Multiple sequence alignment - TraesCS1A01G337200

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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 TraesCS1A01G337200 chr1A 100.000 2357 0 0 1 2357 526739237 526736881 0.000000e+00 4353
1 TraesCS1A01G337200 chr1B 92.327 1225 45 12 998 2189 580438556 580437348 0.000000e+00 1696
2 TraesCS1A01G337200 chr1B 83.476 702 57 25 340 997 580439280 580438594 1.210000e-167 599
3 TraesCS1A01G337200 chr1B 84.524 168 18 4 2190 2357 580437303 580437144 2.420000e-35 159
4 TraesCS1A01G337200 chr1B 96.875 96 2 1 250 344 580439401 580439306 2.420000e-35 159
5 TraesCS1A01G337200 chr1D 90.805 1218 47 20 996 2190 428612949 428611774 0.000000e+00 1568
6 TraesCS1A01G337200 chr1D 86.179 369 33 12 394 755 428618777 428618420 1.320000e-102 383
7 TraesCS1A01G337200 chr1D 91.403 221 15 4 1 218 481422863 481423082 1.370000e-77 300
8 TraesCS1A01G337200 chr1D 84.644 267 18 8 753 997 428613248 428612983 6.510000e-61 244
9 TraesCS1A01G337200 chr1D 93.600 125 8 0 2190 2314 428611730 428611606 1.110000e-43 187
10 TraesCS1A01G337200 chr1D 93.578 109 4 3 238 344 428618990 428618883 2.420000e-35 159
11 TraesCS1A01G337200 chr3D 93.213 221 12 2 1 218 381007057 381006837 2.920000e-84 322
12 TraesCS1A01G337200 chr3D 91.364 220 17 2 1 218 4403936 4403717 1.370000e-77 300
13 TraesCS1A01G337200 chr4D 92.342 222 12 5 1 218 491688248 491688028 6.330000e-81 311
14 TraesCS1A01G337200 chr4D 91.855 221 16 2 1 219 10380955 10381175 8.180000e-80 307
15 TraesCS1A01G337200 chr4D 91.403 221 16 2 1 218 363566439 363566219 1.370000e-77 300
16 TraesCS1A01G337200 chr5A 92.237 219 14 3 3 218 142745317 142745099 8.180000e-80 307
17 TraesCS1A01G337200 chr2D 91.441 222 15 3 2 219 359398055 359397834 3.810000e-78 302
18 TraesCS1A01G337200 chr5D 91.403 221 16 2 1 218 333231369 333231589 1.370000e-77 300
19 TraesCS1A01G337200 chr6A 93.137 102 6 1 2215 2316 29127517 29127417 5.250000e-32 148
20 TraesCS1A01G337200 chr6A 93.814 97 5 1 2215 2311 29022847 29022942 6.790000e-31 145
21 TraesCS1A01G337200 chr6A 92.784 97 6 1 2215 2311 28947948 28948043 3.160000e-29 139
22 TraesCS1A01G337200 chrUn 87.805 123 14 1 2194 2316 103501017 103501138 2.440000e-30 143
23 TraesCS1A01G337200 chrUn 91.753 97 7 1 2215 2311 103546215 103546120 1.470000e-27 134
24 TraesCS1A01G337200 chr6B 91.753 97 7 1 2215 2311 54697238 54697333 1.470000e-27 134
25 TraesCS1A01G337200 chr6B 89.691 97 9 1 2215 2311 54899098 54899003 3.180000e-24 122


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 TraesCS1A01G337200 chr1A 526736881 526739237 2356 True 4353.000000 4353 100.0000 1 2357 1 chr1A.!!$R1 2356
1 TraesCS1A01G337200 chr1B 580437144 580439401 2257 True 653.250000 1696 89.3005 250 2357 4 chr1B.!!$R1 2107
2 TraesCS1A01G337200 chr1D 428611606 428613248 1642 True 666.333333 1568 89.6830 753 2314 3 chr1D.!!$R1 1561
3 TraesCS1A01G337200 chr1D 428618420 428618990 570 True 271.000000 383 89.8785 238 755 2 chr1D.!!$R2 517

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
39 40 0.036952 AGGTGTTGGAGCGATGTCTG 60.037 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2104 0.179142 GAGCGTAACCGGGACTCTTC 60.179 60.0 6.32 0.0 33.68 2.87 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
22 23 3.997021 GGCATCCGACATTAGATGTTAGG 59.003 47.826 9.03 9.03 45.03 2.69
23 24 4.503296 GGCATCCGACATTAGATGTTAGGT 60.503 45.833 12.78 0.00 45.03 3.08
24 25 4.449068 GCATCCGACATTAGATGTTAGGTG 59.551 45.833 12.78 7.72 45.03 4.00
25 26 5.601662 CATCCGACATTAGATGTTAGGTGT 58.398 41.667 12.78 0.00 45.03 4.16
26 27 5.670792 TCCGACATTAGATGTTAGGTGTT 57.329 39.130 12.78 0.00 45.03 3.32
27 28 5.416083 TCCGACATTAGATGTTAGGTGTTG 58.584 41.667 12.78 0.00 45.03 3.33
28 29 4.570772 CCGACATTAGATGTTAGGTGTTGG 59.429 45.833 0.00 0.00 45.03 3.77
