Multiple sequence alignment - TraesCS5D01G329300

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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 TraesCS5D01G329300 chr5D 100.000 2939 0 0 1 2939 421423045 421425983 0.000000e+00 5428.0
1 TraesCS5D01G329300 chr5D 100.000 28 0 0 638 665 303432346 303432319 5.000000e-03 52.8
2 TraesCS5D01G329300 chr2A 85.020 2817 357 43 175 2935 707762170 707759363 0.000000e+00 2804.0
3 TraesCS5D01G329300 chr3D 86.933 2357 281 14 168 2503 391277885 391280235 0.000000e+00 2621.0
4 TraesCS5D01G329300 chr3D 89.904 416 42 0 2522 2937 391280308 391280723 1.200000e-148 536.0
5 TraesCS5D01G329300 chr3D 95.238 84 4 0 65 148 553176485 553176402 1.840000e-27 134.0
6 TraesCS5D01G329300 chr3D 85.294 68 8 2 195 261 475309362 475309296 5.260000e-08 69.4
7 TraesCS5D01G329300 chr4D 82.707 2342 351 31 172 2496 69395967 69393663 0.000000e+00 2032.0
8 TraesCS5D01G329300 chr4D 87.981 416 50 0 2522 2937 69393583 69393168 2.630000e-135 492.0
9 TraesCS5D01G329300 chr4D 95.349 86 4 0 63 148 243305515 243305600 1.420000e-28 137.0
10 TraesCS5D01G329300 chr4D 91.579 95 6 2 55 148 57686963 57687056 2.380000e-26 130.0
11 TraesCS5D01G329300 chr6B 80.771 2257 384 35 183 2416 716220644 716218415 0.000000e+00 1718.0
12 TraesCS5D01G329300 chr6B 94.118 85 5 0 64 148 674059586 674059502 2.380000e-26 130.0
13 TraesCS5D01G329300 chr6B 87.931 58 6 1 175 232 171766348 171766292 1.890000e-07 67.6
14 TraesCS5D01G329300 chr6B 82.432 74 7 5 159 227 604697363 604697291 3.160000e-05 60.2
15 TraesCS5D01G329300 chr4B 79.947 2259 401 40 183 2416 52571341 52573572 0.000000e+00 1615.0
16 TraesCS5D01G329300 chr4B 77.778 117 20 5 162 275 62977605 62977718 1.890000e-07 67.6
17 TraesCS5D01G329300 chr3B 85.714 938 113 13 487 1413 477621593 477620666 0.000000e+00 970.0
18 TraesCS5D01G329300 chr5A 89.726 146 15 0 1 146 535013163 535013308 1.390000e-43 187.0
19 TraesCS5D01G329300 chr5B 94.318 88 5 0 61 148 574992702 574992615 5.110000e-28 135.0
20 TraesCS5D01G329300 chr5B 89.691 97 8 2 53 148 217623000 217623095 3.980000e-24 122.0
21 TraesCS5D01G329300 chr2B 94.048 84 5 0 65 148 476401302 476401219 8.550000e-26 128.0
22 TraesCS5D01G329300 chr2B 73.199 347 88 5 2555 2898 364735479 364735823 1.430000e-23 121.0
23 TraesCS5D01G329300 chr2B 100.000 28 0 0 638 665 545962926 545962953 5.000000e-03 52.8
24 TraesCS5D01G329300 chr2D 93.976 83 5 0 64 146 43079504 43079422 3.070000e-25 126.0
25 TraesCS5D01G329300 chr3A 79.630 162 31 2 2726 2886 466010305 466010465 6.660000e-22 115.0
26 TraesCS5D01G329300 chr3A 75.472 159 22 13 195 348 124196472 124196618 8.790000e-06 62.1
27 TraesCS5D01G329300 chr6D 81.579 76 12 2 199 273 376336904 376336830 8.790000e-06 62.1


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 TraesCS5D01G329300 chr5D 421423045 421425983 2938 False 5428.0 5428 100.0000 1 2939 1 chr5D.!!$F1 2938
1 TraesCS5D01G329300 chr2A 707759363 707762170 2807 True 2804.0 2804 85.0200 175 2935 1 chr2A.!!$R1 2760
2 TraesCS5D01G329300 chr3D 391277885 391280723 2838 False 1578.5 2621 88.4185 168 2937 2 chr3D.!!$F1 2769
3 TraesCS5D01G329300 chr4D 69393168 69395967 2799 True 1262.0 2032 85.3440 172 2937 2 chr4D.!!$R1 2765
4 TraesCS5D01G329300 chr6B 716218415 716220644 2229 True 1718.0 1718 80.7710 183 2416 1 chr6B.!!$R4 2233
5 TraesCS5D01G329300 chr4B 52571341 52573572 2231 False 1615.0 1615 79.9470 183 2416 1 chr4B.!!$F1 2233
6 TraesCS5D01G329300 chr3B 477620666 477621593 927 True 970.0 970 85.7140 487 1413 1 chr3B.!!$R1 926

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
99 100 0.035534 TGCCGCTCTAGATTTTGCCA 60.036 50.0 0.00 0.0 0.0 4.92 F
1375 1446 0.036294 GCCGGAAACTAGCTCAAGGT 60.036 55.0 5.05 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1875 0.029681 ACCCTATCCTGCACCCTCAT 60.030 55.0 0.0 0.0 0.00 2.90 R
2663 2818 0.323451 TCGAGTAGCTCTCTTGGGCA 60.323 55.0 0.0 0.0 40.75 5.36 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
