTTTA 58.212 39.130 0.00 0.00 0.00 1.52
82 83 3.631250 TCAAGTGCCTCTGTTCCTTTTT 58.369 40.909 0.00 0.00 0.00 1.94
83 84 3.297134 TCAAGTGCCTCTGTTCCTTTT 57.703 42.857 0.00 0.00 0.00 2.27
84 85 2.952310 GTTCAAGTGCCTCTGTTCCTTT 59.048 45.455 0.00 0.00 0.00 3.11
85 86 2.173569 AGTTCAAGTGCCTCTGTTCCTT 59.826 45.455 0.00 0.00 0.00 3.36
86 87 1.771255 AGTTCAAGTGCCTCTGTTCCT 59.229 47.619 0.00 0.00 0.00 3.36
87 88 2.262423 AGTTCAAGTGCCTCTGTTCC 57.738 50.000 0.00 0.00 0.00 3.62
88 89 5.505819 GGTTTTAGTTCAAGTGCCTCTGTTC 60.506 44.000 0.00 0.00 0.00 3.18
89 90 4.338400 GGTTTTAGTTCAAGTGCCTCTGTT 59.662 41.667 0.00 0.00 0.00 3.16
90 91 3.883489 GGTTTTAGTTCAAGTGCCTCTGT 59.117 43.478 0.00 0.00 0.00 3.41
91 92 3.882888 TGGTTTTAGTTCAAGTGCCTCTG 59.117 43.478 0.00 0.00 0.00 3.35
92 93 3.883489 GTGGTTTTAGTTCAAGTGCCTCT 59.117 43.478 0.00 0.00 0.00 3.69
93 94 3.303791 CGTGGTTTTAGTTCAAGTGCCTC 60.304 47.826 0.00 0.00 0.00 4.70
94 95 2.616842 CGTGGTTTTAGTTCAAGTGCCT 59.383 45.455 0.00 0.00 0.00 4.75
95 96 2.614983 TCGTGGTTTTAGTTCAAGTGCC 59.385 45.455 0.00 0.00 0.00 5.01
96 97 3.614588 GTCGTGGTTTTAGTTCAAGTGC 58.385 45.455 0.00 0.00 0.00 4.40
97 98 3.552699 TCGTCGTGGTTTTAGTTCAAGTG 59.447 43.478 0.00 0.00 0.00 3.16
98 99 3.784338 TCGTCGTGGTTTTAGTTCAAGT 58.216 40.909 0.00 0.00 0.00 3.16
99 100 3.800506 ACTCGTCGTGGTTTTAGTTCAAG 59.199 43.478 0.00 0.00 0.00 3.02
100 101 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
101 102 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
102 103 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
103 104 6.849588 AAATTACTCGTCGTGGTTTTAGTT 57.150 33.333 0.00 0.00 0.00 2.24
104 105 7.945033 TTAAATTACTCGTCGTGGTTTTAGT 57.055 32.000 0.00 0.00 0.00 2.24
105 106 9.095529 GTTTTAAATTACTCGTCGTGGTTTTAG 57.904 33.333 0.00 0.00 0.00 1.85
106 107 7.791590 CGTTTTAAATTACTCGTCGTGGTTTTA 59.208 33.333 0.00 0.00 0.00 1.52
107 108 6.628461 CGTTTTAAATTACTCGTCGTGGTTTT 59.372 34.615 0.00 0.00 0.00 2.43
108 109 6.128729 CGTTTTAAATTACTCGTCGTGGTTT 58.871 36.000 0.00 0.79 0.00 3.27
109 110 5.333263 CCGTTTTAAATTACTCGTCGTGGTT 60.333 40.000 0.00 0.00 0.00 3.67
110 111 4.150451 CCGTTTTAAATTACTCGTCGTGGT 59.850 41.667 0.00 0.00 0.00 4.16
111 112 4.385447 TCCGTTTTAAATTACTCGTCGTGG 59.615 41.667 0.00 0.00 0.00 4.94
112 113 5.499268 TCCGTTTTAAATTACTCGTCGTG 57.501 39.130 0.00 0.00 0.00 4.35
113 114 5.920273 TCTTCCGTTTTAAATTACTCGTCGT 59.080 36.000 0.00 0.00 0.00 4.34