29 30 5.416083 CGACATTAGATGTTAGGTGTTGGA 58.584 41.667 0.00 0.00 45.03 3.53
30 31 5.520288 CGACATTAGATGTTAGGTGTTGGAG 59.480 44.000 0.00 0.00 45.03 3.86
31 32 5.186198 ACATTAGATGTTAGGTGTTGGAGC 58.814 41.667 0.00 0.00 41.63 4.70
32 33 2.386661 AGATGTTAGGTGTTGGAGCG 57.613 50.000 0.00 0.00 0.00 5.03
33 34 1.899814 AGATGTTAGGTGTTGGAGCGA 59.100 47.619 0.00 0.00 0.00 4.93
34 35 2.501723 AGATGTTAGGTGTTGGAGCGAT 59.498 45.455 0.00 0.00 0.00 4.58
35 36 2.093306 TGTTAGGTGTTGGAGCGATG 57.907 50.000 0.00 0.00 0.00 3.84
36 37 1.346395 TGTTAGGTGTTGGAGCGATGT 59.654 47.619 0.00 0.00 0.00 3.06
37 38 2.000447 GTTAGGTGTTGGAGCGATGTC 59.000 52.381 0.00 0.00 0.00 3.06
38 39 1.557099 TAGGTGTTGGAGCGATGTCT 58.443 50.000 0.00 0.00 0.00 3.41
39 40 0.036952 AGGTGTTGGAGCGATGTCTG 60.037 55.000 0.00 0.00 0.00 3.51
40 41 0.320771 GGTGTTGGAGCGATGTCTGT 60.321 55.000 0.00 0.00 0.00 3.41
41 42 1.512926 GTGTTGGAGCGATGTCTGTT 58.487 50.000 0.00 0.00 0.00 3.16
42 43 1.873591 GTGTTGGAGCGATGTCTGTTT 59.126 47.619 0.00 0.00 0.00 2.83
43 44 1.872952 TGTTGGAGCGATGTCTGTTTG 59.127 47.619 0.00 0.00 0.00 2.93
44 45 1.197721 GTTGGAGCGATGTCTGTTTGG 59.802 52.381 0.00 0.00 0.00 3.28
45 46 0.396435 TGGAGCGATGTCTGTTTGGT 59.604 50.000 0.00 0.00 0.00 3.67
46 47 1.621317 TGGAGCGATGTCTGTTTGGTA 59.379 47.619 0.00 0.00 0.00 3.25
47 48 2.236146 TGGAGCGATGTCTGTTTGGTAT 59.764 45.455 0.00 0.00 0.00 2.73
48 49 3.270877 GGAGCGATGTCTGTTTGGTATT 58.729 45.455 0.00 0.00 0.00 1.89
49 50 4.081365 TGGAGCGATGTCTGTTTGGTATTA 60.081 41.667 0.00 0.00 0.00 0.98
50 51 4.508124 GGAGCGATGTCTGTTTGGTATTAG 59.492 45.833 0.00 0.00 0.00 1.73
51 52 4.442706 AGCGATGTCTGTTTGGTATTAGG 58.557 43.478 0.00 0.00 0.00 2.69
52 53 3.002348 GCGATGTCTGTTTGGTATTAGGC 59.998 47.826 0.00 0.00 0.00 3.93
53 54 4.442706 CGATGTCTGTTTGGTATTAGGCT 58.557 43.478 0.00 0.00 0.00 4.58
54 55 4.876107 CGATGTCTGTTTGGTATTAGGCTT 59.124 41.667 0.00 0.00 0.00 4.35
55 56 5.220662 CGATGTCTGTTTGGTATTAGGCTTG 60.221 44.000 0.00 0.00 0.00 4.01
56 57 4.331968 TGTCTGTTTGGTATTAGGCTTGG 58.668 43.478 0.00 0.00 0.00 3.61
57 58 4.042311 TGTCTGTTTGGTATTAGGCTTGGA 59.958 41.667 0.00 0.00 0.00 3.53
58 59 5.193679 GTCTGTTTGGTATTAGGCTTGGAT 58.806 41.667 0.00 0.00 0.00 3.41
59 60 6.069905 TGTCTGTTTGGTATTAGGCTTGGATA 60.070 38.462 0.00 0.00 0.00 2.59
60 61 6.998673 GTCTGTTTGGTATTAGGCTTGGATAT 59.001 38.462 0.00 0.00 0.00 1.63
61 62 7.502561 GTCTGTTTGGTATTAGGCTTGGATATT 59.497 37.037 0.00 0.00 0.00 1.28
62 63 7.719633 TCTGTTTGGTATTAGGCTTGGATATTC 59.280 37.037 0.00 0.00 0.00 1.75
63 64 6.485313 TGTTTGGTATTAGGCTTGGATATTCG 59.515 38.462 0.00 0.00 0.00 3.34
64 65 5.160607 TGGTATTAGGCTTGGATATTCGG 57.839 43.478 0.00 0.00 0.00 4.30
65 66 3.939592 GGTATTAGGCTTGGATATTCGGC 59.060 47.826 0.00 0.00 0.00 5.54
66 67 3.788227 ATTAGGCTTGGATATTCGGCA 57.212 42.857 0.00 0.00 0.00 5.69
67 68 2.543777 TAGGCTTGGATATTCGGCAC 57.456 50.000 0.00 0.00 0.00 5.01
68 69 0.179018 AGGCTTGGATATTCGGCACC 60.179 55.000 1.99 0.00 0.00 5.01
69 70 1.172812 GGCTTGGATATTCGGCACCC 61.173 60.000 1.99 0.00 0.00 4.61
70 71 1.172812 GCTTGGATATTCGGCACCCC 61.173 60.000 0.00 0.00 0.00 4.95
71 72 0.474184 CTTGGATATTCGGCACCCCT 59.526 55.000 0.00 0.00 0.00 4.79
72 73 0.923358 TTGGATATTCGGCACCCCTT 59.077 50.000 0.00 0.00 0.00 3.95
73 74 0.472471 TGGATATTCGGCACCCCTTC 59.528 55.000 0.00 0.00 0.00 3.46
74 75 0.472471 GGATATTCGGCACCCCTTCA 59.528 55.000 0.00 0.00 0.00 3.02
75 76 1.073923 GGATATTCGGCACCCCTTCAT 59.926 52.381 0.00 0.00 0.00 2.57
76 77 2.427506 GATATTCGGCACCCCTTCATC 58.572 52.381 0.00 0.00 0.00 2.92
77 78 1.208706 TATTCGGCACCCCTTCATCA 58.791 50.000 0.00 0.00 0.00 3.07
78 79 0.394352 ATTCGGCACCCCTTCATCAC 60.394 55.000 0.00 0.00 0.00 3.06
79 80 2.796483 TTCGGCACCCCTTCATCACG 62.796 60.000 0.00 0.00 0.00 4.35