26 27 5.585820 ATGCAAGCATGAACATGAATACA 57.414 34.783 17.40 10.11 41.20 2.29
27 28 4.735985 TGCAAGCATGAACATGAATACAC 58.264 39.130 17.40 0.37 41.20 2.90
28 29 4.217983 TGCAAGCATGAACATGAATACACA 59.782 37.500 17.40 5.58 41.20 3.72
29 30 4.796830 GCAAGCATGAACATGAATACACAG 59.203 41.667 17.40 1.20 41.20 3.66
30 31 5.392272 GCAAGCATGAACATGAATACACAGA 60.392 40.000 17.40 0.00 41.20 3.41
31 32 6.679638 GCAAGCATGAACATGAATACACAGAT 60.680 38.462 17.40 0.00 41.20 2.90
32 33 7.255569 CAAGCATGAACATGAATACACAGATT 58.744 34.615 17.40 0.00 41.20 2.40
33 34 7.400599 AGCATGAACATGAATACACAGATTT 57.599 32.000 17.40 0.00 41.20 2.17
34 35 7.833786 AGCATGAACATGAATACACAGATTTT 58.166 30.769 17.40 0.00 41.20 1.82
35 36 7.758076 AGCATGAACATGAATACACAGATTTTG 59.242 33.333 17.40 0.00 41.20 2.44
36 37 7.463648 GCATGAACATGAATACACAGATTTTGC 60.464 37.037 17.40 0.00 41.20 3.68
37 38 6.979465 TGAACATGAATACACAGATTTTGCA 58.021 32.000 0.00 0.00 0.00 4.08
38 39 7.432059 TGAACATGAATACACAGATTTTGCAA 58.568 30.769 0.00 0.00 0.00 4.08
39 40 8.089597 TGAACATGAATACACAGATTTTGCAAT 58.910 29.630 0.00 0.00 0.00 3.56
40 41 7.821595 ACATGAATACACAGATTTTGCAATG 57.178 32.000 0.00 0.00 0.00 2.82
41 42 6.311935 ACATGAATACACAGATTTTGCAATGC 59.688 34.615 0.00 0.00 0.00 3.56
42 43 5.780984 TGAATACACAGATTTTGCAATGCA 58.219 33.333 2.72 2.72 36.47 3.96
43 44 5.865013 TGAATACACAGATTTTGCAATGCAG 59.135 36.000 8.31 0.00 40.61 4.41
44 45 5.648178 ATACACAGATTTTGCAATGCAGA 57.352 34.783 8.31 0.00 40.61 4.26
45 46 4.325028 ACACAGATTTTGCAATGCAGAA 57.675 36.364 13.54 13.54 40.61 3.02
46 47 4.053295 ACACAGATTTTGCAATGCAGAAC 58.947 39.130 13.44 7.90 40.61 3.01
47 48 4.202182 ACACAGATTTTGCAATGCAGAACT 60.202 37.500 13.44 9.86 40.61 3.01
48 49 4.748102 CACAGATTTTGCAATGCAGAACTT 59.252 37.500 13.44 0.00 40.61 2.66
49 50 4.748102 ACAGATTTTGCAATGCAGAACTTG 59.252 37.500 13.44 15.49 40.61 3.16
64 65 6.929587 CAGAACTTGCATCTTTTCTTCATG 57.070 37.500 0.00 0.00 0.00 3.07
65 66 5.862323 CAGAACTTGCATCTTTTCTTCATGG 59.138 40.000 0.00 0.00 0.00 3.66
66 67 4.796038 ACTTGCATCTTTTCTTCATGGG 57.204 40.909 0.00 0.00 0.00 4.00
67 68 4.410099 ACTTGCATCTTTTCTTCATGGGA 58.590 39.130 0.00 0.00 0.00 4.37
68 69 4.834496 ACTTGCATCTTTTCTTCATGGGAA 59.166 37.500 0.00 0.00 0.00 3.97
69 70 5.305128 ACTTGCATCTTTTCTTCATGGGAAA 59.695 36.000 9.55 9.55 31.35 3.13
70 71 5.804944 TGCATCTTTTCTTCATGGGAAAA 57.195 34.783 18.91 18.91 39.41 2.29
71 72 6.363167 TGCATCTTTTCTTCATGGGAAAAT 57.637 33.333 19.72 9.71 40.41 1.82
72 73 6.771573 TGCATCTTTTCTTCATGGGAAAATT 58.228 32.000 19.72 12.27 40.41 1.82
73 74 7.225725 TGCATCTTTTCTTCATGGGAAAATTT 58.774 30.769 19.72 12.04 40.41 1.82
74 75 7.720515 TGCATCTTTTCTTCATGGGAAAATTTT 59.279 29.630 19.72 2.28 40.41 1.82
75 76 9.218440 GCATCTTTTCTTCATGGGAAAATTTTA 57.782 29.630 19.72 11.31 40.41 1.52
86 87 5.621197 GGGAAAATTTTATTTTTGCCGCT 57.379 34.783 2.75 0.00 43.94 5.52
87 88 5.627172 GGGAAAATTTTATTTTTGCCGCTC 58.373 37.500 2.75 0.00 43.94 5.03
88 89 5.411361 GGGAAAATTTTATTTTTGCCGCTCT 59.589 36.000 2.75 0.00 43.94 4.09
89 90 6.592220 GGGAAAATTTTATTTTTGCCGCTCTA 59.408 34.615 2.75 0.00 43.94 2.43
90 91 7.201522 GGGAAAATTTTATTTTTGCCGCTCTAG 60.202 37.037 2.75 0.00 43.94 2.43
91 92 7.544217 GGAAAATTTTATTTTTGCCGCTCTAGA 59.456 33.333 2.75 0.00 32.62 2.43
92 93 9.087424 GAAAATTTTATTTTTGCCGCTCTAGAT 57.913 29.630 2.75 0.00 0.00 1.98
93 94 9.435688 AAAATTTTATTTTTGCCGCTCTAGATT 57.564 25.926 0.37 0.00 0.00 2.40
94 95 9.435688 AAATTTTATTTTTGCCGCTCTAGATTT 57.564 25.926 0.00 0.00 0.00 2.17
95 96 9.435688 AATTTTATTTTTGCCGCTCTAGATTTT 57.564 25.926 0.00 0.00 0.00 1.82
96 97 7.810766 TTTATTTTTGCCGCTCTAGATTTTG 57.189 32.000 0.00 0.00 0.00 2.44
97 98 2.919666 TTTGCCGCTCTAGATTTTGC 57.080 45.000 0.00 0.00 0.00 3.68
98 99 1.094785 TTGCCGCTCTAGATTTTGCC 58.905 50.000 0.00 0.00 0.00 4.52
99 100 0.035534 TGCCGCTCTAGATTTTGCCA 60.036 50.000 0.00 0.00 0.00 4.92
