Multiple sequence alignment - TraesCS3D01G283400

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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 TraesCS3D01G283400 chr3D 100.000 2777 0 0 1 2777 391638905 391636129 0.000000e+00 5129.0
1 TraesCS3D01G283400 chr3D 82.414 290 43 8 189 474 343275416 343275131 2.140000e-61 246.0
2 TraesCS3D01G283400 chr3D 82.131 291 43 9 189 475 231700861 231701146 9.940000e-60 241.0
3 TraesCS3D01G283400 chr3A 93.351 1880 94 6 929 2777 511997114 511995235 0.000000e+00 2750.0
4 TraesCS3D01G283400 chr3A 86.502 526 58 11 403 923 511998647 511998130 1.440000e-157 566.0
5 TraesCS3D01G283400 chr3B 91.545 1230 65 14 1552 2751 508757108 508755888 0.000000e+00 1659.0
6 TraesCS3D01G283400 chr3B 95.327 642 21 2 881 1513 508759270 508758629 0.000000e+00 1011.0
7 TraesCS3D01G283400 chr3B 89.778 675 57 9 149 819 508763068 508762402 0.000000e+00 854.0
8 TraesCS3D01G283400 chr1A 84.451 328 44 5 155 477 167216749 167216424 1.610000e-82 316.0
9 TraesCS3D01G283400 chr5A 83.793 290 42 5 187 474 562425821 562426107 1.270000e-68 270.0
10 TraesCS3D01G283400 chr5A 80.903 288 46 9 192 475 379960506 379960224 4.660000e-53 219.0
11 TraesCS3D01G283400 chr5A 90.385 156 13 2 1 155 381796194 381796040 1.300000e-48 204.0
12 TraesCS3D01G283400 chr5A 78.853 279 44 13 525 795 480388294 480388023 1.020000e-39 174.0
13 TraesCS3D01G283400 chr6B 80.282 355 54 14 476 819 623177756 623178105 1.280000e-63 254.0
14 TraesCS3D01G283400 chr6B 76.202 416 88 10 479 888 57579394 57579804 2.800000e-50 209.0
15 TraesCS3D01G283400 chr6B 86.957 138 16 2 1 137 226376054 226375918 1.330000e-33 154.0
16 TraesCS3D01G283400 chr5B 80.122 327 58 7 496 819 455754925 455754603 1.290000e-58 237.0
17 TraesCS3D01G283400 chr2B 81.100 291 47 8 187 474 382463775 382463490 2.780000e-55 226.0
18 TraesCS3D01G283400 chr2B 91.667 48 4 0 495 542 496076380 496076333 1.780000e-07 67.6
19 TraesCS3D01G283400 chr2D 81.295 278 45 7 199 474 314254451 314254179 4.660000e-53 219.0
20 TraesCS3D01G283400 chr2D 79.511 327 50 14 155 474 71612742 71612426 1.670000e-52 217.0
21 TraesCS3D01G283400 chr1D 80.345 290 48 9 528 812 437903391 437903676 7.790000e-51 211.0
22 TraesCS3D01G283400 chr1D 79.389 131 18 9 496 621 413660589 413660463 1.770000e-12 84.2
23 TraesCS3D01G283400 chr1D 93.878 49 3 0 494 542 416406925 416406973 1.070000e-09 75.0
24 TraesCS3D01G283400 chr1B 80.135 297 46 8 527 812 336073401 336073107 2.800000e-50 209.0
25 TraesCS3D01G283400 chr5D 75.750 400 71 20 476 868 547453738 547454118 7.900000e-41 178.0
26 TraesCS3D01G283400 chr7B 81.457 151 24 4 7 155 505358003 505357855 1.350000e-23 121.0
27 TraesCS3D01G283400 chr2A 87.500 64 8 0 479 542 733449345 733449282 1.070000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G283400 chr3D 391636129 391638905 2776 True 5129.000000 5129 100.000000 1 2777 1 chr3D.!!$R2 2776
1 TraesCS3D01G283400 chr3A 511995235 511998647 3412 True 1658.000000 2750 89.926500 403 2777 2 chr3A.!!$R1 2374
2 TraesCS3D01G283400 chr3B 508755888 508763068 7180 True 1174.666667 1659 92.216667 149 2751 3 chr3B.!!$R1 2602

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
50 51 0.037590 TTGCTTCTTGGGCCGTACAT 59.962 50.0 0.00 0.00 0.0 2.29 F
209 211 0.109342 CAAAGGCCTGAGTCTGGTGT 59.891 55.0 5.69 2.66 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 5361 0.617820 GGAGGTAGTCCCAGCCAAGA 60.618 60.0 0.0 0.0 39.88 3.02 R
2186 7808 0.037326 GTGGACGACAGAATGGAGCA 60.037 55.0 0.0 0.0 43.62 4.26 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.650647 TCTTGGGCATGACAGGAAC 57.349 52.632 0.00 0.00 0.00 3.62
19 20 0.321564 TCTTGGGCATGACAGGAACG 60.322 55.000 0.00 0.00 0.00 3.95
20 21 1.303236 TTGGGCATGACAGGAACGG 60.303 57.895 0.00 0.00 0.00 4.44
21 22 2.438434 GGGCATGACAGGAACGGG 60.438 66.667 0.00 0.00 0.00 5.28
22 23 2.351276 GGCATGACAGGAACGGGT 59.649 61.111 0.00 0.00 0.00 5.28
23 24 1.303317 GGCATGACAGGAACGGGTT 60.303 57.895 0.00 0.00 0.00 4.11
24 25 1.586154 GGCATGACAGGAACGGGTTG 61.586 60.000 0.00 0.00 0.00 3.77
25 26 0.605319 GCATGACAGGAACGGGTTGA 60.605 55.000 0.00 0.00 0.00 3.18
26 27 1.890876 CATGACAGGAACGGGTTGAA 58.109 50.000 0.00 0.00 0.00 2.69
27 28 1.806542 CATGACAGGAACGGGTTGAAG 59.193 52.381 0.00 0.00 0.00 3.02
28 29 1.124780 TGACAGGAACGGGTTGAAGA 58.875 50.000 0.00 0.00 0.00 2.87
29 30 1.697432 TGACAGGAACGGGTTGAAGAT 59.303 47.619 0.00 0.00 0.00 2.40
30 31 2.105821 TGACAGGAACGGGTTGAAGATT 59.894 45.455 0.00 0.00 0.00 2.40
31 32 3.146847 GACAGGAACGGGTTGAAGATTT 58.853 45.455 0.00 0.00 0.00 2.17