80 81 2.438434 GGCACCCCTTCATCACGG 60.438 66.667 0.00 0.00 0.00 4.94
81 82 2.438434 GCACCCCTTCATCACGGG 60.438 66.667 0.00 0.00 43.05 5.28
87 88 0.687354 CCCTTCATCACGGGGATAGG 59.313 60.000 2.54 2.54 42.58 2.57
88 89 1.717032 CCTTCATCACGGGGATAGGA 58.283 55.000 3.34 0.00 34.78 2.94
89 90 1.620819 CCTTCATCACGGGGATAGGAG 59.379 57.143 3.34 0.00 34.78 3.69
90 91 2.320781 CTTCATCACGGGGATAGGAGT 58.679 52.381 0.00 0.00 33.95 3.85
91 92 3.497332 CTTCATCACGGGGATAGGAGTA 58.503 50.000 0.00 0.00 33.95 2.59
92 93 3.156288 TCATCACGGGGATAGGAGTAG 57.844 52.381 0.00 0.00 33.95 2.57
93 94 1.546476 CATCACGGGGATAGGAGTAGC 59.454 57.143 0.00 0.00 33.95 3.58
94 95 0.536687 TCACGGGGATAGGAGTAGCG 60.537 60.000 0.00 0.00 0.00 4.26
95 96 0.536687 CACGGGGATAGGAGTAGCGA 60.537 60.000 0.00 0.00 0.00 4.93
96 97 0.536915 ACGGGGATAGGAGTAGCGAC 60.537 60.000 0.00 0.00 0.00 5.19
97 98 0.536687 CGGGGATAGGAGTAGCGACA 60.537 60.000 0.00 0.00 0.00 4.35
98 99 1.249407 GGGGATAGGAGTAGCGACAG 58.751 60.000 0.00 0.00 0.00 3.51
99 100 1.249407 GGGATAGGAGTAGCGACAGG 58.751 60.000 0.00 0.00 0.00 4.00
100 101 1.479021 GGGATAGGAGTAGCGACAGGT 60.479 57.143 0.00 0.00 0.00 4.00
101 102 1.609555 GGATAGGAGTAGCGACAGGTG 59.390 57.143 0.00 0.00 0.00 4.00
102 103 2.299521 GATAGGAGTAGCGACAGGTGT 58.700 52.381 0.00 0.00 0.00 4.16
103 104 2.211250 TAGGAGTAGCGACAGGTGTT 57.789 50.000 0.00 0.00 0.00 3.32
104 105 0.603569 AGGAGTAGCGACAGGTGTTG 59.396 55.000 0.00 0.00 0.00 3.33
110 111 4.454948 CGACAGGTGTTGCCAAGA 57.545 55.556 0.00 0.00 40.61 3.02
111 112 2.932663 CGACAGGTGTTGCCAAGAT 58.067 52.632 0.00 0.00 40.61 2.40
112 113 0.518636 CGACAGGTGTTGCCAAGATG 59.481 55.000 0.00 0.00 40.61 2.90
113 114 0.883833 GACAGGTGTTGCCAAGATGG 59.116 55.000 0.00 0.00 41.55 3.51
114 115 0.185901 ACAGGTGTTGCCAAGATGGT 59.814 50.000 0.00 0.00 40.46 3.55
115 116 1.423541 ACAGGTGTTGCCAAGATGGTA 59.576 47.619 0.00 0.00 40.46 3.25
116 117 2.086869 CAGGTGTTGCCAAGATGGTAG 58.913 52.381 0.00 0.00 40.46 3.18
117 118 1.705186 AGGTGTTGCCAAGATGGTAGT 59.295 47.619 0.00 0.00 40.46 2.73
118 119 2.108250 AGGTGTTGCCAAGATGGTAGTT 59.892 45.455 0.00 0.00 40.46 2.24
119 120 2.890945 GGTGTTGCCAAGATGGTAGTTT 59.109 45.455 0.00 0.00 40.46 2.66
120 121 3.057526 GGTGTTGCCAAGATGGTAGTTTC 60.058 47.826 0.00 0.00 40.46 2.78
121 122 3.568007 GTGTTGCCAAGATGGTAGTTTCA 59.432 43.478 0.00 0.00 40.46 2.69
122 123 3.820467 TGTTGCCAAGATGGTAGTTTCAG 59.180 43.478 0.00 0.00 40.46 3.02
123 124 3.071874 TGCCAAGATGGTAGTTTCAGG 57.928 47.619 0.00 0.00 40.46 3.86
124 125 1.745653 GCCAAGATGGTAGTTTCAGGC 59.254 52.381 0.00 0.00 40.46 4.85
125 126 2.619074 GCCAAGATGGTAGTTTCAGGCT 60.619 50.000 0.00 0.00 40.46 4.58
126 127 3.690460 CCAAGATGGTAGTTTCAGGCTT 58.310 45.455 0.00 0.00 31.35 4.35
127 128 4.843728 CCAAGATGGTAGTTTCAGGCTTA 58.156 43.478 0.00 0.00 31.35 3.09
128 129 4.636206 CCAAGATGGTAGTTTCAGGCTTAC 59.364 45.833 0.00 0.00 31.35 2.34
129 130 5.491982 CAAGATGGTAGTTTCAGGCTTACT 58.508 41.667 0.00 0.00 0.00 2.24
130 131 7.568325 CCAAGATGGTAGTTTCAGGCTTACTG 61.568 46.154 4.43 0.00 39.66 2.74
131 132 9.630391 CCAAGATGGTAGTTTCAGGCTTACTGA 62.630 44.444 4.43 0.00 42.82 3.41
143 144 5.552870 AGGCTTACTGATGTATTACCCTG 57.447 43.478 0.00 0.00 0.00 4.45
144 145 4.969359 AGGCTTACTGATGTATTACCCTGT 59.031 41.667 0.00 0.00 0.00 4.00
145 146 6.141083 AGGCTTACTGATGTATTACCCTGTA 58.859 40.000 0.00 0.00 0.00 2.74
146 147 6.614087 AGGCTTACTGATGTATTACCCTGTAA 59.386 38.462 11.51 11.51 0.00 2.41
147 148 6.929606 GGCTTACTGATGTATTACCCTGTAAG 59.070 42.308 21.99 21.99 40.66 2.34
185 186 7.862741 ATTAATAAAATGACTGCATGCATCG 57.137 32.000 22.97 13.40 34.26 3.84
186 187 1.917273 AAAATGACTGCATGCATCGC 58.083 45.000 22.97 13.76 34.26 4.58
187 188 0.101759 AAATGACTGCATGCATCGCC 59.898 50.000 22.97 10.95 34.26 5.54