100 101 1.094785 GCCGCTCTAGATTTTGCCAA 58.905 50.000 0.00 0.00 0.00 4.52
101 102 1.678101 GCCGCTCTAGATTTTGCCAAT 59.322 47.619 0.00 0.00 0.00 3.16
102 103 2.099756 GCCGCTCTAGATTTTGCCAATT 59.900 45.455 0.00 0.00 0.00 2.32
103 104 3.429410 GCCGCTCTAGATTTTGCCAATTT 60.429 43.478 0.00 0.00 0.00 1.82
104 105 4.747810 CCGCTCTAGATTTTGCCAATTTT 58.252 39.130 0.00 0.00 0.00 1.82
105 106 4.800471 CCGCTCTAGATTTTGCCAATTTTC 59.200 41.667 0.00 0.00 0.00 2.29
106 107 4.800471 CGCTCTAGATTTTGCCAATTTTCC 59.200 41.667 0.00 0.00 0.00 3.13
107 108 5.393461 CGCTCTAGATTTTGCCAATTTTCCT 60.393 40.000 0.00 0.00 0.00 3.36
108 109 6.401394 GCTCTAGATTTTGCCAATTTTCCTT 58.599 36.000 0.00 0.00 0.00 3.36
109 110 7.547227 GCTCTAGATTTTGCCAATTTTCCTTA 58.453 34.615 0.00 0.00 0.00 2.69
110 111 8.200120 GCTCTAGATTTTGCCAATTTTCCTTAT 58.800 33.333 0.00 0.00 0.00 1.73
111 112 9.525409 CTCTAGATTTTGCCAATTTTCCTTATG 57.475 33.333 0.00 0.00 0.00 1.90
112 113 9.034800 TCTAGATTTTGCCAATTTTCCTTATGT 57.965 29.630 0.00 0.00 0.00 2.29
113 114 9.305925 CTAGATTTTGCCAATTTTCCTTATGTC 57.694 33.333 0.00 0.00 0.00 3.06
114 115 7.678837 AGATTTTGCCAATTTTCCTTATGTCA 58.321 30.769 0.00 0.00 0.00 3.58
115 116 7.603784 AGATTTTGCCAATTTTCCTTATGTCAC 59.396 33.333 0.00 0.00 0.00 3.67
116 117 6.418057 TTTGCCAATTTTCCTTATGTCACT 57.582 33.333 0.00 0.00 0.00 3.41
117 118 5.643379 TGCCAATTTTCCTTATGTCACTC 57.357 39.130 0.00 0.00 0.00 3.51
118 119 5.324409 TGCCAATTTTCCTTATGTCACTCT 58.676 37.500 0.00 0.00 0.00 3.24
119 120 6.480763 TGCCAATTTTCCTTATGTCACTCTA 58.519 36.000 0.00 0.00 0.00 2.43
120 121 6.599244 TGCCAATTTTCCTTATGTCACTCTAG 59.401 38.462 0.00 0.00 0.00 2.43
121 122 6.823689 GCCAATTTTCCTTATGTCACTCTAGA 59.176 38.462 0.00 0.00 0.00 2.43
122 123 7.500559 GCCAATTTTCCTTATGTCACTCTAGAT 59.499 37.037 0.00 0.00 0.00 1.98
123 124 9.401058 CCAATTTTCCTTATGTCACTCTAGATT 57.599 33.333 0.00 0.00 0.00 2.40
126 127 8.703604 TTTTCCTTATGTCACTCTAGATTTCG 57.296 34.615 0.00 0.00 0.00 3.46
127 128 7.640597 TTCCTTATGTCACTCTAGATTTCGA 57.359 36.000 0.00 0.00 0.00 3.71
128 129 7.028926 TCCTTATGTCACTCTAGATTTCGAC 57.971 40.000 0.00 0.00 0.00 4.20
129 130 6.602009 TCCTTATGTCACTCTAGATTTCGACA 59.398 38.462 13.02 13.02 37.74 4.35
130 131 7.285629 TCCTTATGTCACTCTAGATTTCGACAT 59.714 37.037 20.79 20.79 44.11 3.06
131 132 7.923344 CCTTATGTCACTCTAGATTTCGACATT 59.077 37.037 21.58 12.15 40.26 2.71
132 133 9.307121 CTTATGTCACTCTAGATTTCGACATTT 57.693 33.333 21.58 9.97 40.26 2.32
133 134 7.763172 ATGTCACTCTAGATTTCGACATTTC 57.237 36.000 15.38 0.00 40.26 2.17
134 135 6.687604 TGTCACTCTAGATTTCGACATTTCA 58.312 36.000 0.00 0.00 0.00 2.69
135 136 6.586463 TGTCACTCTAGATTTCGACATTTCAC 59.414 38.462 0.00 0.00 0.00 3.18
136 137 6.809196 GTCACTCTAGATTTCGACATTTCACT 59.191 38.462 0.00 0.00 0.00 3.41
137 138 7.329717 GTCACTCTAGATTTCGACATTTCACTT 59.670 37.037 0.00 0.00 0.00 3.16
138 139 7.872993 TCACTCTAGATTTCGACATTTCACTTT 59.127 33.333 0.00 0.00 0.00 2.66
139 140 8.499162 CACTCTAGATTTCGACATTTCACTTTT 58.501 33.333 0.00 0.00 0.00 2.27
140 141 8.499162 ACTCTAGATTTCGACATTTCACTTTTG 58.501 33.333 0.00 0.00 0.00 2.44
141 142 7.298122 TCTAGATTTCGACATTTCACTTTTGC 58.702 34.615 0.00 0.00 0.00 3.68
142 143 5.830912 AGATTTCGACATTTCACTTTTGCA 58.169 33.333 0.00 0.00 0.00 4.08
143 144 6.272318 AGATTTCGACATTTCACTTTTGCAA 58.728 32.000 0.00 0.00 0.00 4.08
144 145 5.694674 TTTCGACATTTCACTTTTGCAAC 57.305 34.783 0.00 0.00 0.00 4.17
145 146 4.630894 TCGACATTTCACTTTTGCAACT 57.369 36.364 0.00 0.00 0.00 3.16
146 147 4.597079 TCGACATTTCACTTTTGCAACTC 58.403 39.130 0.00 0.00 0.00 3.01
147 148 4.335315 TCGACATTTCACTTTTGCAACTCT 59.665 37.500 0.00 0.00 0.00 3.24
148 149 4.438797 CGACATTTCACTTTTGCAACTCTG 59.561 41.667 0.00 0.00 0.00 3.35
149 150 4.685924 ACATTTCACTTTTGCAACTCTGG 58.314 39.130 0.00 0.00 0.00 3.86
150 151 4.402155 ACATTTCACTTTTGCAACTCTGGA 59.598 37.500 0.00 0.00 0.00 3.86