32 33 3.562182 ACAGGAACGGGTTGAAGATTTT 58.438 40.909 0.00 0.00 0.00 1.82
33 34 3.317993 ACAGGAACGGGTTGAAGATTTTG 59.682 43.478 0.00 0.00 0.00 2.44
34 35 2.296190 AGGAACGGGTTGAAGATTTTGC 59.704 45.455 0.00 0.00 0.00 3.68
35 36 2.296190 GGAACGGGTTGAAGATTTTGCT 59.704 45.455 0.00 0.00 0.00 3.91
36 37 3.243737 GGAACGGGTTGAAGATTTTGCTT 60.244 43.478 0.00 0.00 0.00 3.91
37 38 3.643159 ACGGGTTGAAGATTTTGCTTC 57.357 42.857 0.00 0.00 43.53 3.86
38 39 3.222603 ACGGGTTGAAGATTTTGCTTCT 58.777 40.909 0.00 0.00 43.60 2.85
39 40 3.636764 ACGGGTTGAAGATTTTGCTTCTT 59.363 39.130 0.00 0.00 43.60 2.52
40 41 3.983344 CGGGTTGAAGATTTTGCTTCTTG 59.017 43.478 0.00 0.00 43.60 3.02
41 42 4.309933 GGGTTGAAGATTTTGCTTCTTGG 58.690 43.478 0.00 0.00 43.60 3.61
42 43 4.309933 GGTTGAAGATTTTGCTTCTTGGG 58.690 43.478 0.00 0.00 43.60 4.12
43 44 3.665745 TGAAGATTTTGCTTCTTGGGC 57.334 42.857 0.00 0.00 43.60 5.36
44 45 2.299867 TGAAGATTTTGCTTCTTGGGCC 59.700 45.455 0.00 0.00 43.60 5.80
45 46 0.890683 AGATTTTGCTTCTTGGGCCG 59.109 50.000 0.00 0.00 0.00 6.13
46 47 0.603065 GATTTTGCTTCTTGGGCCGT 59.397 50.000 0.00 0.00 0.00 5.68
47 48 1.816224 GATTTTGCTTCTTGGGCCGTA 59.184 47.619 0.00 0.00 0.00 4.02
48 49 0.955905 TTTTGCTTCTTGGGCCGTAC 59.044 50.000 0.00 0.00 0.00 3.67
49 50 0.179015 TTTGCTTCTTGGGCCGTACA 60.179 50.000 0.00 0.00 0.00 2.90
50 51 0.037590 TTGCTTCTTGGGCCGTACAT 59.962 50.000 0.00 0.00 0.00 2.29
51 52 0.392461 TGCTTCTTGGGCCGTACATC 60.392 55.000 0.00 0.00 0.00 3.06
52 53 0.392461 GCTTCTTGGGCCGTACATCA 60.392 55.000 0.00 0.00 0.00 3.07
53 54 1.948611 GCTTCTTGGGCCGTACATCAA 60.949 52.381 0.00 0.00 0.00 2.57
54 55 2.432444 CTTCTTGGGCCGTACATCAAA 58.568 47.619 0.00 0.00 0.00 2.69
55 56 2.799126 TCTTGGGCCGTACATCAAAT 57.201 45.000 0.00 0.00 0.00 2.32
56 57 3.916359 TCTTGGGCCGTACATCAAATA 57.084 42.857 0.00 0.00 0.00 1.40
57 58 3.537580 TCTTGGGCCGTACATCAAATAC 58.462 45.455 0.00 0.00 0.00 1.89
58 59 3.199071 TCTTGGGCCGTACATCAAATACT 59.801 43.478 0.00 0.00 0.00 2.12
59 60 2.912771 TGGGCCGTACATCAAATACTG 58.087 47.619 0.00 0.00 0.00 2.74
60 61 2.502130 TGGGCCGTACATCAAATACTGA 59.498 45.455 0.00 0.00 38.81 3.41
61 62 3.135712 TGGGCCGTACATCAAATACTGAT 59.864 43.478 0.00 0.00 46.25 2.90
62 63 3.746492 GGGCCGTACATCAAATACTGATC 59.254 47.826 0.00 0.00 43.28 2.92
63 64 4.503296 GGGCCGTACATCAAATACTGATCT 60.503 45.833 0.00 0.00 43.28 2.75
64 65 5.057149 GGCCGTACATCAAATACTGATCTT 58.943 41.667 0.00 0.00 43.28 2.40
65 66 5.050091 GGCCGTACATCAAATACTGATCTTG 60.050 44.000 0.00 0.00 43.28 3.02
66 67 5.050091 GCCGTACATCAAATACTGATCTTGG 60.050 44.000 0.00 0.00 43.28 3.61
67 68 6.280643 CCGTACATCAAATACTGATCTTGGA 58.719 40.000 0.00 0.00 43.28 3.53
68 69 6.422100 CCGTACATCAAATACTGATCTTGGAG 59.578 42.308 0.00 0.00 43.28 3.86
69 70 7.203218 CGTACATCAAATACTGATCTTGGAGA 58.797 38.462 0.00 0.00 43.28 3.71
70 71 7.168302 CGTACATCAAATACTGATCTTGGAGAC 59.832 40.741 0.00 0.00 43.28 3.36
71 72 6.352516 ACATCAAATACTGATCTTGGAGACC 58.647 40.000 0.00 0.00 43.28 3.85
72 73 5.359194 TCAAATACTGATCTTGGAGACCC 57.641 43.478 0.00 0.00 0.00 4.46
73 74 4.782691 TCAAATACTGATCTTGGAGACCCA 59.217 41.667 0.00 0.00 41.64 4.51
74 75 5.104776 TCAAATACTGATCTTGGAGACCCAG 60.105 44.000 0.00 0.00 44.60 4.45
75 76 2.334006 ACTGATCTTGGAGACCCAGT 57.666 50.000 8.24 8.24 44.60 4.00
76 77 3.474798 ACTGATCTTGGAGACCCAGTA 57.525 47.619 10.97 0.00 44.60 2.74
77 78 3.370104 ACTGATCTTGGAGACCCAGTAG 58.630 50.000 10.97 0.00 44.60 2.57
78 79 3.011821 ACTGATCTTGGAGACCCAGTAGA 59.988 47.826 10.97 0.00 44.60 2.59
79 80 4.026744 CTGATCTTGGAGACCCAGTAGAA 58.973 47.826 0.00 0.00 44.60 2.10
80 81 4.624913 TGATCTTGGAGACCCAGTAGAAT 58.375 43.478 0.00 0.00 44.60 2.40
81 82 4.651503 TGATCTTGGAGACCCAGTAGAATC 59.348 45.833 0.00 0.00 44.60 2.52
82 83 4.338795 TCTTGGAGACCCAGTAGAATCT 57.661 45.455 0.00 0.00 44.60 2.40
83 84 4.689062 TCTTGGAGACCCAGTAGAATCTT 58.311 43.478 0.00 0.00 44.60 2.40
84 85 4.467795 TCTTGGAGACCCAGTAGAATCTTG 59.532 45.833 0.00 0.00 44.60 3.02
85 86 4.061131 TGGAGACCCAGTAGAATCTTGA 57.939 45.455 0.00 0.00 37.58 3.02
86 87 4.026744 TGGAGACCCAGTAGAATCTTGAG 58.973 47.826 0.00 0.00 37.58 3.02
87 88 3.386402 GGAGACCCAGTAGAATCTTGAGG 59.614 52.174 0.00 0.00 0.00 3.86
88 89 4.282496 GAGACCCAGTAGAATCTTGAGGA 58.718 47.826 0.00 0.00 0.00 3.71
89 90 4.889780 AGACCCAGTAGAATCTTGAGGAT 58.110 43.478 0.00 0.00 35.97 3.24
90 91 4.898861 AGACCCAGTAGAATCTTGAGGATC 59.101 45.833 0.00 0.00 32.76 3.36
104 105 4.732672 TGAGGATCAGTCACATCAAGAG 57.267 45.455 0.00 0.00 42.56 2.85
105 106 4.347607 TGAGGATCAGTCACATCAAGAGA 58.652 43.478 0.00 0.00 42.56 3.10