188 189 1.731433 AATGACTGCATGCATCGCCC 61.731 55.000 22.97 9.17 34.26 6.13
189 190 2.825387 GACTGCATGCATCGCCCA 60.825 61.111 22.97 0.00 0.00 5.36
190 191 2.827190 ACTGCATGCATCGCCCAG 60.827 61.111 22.97 10.18 0.00 4.45
191 192 2.515290 CTGCATGCATCGCCCAGA 60.515 61.111 22.97 0.00 0.00 3.86
192 193 1.897137 CTGCATGCATCGCCCAGAT 60.897 57.895 22.97 0.00 41.01 2.90
199 200 2.827423 ATCGCCCAGATGCAGAGG 59.173 61.111 0.00 0.00 38.36 3.69
200 201 3.472943 ATCGCCCAGATGCAGAGGC 62.473 63.158 8.59 8.59 42.18 4.70
203 204 4.559063 CCCAGATGCAGAGGCCGG 62.559 72.222 0.00 0.00 40.13 6.13
204 205 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
205 206 3.790437 CAGATGCAGAGGCCGGGT 61.790 66.667 2.18 0.00 40.13 5.28
206 207 2.041922 AGATGCAGAGGCCGGGTA 60.042 61.111 2.18 0.00 40.13 3.69
207 208 2.109181 GATGCAGAGGCCGGGTAC 59.891 66.667 2.18 0.00 40.13 3.34
208 209 2.687200 ATGCAGAGGCCGGGTACA 60.687 61.111 2.18 0.00 40.13 2.90
209 210 2.044806 GATGCAGAGGCCGGGTACAT 62.045 60.000 2.18 0.00 40.13 2.29
210 211 2.044806 ATGCAGAGGCCGGGTACATC 62.045 60.000 2.18 0.00 40.13 3.06
211 212 2.435693 GCAGAGGCCGGGTACATCT 61.436 63.158 2.18 0.00 0.00 2.90
212 213 1.742768 CAGAGGCCGGGTACATCTC 59.257 63.158 2.18 0.00 0.00 2.75
213 214 1.457831 AGAGGCCGGGTACATCTCC 60.458 63.158 2.18 0.00 0.00 3.71
214 215 1.457831 GAGGCCGGGTACATCTCCT 60.458 63.158 2.18 0.00 0.00 3.69
215 216 1.003051 AGGCCGGGTACATCTCCTT 59.997 57.895 2.18 0.00 0.00 3.36
216 217 0.620700 AGGCCGGGTACATCTCCTTT 60.621 55.000 2.18 0.00 0.00 3.11
217 218 0.255033 GGCCGGGTACATCTCCTTTT 59.745 55.000 2.18 0.00 0.00 2.27
218 219 1.340697 GGCCGGGTACATCTCCTTTTT 60.341 52.381 2.18 0.00 0.00 1.94
364 395 4.378459 GCTACCAGTGCAATTGTGTTCTAC 60.378 45.833 7.40 0.00 0.00 2.59
365 396 3.820557 ACCAGTGCAATTGTGTTCTACT 58.179 40.909 7.40 0.37 0.00 2.57
366 397 3.565482 ACCAGTGCAATTGTGTTCTACTG 59.435 43.478 7.40 11.26 35.17 2.74
367 398 3.565482 CCAGTGCAATTGTGTTCTACTGT 59.435 43.478 7.40 0.00 33.95 3.55
368 399 4.754618 CCAGTGCAATTGTGTTCTACTGTA 59.245 41.667 7.40 0.00 33.95 2.74
383 414 2.964740 ACTGTAGCAGCTGTATGTGTG 58.035 47.619 16.64 2.93 34.37 3.82
421 483 1.793258 CTGCTAGCAATGATCCTCGG 58.207 55.000 19.86 0.00 0.00 4.63
453 519 0.249073 CTATTGCGGTGGTCCTCTCG 60.249 60.000 0.00 0.00 0.00 4.04
464 530 3.318275 GTGGTCCTCTCGCTAATGATACA 59.682 47.826 0.00 0.00 0.00 2.29
546 615 5.256806 AGGAGGCTTAATAAACAAGTGGT 57.743 39.130 0.00 0.00 0.00 4.16
568 637 7.547722 GTGGTCACCTTTAAGTTCAAAACAAAT 59.452 33.333 0.00 0.00 0.00 2.32
569 638 8.750298 TGGTCACCTTTAAGTTCAAAACAAATA 58.250 29.630 0.00 0.00 0.00 1.40
570 639 9.027129 GGTCACCTTTAAGTTCAAAACAAATAC 57.973 33.333 0.00 0.00 0.00 1.89
571 640 8.739461 GTCACCTTTAAGTTCAAAACAAATACG 58.261 33.333 0.00 0.00 0.00 3.06
616 685 6.356714 GTGCACGCCTTTGAAAATTTAAATTG 59.643 34.615 14.04 1.55 0.00 2.32
619 688 6.017523 CACGCCTTTGAAAATTTAAATTGGGT 60.018 34.615 14.04 10.61 0.00 4.51
696 765 8.947055 ATACCATTGGATTCACATTTAAAAGC 57.053 30.769 10.37 0.00 0.00 3.51
702 771 8.729805 TTGGATTCACATTTAAAAGCAGTTTT 57.270 26.923 0.00 0.00 39.31 2.43
704 774 9.474920 TGGATTCACATTTAAAAGCAGTTTTAG 57.525 29.630 0.00 0.00 38.93 1.85
711 781 7.491048 ACATTTAAAAGCAGTTTTAGTGGTGTG 59.509 33.333 0.00 0.00 38.93 3.82
712 782 3.436700 AAAGCAGTTTTAGTGGTGTGC 57.563 42.857 0.00 0.00 28.47 4.57
718 788 4.032786 GCAGTTTTAGTGGTGTGCTTTTTG 59.967 41.667 0.00 0.00 0.00 2.44
761 834 7.811117 AATTGTTGTAAGCACCTAGTAAACA 57.189 32.000 0.00 0.00 0.00 2.83
821 897 6.071463 CGAACCGAAAGACAAAATAACTGAG 58.929 40.000 0.00 0.00 0.00 3.35
846 922 7.013369 AGACTTCTGAATTTTTAAGTGGTGACC 59.987 37.037 0.00 0.00 32.51 4.02
865 941 1.480545 CCGAAATTTGGAACCATCCCC 59.519 52.381 1.22 0.00 45.95 4.81
866 942 1.480545 CGAAATTTGGAACCATCCCCC 59.519 52.381 0.00 0.00 45.95 5.40