114 115 6.380111 TCTTCCGTTTTAAATTACTCGTCG 57.620 37.500 0.00 0.00 0.00 5.12
115 116 6.735510 GCTTCTTCCGTTTTAAATTACTCGTC 59.264 38.462 0.00 0.00 0.00 4.20
116 117 6.203338 TGCTTCTTCCGTTTTAAATTACTCGT 59.797 34.615 0.00 0.00 0.00 4.18
117 118 6.595794 TGCTTCTTCCGTTTTAAATTACTCG 58.404 36.000 0.00 0.00 0.00 4.18
118 119 7.582352 ACTGCTTCTTCCGTTTTAAATTACTC 58.418 34.615 0.00 0.00 0.00 2.59
119 120 7.506328 ACTGCTTCTTCCGTTTTAAATTACT 57.494 32.000 0.00 0.00 0.00 2.24
120 121 9.110617 GTTACTGCTTCTTCCGTTTTAAATTAC 57.889 33.333 0.00 0.00 0.00 1.89
121 122 8.011106 CGTTACTGCTTCTTCCGTTTTAAATTA 58.989 33.333 0.00 0.00 0.00 1.40
122 123 6.854381 CGTTACTGCTTCTTCCGTTTTAAATT 59.146 34.615 0.00 0.00 0.00 1.82
123 124 6.203338 TCGTTACTGCTTCTTCCGTTTTAAAT 59.797 34.615 0.00 0.00 0.00 1.40
124 125 5.523188 TCGTTACTGCTTCTTCCGTTTTAAA 59.477 36.000 0.00 0.00 0.00 1.52
125 126 5.049167 TCGTTACTGCTTCTTCCGTTTTAA 58.951 37.500 0.00 0.00 0.00 1.52
126 127 4.619973 TCGTTACTGCTTCTTCCGTTTTA 58.380 39.130 0.00 0.00 0.00 1.52
127 128 3.460103 TCGTTACTGCTTCTTCCGTTTT 58.540 40.909 0.00 0.00 0.00 2.43
128 129 3.102052 TCGTTACTGCTTCTTCCGTTT 57.898 42.857 0.00 0.00 0.00 3.60
129 130 2.806608 TCGTTACTGCTTCTTCCGTT 57.193 45.000 0.00 0.00 0.00 4.44
130 131 2.806608 TTCGTTACTGCTTCTTCCGT 57.193 45.000 0.00 0.00 0.00 4.69
131 132 4.663636 ATTTTCGTTACTGCTTCTTCCG 57.336 40.909 0.00 0.00 0.00 4.30
132 133 7.303634 TCATATTTTCGTTACTGCTTCTTCC 57.696 36.000 0.00 0.00 0.00 3.46
133 134 8.391106 ACATCATATTTTCGTTACTGCTTCTTC 58.609 33.333 0.00 0.00 0.00 2.87
134 135 8.268850 ACATCATATTTTCGTTACTGCTTCTT 57.731 30.769 0.00 0.00 0.00 2.52
135 136 7.849804 ACATCATATTTTCGTTACTGCTTCT 57.150 32.000 0.00 0.00 0.00 2.85
136 137 9.422196 GTTACATCATATTTTCGTTACTGCTTC 57.578 33.333 0.00 0.00 0.00 3.86
137 138 8.395633 GGTTACATCATATTTTCGTTACTGCTT 58.604 33.333 0.00 0.00 0.00 3.91
138 139 7.254319 CGGTTACATCATATTTTCGTTACTGCT 60.254 37.037 0.00 0.00 0.00 4.24
139 140 6.844279 CGGTTACATCATATTTTCGTTACTGC 59.156 38.462 0.00 0.00 0.00 4.40
140 141 7.902032 ACGGTTACATCATATTTTCGTTACTG 58.098 34.615 0.00 0.00 0.00 2.74
141 142 9.023967 GTACGGTTACATCATATTTTCGTTACT 57.976 33.333 0.00 0.00 0.00 2.24
142 143 7.992692 CGTACGGTTACATCATATTTTCGTTAC 59.007 37.037 7.57 0.00 0.00 2.50
143 144 7.700234 ACGTACGGTTACATCATATTTTCGTTA 59.300 33.333 21.06 0.00 0.00 3.18
144 145 6.531240 ACGTACGGTTACATCATATTTTCGTT 59.469 34.615 21.06 0.00 0.00 3.85