106 107 4.961099 TGAGGATCAGTCACATCAAGAGAT 59.039 41.667 0.00 0.00 42.56 2.75
107 108 5.424573 TGAGGATCAGTCACATCAAGAGATT 59.575 40.000 0.00 0.00 42.56 2.40
108 109 6.070366 TGAGGATCAGTCACATCAAGAGATTT 60.070 38.462 0.00 0.00 42.56 2.17
109 110 6.114089 AGGATCAGTCACATCAAGAGATTTG 58.886 40.000 0.00 0.00 34.07 2.32
110 111 5.220815 GGATCAGTCACATCAAGAGATTTGC 60.221 44.000 0.00 0.00 33.06 3.68
111 112 4.644498 TCAGTCACATCAAGAGATTTGCA 58.356 39.130 0.00 0.00 33.06 4.08
112 113 5.065235 TCAGTCACATCAAGAGATTTGCAA 58.935 37.500 0.00 0.00 33.06 4.08
113 114 5.532032 TCAGTCACATCAAGAGATTTGCAAA 59.468 36.000 15.44 15.44 33.06 3.68
114 115 6.208007 TCAGTCACATCAAGAGATTTGCAAAT 59.792 34.615 24.33 24.33 33.06 2.32
115 116 6.866770 CAGTCACATCAAGAGATTTGCAAATT 59.133 34.615 24.81 14.80 33.06 1.82
116 117 7.384115 CAGTCACATCAAGAGATTTGCAAATTT 59.616 33.333 24.81 19.75 33.06 1.82
117 118 7.597743 AGTCACATCAAGAGATTTGCAAATTTC 59.402 33.333 27.05 27.05 33.06 2.17
118 119 6.869913 TCACATCAAGAGATTTGCAAATTTCC 59.130 34.615 29.29 19.48 33.06 3.13
119 120 6.872020 CACATCAAGAGATTTGCAAATTTCCT 59.128 34.615 29.29 20.74 31.79 3.36
120 121 7.063074 CACATCAAGAGATTTGCAAATTTCCTC 59.937 37.037 29.29 25.82 31.79 3.71
121 122 6.653526 TCAAGAGATTTGCAAATTTCCTCA 57.346 33.333 29.29 16.04 31.79 3.86
122 123 6.684686 TCAAGAGATTTGCAAATTTCCTCAG 58.315 36.000 29.29 22.35 31.79 3.35
123 124 5.069501 AGAGATTTGCAAATTTCCTCAGC 57.930 39.130 29.29 14.63 31.79 4.26
124 125 4.525487 AGAGATTTGCAAATTTCCTCAGCA 59.475 37.500 29.29 0.66 31.79 4.41
125 126 4.817517 AGATTTGCAAATTTCCTCAGCAG 58.182 39.130 24.81 0.00 36.47 4.24
126 127 4.282703 AGATTTGCAAATTTCCTCAGCAGT 59.717 37.500 24.81 0.00 36.47 4.40
127 128 3.374220 TTGCAAATTTCCTCAGCAGTG 57.626 42.857 0.00 0.00 36.47 3.66
128 129 1.614903 TGCAAATTTCCTCAGCAGTGG 59.385 47.619 0.00 0.00 0.00 4.00
129 130 1.670967 GCAAATTTCCTCAGCAGTGGC 60.671 52.381 0.00 0.00 41.61 5.01
130 131 1.614903 CAAATTTCCTCAGCAGTGGCA 59.385 47.619 0.00 0.00 44.61 4.92
131 132 1.542492 AATTTCCTCAGCAGTGGCAG 58.458 50.000 0.00 0.00 44.61 4.85
132 133 0.403271 ATTTCCTCAGCAGTGGCAGT 59.597 50.000 0.00 0.00 44.61 4.40
133 134 0.183492 TTTCCTCAGCAGTGGCAGTT 59.817 50.000 0.00 0.00 44.61 3.16
134 135 0.535780 TTCCTCAGCAGTGGCAGTTG 60.536 55.000 0.00 0.00 44.61 3.16
135 136 1.970114 CCTCAGCAGTGGCAGTTGG 60.970 63.158 0.00 0.00 44.61 3.77
136 137 1.071987 CTCAGCAGTGGCAGTTGGA 59.928 57.895 0.00 0.00 44.61 3.53
137 138 0.954449 CTCAGCAGTGGCAGTTGGAG 60.954 60.000 0.00 0.00 44.61 3.86
138 139 2.282040 AGCAGTGGCAGTTGGAGC 60.282 61.111 0.00 0.00 44.61 4.70
139 140 2.595463 GCAGTGGCAGTTGGAGCA 60.595 61.111 0.00 0.00 40.72 4.26
140 141 2.623915 GCAGTGGCAGTTGGAGCAG 61.624 63.158 0.00 0.00 40.72 4.24
141 142 1.228063 CAGTGGCAGTTGGAGCAGT 60.228 57.895 0.00 0.00 0.00 4.40
142 143 1.228063 AGTGGCAGTTGGAGCAGTG 60.228 57.895 0.00 0.00 0.00 3.66
143 144 1.526917 GTGGCAGTTGGAGCAGTGT 60.527 57.895 0.00 0.00 0.00 3.55
144 145 1.227943 TGGCAGTTGGAGCAGTGTC 60.228 57.895 0.00 0.00 0.00 3.67
145 146 1.072159 GGCAGTTGGAGCAGTGTCT 59.928 57.895 0.00 0.00 0.00 3.41
146 147 1.233285 GGCAGTTGGAGCAGTGTCTG 61.233 60.000 0.00 0.00 34.12 3.51
147 148 0.533755 GCAGTTGGAGCAGTGTCTGT 60.534 55.000 0.00 0.00 33.43 3.41
148 149 1.270305 GCAGTTGGAGCAGTGTCTGTA 60.270 52.381 0.00 0.00 33.43 2.74
149 150 2.613977 GCAGTTGGAGCAGTGTCTGTAT 60.614 50.000 0.00 0.00 33.43 2.29
150 151 3.257393 CAGTTGGAGCAGTGTCTGTATC 58.743 50.000 0.00 0.00 33.43 2.24
151 152 3.056250 CAGTTGGAGCAGTGTCTGTATCT 60.056 47.826 0.00 0.00 33.43 1.98
152 153 3.056250 AGTTGGAGCAGTGTCTGTATCTG 60.056 47.826 0.00 0.00 33.43 2.90
167 168 6.818644 GTCTGTATCTGCTTTGGATCACTTTA 59.181 38.462 0.00 0.00 0.00 1.85
176 177 8.458573 TGCTTTGGATCACTTTAGAAAAGTTA 57.541 30.769 2.36 0.00 0.00 2.24
209 211 0.109342 CAAAGGCCTGAGTCTGGTGT 59.891 55.000 5.69 2.66 0.00 4.16
210 212 0.109342 AAAGGCCTGAGTCTGGTGTG 59.891 55.000 5.69 0.00 0.00 3.82
213 215 1.963338 GCCTGAGTCTGGTGTGTGC 60.963 63.158 16.61 0.00 0.00 4.57
219 221 1.331756 GAGTCTGGTGTGTGCAACTTG 59.668 52.381 0.00 0.00 38.04 3.16
222 224 0.381801 CTGGTGTGTGCAACTTGTCC 59.618 55.000 0.00 0.00 38.04 4.02
224 226 1.092921 GGTGTGTGCAACTTGTCCGA 61.093 55.000 0.00 0.00 38.04 4.55
273 275 2.358737 CAAGTCCACGGACAGGCC 60.359 66.667 18.21 0.00 46.76 5.19
284 286 1.472728 CGGACAGGCCAACATACCTAC 60.473 57.143 5.01 0.00 33.38 3.18
293 295 4.076394 GCCAACATACCTACAAAGACCAA 58.924 43.478 0.00 0.00 0.00 3.67
359 361 2.161808 TGCAACGAACTTGGAAAAACGA 59.838 40.909 0.00 0.00 0.00 3.85