867 943 2.832838 GAAATTTGGAACCATCCCCCT 58.167 47.619 0.00 0.00 45.95 4.79
869 945 3.290039 AATTTGGAACCATCCCCCTTT 57.710 42.857 0.00 0.00 45.95 3.11
870 946 2.022718 TTTGGAACCATCCCCCTTTG 57.977 50.000 0.00 0.00 45.95 2.77
905 992 4.033709 CTCCTAATCCAACCCTCTCTGAA 58.966 47.826 0.00 0.00 0.00 3.02
908 995 2.770164 ATCCAACCCTCTCTGAAACG 57.230 50.000 0.00 0.00 0.00 3.60
1119 1256 2.584391 GCGGTTCCACCTCCTGTCT 61.584 63.158 0.00 0.00 35.66 3.41
1275 1412 1.604693 GCCAAGAACTTCGACGAAGGA 60.605 52.381 34.04 5.07 43.25 3.36
1384 1533 2.312722 TTTTCCTTGTCGTCGGTTCA 57.687 45.000 0.00 0.00 0.00 3.18
1387 1536 1.299620 CCTTGTCGTCGGTTCACGT 60.300 57.895 0.00 0.00 44.69 4.49
1401 1550 2.864343 GTTCACGTGTAGCTGTTGTTCT 59.136 45.455 16.51 0.00 0.00 3.01
1483 1632 4.514441 CAGAAGATGCAGACTGTTCTTGTT 59.486 41.667 20.61 10.55 0.00 2.83
1528 1686 1.395608 CGTCTCGTCTCTCCTTGTCTC 59.604 57.143 0.00 0.00 0.00 3.36
1533 1691 0.534873 GTCTCTCCTTGTCTCCCTGC 59.465 60.000 0.00 0.00 0.00 4.85
1550 1708 0.660300 TGCGATGATCCGATCGAACG 60.660 55.000 18.66 8.26 46.72 3.95
1551 1709 0.385598 GCGATGATCCGATCGAACGA 60.386 55.000 18.66 5.77 46.72 3.85
1552 1710 1.924629 GCGATGATCCGATCGAACGAA 60.925 52.381 18.66 0.00 46.72 3.85
1553 1711 1.709203 CGATGATCCGATCGAACGAAC 59.291 52.381 18.66 4.94 46.72 3.95
1645 1805 2.159881 CGTCAATTTCCGTTTCGTCCTC 60.160 50.000 0.00 0.00 0.00 3.71
1662 1822 1.474320 CCTCGACAAACCACAAGGACA 60.474 52.381 0.00 0.00 38.69 4.02
1777 1938 0.606673 GGGGAATAGATTCGCTGGGC 60.607 60.000 16.17 0.10 45.66 5.36
1830 1991 2.671963 GGTGGAGCCGGGAACAAC 60.672 66.667 2.18 0.00 0.00 3.32
1837 1998 2.867472 CCGGGAACAACATGACGC 59.133 61.111 0.00 0.00 0.00 5.19
1841 2002 1.399727 CGGGAACAACATGACGCTTTC 60.400 52.381 0.00 0.00 0.00 2.62
1846 2007 5.147162 GGAACAACATGACGCTTTCTTTAG 58.853 41.667 0.00 0.00 0.00 1.85
1985 2146 2.997315 TGTCGGCCTCTGGTCCAG 60.997 66.667 13.21 13.21 0.00 3.86
2086 2260 1.922447 AGGGCAACATGGTTAGATCCA 59.078 47.619 0.00 0.00 42.01 3.41
2182 2362 1.512926 AGTTCGTTGTGATGTCAGGC 58.487 50.000 0.00 0.00 0.00 4.85
2186 2366 0.603707 CGTTGTGATGTCAGGCCTGT 60.604 55.000 31.58 13.82 0.00 4.00
2188 2368 1.267806 GTTGTGATGTCAGGCCTGTTG 59.732 52.381 31.58 8.56 0.00 3.33
2211 2436 0.250467 AACTAGTGCCTGCTGGTGTG 60.250 55.000 11.69 0.87 35.27 3.82
2215 2440 1.601759 GTGCCTGCTGGTGTGATGT 60.602 57.895 11.69 0.00 35.27 3.06
2236 2461 8.283992 TGATGTTAACGTTTGATTACATTCGTT 58.716 29.630 5.91 0.00 42.65 3.85
2245 2470 7.061905 CGTTTGATTACATTCGTTAGTGACTCT 59.938 37.037 0.00 0.00 0.00 3.24
2311 2536 1.272147 GGTTTGATCCCCAGCAGAGTT 60.272 52.381 0.00 0.00 0.00 3.01
2314 2539 0.615331 TGATCCCCAGCAGAGTTGAC 59.385 55.000 0.00 0.00 0.00 3.18
2315 2540 0.908198 GATCCCCAGCAGAGTTGACT 59.092 55.000 0.00 0.00 0.00 3.41
2316 2541 0.617413 ATCCCCAGCAGAGTTGACTG 59.383 55.000 0.00 0.00 40.43 3.51
2328 2553 3.381590 AGAGTTGACTGCCTTTTGTTTCC 59.618 43.478 0.00 0.00 0.00 3.13
2335 2560 1.179174 GCCTTTTGTTTCCGCCCTCT 61.179 55.000 0.00 0.00 0.00 3.69
2348 2573 3.325716 TCCGCCCTCTTAGTTTTTAGTGT 59.674 43.478 0.00 0.00 0.00 3.55
2354 2579 6.092807 GCCCTCTTAGTTTTTAGTGTGATCAG 59.907 42.308 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.997021 CCTAACATCTAATGTCGGATGCC 59.003 47.826 0.00 0.00 44.07 4.40
1 2 4.449068 CACCTAACATCTAATGTCGGATGC 59.551 45.833 12.55 0.00 44.07 3.91
2 3 5.601662 ACACCTAACATCTAATGTCGGATG 58.398 41.667 12.55 0.00 44.07 3.51
3 4 5.871396 ACACCTAACATCTAATGTCGGAT 57.129 39.130 12.55 0.00 44.07 4.18
4 5 5.416083 CAACACCTAACATCTAATGTCGGA 58.584 41.667 12.55 0.00 44.07 4.55
5 6 4.570772 CCAACACCTAACATCTAATGTCGG 59.429 45.833 0.00 0.83 44.07 4.79
6 7 5.416083 TCCAACACCTAACATCTAATGTCG 58.584 41.667 0.00 0.00 44.07 4.35
10 11 4.161565 TCGCTCCAACACCTAACATCTAAT 59.838 41.667 0.00 0.00 0.00 1.73