145 146 6.035843 ACGTACGGTTACATCATATTTTCGT 58.964 36.000 21.06 0.00 0.00 3.85
146 147 6.500775 ACGTACGGTTACATCATATTTTCG 57.499 37.500 21.06 0.00 0.00 3.46
161 162 4.074259 TGATGCAGGTATATACGTACGGT 58.926 43.478 21.06 10.38 0.00 4.83
162 163 4.690184 TGATGCAGGTATATACGTACGG 57.310 45.455 21.06 1.43 0.00 4.02
250 251 2.128507 GGCCTGGACTACCCTCTCG 61.129 68.421 0.00 0.00 35.38 4.04
254 255 1.988406 GAACGGCCTGGACTACCCT 60.988 63.158 0.00 0.00 35.38 4.34
592 602 2.034879 GCCACCATGGTGTCGTCAG 61.035 63.158 36.62 23.84 44.02 3.51
596 606 3.055719 GTGGCCACCATGGTGTCG 61.056 66.667 36.62 25.79 44.02 4.35
632 642 0.304705 GCTACCCACATTTCGCATCG 59.695 55.000 0.00 0.00 0.00 3.84
651 664 1.803519 GCTGTCTCGAAGCCTCACG 60.804 63.158 0.00 0.00 34.45 4.35
657 670 2.564553 ATCCCGTGCTGTCTCGAAGC 62.565 60.000 0.49 0.49 41.22 3.86
912 932 0.961358 CCGAGGAGAAGACCACGAGT 60.961 60.000 0.00 0.00 44.27 4.18
923 943 4.779733 GTGGGAGGGCCGAGGAGA 62.780 72.222 0.00 0.00 33.83 3.71
930 950 2.956077 TTTTTGGGTGTGGGAGGGCC 62.956 60.000 0.00 0.00 0.00 5.80
1059 1079 1.377856 GGTGCCCTTCTTCTGGAGC 60.378 63.158 0.00 0.00 0.00 4.70
1079 1099 3.758133 GAGAGGGGCGGGAGGATGA 62.758 68.421 0.00 0.00 0.00 2.92
1123 1143 2.156774 GGATAAGGGGGCAGGGAGG 61.157 68.421 0.00 0.00 0.00 4.30
1125 1145 0.772124 GATGGATAAGGGGGCAGGGA 60.772 60.000 0.00 0.00 0.00 4.20
1128 1148 0.773700 AGGGATGGATAAGGGGGCAG 60.774 60.000 0.00 0.00 0.00 4.85
1129 1149 0.329434 AAGGGATGGATAAGGGGGCA 60.329 55.000 0.00 0.00 0.00 5.36
1130 1150 0.405973 GAAGGGATGGATAAGGGGGC 59.594 60.000 0.00 0.00 0.00 5.80
1168 1197 4.051922 GGCGTCATCCATCTAACAGTAAG 58.948 47.826 0.00 0.00 0.00 2.34
1181 1215 4.162690 AAGAGGGCGGCGTCATCC 62.163 66.667 29.75 12.09 0.00 3.51
1329 1363 4.709250 GAGAAGAGAAACACAAGGGAGTT 58.291 43.478 0.00 0.00 0.00 3.01
1361 1395 1.151668 GTCATCATGCGGCATCCTAC 58.848 55.000 13.53 5.58 0.00 3.18
1376 1432 0.955428 ACAAACGCCGCATCAGTCAT 60.955 50.000 0.00 0.00 0.00 3.06
1556 1613 6.948228 CGTAAAACTATGATGACGAACTTGTG 59.052 38.462 0.00 0.00 32.20 3.33
1831 1920 5.741388 AGTTTGTGCAAGAGAAACTACAG 57.259 39.130 10.92 0.00 44.30 2.74
1863 1952 9.547753 TGAGAGTTGGAATATTATAGCAAGAAC 57.452 33.333 0.00 0.00 0.00 3.01
1881 1970 5.222631 GCCTAAAATTGTTGGTGAGAGTTG 58.777 41.667 0.00 0.00 0.00 3.16
2132 4654 2.961741 CAGTAGCAGGCTAGAATCTGGA 59.038 50.000 0.32 0.00 0.00 3.86