366 368 5.202640 CGAACTTGGAAAAACGAGTAAAGG 58.797 41.667 0.00 0.00 34.00 3.11
369 371 1.874872 TGGAAAAACGAGTAAAGGCCG 59.125 47.619 0.00 0.00 0.00 6.13
386 388 2.622942 GGCCGAAAATTATGCATGGAGA 59.377 45.455 10.16 0.00 0.00 3.71
390 392 5.737063 GCCGAAAATTATGCATGGAGAACAT 60.737 40.000 10.16 0.00 41.57 2.71
539 541 3.327404 TCCCCTCCCGTTGAAGCC 61.327 66.667 0.00 0.00 0.00 4.35
543 545 0.825840 CCCTCCCGTTGAAGCCAAAA 60.826 55.000 0.00 0.00 33.49 2.44
544 546 0.313987 CCTCCCGTTGAAGCCAAAAC 59.686 55.000 0.00 0.00 33.49 2.43
546 548 1.681264 CTCCCGTTGAAGCCAAAACTT 59.319 47.619 0.00 0.00 33.49 2.66
547 549 1.407258 TCCCGTTGAAGCCAAAACTTG 59.593 47.619 0.00 0.00 33.49 3.16
548 550 1.407258 CCCGTTGAAGCCAAAACTTGA 59.593 47.619 0.00 0.00 33.49 3.02
549 551 2.459934 CCGTTGAAGCCAAAACTTGAC 58.540 47.619 0.00 0.00 33.49 3.18
568 570 2.483745 GCTCGTCATCGTCGACCA 59.516 61.111 10.58 0.00 38.33 4.02
575 577 2.607187 GTCATCGTCGACCAATTGACT 58.393 47.619 19.40 0.00 37.12 3.41
585 587 2.749621 GACCAATTGACTGCTTGTAGGG 59.250 50.000 7.12 0.00 0.00 3.53
645 647 0.389817 CGAACATGAGAAGCGGGTGA 60.390 55.000 0.00 0.00 0.00 4.02
665 667 3.004419 TGACGGCGATCATTTAGACTAGG 59.996 47.826 16.62 0.00 0.00 3.02
884 3957 4.238514 GACTCCTATATCAATGTCCGCAC 58.761 47.826 0.00 0.00 0.00 5.34
901 3974 3.374402 CACTGGTCCCGCTCGACT 61.374 66.667 0.75 0.00 33.07 4.18
949 5032 6.704310 CATCCCCAAAAGAACATCAGATTTT 58.296 36.000 0.00 0.00 0.00 1.82
963 5046 7.833786 ACATCAGATTTTGTAAGCATTCACAT 58.166 30.769 0.00 0.00 0.00 3.21
1099 5182 1.203313 TGCTAGTCTTCCCACCTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
1246 5329 2.434185 GCCGAATCGCCTCACACA 60.434 61.111 0.00 0.00 0.00 3.72
1257 5340 3.895041 TCGCCTCACACATATCCATTCTA 59.105 43.478 0.00 0.00 0.00 2.10
1341 5424 2.586792 GGATGCGGCTTCTCCTGT 59.413 61.111 14.51 0.00 0.00 4.00
1473 5556 0.454600 CTACGCAGCTCCTAAACGGA 59.545 55.000 0.00 0.00 40.30 4.69
1482 5565 2.025898 CTCCTAAACGGACTCCTCTCC 58.974 57.143 0.00 0.00 36.69 3.71
1507 5590 2.388735 TCTCCGAGCAGGTACATGATT 58.611 47.619 12.53 0.00 41.99 2.57
1520 5603 6.656693 CAGGTACATGATTTGGTCTTCTTCTT 59.343 38.462 0.00 0.00 0.00 2.52
1580 7176 3.735820 CGAACCATATTGCAGCAATGCTT 60.736 43.478 27.91 14.05 36.40 3.91
1650 7246 2.582052 GTGTTGGATGTGAAGTGGGAA 58.418 47.619 0.00 0.00 0.00 3.97
1842 7438 3.338249 TCACATTCCTGCTTACTTGCTC 58.662 45.455 0.00 0.00 0.00 4.26
1845 7441 2.370281 TTCCTGCTTACTTGCTCTCG 57.630 50.000 0.00 0.00 0.00 4.04
1852 7448 5.333299 TGCTTACTTGCTCTCGGTTTATA 57.667 39.130 0.00 0.00 0.00 0.98
1863 7459 6.127842 TGCTCTCGGTTTATAATTTTGGAACC 60.128 38.462 0.00 0.00 37.10 3.62
1866 7462 9.338622 CTCTCGGTTTATAATTTTGGAACCTAT 57.661 33.333 11.40 0.00 38.04 2.57
1887 7483 9.839185 ACCTATAACTGTTATACATCCTACCAT 57.161 33.333 14.61 0.00 0.00 3.55
1893 7489 8.045720 ACTGTTATACATCCTACCATGGAATT 57.954 34.615 21.47 0.00 39.85 2.17
1909 7505 4.415596 TGGAATTAAACCAGCATCCTGTT 58.584 39.130 1.37 0.00 37.38 3.16
1913 7509 2.215942 AAACCAGCATCCTGTTACCC 57.784 50.000 0.00 0.00 37.38 3.69
1943 7539 3.092301 TCGAGAGAGTGGATGTGTGAAT 58.908 45.455 0.00 0.00 34.84 2.57
1948 7544 6.638873 CGAGAGAGTGGATGTGTGAATAATAC 59.361 42.308 0.00 0.00 0.00 1.89
1955 7551 7.012704 AGTGGATGTGTGAATAATACAAGATGC 59.987 37.037 0.00 0.00 0.00 3.91
2011 7630 3.637998 AGCATGTTCTGTTTGCTCTTG 57.362 42.857 0.00 0.00 42.88 3.02
2122 7744 2.168313 TGCACATACGTGATCTGTCCAT 59.832 45.455 0.00 0.00 46.80 3.41
2186 7808 2.972713 TCCTGACCAAGAAACTACAGCT 59.027 45.455 0.00 0.00 0.00 4.24
2200 7822 0.390866 ACAGCTGCTCCATTCTGTCG 60.391 55.000 15.27 0.00 35.05 4.35
2206 7828 0.247736 GCTCCATTCTGTCGTCCACT 59.752 55.000 0.00 0.00 0.00 4.00
2211 7833 2.354103 CCATTCTGTCGTCCACTGATGT 60.354 50.000 0.00 0.00 33.30 3.06
2234 7862 4.515361 AGAATGCTTCAGATCTTCACCTG 58.485 43.478 0.00 0.00 0.00 4.00
2252 7880 2.229543 CCTGCACAATTAAAGCTGCTCA 59.770 45.455 1.00 0.00 0.00 4.26
2253 7881 3.119245 CCTGCACAATTAAAGCTGCTCAT 60.119 43.478 1.00 0.00 0.00 2.90
2260 7888 3.302365 TTAAAGCTGCTCATGTTTGGC 57.698 42.857 1.00 0.00 0.00 4.52
2274 7902 1.394917 GTTTGGCGACTCTGCATACAG 59.605 52.381 0.00 0.00 45.95 2.74
2295 7923 3.993081 AGCGCATCATGTTAAGCTATCTC 59.007 43.478 11.47 0.00 32.73 2.75
2307 7935 2.524306 AGCTATCTCATCTCTTCGGGG 58.476 52.381 0.00 0.00 0.00 5.73
2353 7982 5.104693 TGTCCAGTAGTTCCTGAACAGAAAA 60.105 40.000 12.21 0.00 43.47 2.29
2383 8012 4.321452 CCTGCTGTTTAATGACATTGCAGT 60.321 41.667 24.49 0.51 42.57 4.40
2388 8017 7.871973 TGCTGTTTAATGACATTGCAGTTTTAT 59.128 29.630 20.28 0.00 30.31 1.40
2446 8075 5.357257 GTTCTGTTGACTTTGGAGTACTGA 58.643 41.667 0.00 0.00 35.88 3.41