151 152 5.105392 ACATTTCACTTTTGCAACTCTGGAA 60.105 36.000 0.00 0.00 0.00 3.53
152 153 5.398603 TTTCACTTTTGCAACTCTGGAAA 57.601 34.783 0.00 3.62 40.68 3.13
153 154 5.398603 TTCACTTTTGCAACTCTGGAAAA 57.601 34.783 0.00 4.77 46.73 2.29
154 155 4.743493 TCACTTTTGCAACTCTGGAAAAC 58.257 39.130 0.00 0.00 44.85 2.43
155 156 3.865164 CACTTTTGCAACTCTGGAAAACC 59.135 43.478 0.00 0.00 44.85 3.27
156 157 2.861462 TTTGCAACTCTGGAAAACCG 57.139 45.000 0.00 0.00 39.61 4.44
157 158 1.028905 TTGCAACTCTGGAAAACCGG 58.971 50.000 0.00 0.00 28.70 5.28
158 159 1.285950 GCAACTCTGGAAAACCGGC 59.714 57.895 0.00 0.00 0.00 6.13
159 160 1.956802 CAACTCTGGAAAACCGGCC 59.043 57.895 0.00 0.00 0.00 6.13
160 161 0.537371 CAACTCTGGAAAACCGGCCT 60.537 55.000 0.00 0.00 0.00 5.19
161 162 0.250770 AACTCTGGAAAACCGGCCTC 60.251 55.000 0.00 0.00 0.00 4.70
162 163 1.741770 CTCTGGAAAACCGGCCTCG 60.742 63.158 0.00 0.00 0.00 4.63
163 164 3.431725 CTGGAAAACCGGCCTCGC 61.432 66.667 0.00 0.00 34.56 5.03
288 318 2.444895 CCTCTTCCCCCTCTCCGG 60.445 72.222 0.00 0.00 0.00 5.14
308 338 4.148825 CCGTCTTCCTCCCTGGCG 62.149 72.222 0.00 0.00 35.26 5.69
607 639 3.453070 GAGGTGATCCCGGAGCTGC 62.453 68.421 0.73 0.00 38.74 5.25
608 640 3.785859 GGTGATCCCGGAGCTGCA 61.786 66.667 0.73 0.00 0.00 4.41
636 668 0.315251 GCTTCAGGTGCCTGGAAAAC 59.685 55.000 17.23 0.00 43.75 2.43
685 719 1.525077 GAGGTGTGTTTCCGGTGCA 60.525 57.895 0.00 0.00 0.00 4.57
748 790 2.178890 CCTTCCTCTGCTGATGCGC 61.179 63.158 0.00 0.00 43.34 6.09
857 928 1.820056 CTCTCCTACTCGCTGCCGA 60.820 63.158 0.00 0.00 42.01 5.54
943 1014 0.681564 AAGGCGAGTCCGAGATCTGT 60.682 55.000 0.00 0.00 40.77 3.41
948 1019 1.178276 GAGTCCGAGATCTGTGTGGT 58.822 55.000 0.00 0.00 0.00 4.16
949 1020 1.546476 GAGTCCGAGATCTGTGTGGTT 59.454 52.381 0.00 0.00 0.00 3.67
961 1032 1.814586 TGTGGTTTTCGGCGTTCGT 60.815 52.632 6.85 0.00 40.32 3.85
1164 1235 0.526524 CGGCGATCAGGAACAGAGTC 60.527 60.000 0.00 0.00 0.00 3.36
1212 1283 3.205507 AGGGAGATAGGCTGTACTTCAGA 59.794 47.826 0.00 0.00 46.27 3.27
1230 1301 4.308458 CCGTGGAACCGGCAGTCA 62.308 66.667 0.00 0.00 41.78 3.41
1256 1327 1.137872 AGTGCACTCGATCTTGGGATC 59.862 52.381 15.25 0.00 43.48 3.36
1257 1328 1.137872 GTGCACTCGATCTTGGGATCT 59.862 52.381 10.32 0.00 44.42 2.75
1326 1397 1.751927 GACGGCGGAGGACCTTCTA 60.752 63.158 13.24 0.00 0.00 2.10
1375 1446 0.036294 GCCGGAAACTAGCTCAAGGT 60.036 55.000 5.05 0.00 0.00 3.50
1377 1448 1.275291 CCGGAAACTAGCTCAAGGTCA 59.725 52.381 0.00 0.00 0.00 4.02
1398 1469 1.601430 GATCTTTCGGCATTCAGGCTC 59.399 52.381 0.00 0.00 41.46 4.70
1419 1490 1.220749 GGCGTGGACTGCTAATCCA 59.779 57.895 0.60 0.60 44.20 3.41
1506 1577 5.222079 TGTTGCAGTACAAGGTTCTCATA 57.778 39.130 0.00 0.00 39.50 2.15
1532 1603 3.312404 ACGCAGTTGCAGACTTCAT 57.688 47.368 4.84 0.00 37.78 2.57
1578 1649 4.279326 GGCTCCTCCGATAGTGGT 57.721 61.111 0.00 0.00 0.00 4.16
1617 1688 1.745489 GCCGGATGGGTTCAGTGAC 60.745 63.158 5.05 0.00 38.44 3.67
1660 1731 0.249031 GCAGCGAGTTTGGCAGTTTT 60.249 50.000 0.00 0.00 0.00 2.43
1744 1815 2.826287 CGAGGAGCGCAGAGAGGA 60.826 66.667 11.47 0.00 0.00 3.71
1827 1898 1.271840 GGGTGCAGGATAGGGTGACA 61.272 60.000 0.00 0.00 0.00 3.58
1924 1995 4.539083 TGAACAGTGGTGGCGCGT 62.539 61.111 8.43 0.00 0.00 6.01
1928 1999 1.939769 AACAGTGGTGGCGCGTTTTT 61.940 50.000 8.43 0.00 0.00 1.94
1932 2003 2.354188 GGTGGCGCGTTTTTGACC 60.354 61.111 8.43 0.00 0.00 4.02
1940 2011 1.871077 CGTTTTTGACCGGGTAGGC 59.129 57.895 6.32 0.00 46.52 3.93
1976 2047 0.033781 TTACCGTTGGGAGAACGTGG 59.966 55.000 6.24 0.00 41.64 4.94
2011 2082 4.414956 AGGGTGCGGATCCCCAGA 62.415 66.667 1.00 0.00 45.64 3.86
2095 2166 0.526954 GGTTACGTCGATGGATGCGT 60.527 55.000 9.90 5.65 40.76 5.24
2096 2167 0.844503 GTTACGTCGATGGATGCGTC 59.155 55.000 9.90 0.00 38.56 5.19
2129 2200 0.394899 CCAATGGGGACTCTTCTGCC 60.395 60.000 0.00 0.00 40.01 4.85
2151 2222 3.071206 GCTGGAGAGGACGAGGCA 61.071 66.667 0.00 0.00 0.00 4.75