13 14 1.899814 TCGCTCCAACACCTAACATCT 59.100 47.619 0.00 0.00 0.00 2.90
14 15 2.380084 TCGCTCCAACACCTAACATC 57.620 50.000 0.00 0.00 0.00 3.06
15 16 2.027192 ACATCGCTCCAACACCTAACAT 60.027 45.455 0.00 0.00 0.00 2.71
17 18 2.000447 GACATCGCTCCAACACCTAAC 59.000 52.381 0.00 0.00 0.00 2.34
19 20 1.204704 CAGACATCGCTCCAACACCTA 59.795 52.381 0.00 0.00 0.00 3.08
20 21 0.036952 CAGACATCGCTCCAACACCT 60.037 55.000 0.00 0.00 0.00 4.00
21 22 0.320771 ACAGACATCGCTCCAACACC 60.321 55.000 0.00 0.00 0.00 4.16
22 23 1.512926 AACAGACATCGCTCCAACAC 58.487 50.000 0.00 0.00 0.00 3.32
23 24 1.872952 CAAACAGACATCGCTCCAACA 59.127 47.619 0.00 0.00 0.00 3.33
24 25 1.197721 CCAAACAGACATCGCTCCAAC 59.802 52.381 0.00 0.00 0.00 3.77
25 26 1.202758 ACCAAACAGACATCGCTCCAA 60.203 47.619 0.00 0.00 0.00 3.53
26 27 0.396435 ACCAAACAGACATCGCTCCA 59.604 50.000 0.00 0.00 0.00 3.86
27 28 2.380084 TACCAAACAGACATCGCTCC 57.620 50.000 0.00 0.00 0.00 4.70
28 29 4.508124 CCTAATACCAAACAGACATCGCTC 59.492 45.833 0.00 0.00 0.00 5.03
29 30 4.442706 CCTAATACCAAACAGACATCGCT 58.557 43.478 0.00 0.00 0.00 4.93
30 31 3.002348 GCCTAATACCAAACAGACATCGC 59.998 47.826 0.00 0.00 0.00 4.58
31 32 4.442706 AGCCTAATACCAAACAGACATCG 58.557 43.478 0.00 0.00 0.00 3.84
32 33 5.066505 CCAAGCCTAATACCAAACAGACATC 59.933 44.000 0.00 0.00 0.00 3.06
33 34 4.949856 CCAAGCCTAATACCAAACAGACAT 59.050 41.667 0.00 0.00 0.00 3.06
34 35 4.042311 TCCAAGCCTAATACCAAACAGACA 59.958 41.667 0.00 0.00 0.00 3.41
35 36 4.585879 TCCAAGCCTAATACCAAACAGAC 58.414 43.478 0.00 0.00 0.00 3.51
36 37 4.919774 TCCAAGCCTAATACCAAACAGA 57.080 40.909 0.00 0.00 0.00 3.41
37 38 7.307989 CGAATATCCAAGCCTAATACCAAACAG 60.308 40.741 0.00 0.00 0.00 3.16
38 39 6.485313 CGAATATCCAAGCCTAATACCAAACA 59.515 38.462 0.00 0.00 0.00 2.83
39 40 6.072673 CCGAATATCCAAGCCTAATACCAAAC 60.073 42.308 0.00 0.00 0.00 2.93
40 41 6.001460 CCGAATATCCAAGCCTAATACCAAA 58.999 40.000 0.00 0.00 0.00 3.28
41 42 5.556915 CCGAATATCCAAGCCTAATACCAA 58.443 41.667 0.00 0.00 0.00 3.67
42 43 4.564821 GCCGAATATCCAAGCCTAATACCA 60.565 45.833 0.00 0.00 0.00 3.25
43 44 3.939592 GCCGAATATCCAAGCCTAATACC 59.060 47.826 0.00 0.00 0.00 2.73
44 45 4.392138 GTGCCGAATATCCAAGCCTAATAC 59.608 45.833 0.00 0.00 0.00 1.89
45 46 4.564821 GGTGCCGAATATCCAAGCCTAATA 60.565 45.833 0.00 0.00 0.00 0.98
46 47 3.412386 GTGCCGAATATCCAAGCCTAAT 58.588 45.455 0.00 0.00 0.00 1.73
47 48 2.486548 GGTGCCGAATATCCAAGCCTAA 60.487 50.000 0.00 0.00 0.00 2.69
48 49 1.071699 GGTGCCGAATATCCAAGCCTA 59.928 52.381 0.00 0.00 0.00 3.93
49 50 0.179018 GGTGCCGAATATCCAAGCCT 60.179 55.000 0.00 0.00 0.00 4.58
50 51 1.172812 GGGTGCCGAATATCCAAGCC 61.173 60.000 0.00 0.00 0.00 4.35
51 52 1.172812 GGGGTGCCGAATATCCAAGC 61.173 60.000 0.00 0.00 0.00 4.01
52 53 0.474184 AGGGGTGCCGAATATCCAAG 59.526 55.000 0.00 0.00 0.00 3.61
53 54 0.923358 AAGGGGTGCCGAATATCCAA 59.077 50.000 0.00 0.00 0.00 3.53
54 55 0.472471 GAAGGGGTGCCGAATATCCA 59.528 55.000 0.00 0.00 0.00 3.41
55 56 0.472471 TGAAGGGGTGCCGAATATCC 59.528 55.000 0.00 0.00 0.00 2.59
56 57 2.224523 TGATGAAGGGGTGCCGAATATC 60.225 50.000 0.00 0.00 0.00 1.63
57 58 1.774254 TGATGAAGGGGTGCCGAATAT 59.226 47.619 0.00 0.00 0.00 1.28
58 59 1.134220 GTGATGAAGGGGTGCCGAATA 60.134 52.381 0.00 0.00 0.00 1.75
59 60 0.394352 GTGATGAAGGGGTGCCGAAT 60.394 55.000 0.00 0.00 0.00 3.34
60 61 1.002624 GTGATGAAGGGGTGCCGAA 60.003 57.895 0.00 0.00 0.00 4.30
61 62 2.668632 GTGATGAAGGGGTGCCGA 59.331 61.111 0.00 0.00 0.00 5.54
62 63 2.819595 CGTGATGAAGGGGTGCCG 60.820 66.667 0.00 0.00 0.00 5.69
63 64 2.438434 CCGTGATGAAGGGGTGCC 60.438 66.667 0.00 0.00 0.00 5.01
69 70 1.620819 CTCCTATCCCCGTGATGAAGG 59.379 57.143 0.00 0.00 34.76 3.46
70 71 2.320781 ACTCCTATCCCCGTGATGAAG 58.679 52.381 0.00 0.00 34.76 3.02
71 72 2.471815 ACTCCTATCCCCGTGATGAA 57.528 50.000 0.00 0.00 34.76 2.57