2459 8088 5.245531 TGGAGTACTGATTTTGCTAAGTGG 58.754 41.667 0.00 0.00 0.00 4.00
2529 8158 4.832248 TGTAGGATCCATGTGAACAGTTC 58.168 43.478 15.82 6.32 0.00 3.01
2543 8172 4.421058 GAACAGTTCCCAGTTCAAAACAC 58.579 43.478 1.29 0.00 42.72 3.32
2625 8254 1.688735 TCCTTCGTCCATGCATAGGAG 59.311 52.381 15.50 10.98 35.42 3.69
2670 8299 8.475639 ACTAGTTTACCTACAACATCTACCATG 58.524 37.037 0.00 0.00 0.00 3.66
2721 8350 5.324832 TGTTTTCCTCTTTCCCTTCTGAT 57.675 39.130 0.00 0.00 0.00 2.90
2761 8390 7.664758 TCTTGACTAGTGTTACTTTAACTCCC 58.335 38.462 0.00 0.00 39.38 4.30
2762 8391 6.350629 TGACTAGTGTTACTTTAACTCCCC 57.649 41.667 0.00 0.00 39.38 4.81
2766 8395 1.338011 TGTTACTTTAACTCCCCGCGG 60.338 52.381 21.04 21.04 39.38 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.321564 CGTTCCTGTCATGCCCAAGA 60.322 55.000 0.00 0.00 0.00 3.02
1 2 1.308069 CCGTTCCTGTCATGCCCAAG 61.308 60.000 0.00 0.00 0.00 3.61
2 3 1.303236 CCGTTCCTGTCATGCCCAA 60.303 57.895 0.00 0.00 0.00 4.12
4 5 2.438434 CCCGTTCCTGTCATGCCC 60.438 66.667 0.00 0.00 0.00 5.36
6 7 0.605319 TCAACCCGTTCCTGTCATGC 60.605 55.000 0.00 0.00 0.00 4.06
7 8 1.806542 CTTCAACCCGTTCCTGTCATG 59.193 52.381 0.00 0.00 0.00 3.07
8 9 1.697432 TCTTCAACCCGTTCCTGTCAT 59.303 47.619 0.00 0.00 0.00 3.06
9 10 1.124780 TCTTCAACCCGTTCCTGTCA 58.875 50.000 0.00 0.00 0.00 3.58
10 11 2.474410 ATCTTCAACCCGTTCCTGTC 57.526 50.000 0.00 0.00 0.00 3.51
11 12 2.951229 AATCTTCAACCCGTTCCTGT 57.049 45.000 0.00 0.00 0.00 4.00
12 13 3.857010 GCAAAATCTTCAACCCGTTCCTG 60.857 47.826 0.00 0.00 0.00 3.86
13 14 2.296190 GCAAAATCTTCAACCCGTTCCT 59.704 45.455 0.00 0.00 0.00 3.36
14 15 2.296190 AGCAAAATCTTCAACCCGTTCC 59.704 45.455 0.00 0.00 0.00 3.62
15 16 3.643159 AGCAAAATCTTCAACCCGTTC 57.357 42.857 0.00 0.00 0.00 3.95
16 17 3.636764 AGAAGCAAAATCTTCAACCCGTT 59.363 39.130 6.33 0.00 43.64 4.44
17 18 3.222603 AGAAGCAAAATCTTCAACCCGT 58.777 40.909 6.33 0.00 43.64 5.28
18 19 3.923017 AGAAGCAAAATCTTCAACCCG 57.077 42.857 6.33 0.00 43.64 5.28
19 20 4.309933 CCAAGAAGCAAAATCTTCAACCC 58.690 43.478 6.33 0.00 43.64 4.11
20 21 4.309933 CCCAAGAAGCAAAATCTTCAACC 58.690 43.478 6.33 0.00 43.64 3.77
21 22 3.742882 GCCCAAGAAGCAAAATCTTCAAC 59.257 43.478 6.33 0.00 43.64 3.18
22 23 3.244181 GGCCCAAGAAGCAAAATCTTCAA 60.244 43.478 0.00 0.00 43.64 2.69
23 24 2.299867 GGCCCAAGAAGCAAAATCTTCA 59.700 45.455 0.00 0.00 43.64 3.02
24 25 2.672195 CGGCCCAAGAAGCAAAATCTTC 60.672 50.000 0.00 0.00 42.01 2.87
25 26 1.273327 CGGCCCAAGAAGCAAAATCTT 59.727 47.619 0.00 0.00 37.62 2.40
26 27 0.890683 CGGCCCAAGAAGCAAAATCT 59.109 50.000 0.00 0.00 0.00 2.40
27 28 0.603065 ACGGCCCAAGAAGCAAAATC 59.397 50.000 0.00 0.00 0.00 2.17
28 29 1.544246 GTACGGCCCAAGAAGCAAAAT 59.456 47.619 0.00 0.00 0.00 1.82
29 30 0.955905 GTACGGCCCAAGAAGCAAAA 59.044 50.000 0.00 0.00 0.00 2.44
30 31 0.179015 TGTACGGCCCAAGAAGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
31 32 0.037590 ATGTACGGCCCAAGAAGCAA 59.962 50.000 0.00 0.00 0.00 3.91
32 33 0.392461 GATGTACGGCCCAAGAAGCA 60.392 55.000 0.00 0.00 0.00 3.91
33 34 0.392461 TGATGTACGGCCCAAGAAGC 60.392 55.000 0.00 0.00 0.00 3.86
34 35 2.107950 TTGATGTACGGCCCAAGAAG 57.892 50.000 0.00 0.00 0.00 2.85
35 36 2.570415 TTTGATGTACGGCCCAAGAA 57.430 45.000 0.00 0.00 0.00 2.52
36 37 2.799126 ATTTGATGTACGGCCCAAGA 57.201 45.000 0.00 0.00 0.00 3.02
37 38 3.312421 CAGTATTTGATGTACGGCCCAAG 59.688 47.826 0.00 0.00 0.00 3.61
38 39 3.055021 TCAGTATTTGATGTACGGCCCAA 60.055 43.478 0.00 0.00 0.00 4.12
39 40 2.502130 TCAGTATTTGATGTACGGCCCA 59.498 45.455 0.00 0.00 0.00 5.36
40 41 3.188159 TCAGTATTTGATGTACGGCCC 57.812 47.619 0.00 0.00 0.00 5.80
41 42 4.632153 AGATCAGTATTTGATGTACGGCC 58.368 43.478 0.00 0.00 46.51 6.13
42 43 5.050091 CCAAGATCAGTATTTGATGTACGGC 60.050 44.000 0.00 0.00 46.51 5.68
43 44 6.280643 TCCAAGATCAGTATTTGATGTACGG 58.719 40.000 0.00 0.00 46.51 4.02
44 45 7.168302 GTCTCCAAGATCAGTATTTGATGTACG 59.832 40.741 0.00 0.00 46.51 3.67
45 46 7.439655 GGTCTCCAAGATCAGTATTTGATGTAC 59.560 40.741 0.00 0.00 46.51 2.90
46 47 7.419057 GGGTCTCCAAGATCAGTATTTGATGTA 60.419 40.741 0.00 0.00 46.51 2.29
47 48 6.352516 GGTCTCCAAGATCAGTATTTGATGT 58.647 40.000 0.00 0.00 46.51 3.06
48 49 5.762218 GGGTCTCCAAGATCAGTATTTGATG 59.238 44.000 0.00 0.00 46.51 3.07
49 50 5.429762 TGGGTCTCCAAGATCAGTATTTGAT 59.570 40.000 0.00 0.00 43.94 2.57
50 51 4.782691 TGGGTCTCCAAGATCAGTATTTGA 59.217 41.667 0.00 0.00 40.73 2.69
51 52 5.102953 TGGGTCTCCAAGATCAGTATTTG 57.897 43.478 0.00 0.00 40.73 2.32
52 53 4.785376 ACTGGGTCTCCAAGATCAGTATTT 59.215 41.667 11.57 0.00 43.51 1.40