2194 2268 0.976073 GGACCCACCGGAGATTCTCA 60.976 60.000 9.46 0.00 31.08 3.27
2205 2279 2.288152 GGAGATTCTCACTGATCGCTCC 60.288 54.545 15.36 0.00 33.06 4.70
2290 2364 1.229145 AGAGGTGAGCAGCAGGAGT 60.229 57.895 0.00 0.00 0.00 3.85
2336 2410 0.475906 ATAATGGAGGGACTGGCAGC 59.524 55.000 15.89 7.42 41.55 5.25
2358 2432 2.991540 GCTGAAGGTGGGGCCAAC 60.992 66.667 4.39 3.29 40.61 3.77
2431 2505 6.046593 GTCACCGATGATACAAGTATGGAAA 58.953 40.000 0.00 0.00 37.14 3.13
2441 2515 3.333680 ACAAGTATGGAAATGGAGGGTGT 59.666 43.478 0.00 0.00 0.00 4.16
2451 2525 2.584391 GGAGGGTGTTCTCGCTGGT 61.584 63.158 0.00 0.00 34.74 4.00
2462 2536 4.100084 CGCTGGTGGGCTGGATGA 62.100 66.667 0.00 0.00 0.00 2.92
2473 2574 2.611800 TGGATGAGGGCAGGCTGT 60.612 61.111 17.16 0.00 0.00 4.40
2478 2579 3.775654 GAGGGCAGGCTGTAGCGT 61.776 66.667 17.16 0.00 43.26 5.07
2518 2619 3.362399 ATCGAGGCAGAGGCACACG 62.362 63.158 0.00 0.00 43.71 4.49
2539 2694 1.519455 GAGACGGAAGGCATGACCG 60.519 63.158 14.04 14.04 46.78 4.79
2592 2747 4.660168 AGAGTTTCTGCTCCAACATCATT 58.340 39.130 0.00 0.00 36.20 2.57
2614 2769 4.658786 AACTCGCCCCTCCCCTGT 62.659 66.667 0.00 0.00 0.00 4.00
2616 2771 2.365105 CTCGCCCCTCCCCTGTTA 60.365 66.667 0.00 0.00 0.00 2.41
2663 2818 3.879295 CGTCCAGATGCATAACCTTTCAT 59.121 43.478 0.00 0.00 0.00 2.57
2697 2852 1.432251 TCGATCGTCGAAGAAGGCC 59.568 57.895 15.94 0.00 46.90 5.19
2698 2853 1.138883 CGATCGTCGAAGAAGGCCA 59.861 57.895 5.01 0.00 43.74 5.36
2898 3053 1.202855 CCATCGGCAGAGGAATTGGAT 60.203 52.381 0.00 0.00 0.00 3.41
2922 3077 2.100584 GAGCAACTCGGTGATGATCTCT 59.899 50.000 0.00 0.00 32.26 3.10
2937 3092 2.909504 TCTCTGTCAACTAGGAGGCT 57.090 50.000 0.00 0.00 0.00 4.58
2938 3093 3.176924 TCTCTGTCAACTAGGAGGCTT 57.823 47.619 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.086282 TCATGTTCATGCTTGCATGAGT 58.914 40.909 29.15 19.89 41.60 3.41
2 3 4.729227 ATTCATGTTCATGCTTGCATGA 57.271 36.364 27.91 27.91 43.81 3.07
4 5 5.105675 TGTGTATTCATGTTCATGCTTGCAT 60.106 36.000 1.81 1.81 0.00 3.96
5 6 4.217983 TGTGTATTCATGTTCATGCTTGCA 59.782 37.500 7.80 0.00 0.00 4.08
6 7 4.735985 TGTGTATTCATGTTCATGCTTGC 58.264 39.130 7.80 3.00 0.00 4.01
7 8 6.185852 TCTGTGTATTCATGTTCATGCTTG 57.814 37.500 7.80 0.00 0.00 4.01
8 9 7.400599 AATCTGTGTATTCATGTTCATGCTT 57.599 32.000 7.80 1.43 0.00 3.91
9 10 7.400599 AAATCTGTGTATTCATGTTCATGCT 57.599 32.000 7.80 1.58 0.00 3.79
10 11 7.463648 GCAAAATCTGTGTATTCATGTTCATGC 60.464 37.037 7.80 0.00 0.00 4.06
11 12 7.542824 TGCAAAATCTGTGTATTCATGTTCATG 59.457 33.333 6.46 6.46 0.00 3.07
12 13 7.604549 TGCAAAATCTGTGTATTCATGTTCAT 58.395 30.769 0.00 0.00 0.00 2.57
13 14 6.979465 TGCAAAATCTGTGTATTCATGTTCA 58.021 32.000 0.00 0.00 0.00 3.18
14 15 7.872163 TTGCAAAATCTGTGTATTCATGTTC 57.128 32.000 0.00 0.00 0.00 3.18
15 16 7.148540 GCATTGCAAAATCTGTGTATTCATGTT 60.149 33.333 1.71 0.00 0.00 2.71
16 17 6.311935 GCATTGCAAAATCTGTGTATTCATGT 59.688 34.615 1.71 0.00 0.00 3.21
17 18 6.311690 TGCATTGCAAAATCTGTGTATTCATG 59.688 34.615 9.33 0.00 34.76 3.07
18 19 6.399743 TGCATTGCAAAATCTGTGTATTCAT 58.600 32.000 9.33 0.00 34.76 2.57
19 20 5.780984 TGCATTGCAAAATCTGTGTATTCA 58.219 33.333 9.33 0.00 34.76 2.57
20 21 6.094719 TCTGCATTGCAAAATCTGTGTATTC 58.905 36.000 13.18 0.00 38.41 1.75
21 22 6.028146 TCTGCATTGCAAAATCTGTGTATT 57.972 33.333 13.18 0.00 38.41 1.89
22 23 5.648178 TCTGCATTGCAAAATCTGTGTAT 57.352 34.783 13.18 0.00 38.41 2.29
23 24 5.009911 AGTTCTGCATTGCAAAATCTGTGTA 59.990 36.000 13.18 0.00 38.41 2.90
24 25 4.053295 GTTCTGCATTGCAAAATCTGTGT 58.947 39.130 13.18 0.00 38.41 3.72
25 26 4.304110 AGTTCTGCATTGCAAAATCTGTG 58.696 39.130 13.18 0.00 38.41 3.66
26 27 4.595762 AGTTCTGCATTGCAAAATCTGT 57.404 36.364 13.18 0.00 38.41 3.41
27 28 5.264060 CAAGTTCTGCATTGCAAAATCTG 57.736 39.130 13.18 3.99 38.41 2.90
41 42 5.862323 CCATGAAGAAAAGATGCAAGTTCTG 59.138 40.000 0.00 0.00 30.85 3.02
42 43 5.047519 CCCATGAAGAAAAGATGCAAGTTCT 60.048 40.000 0.00 0.00 31.69 3.01