2778 5304 1.977854 TGATGCACACAAGTAGGGAGT 59.022 47.619 0.00 0.00 0.00 3.85
2865 5392 3.202818 TCCCTATCAATGCCAGAACACAT 59.797 43.478 0.00 0.00 0.00 3.21
2904 5431 9.708092 AATCTCTAGGTTTTCTACAAACACTAC 57.292 33.333 0.25 0.00 32.04 2.73
2922 5449 4.202264 ACCGATGGCAGGTAAAATCTCTAG 60.202 45.833 0.00 0.00 40.80 2.43
2930 5457 0.676466 CAGCACCGATGGCAGGTAAA 60.676 55.000 0.00 0.00 40.59 2.01
2947 5474 5.283717 GTGCGTAAATCATTAACAAGTGCAG 59.716 40.000 0.00 0.00 0.00 4.41
2984 5511 4.508124 GTGCAATAGTCTCAATAGTTCCCG 59.492 45.833 0.00 0.00 0.00 5.14
3068 5595 7.452880 TTGAAACAGAAGGATTTGACATAGG 57.547 36.000 0.00 0.00 0.00 2.57
3077 5604 6.266103 TGAAGATTGCTTGAAACAGAAGGATT 59.734 34.615 0.00 0.00 33.61 3.01
3166 5693 4.344679 TGCTTTCCAGGTTCACAAATCAAT 59.655 37.500 0.00 0.00 0.00 2.57
3298 5836 3.948196 GTTGGTAACGCAACAGTTGTA 57.052 42.857 14.88 0.00 42.51 2.41
3371 5910 4.400251 GCCTCATTCTGATGACCATCAAAA 59.600 41.667 13.02 7.55 46.10 2.44
3460 5999 0.037303 ACTGAGTGGCCACCTGAATG 59.963 55.000 32.29 17.83 0.00 2.67
3557 6096 5.452216 GCCATATCTTTCATTGTGCAATGGA 60.452 40.000 20.58 12.39 46.08 3.41
3647 6214 2.567615 GCTTTGGGGTGAGTCTCTCTAA 59.432 50.000 0.65 0.00 0.00 2.10
3649 6216 0.980423 GCTTTGGGGTGAGTCTCTCT 59.020 55.000 0.65 0.00 0.00 3.10
3650 6217 0.687354 TGCTTTGGGGTGAGTCTCTC 59.313 55.000 0.65 0.00 0.00 3.20
3664 6233 0.990374 AGGTGAGAGATGGCTGCTTT 59.010 50.000 0.00 0.00 0.00 3.51
4053 6624 8.896320 TTAACTAGCAAGTACATGTTCTCAAA 57.104 30.769 2.30 0.00 33.75 2.69
4076 6647 6.588756 CGTCATAAGCTTGGTGTAAGAGTTTA 59.411 38.462 9.86 0.00 38.76 2.01
4167 6739 1.271597 ACCCATGTTCCTGCTTCACTC 60.272 52.381 0.00 0.00 0.00 3.51
4285 6857 2.401351 GCAGCAAAAAGGAAGAAGCAG 58.599 47.619 0.00 0.00 0.00 4.24
4286 6858 1.069049 GGCAGCAAAAAGGAAGAAGCA 59.931 47.619 0.00 0.00 0.00 3.91
4287 6859 1.788258 GGCAGCAAAAAGGAAGAAGC 58.212 50.000 0.00 0.00 0.00 3.86
4290 6862 1.202758 TCTCGGCAGCAAAAAGGAAGA 60.203 47.619 0.00 0.00 0.00 2.87
4907 7550 4.261801 ACAGCTTCAGTACAAAGTTGTGT 58.738 39.130 21.40 13.80 43.64 3.72
4908 7551 4.882671 ACAGCTTCAGTACAAAGTTGTG 57.117 40.909 21.40 13.36 43.64 3.33
4922 7565 6.074088 CGATCCATATTACTTGTCACAGCTTC 60.074 42.308 0.00 0.00 0.00 3.86
4926 7569 6.422100 CCTTCGATCCATATTACTTGTCACAG 59.578 42.308 0.00 0.00 0.00 3.66
5011 7666 3.976793 TCTCACGGTTATCGGATACAC 57.023 47.619 0.00 0.38 44.45 2.90
5077 7733 3.642503 CCCTACCCCACCACGCAA 61.643 66.667 0.00 0.00 0.00 4.85