53 54 4.366267 ACTGGGTCTCCAAGATCAGTATT 58.634 43.478 11.57 0.00 43.51 1.89
54 55 4.000928 ACTGGGTCTCCAAGATCAGTAT 57.999 45.455 11.57 0.00 43.51 2.12
55 56 3.474798 ACTGGGTCTCCAAGATCAGTA 57.525 47.619 11.57 0.00 43.51 2.74
56 57 2.334006 ACTGGGTCTCCAAGATCAGT 57.666 50.000 0.00 8.92 43.51 3.41
57 58 3.636679 TCTACTGGGTCTCCAAGATCAG 58.363 50.000 0.00 8.01 43.51 2.90
58 59 3.757947 TCTACTGGGTCTCCAAGATCA 57.242 47.619 0.00 0.00 43.51 2.92
59 60 4.898861 AGATTCTACTGGGTCTCCAAGATC 59.101 45.833 0.00 0.00 43.51 2.75
60 61 4.889780 AGATTCTACTGGGTCTCCAAGAT 58.110 43.478 0.00 0.00 43.51 2.40
61 62 4.338795 AGATTCTACTGGGTCTCCAAGA 57.661 45.455 0.00 0.00 43.51 3.02
62 63 4.467795 TCAAGATTCTACTGGGTCTCCAAG 59.532 45.833 0.00 0.00 43.51 3.61
63 64 4.425772 TCAAGATTCTACTGGGTCTCCAA 58.574 43.478 0.00 0.00 43.51 3.53
64 65 4.026744 CTCAAGATTCTACTGGGTCTCCA 58.973 47.826 0.00 0.00 41.58 3.86
65 66 3.386402 CCTCAAGATTCTACTGGGTCTCC 59.614 52.174 0.00 0.00 0.00 3.71
66 67 4.282496 TCCTCAAGATTCTACTGGGTCTC 58.718 47.826 0.00 0.00 0.00 3.36
67 68 4.338795 TCCTCAAGATTCTACTGGGTCT 57.661 45.455 0.00 0.00 0.00 3.85
68 69 4.651503 TGATCCTCAAGATTCTACTGGGTC 59.348 45.833 0.00 5.54 34.42 4.46
69 70 4.624913 TGATCCTCAAGATTCTACTGGGT 58.375 43.478 0.00 0.00 34.42 4.51
70 71 4.653341 ACTGATCCTCAAGATTCTACTGGG 59.347 45.833 0.00 0.00 34.42 4.45
71 72 5.362143 TGACTGATCCTCAAGATTCTACTGG 59.638 44.000 0.00 0.00 34.42 4.00
72 73 6.127507 TGTGACTGATCCTCAAGATTCTACTG 60.128 42.308 0.00 0.00 34.42 2.74
73 74 5.954752 TGTGACTGATCCTCAAGATTCTACT 59.045 40.000 0.00 0.00 34.42 2.57
74 75 6.214191 TGTGACTGATCCTCAAGATTCTAC 57.786 41.667 0.00 0.00 34.42 2.59
75 76 6.608808 TGATGTGACTGATCCTCAAGATTCTA 59.391 38.462 0.00 0.00 34.42 2.10
76 77 5.424573 TGATGTGACTGATCCTCAAGATTCT 59.575 40.000 0.00 0.00 34.42 2.40
77 78 5.668471 TGATGTGACTGATCCTCAAGATTC 58.332 41.667 0.00 0.00 34.42 2.52
78 79 5.688814 TGATGTGACTGATCCTCAAGATT 57.311 39.130 0.00 0.00 34.42 2.40
79 80 5.424573 TCTTGATGTGACTGATCCTCAAGAT 59.575 40.000 8.32 0.00 41.99 2.40
80 81 4.774200 TCTTGATGTGACTGATCCTCAAGA 59.226 41.667 8.32 8.32 43.62 3.02
81 82 5.082251 TCTTGATGTGACTGATCCTCAAG 57.918 43.478 0.00 0.00 40.42 3.02
82 83 4.774200 TCTCTTGATGTGACTGATCCTCAA 59.226 41.667 0.00 0.00 0.00 3.02
83 84 4.347607 TCTCTTGATGTGACTGATCCTCA 58.652 43.478 0.00 0.00 0.00 3.86
84 85 4.998671 TCTCTTGATGTGACTGATCCTC 57.001 45.455 0.00 0.00 0.00 3.71
85 86 5.954153 AATCTCTTGATGTGACTGATCCT 57.046 39.130 0.00 0.00 32.44 3.24
86 87 5.220815 GCAAATCTCTTGATGTGACTGATCC 60.221 44.000 0.81 0.00 39.67 3.36
87 88 5.353400 TGCAAATCTCTTGATGTGACTGATC 59.647 40.000 0.81 0.00 39.67 2.92
88 89 5.250982 TGCAAATCTCTTGATGTGACTGAT 58.749 37.500 0.81 0.00 39.67 2.90
89 90 4.644498 TGCAAATCTCTTGATGTGACTGA 58.356 39.130 0.81 0.00 39.67 3.41
90 91 5.366829 TTGCAAATCTCTTGATGTGACTG 57.633 39.130 0.00 0.00 39.67 3.51
91 92 6.585695 ATTTGCAAATCTCTTGATGTGACT 57.414 33.333 18.99 0.00 39.67 3.41
92 93 7.148689 GGAAATTTGCAAATCTCTTGATGTGAC 60.149 37.037 24.28 1.51 39.67 3.67
93 94 6.869913 GGAAATTTGCAAATCTCTTGATGTGA 59.130 34.615 24.28 0.00 39.67 3.58
94 95 6.872020 AGGAAATTTGCAAATCTCTTGATGTG 59.128 34.615 24.28 0.00 40.14 3.21
95 96 7.001099 AGGAAATTTGCAAATCTCTTGATGT 57.999 32.000 24.28 3.32 32.44 3.06
96 97 7.094631 TGAGGAAATTTGCAAATCTCTTGATG 58.905 34.615 26.78 0.00 32.44 3.07
97 98 7.235935 TGAGGAAATTTGCAAATCTCTTGAT 57.764 32.000 26.78 13.34 33.70 2.57
98 99 6.653526 TGAGGAAATTTGCAAATCTCTTGA 57.346 33.333 26.78 14.18 0.00 3.02
99 100 5.347907 GCTGAGGAAATTTGCAAATCTCTTG 59.652 40.000 26.78 21.97 0.00 3.02
100 101 5.011329 TGCTGAGGAAATTTGCAAATCTCTT 59.989 36.000 26.78 20.21 0.00 2.85
101 102 4.525487 TGCTGAGGAAATTTGCAAATCTCT 59.475 37.500 26.78 21.99 0.00 3.10
102 103 4.813027 TGCTGAGGAAATTTGCAAATCTC 58.187 39.130 24.28 23.51 0.00 2.75
103 104 4.282703 ACTGCTGAGGAAATTTGCAAATCT 59.717 37.500 24.28 16.97 33.07 2.40
104 105 4.387862 CACTGCTGAGGAAATTTGCAAATC 59.612 41.667 24.28 14.05 33.07 2.17
105 106 4.312443 CACTGCTGAGGAAATTTGCAAAT 58.688 39.130 18.99 18.99 33.07 2.32
106 107 3.493002 CCACTGCTGAGGAAATTTGCAAA 60.493 43.478 15.44 15.44 33.07 3.68
107 108 2.036217 CCACTGCTGAGGAAATTTGCAA 59.964 45.455 12.54 0.00 33.07 4.08
108 109 1.614903 CCACTGCTGAGGAAATTTGCA 59.385 47.619 12.54 6.24 0.00 4.08
109 110 1.670967 GCCACTGCTGAGGAAATTTGC 60.671 52.381 11.22 0.68 33.53 3.68
110 111 1.614903 TGCCACTGCTGAGGAAATTTG 59.385 47.619 11.22 0.00 38.71 2.32
111 112 1.891150 CTGCCACTGCTGAGGAAATTT 59.109 47.619 11.22 0.00 38.61 1.82