43 44 5.047802 TCCCATGAAGAAAAGATGCAAGTTC 60.048 40.000 0.00 0.00 0.00 3.01
44 45 4.834496 TCCCATGAAGAAAAGATGCAAGTT 59.166 37.500 0.00 0.00 0.00 2.66
45 46 4.410099 TCCCATGAAGAAAAGATGCAAGT 58.590 39.130 0.00 0.00 0.00 3.16
46 47 5.395682 TTCCCATGAAGAAAAGATGCAAG 57.604 39.130 0.00 0.00 0.00 4.01
47 48 5.804944 TTTCCCATGAAGAAAAGATGCAA 57.195 34.783 8.03 0.00 30.48 4.08
48 49 5.804944 TTTTCCCATGAAGAAAAGATGCA 57.195 34.783 15.51 0.00 38.08 3.96
49 50 7.677454 AAATTTTCCCATGAAGAAAAGATGC 57.323 32.000 20.85 0.00 44.12 3.91
57 58 8.791675 GGCAAAAATAAAATTTTCCCATGAAGA 58.208 29.630 6.72 0.00 31.61 2.87
58 59 7.750014 CGGCAAAAATAAAATTTTCCCATGAAG 59.250 33.333 6.72 0.00 30.85 3.02
59 60 7.588512 CGGCAAAAATAAAATTTTCCCATGAA 58.411 30.769 6.72 0.00 30.85 2.57
60 61 6.348868 GCGGCAAAAATAAAATTTTCCCATGA 60.349 34.615 6.72 0.00 30.85 3.07
61 62 5.799435 GCGGCAAAAATAAAATTTTCCCATG 59.201 36.000 6.72 3.41 30.85 3.66
62 63 5.709631 AGCGGCAAAAATAAAATTTTCCCAT 59.290 32.000 6.72 0.00 30.85 4.00
63 64 5.066593 AGCGGCAAAAATAAAATTTTCCCA 58.933 33.333 6.72 0.00 30.85 4.37
64 65 5.411361 AGAGCGGCAAAAATAAAATTTTCCC 59.589 36.000 6.72 2.64 30.31 3.97
65 66 6.480524 AGAGCGGCAAAAATAAAATTTTCC 57.519 33.333 6.72 0.00 30.31 3.13
66 67 8.460831 TCTAGAGCGGCAAAAATAAAATTTTC 57.539 30.769 6.72 0.00 30.31 2.29
67 68 9.435688 AATCTAGAGCGGCAAAAATAAAATTTT 57.564 25.926 8.75 8.75 32.89 1.82
68 69 9.435688 AAATCTAGAGCGGCAAAAATAAAATTT 57.564 25.926 1.45 0.00 0.00 1.82
69 70 9.435688 AAAATCTAGAGCGGCAAAAATAAAATT 57.564 25.926 1.45 0.00 0.00 1.82
70 71 8.872845 CAAAATCTAGAGCGGCAAAAATAAAAT 58.127 29.630 1.45 0.00 0.00 1.82
71 72 7.148656 GCAAAATCTAGAGCGGCAAAAATAAAA 60.149 33.333 1.45 0.00 0.00 1.52
72 73 6.310224 GCAAAATCTAGAGCGGCAAAAATAAA 59.690 34.615 1.45 0.00 0.00 1.40
73 74 5.804979 GCAAAATCTAGAGCGGCAAAAATAA 59.195 36.000 1.45 0.00 0.00 1.40
74 75 5.339990 GCAAAATCTAGAGCGGCAAAAATA 58.660 37.500 1.45 0.00 0.00 1.40
75 76 4.176271 GCAAAATCTAGAGCGGCAAAAAT 58.824 39.130 1.45 0.00 0.00 1.82
76 77 3.574614 GCAAAATCTAGAGCGGCAAAAA 58.425 40.909 1.45 0.00 0.00 1.94
77 78 2.094752 GGCAAAATCTAGAGCGGCAAAA 60.095 45.455 1.45 0.00 0.00 2.44
78 79 1.472480 GGCAAAATCTAGAGCGGCAAA 59.528 47.619 1.45 0.00 0.00 3.68
79 80 1.094785 GGCAAAATCTAGAGCGGCAA 58.905 50.000 1.45 0.00 0.00 4.52
80 81 0.035534 TGGCAAAATCTAGAGCGGCA 60.036 50.000 1.45 2.26 0.00 5.69
81 82 1.094785 TTGGCAAAATCTAGAGCGGC 58.905 50.000 0.00 0.00 0.00 6.53
82 83 4.376340 AAATTGGCAAAATCTAGAGCGG 57.624 40.909 3.01 0.00 0.00 5.52
83 84 4.800471 GGAAAATTGGCAAAATCTAGAGCG 59.200 41.667 3.01 0.00 0.00 5.03
84 85 5.970592 AGGAAAATTGGCAAAATCTAGAGC 58.029 37.500 3.01 0.00 0.00 4.09
85 86 9.525409 CATAAGGAAAATTGGCAAAATCTAGAG 57.475 33.333 3.01 0.00 0.00 2.43
86 87 9.034800 ACATAAGGAAAATTGGCAAAATCTAGA 57.965 29.630 3.01 0.00 0.00 2.43
87 88 9.305925 GACATAAGGAAAATTGGCAAAATCTAG 57.694 33.333 3.01 0.00 0.00 2.43
88 89 8.811017 TGACATAAGGAAAATTGGCAAAATCTA 58.189 29.630 3.01 0.00 0.00 1.98
89 90 7.603784 GTGACATAAGGAAAATTGGCAAAATCT 59.396 33.333 3.01 0.00 0.00 2.40
90 91 7.603784 AGTGACATAAGGAAAATTGGCAAAATC 59.396 33.333 3.01 2.81 0.00 2.17
91 92 7.452562 AGTGACATAAGGAAAATTGGCAAAAT 58.547 30.769 3.01 0.00 0.00 1.82
92 93 6.825610 AGTGACATAAGGAAAATTGGCAAAA 58.174 32.000 3.01 0.00 0.00 2.44
93 94 6.267471 AGAGTGACATAAGGAAAATTGGCAAA 59.733 34.615 3.01 0.00 0.00 3.68
94 95 5.774690 AGAGTGACATAAGGAAAATTGGCAA 59.225 36.000 0.68 0.68 0.00 4.52
95 96 5.324409 AGAGTGACATAAGGAAAATTGGCA 58.676 37.500 0.00 0.00 0.00 4.92
96 97 5.904362 AGAGTGACATAAGGAAAATTGGC 57.096 39.130 0.00 0.00 0.00 4.52
97 98 8.970859 ATCTAGAGTGACATAAGGAAAATTGG 57.029 34.615 0.00 0.00 0.00 3.16
100 101 9.319143 CGAAATCTAGAGTGACATAAGGAAAAT 57.681 33.333 0.00 0.00 0.00 1.82
101 102 8.528643 TCGAAATCTAGAGTGACATAAGGAAAA 58.471 33.333 0.00 0.00 0.00 2.29
102 103 7.974501 GTCGAAATCTAGAGTGACATAAGGAAA 59.025 37.037 0.00 0.00 0.00 3.13