5103 7759 6.016693 CACAATGTATGTTAAGTGTTCCACCA 60.017 38.462 0.00 0.00 41.46 4.17
5132 7788 3.750130 CCAGTATTGCCTATCATCACTGC 59.250 47.826 0.00 0.00 36.39 4.40
5133 7789 5.219343 TCCAGTATTGCCTATCATCACTG 57.781 43.478 0.00 0.00 36.96 3.66
5179 7918 6.842437 TCTATCAAGGAGATACTGCCATAC 57.158 41.667 0.00 0.00 38.19 2.39
5375 8189 1.349542 TGGTGCCTGTGGTTGTAGGT 61.350 55.000 0.00 0.00 36.44 3.08
5487 8301 0.937441 TCCTCCCTCTACTCCAGCAT 59.063 55.000 0.00 0.00 0.00 3.79
5568 8388 3.306364 CCCACACAACCAAAACAGTTTCA 60.306 43.478 0.00 0.00 0.00 2.69
5569 8389 3.258228 CCCACACAACCAAAACAGTTTC 58.742 45.455 0.00 0.00 0.00 2.78
5650 8727 4.996122 CAGAGCATATCAGGTGGAAATCTC 59.004 45.833 0.00 0.00 0.00 2.75
5703 8780 0.768221 AGTCCCAAGAGAAGCACCCA 60.768 55.000 0.00 0.00 0.00 4.51
5712 8789 9.610705 CATGAATTCCATATATAGTCCCAAGAG 57.389 37.037 2.27 0.00 33.31 2.85
5816 8893 5.221048 GCTGAATTTGCATATCCGTAACCTT 60.221 40.000 0.00 0.00 0.00 3.50
5962 9051 0.541530 AGCAGAGGTCAGAGAGCACA 60.542 55.000 0.00 0.00 31.89 4.57
6159 9253 2.034048 GATCCTTCCCTCGGGCTGAC 62.034 65.000 0.00 0.00 34.68 3.51
6384 9492 6.766467 ACAGGAGATTTTACGAACTTCTGTTT 59.234 34.615 0.00 0.00 43.86 2.83
6480 9588 0.586319 AACACGCACACAAGATTCGG 59.414 50.000 0.00 0.00 0.00 4.30
6525 9635 4.690280 CCCACGCATTCTTAAAAGCAAAAT 59.310 37.500 0.00 0.00 0.00 1.82
6620 9733 1.294459 GGCCTAACGGAACCGAAGT 59.706 57.895 20.14 7.10 42.83 3.01
6632 9745 0.704076 AACCATCAGCAAGGGCCTAA 59.296 50.000 6.41 0.00 42.56 2.69
6700 9813 4.093011 AGGTACAGCAAATATTTTGCCCA 58.907 39.130 18.48 4.52 45.98 5.36
6898 10046 0.247185 ATTTGGCAGCATGGGAAACG 59.753 50.000 0.00 0.00 35.86 3.60
6899 10047 1.275856 TCATTTGGCAGCATGGGAAAC 59.724 47.619 8.43 0.00 35.86 2.78
7105 10270 1.064314 ACAAAACTGTGCCTACCACCA 60.064 47.619 0.00 0.00 44.01 4.17
7111 10276 1.133945 TGCTGGACAAAACTGTGCCTA 60.134 47.619 0.00 0.00 0.00 3.93
7113 10278 0.459489 TTGCTGGACAAAACTGTGCC 59.541 50.000 0.00 0.00 34.56 5.01
7131 10296 8.957466 GTTGACCTAACCTAGCTAATCAAATTT 58.043 33.333 0.00 0.00 33.01 1.82
7196 10369 9.282247 CTGATGTGAAATTCTTAATCTTTTCCG 57.718 33.333 0.00 0.00 0.00 4.30
7212 10385 1.522668 CCAAGGCGACTGATGTGAAA 58.477 50.000 0.00 0.00 42.68 2.69
7217 10390 0.742281 CTGACCCAAGGCGACTGATG 60.742 60.000 0.00 0.00 42.68 3.07


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

AutoCloner maintained by Alex Coulton.