112 113 1.202976 ACTGCCACTGCTGAGGAAATT 60.203 47.619 11.22 0.00 39.51 1.82
113 114 0.403271 ACTGCCACTGCTGAGGAAAT 59.597 50.000 11.22 0.00 39.51 2.17
114 115 0.183492 AACTGCCACTGCTGAGGAAA 59.817 50.000 11.22 0.00 39.51 3.13
115 116 0.535780 CAACTGCCACTGCTGAGGAA 60.536 55.000 11.22 0.00 39.51 3.36
116 117 1.071987 CAACTGCCACTGCTGAGGA 59.928 57.895 11.22 0.00 39.51 3.71
117 118 1.970114 CCAACTGCCACTGCTGAGG 60.970 63.158 2.60 2.60 39.51 3.86
118 119 0.954449 CTCCAACTGCCACTGCTGAG 60.954 60.000 0.00 0.00 39.51 3.35
119 120 1.071987 CTCCAACTGCCACTGCTGA 59.928 57.895 0.00 0.00 39.51 4.26
120 121 2.623915 GCTCCAACTGCCACTGCTG 61.624 63.158 0.00 0.00 41.75 4.41
121 122 2.282040 GCTCCAACTGCCACTGCT 60.282 61.111 0.00 0.00 38.71 4.24
122 123 2.595463 TGCTCCAACTGCCACTGC 60.595 61.111 0.00 0.00 38.26 4.40
123 124 1.228063 ACTGCTCCAACTGCCACTG 60.228 57.895 0.00 0.00 0.00 3.66
124 125 1.228063 CACTGCTCCAACTGCCACT 60.228 57.895 0.00 0.00 0.00 4.00
125 126 1.510480 GACACTGCTCCAACTGCCAC 61.510 60.000 0.00 0.00 0.00 5.01
126 127 1.227943 GACACTGCTCCAACTGCCA 60.228 57.895 0.00 0.00 0.00 4.92
127 128 1.072159 AGACACTGCTCCAACTGCC 59.928 57.895 0.00 0.00 0.00 4.85
128 129 0.533755 ACAGACACTGCTCCAACTGC 60.534 55.000 0.00 0.00 34.37 4.40
129 130 2.820059 TACAGACACTGCTCCAACTG 57.180 50.000 0.00 0.00 34.37 3.16
130 131 3.056250 CAGATACAGACACTGCTCCAACT 60.056 47.826 0.00 0.00 34.37 3.16
131 132 3.257393 CAGATACAGACACTGCTCCAAC 58.743 50.000 0.00 0.00 34.37 3.77
132 133 3.599730 CAGATACAGACACTGCTCCAA 57.400 47.619 0.00 0.00 34.37 3.53
138 139 3.930336 TCCAAAGCAGATACAGACACTG 58.070 45.455 0.00 0.00 37.52 3.66
139 140 4.223700 TGATCCAAAGCAGATACAGACACT 59.776 41.667 0.00 0.00 0.00 3.55
140 141 4.331168 GTGATCCAAAGCAGATACAGACAC 59.669 45.833 0.00 0.00 0.00 3.67
141 142 4.223700 AGTGATCCAAAGCAGATACAGACA 59.776 41.667 0.00 0.00 0.00 3.41
142 143 4.764172 AGTGATCCAAAGCAGATACAGAC 58.236 43.478 0.00 0.00 0.00 3.51
143 144 5.426689 AAGTGATCCAAAGCAGATACAGA 57.573 39.130 0.00 0.00 0.00 3.41
144 145 7.044181 TCTAAAGTGATCCAAAGCAGATACAG 58.956 38.462 0.00 0.00 0.00 2.74
145 146 6.946340 TCTAAAGTGATCCAAAGCAGATACA 58.054 36.000 0.00 0.00 0.00 2.29
146 147 7.849804 TTCTAAAGTGATCCAAAGCAGATAC 57.150 36.000 0.00 0.00 0.00 2.24
147 148 8.862325 TTTTCTAAAGTGATCCAAAGCAGATA 57.138 30.769 0.00 0.00 0.00 1.98
148 149 7.449704 ACTTTTCTAAAGTGATCCAAAGCAGAT 59.550 33.333 4.14 0.00 0.00 2.90
149 150 6.772716 ACTTTTCTAAAGTGATCCAAAGCAGA 59.227 34.615 4.14 0.00 0.00 4.26
150 151 6.974965 ACTTTTCTAAAGTGATCCAAAGCAG 58.025 36.000 4.14 0.00 0.00 4.24
151 152 6.959639 ACTTTTCTAAAGTGATCCAAAGCA 57.040 33.333 4.14 0.00 0.00 3.91
152 153 8.568794 AGTAACTTTTCTAAAGTGATCCAAAGC 58.431 33.333 5.64 0.00 0.00 3.51
194 196 1.302033 CACACACCAGACTCAGGCC 60.302 63.158 0.00 0.00 0.00 5.19
198 200 0.541392 AGTTGCACACACCAGACTCA 59.459 50.000 0.00 0.00 0.00 3.41
209 211 3.003897 GGTTAAATCGGACAAGTTGCACA 59.996 43.478 1.81 0.00 0.00 4.57
210 212 3.561503 GGTTAAATCGGACAAGTTGCAC 58.438 45.455 1.81 0.00 0.00 4.57
213 215 3.150767 TGGGGTTAAATCGGACAAGTTG 58.849 45.455 0.00 0.00 0.00 3.16
219 221 3.414269 TCAAGTTGGGGTTAAATCGGAC 58.586 45.455 2.34 0.00 0.00 4.79
222 224 3.380320 GGGATCAAGTTGGGGTTAAATCG 59.620 47.826 2.34 0.00 0.00 3.34
224 226 4.692523 AGGGATCAAGTTGGGGTTAAAT 57.307 40.909 2.34 0.00 0.00 1.40
328 330 6.276847 TCCAAGTTCGTTGCACAATTTTTAT 58.723 32.000 0.00 0.00 34.45 1.40
334 336 3.791973 TTTCCAAGTTCGTTGCACAAT 57.208 38.095 0.00 0.00 34.45 2.71
336 338 3.246619 GTTTTTCCAAGTTCGTTGCACA 58.753 40.909 0.00 0.00 34.45 4.57
337 339 2.277834 CGTTTTTCCAAGTTCGTTGCAC 59.722 45.455 0.00 0.00 34.45 4.57
338 340 2.161808 TCGTTTTTCCAAGTTCGTTGCA 59.838 40.909 0.00 0.00 34.45 4.08
339 341 2.781646 CTCGTTTTTCCAAGTTCGTTGC 59.218 45.455 0.00 0.00 34.45 4.17
340 342 4.011058 ACTCGTTTTTCCAAGTTCGTTG 57.989 40.909 0.00 0.00 35.71 4.10
342 344 5.220719 CCTTTACTCGTTTTTCCAAGTTCGT 60.221 40.000 0.00 0.00 0.00 3.85
343 345 5.202640 CCTTTACTCGTTTTTCCAAGTTCG 58.797 41.667 0.00 0.00 0.00 3.95
344 346 4.974275 GCCTTTACTCGTTTTTCCAAGTTC 59.026 41.667 0.00 0.00 0.00 3.01
345 347 4.202080 GGCCTTTACTCGTTTTTCCAAGTT 60.202 41.667 0.00 0.00 0.00 2.66
359 361 5.451798 CCATGCATAATTTTCGGCCTTTACT 60.452 40.000 0.00 0.00 0.00 2.24
366 368 3.988379 TCTCCATGCATAATTTTCGGC 57.012 42.857 0.00 0.00 0.00 5.54
504 506 1.353091 GAGGAGTGGTGGTCTTCCTT 58.647 55.000 0.00 0.00 34.23 3.36
548 550 3.122971 TCGACGATGACGAGCCGT 61.123 61.111 0.00 0.00 45.10 5.68
549 551 2.648102 GTCGACGATGACGAGCCG 60.648 66.667 0.00 0.00 42.66 5.52