103 104 7.122204 TGTCGAAATCTAGAGTGACATAAGGAA 59.878 37.037 8.73 0.00 31.93 3.36
104 105 6.602009 TGTCGAAATCTAGAGTGACATAAGGA 59.398 38.462 8.73 0.00 31.93 3.36
105 106 6.796426 TGTCGAAATCTAGAGTGACATAAGG 58.204 40.000 8.73 0.00 31.93 2.69
106 107 8.864069 AATGTCGAAATCTAGAGTGACATAAG 57.136 34.615 20.11 0.00 43.93 1.73
107 108 9.302345 GAAATGTCGAAATCTAGAGTGACATAA 57.698 33.333 20.11 0.90 43.93 1.90
108 109 8.466798 TGAAATGTCGAAATCTAGAGTGACATA 58.533 33.333 20.11 7.95 43.93 2.29
109 110 7.276658 GTGAAATGTCGAAATCTAGAGTGACAT 59.723 37.037 16.23 16.23 45.93 3.06
110 111 6.586463 GTGAAATGTCGAAATCTAGAGTGACA 59.414 38.462 13.63 13.63 40.24 3.58
111 112 6.809196 AGTGAAATGTCGAAATCTAGAGTGAC 59.191 38.462 0.00 1.12 0.00 3.67
112 113 6.925211 AGTGAAATGTCGAAATCTAGAGTGA 58.075 36.000 0.00 0.00 0.00 3.41
113 114 7.588143 AAGTGAAATGTCGAAATCTAGAGTG 57.412 36.000 0.00 0.00 0.00 3.51
114 115 8.499162 CAAAAGTGAAATGTCGAAATCTAGAGT 58.501 33.333 0.00 0.00 0.00 3.24
115 116 7.479916 GCAAAAGTGAAATGTCGAAATCTAGAG 59.520 37.037 0.00 0.00 0.00 2.43
116 117 7.041440 TGCAAAAGTGAAATGTCGAAATCTAGA 60.041 33.333 0.00 0.00 0.00 2.43
117 118 7.077605 TGCAAAAGTGAAATGTCGAAATCTAG 58.922 34.615 0.00 0.00 0.00 2.43
118 119 6.964908 TGCAAAAGTGAAATGTCGAAATCTA 58.035 32.000 0.00 0.00 0.00 1.98
119 120 5.830912 TGCAAAAGTGAAATGTCGAAATCT 58.169 33.333 0.00 0.00 0.00 2.40
120 121 6.198966 AGTTGCAAAAGTGAAATGTCGAAATC 59.801 34.615 0.00 0.00 0.00 2.17
121 122 6.042143 AGTTGCAAAAGTGAAATGTCGAAAT 58.958 32.000 0.00 0.00 0.00 2.17
122 123 5.406649 AGTTGCAAAAGTGAAATGTCGAAA 58.593 33.333 0.00 0.00 0.00 3.46
123 124 4.992688 AGTTGCAAAAGTGAAATGTCGAA 58.007 34.783 0.00 0.00 0.00 3.71
124 125 4.335315 AGAGTTGCAAAAGTGAAATGTCGA 59.665 37.500 0.00 0.00 0.00 4.20
125 126 4.438797 CAGAGTTGCAAAAGTGAAATGTCG 59.561 41.667 0.00 0.00 0.00 4.35
126 127 4.741676 CCAGAGTTGCAAAAGTGAAATGTC 59.258 41.667 0.00 0.00 0.00 3.06
127 128 4.402155 TCCAGAGTTGCAAAAGTGAAATGT 59.598 37.500 0.00 0.00 0.00 2.71
128 129 4.935702 TCCAGAGTTGCAAAAGTGAAATG 58.064 39.130 0.00 0.00 0.00 2.32
129 130 5.596836 TTCCAGAGTTGCAAAAGTGAAAT 57.403 34.783 0.00 0.00 0.00 2.17
130 131 5.398603 TTTCCAGAGTTGCAAAAGTGAAA 57.601 34.783 0.00 4.62 0.00 2.69
131 132 5.167845 GTTTTCCAGAGTTGCAAAAGTGAA 58.832 37.500 0.00 0.00 0.00 3.18
132 133 4.381505 GGTTTTCCAGAGTTGCAAAAGTGA 60.382 41.667 0.00 0.00 40.31 3.41
133 134 3.865164 GGTTTTCCAGAGTTGCAAAAGTG 59.135 43.478 0.00 0.00 40.31 3.16
134 135 3.428862 CGGTTTTCCAGAGTTGCAAAAGT 60.429 43.478 0.00 0.00 40.70 2.66
135 136 3.115554 CGGTTTTCCAGAGTTGCAAAAG 58.884 45.455 0.00 0.00 40.70 2.27
136 137 2.159170 CCGGTTTTCCAGAGTTGCAAAA 60.159 45.455 0.00 0.00 40.70 2.44
137 138 1.407258 CCGGTTTTCCAGAGTTGCAAA 59.593 47.619 0.00 0.00 40.70 3.68
138 139 1.028905 CCGGTTTTCCAGAGTTGCAA 58.971 50.000 0.00 0.00 40.70 4.08
139 140 1.452145 GCCGGTTTTCCAGAGTTGCA 61.452 55.000 1.90 0.00 40.70 4.08
140 141 1.285950 GCCGGTTTTCCAGAGTTGC 59.714 57.895 1.90 0.00 40.70 4.17
141 142 0.537371 AGGCCGGTTTTCCAGAGTTG 60.537 55.000 1.90 0.00 40.70 3.16
142 143 0.250770 GAGGCCGGTTTTCCAGAGTT 60.251 55.000 1.90 0.00 40.70 3.01
143 144 1.375326 GAGGCCGGTTTTCCAGAGT 59.625 57.895 1.90 0.00 40.70 3.24
144 145 1.741770 CGAGGCCGGTTTTCCAGAG 60.742 63.158 1.90 0.00 40.70 3.35
145 146 2.345991 CGAGGCCGGTTTTCCAGA 59.654 61.111 1.90 0.00 40.70 3.86
146 147 3.431725 GCGAGGCCGGTTTTCCAG 61.432 66.667 1.90 0.00 40.70 3.86
261 267 2.680370 GGGAAGAGGTGGCCGGAAT 61.680 63.158 5.05 0.00 0.00 3.01
288 318 2.359967 CCAGGGAGGAAGACGGGAC 61.360 68.421 0.00 0.00 41.22 4.46
607 639 1.233019 CACCTGAAGCACTTGTCCTG 58.767 55.000 0.00 0.00 0.00 3.86
608 640 0.536006 GCACCTGAAGCACTTGTCCT 60.536 55.000 0.00 0.00 0.00 3.85
685 719 1.992519 GATCCATGTCCAGGCAGCCT 61.993 60.000 8.70 8.70 0.00 4.58
696 730 2.501128 CAGTCGCGGGATCCATGT 59.499 61.111 15.23 0.00 0.00 3.21
840 891 1.820056 CTCGGCAGCGAGTAGGAGA 60.820 63.158 4.42 0.00 0.00 3.71