72 73 2.818216 GCTACTCCTATCCCCGTGATGA 60.818 54.545 0.00 0.00 34.76 2.92
73 74 1.546476 GCTACTCCTATCCCCGTGATG 59.454 57.143 0.00 0.00 34.76 3.07
74 75 1.887088 CGCTACTCCTATCCCCGTGAT 60.887 57.143 0.00 0.00 37.49 3.06
75 76 0.536687 CGCTACTCCTATCCCCGTGA 60.537 60.000 0.00 0.00 0.00 4.35
76 77 0.536687 TCGCTACTCCTATCCCCGTG 60.537 60.000 0.00 0.00 0.00 4.94
77 78 0.536915 GTCGCTACTCCTATCCCCGT 60.537 60.000 0.00 0.00 0.00 5.28
78 79 0.536687 TGTCGCTACTCCTATCCCCG 60.537 60.000 0.00 0.00 0.00 5.73
79 80 1.249407 CTGTCGCTACTCCTATCCCC 58.751 60.000 0.00 0.00 0.00 4.81
80 81 1.249407 CCTGTCGCTACTCCTATCCC 58.751 60.000 0.00 0.00 0.00 3.85
81 82 1.609555 CACCTGTCGCTACTCCTATCC 59.390 57.143 0.00 0.00 0.00 2.59
82 83 2.299521 ACACCTGTCGCTACTCCTATC 58.700 52.381 0.00 0.00 0.00 2.08
83 84 2.427453 CAACACCTGTCGCTACTCCTAT 59.573 50.000 0.00 0.00 0.00 2.57
84 85 1.816835 CAACACCTGTCGCTACTCCTA 59.183 52.381 0.00 0.00 0.00 2.94
85 86 0.603569 CAACACCTGTCGCTACTCCT 59.396 55.000 0.00 0.00 0.00 3.69
86 87 1.014564 GCAACACCTGTCGCTACTCC 61.015 60.000 0.00 0.00 0.00 3.85
87 88 1.014564 GGCAACACCTGTCGCTACTC 61.015 60.000 0.00 0.00 34.51 2.59
88 89 1.004918 GGCAACACCTGTCGCTACT 60.005 57.895 0.00 0.00 34.51 2.57
89 90 1.301401 TGGCAACACCTGTCGCTAC 60.301 57.895 0.00 0.00 46.17 3.58
90 91 3.143338 TGGCAACACCTGTCGCTA 58.857 55.556 0.00 0.00 46.17 4.26
101 102 3.191371 CCTGAAACTACCATCTTGGCAAC 59.809 47.826 0.00 0.00 42.67 4.17
102 103 3.420893 CCTGAAACTACCATCTTGGCAA 58.579 45.455 0.00 0.00 42.67 4.52
103 104 2.879756 GCCTGAAACTACCATCTTGGCA 60.880 50.000 0.00 0.00 42.67 4.92
104 105 1.745653 GCCTGAAACTACCATCTTGGC 59.254 52.381 0.00 0.00 42.67 4.52
105 106 3.356529 AGCCTGAAACTACCATCTTGG 57.643 47.619 0.00 0.00 45.02 3.61
106 107 5.352569 CAGTAAGCCTGAAACTACCATCTTG 59.647 44.000 0.00 0.00 44.49 3.02
107 108 5.491982 CAGTAAGCCTGAAACTACCATCTT 58.508 41.667 0.00 0.00 44.49 2.40
108 109 5.091261 CAGTAAGCCTGAAACTACCATCT 57.909 43.478 0.00 0.00 44.49 2.90
120 121 5.300752 CAGGGTAATACATCAGTAAGCCTG 58.699 45.833 9.73 9.73 44.13 4.85
121 122 4.969359 ACAGGGTAATACATCAGTAAGCCT 59.031 41.667 0.00 0.00 38.73 4.58
122 123 5.291905 ACAGGGTAATACATCAGTAAGCC 57.708 43.478 0.00 0.00 33.13 4.35
123 124 6.929606 CCTTACAGGGTAATACATCAGTAAGC 59.070 42.308 15.56 0.00 37.13 3.09
124 125 8.142551 GTCCTTACAGGGTAATACATCAGTAAG 58.857 40.741 14.75 14.75 37.80 2.34
125 126 7.842743 AGTCCTTACAGGGTAATACATCAGTAA 59.157 37.037 0.00 0.00 35.59 2.24
126 127 7.359849 AGTCCTTACAGGGTAATACATCAGTA 58.640 38.462 0.00 0.00 35.59 2.74
127 128 6.203072 AGTCCTTACAGGGTAATACATCAGT 58.797 40.000 0.00 0.00 35.59 3.41
128 129 6.732896 AGTCCTTACAGGGTAATACATCAG 57.267 41.667 0.00 0.00 35.59 2.90
129 130 7.037873 ACAAAGTCCTTACAGGGTAATACATCA 60.038 37.037 0.00 0.00 35.59 3.07
130 131 7.280205 CACAAAGTCCTTACAGGGTAATACATC 59.720 40.741 0.00 0.00 35.59 3.06
131 132 7.037873 TCACAAAGTCCTTACAGGGTAATACAT 60.038 37.037 0.00 0.00 35.59 2.29
132 133 6.270463 TCACAAAGTCCTTACAGGGTAATACA 59.730 38.462 0.00 0.00 35.59 2.29
133 134 6.704310 TCACAAAGTCCTTACAGGGTAATAC 58.296 40.000 0.00 0.00 35.59 1.89
134 135 6.938698 TCACAAAGTCCTTACAGGGTAATA 57.061 37.500 0.00 0.00 35.59 0.98
135 136 5.836024 TCACAAAGTCCTTACAGGGTAAT 57.164 39.130 0.00 0.00 35.59 1.89
136 137 5.633655 TTCACAAAGTCCTTACAGGGTAA 57.366 39.130 0.00 0.00 35.59 2.85
137 138 5.836024 ATTCACAAAGTCCTTACAGGGTA 57.164 39.130 0.00 0.00 35.59 3.69
138 139 4.724279 ATTCACAAAGTCCTTACAGGGT 57.276 40.909 0.00 0.00 35.59 4.34
139 140 7.703058 AATTATTCACAAAGTCCTTACAGGG 57.297 36.000 0.00 0.00 35.59 4.45
159 160 9.396938 CGATGCATGCAGTCATTTTATTAATTA 57.603 29.630 26.69 0.00 0.00 1.40
160 161 7.095940 GCGATGCATGCAGTCATTTTATTAATT 60.096 33.333 26.69 2.43 0.00 1.40