568 570 2.162681 GCACCCTACAAGCAGTCAATT 58.837 47.619 0.00 0.00 0.00 2.32
575 577 1.003839 CCTTCGCACCCTACAAGCA 60.004 57.895 0.00 0.00 0.00 3.91
585 587 1.023513 ATGAAGCTCTGCCTTCGCAC 61.024 55.000 0.00 0.00 43.21 5.34
596 598 1.133216 GAGCCCCGAAAAATGAAGCTC 59.867 52.381 0.00 0.00 38.56 4.09
628 630 0.670546 CGTCACCCGCTTCTCATGTT 60.671 55.000 0.00 0.00 0.00 2.71
645 647 2.957006 ACCTAGTCTAAATGATCGCCGT 59.043 45.455 0.00 0.00 0.00 5.68
695 697 8.419076 AAACCGGCACAAATTCATTATATTTC 57.581 30.769 0.00 0.00 0.00 2.17
755 757 6.677913 ACCAAACGATTTTCATTCTACTTGG 58.322 36.000 0.00 0.00 36.50 3.61
819 822 9.487790 CCATAAATATACGGGCATTTCAATTTT 57.512 29.630 0.00 0.00 0.00 1.82
820 823 7.602265 GCCATAAATATACGGGCATTTCAATTT 59.398 33.333 0.00 0.00 44.01 1.82
821 824 7.039082 AGCCATAAATATACGGGCATTTCAATT 60.039 33.333 0.00 0.00 46.96 2.32
822 825 6.437162 AGCCATAAATATACGGGCATTTCAAT 59.563 34.615 0.00 0.00 46.96 2.57
825 828 5.897377 AGCCATAAATATACGGGCATTTC 57.103 39.130 0.00 0.00 46.96 2.17
833 836 7.412563 CCATTCAACCGTAGCCATAAATATACG 60.413 40.741 0.00 0.00 40.41 3.06
834 837 7.625606 GCCATTCAACCGTAGCCATAAATATAC 60.626 40.741 0.00 0.00 0.00 1.47
835 838 6.373216 GCCATTCAACCGTAGCCATAAATATA 59.627 38.462 0.00 0.00 0.00 0.86
884 3957 3.374402 AGTCGAGCGGGACCAGTG 61.374 66.667 6.57 0.00 37.66 3.66
901 3974 0.320073 GACCCAAATCGGACACGTCA 60.320 55.000 0.00 0.00 41.85 4.35
949 5032 5.874810 GGACAAGTCTATGTGAATGCTTACA 59.125 40.000 0.00 0.00 32.57 2.41
963 5046 3.236896 ACGGAAGAAAGGGACAAGTCTA 58.763 45.455 0.00 0.00 0.00 2.59
1246 5329 2.695666 CGCGGGAGGATAGAATGGATAT 59.304 50.000 0.00 0.00 0.00 1.63
1278 5361 0.617820 GGAGGTAGTCCCAGCCAAGA 60.618 60.000 0.00 0.00 39.88 3.02
1281 5364 2.363795 CGGAGGTAGTCCCAGCCA 60.364 66.667 0.00 0.00 43.47 4.75
1473 5556 1.380650 GGAGAAGGCGGAGAGGAGT 60.381 63.158 0.00 0.00 0.00 3.85
1482 5565 2.415608 TACCTGCTCGGAGAAGGCG 61.416 63.158 28.80 9.55 38.05 5.52
1507 5590 9.681062 TTTCTAAAGAAAGAAGAAGAAGACCAA 57.319 29.630 1.00 0.00 38.94 3.67
1520 5603 6.715264 GGGACCAAGTCATTTCTAAAGAAAGA 59.285 38.462 10.64 6.08 45.87 2.52
1580 7176 6.202570 ACAAGCGTACAAAAATTTACCGACTA 59.797 34.615 0.00 0.00 0.00 2.59
1866 7462 8.555896 TTCCATGGTAGGATGTATAACAGTTA 57.444 34.615 12.58 0.00 37.56 2.24
1887 7483 4.046286 ACAGGATGCTGGTTTAATTCCA 57.954 40.909 19.22 0.99 42.53 3.53
1893 7489 2.645297 TGGGTAACAGGATGCTGGTTTA 59.355 45.455 19.22 6.21 42.53 2.01
1909 7505 4.038042 CACTCTCTCGAATGCTTATGGGTA 59.962 45.833 0.00 0.00 0.00 3.69
1913 7509 4.313277 TCCACTCTCTCGAATGCTTATG 57.687 45.455 0.00 0.00 0.00 1.90
1943 7539 9.657419 CATGTATGGACTATGCATCTTGTATTA 57.343 33.333 0.19 0.00 39.68 0.98
1970 7566 2.819608 TCCAAAATACTCTGCAACAGGC 59.180 45.455 0.00 0.00 45.13 4.85
2084 7706 1.986413 CAGCTACTGCAAGAGGGGT 59.014 57.895 0.00 0.00 42.74 4.95
2122 7744 6.039047 GGTACTATGGTCAGTGATTCTCGTAA 59.961 42.308 0.00 0.00 0.00 3.18
2186 7808 0.037326 GTGGACGACAGAATGGAGCA 60.037 55.000 0.00 0.00 43.62 4.26
2234 7862 3.841643 ACATGAGCAGCTTTAATTGTGC 58.158 40.909 0.00 0.00 36.10 4.57
2252 7880 2.009774 GTATGCAGAGTCGCCAAACAT 58.990 47.619 0.00 0.00 0.00 2.71
2253 7881 1.270571 TGTATGCAGAGTCGCCAAACA 60.271 47.619 0.00 4.21 0.00 2.83
2260 7888 0.873312 ATGCGCTGTATGCAGAGTCG 60.873 55.000 15.68 9.75 46.98 4.18
2274 7902 3.742882 TGAGATAGCTTAACATGATGCGC 59.257 43.478 0.00 0.00 0.00 6.09
2295 7923 2.789409 ACCTTTTCCCCGAAGAGATG 57.211 50.000 0.00 0.00 0.00 2.90
2353 7982 6.909550 TGTCATTAAACAGCAGGGTTAATT 57.090 33.333 8.26 0.00 0.00 1.40
2388 8017 6.351881 GGACCCACTTCTATTACAATCACAGA 60.352 42.308 0.00 0.00 0.00 3.41
2406 8035 2.032071 CGGACACAAGGGACCCAC 59.968 66.667 14.60 0.00 0.00 4.61
2409 8038 0.602905 CAGAACGGACACAAGGGACC 60.603 60.000 0.00 0.00 0.00 4.46
2459 8088 5.048013 AGCCTTGCAACCATCTAAAAGTTAC 60.048 40.000 0.00 0.00 0.00 2.50
2529 8158 4.565022 ACAAAGTTGTGTTTTGAACTGGG 58.435 39.130 4.87 0.00 40.49 4.45
2543 8172 6.925165 AGAAAATCTACCATGCAACAAAGTTG 59.075 34.615 5.56 5.56 0.00 3.16
2603 8232 1.414181 CCTATGCATGGACGAAGGACT 59.586 52.381 12.26 0.00 0.00 3.85
2648 8277 5.820947 CCCATGGTAGATGTTGTAGGTAAAC 59.179 44.000 11.73 0.00 0.00 2.01
2651 8280 3.389983 GCCCATGGTAGATGTTGTAGGTA 59.610 47.826 11.73 0.00 0.00 3.08
2687 8316 5.438761 AGAGGAAAACAAACATAGTGCAC 57.561 39.130 9.40 9.40 0.00 4.57
2688 8317 6.460953 GGAAAGAGGAAAACAAACATAGTGCA 60.461 38.462 0.00 0.00 0.00 4.57
2721 8350 1.110442 CAAGAACAGGTGTTTGGCCA 58.890 50.000 0.00 0.00 38.56 5.36


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

AutoCloner maintained by Alex Coulton.