922 993 1.009449 GATCTCGGACTCGCCTTCG 60.009 63.158 0.00 0.00 36.13 3.79
943 1014 0.529337 TACGAACGCCGAAAACCACA 60.529 50.000 4.79 0.00 41.76 4.17
948 1019 0.031857 TGGACTACGAACGCCGAAAA 59.968 50.000 4.79 0.00 41.76 2.29
949 1020 0.664166 GTGGACTACGAACGCCGAAA 60.664 55.000 4.79 0.00 41.76 3.46
961 1032 0.704664 TCCAGCTCCTCTGTGGACTA 59.295 55.000 0.00 0.00 40.56 2.59
1197 1268 1.816835 CACGGTCTGAAGTACAGCCTA 59.183 52.381 0.00 0.00 45.38 3.93
1215 1286 1.961277 CTGTGACTGCCGGTTCCAC 60.961 63.158 1.90 7.36 0.00 4.02
1230 1301 1.079543 GATCGAGTGCACTGCCTGT 60.080 57.895 27.27 5.25 0.00 4.00
1256 1327 4.122776 CTCCATGACGATCCAAACCTTAG 58.877 47.826 0.00 0.00 0.00 2.18
1257 1328 3.118408 CCTCCATGACGATCCAAACCTTA 60.118 47.826 0.00 0.00 0.00 2.69
1375 1446 2.910199 CCTGAATGCCGAAAGATCTGA 58.090 47.619 0.00 0.00 0.00 3.27
1377 1448 1.211457 AGCCTGAATGCCGAAAGATCT 59.789 47.619 0.00 0.00 0.00 2.75
1398 1469 1.421410 GATTAGCAGTCCACGCCGTG 61.421 60.000 10.95 10.95 0.00 4.94
1419 1490 1.003573 AAGGGAAGGGATCGCCTCT 59.996 57.895 6.09 0.00 41.76 3.69
1506 1577 3.327754 GCAACTGCGTCGACGTGT 61.328 61.111 35.48 29.60 42.22 4.49
1532 1603 1.274703 CCAAGGCTCCCCAGCTTCTA 61.275 60.000 0.00 0.00 46.03 2.10
1578 1649 3.385384 CCTGGCAGACCGCTCTGA 61.385 66.667 17.94 0.00 46.32 3.27
1660 1731 2.810887 GCGCGCATCTCTCACACA 60.811 61.111 29.10 0.00 0.00 3.72
1735 1806 1.217779 GCCAGTCTGTCCTCTCTGC 59.782 63.158 0.00 0.00 0.00 4.26
1737 1808 2.347322 GCGCCAGTCTGTCCTCTCT 61.347 63.158 0.00 0.00 0.00 3.10
1804 1875 0.029681 ACCCTATCCTGCACCCTCAT 60.030 55.000 0.00 0.00 0.00 2.90
1810 1881 0.462759 GCTGTCACCCTATCCTGCAC 60.463 60.000 0.00 0.00 0.00 4.57
1827 1898 1.143684 TCAAAAGCTGACTTCCTGGCT 59.856 47.619 0.00 0.00 34.05 4.75
1849 1920 1.301716 GCTGCTGACCCGAAAGACA 60.302 57.895 0.00 0.00 0.00 3.41
1924 1995 1.302671 CCGCCTACCCGGTCAAAAA 60.303 57.895 0.00 0.00 43.24 1.94
1932 2003 4.301027 GCTCCATCCGCCTACCCG 62.301 72.222 0.00 0.00 0.00 5.28
1940 2011 1.732259 GTAACACTTGTGCTCCATCCG 59.268 52.381 0.10 0.00 0.00 4.18
1976 2047 0.537371 CTCAACAACCAGGGTCACCC 60.537 60.000 3.85 3.85 45.90 4.61
2108 2179 0.745845 CAGAAGAGTCCCCATTGGCG 60.746 60.000 0.00 0.00 0.00 5.69
2194 2268 2.418910 CCTGGACGGAGCGATCAGT 61.419 63.158 6.06 6.06 32.51 3.41
2306 2380 2.922283 CCCTCCATTATTGGCTCCCTAT 59.078 50.000 0.00 0.00 43.29 2.57
2336 2410 4.760047 CCCCACCTTCAGCGTCCG 62.760 72.222 0.00 0.00 0.00 4.79
2341 2415 2.991540 GTTGGCCCCACCTTCAGC 60.992 66.667 0.00 0.00 40.22 4.26
2358 2432 1.335597 GCATGTGCATGATTCCCATCG 60.336 52.381 15.53 0.00 41.20 3.84
2417 2491 5.193728 ACACCCTCCATTTCCATACTTGTAT 59.806 40.000 0.00 0.00 0.00 2.29
2431 2505 1.599047 CAGCGAGAACACCCTCCAT 59.401 57.895 0.00 0.00 0.00 3.41
2441 2515 4.020617 CCAGCCCACCAGCGAGAA 62.021 66.667 0.00 0.00 38.01 2.87
2451 2525 3.414193 CTGCCCTCATCCAGCCCA 61.414 66.667 0.00 0.00 0.00 5.36
2462 2536 4.087892 CACGCTACAGCCTGCCCT 62.088 66.667 0.00 0.00 37.91 5.19
2473 2574 2.345991 GGCCAGTTGGTCACGCTA 59.654 61.111 0.00 0.00 40.23 4.26
2518 2619 2.190578 CATGCCTTCCGTCTCCCC 59.809 66.667 0.00 0.00 0.00 4.81
2601 2756 0.679960 CTTTTAACAGGGGAGGGGCG 60.680 60.000 0.00 0.00 0.00 6.13
2614 2769 1.673626 CGCCGCCTGTACCTCTTTTAA 60.674 52.381 0.00 0.00 0.00 1.52
2616 2771 1.375523 CGCCGCCTGTACCTCTTTT 60.376 57.895 0.00 0.00 0.00 2.27
2653 2808 3.873801 GCTCTCTTGGGCATGAAAGGTTA 60.874 47.826 0.00 0.00 0.00 2.85
2663 2818 0.323451 TCGAGTAGCTCTCTTGGGCA 60.323 55.000 0.00 0.00 40.75 5.36
2697 2852 2.401583 TTGATCTTCGTGTCCCCATG 57.598 50.000 0.00 0.00 0.00 3.66
2698 2853 2.356125 CCTTTGATCTTCGTGTCCCCAT 60.356 50.000 0.00 0.00 0.00 4.00
2763 2918 1.460689 AACCACCAAGTCCTCCGGA 60.461 57.895 2.93 2.93 0.00 5.14
2835 2990 3.442625 CAGCAATGATCCTCACATGTTGT 59.557 43.478 0.00 0.00 29.48 3.32


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

AutoCloner maintained by Alex Coulton.