161 162 6.364165 GCGATGCATGCAGTCATTTTATTAAT 59.636 34.615 26.69 3.17 0.00 1.40
162 163 5.686841 GCGATGCATGCAGTCATTTTATTAA 59.313 36.000 26.69 0.00 0.00 1.40
163 164 5.214417 GCGATGCATGCAGTCATTTTATTA 58.786 37.500 26.69 0.00 0.00 0.98
164 165 4.046462 GCGATGCATGCAGTCATTTTATT 58.954 39.130 26.69 4.49 0.00 1.40
165 166 3.551454 GGCGATGCATGCAGTCATTTTAT 60.551 43.478 26.69 5.33 0.00 1.40
166 167 2.223548 GGCGATGCATGCAGTCATTTTA 60.224 45.455 26.69 0.00 0.00 1.52
167 168 1.470285 GGCGATGCATGCAGTCATTTT 60.470 47.619 26.69 7.01 0.00 1.82
168 169 0.101759 GGCGATGCATGCAGTCATTT 59.898 50.000 26.69 7.85 0.00 2.32
169 170 1.731433 GGGCGATGCATGCAGTCATT 61.731 55.000 26.69 8.70 0.00 2.57
170 171 2.191513 GGGCGATGCATGCAGTCAT 61.192 57.895 26.69 9.13 0.00 3.06
171 172 2.825387 GGGCGATGCATGCAGTCA 60.825 61.111 26.69 1.47 0.00 3.41
172 173 2.825387 TGGGCGATGCATGCAGTC 60.825 61.111 26.69 20.23 0.00 3.51
173 174 2.619941 ATCTGGGCGATGCATGCAGT 62.620 55.000 26.69 14.02 0.00 4.40
174 175 1.897137 ATCTGGGCGATGCATGCAG 60.897 57.895 26.69 14.50 0.00 4.41
175 176 2.190841 CATCTGGGCGATGCATGCA 61.191 57.895 25.04 25.04 42.75 3.96
176 177 2.643272 CATCTGGGCGATGCATGC 59.357 61.111 11.82 11.82 42.75 4.06
182 183 2.827423 CCTCTGCATCTGGGCGAT 59.173 61.111 0.00 0.00 36.28 4.58
183 184 4.166888 GCCTCTGCATCTGGGCGA 62.167 66.667 0.00 0.00 37.47 5.54
186 187 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
187 188 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
188 189 2.434843 TACCCGGCCTCTGCATCTG 61.435 63.158 0.00 0.00 40.13 2.90
189 190 2.041922 TACCCGGCCTCTGCATCT 60.042 61.111 0.00 0.00 40.13 2.90
190 191 2.044806 ATGTACCCGGCCTCTGCATC 62.045 60.000 0.00 0.00 40.13 3.91
191 192 2.044806 GATGTACCCGGCCTCTGCAT 62.045 60.000 0.00 0.00 40.13 3.96
192 193 2.687200 ATGTACCCGGCCTCTGCA 60.687 61.111 0.00 0.00 40.13 4.41
193 194 2.109181 GATGTACCCGGCCTCTGC 59.891 66.667 0.00 0.00 0.00 4.26
194 195 1.742768 GAGATGTACCCGGCCTCTG 59.257 63.158 0.00 0.00 0.00 3.35
195 196 1.457831 GGAGATGTACCCGGCCTCT 60.458 63.158 0.00 0.00 0.00 3.69
196 197 1.049289 AAGGAGATGTACCCGGCCTC 61.049 60.000 0.00 0.00 0.00 4.70
197 198 0.620700 AAAGGAGATGTACCCGGCCT 60.621 55.000 0.00 0.00 0.00 5.19
198 199 0.255033 AAAAGGAGATGTACCCGGCC 59.745 55.000 0.00 0.00 0.00 6.13
199 200 2.124277 AAAAAGGAGATGTACCCGGC 57.876 50.000 0.00 0.00 0.00 6.13
251 252 5.483583 CCACAATATCCAAGGGAAGGAAAAA 59.516 40.000 0.00 0.00 38.93 1.94
252 253 5.022787 CCACAATATCCAAGGGAAGGAAAA 58.977 41.667 0.00 0.00 38.93 2.29
253 254 4.571792 CCCACAATATCCAAGGGAAGGAAA 60.572 45.833 0.00 0.00 42.25 3.13
254 255 3.052944 CCCACAATATCCAAGGGAAGGAA 60.053 47.826 0.00 0.00 42.25 3.36
255 256 2.513738 CCCACAATATCCAAGGGAAGGA 59.486 50.000 0.00 0.00 42.25 3.36
269 270 0.038166 CAGGTACACAGCCCCACAAT 59.962 55.000 0.00 0.00 0.00 2.71
364 395 1.662629 GCACACATACAGCTGCTACAG 59.337 52.381 15.27 3.96 34.12 2.74
365 396 1.276138 AGCACACATACAGCTGCTACA 59.724 47.619 15.27 0.00 38.22 2.74
366 397 2.015736 AGCACACATACAGCTGCTAC 57.984 50.000 15.27 0.00 38.22 3.58
383 414 1.517242 GCTGCATACTATCCCACAGC 58.483 55.000 0.00 0.00 43.09 4.40
385 416 1.202687 GCAGCTGCATACTATCCCACA 60.203 52.381 33.36 0.00 41.59 4.17
441 507 1.112113 TCATTAGCGAGAGGACCACC 58.888 55.000 0.00 0.00 0.00 4.61
464 530 6.687081 TGACACGAGTTTAAAACCTCAAAT 57.313 33.333 6.63 0.00 0.00 2.32
531 600 9.411189 ACTTAAAGGTGACCACTTGTTTATTAA 57.589 29.630 3.63 0.00 0.00 1.40
532 601 8.983702 ACTTAAAGGTGACCACTTGTTTATTA 57.016 30.769 3.63 0.00 0.00 0.98
546 615 8.460428 ACGTATTTGTTTTGAACTTAAAGGTGA 58.540 29.630 0.00 0.00 0.00 4.02
571 640 4.792189 GCACACGTACTAACTCATGAGTAC 59.208 45.833 28.10 20.27 43.02 2.73
597 666 7.503521 TGACCCAATTTAAATTTTCAAAGGC 57.496 32.000 10.77 0.21 0.00 4.35
599 668 9.336171 TCCTTGACCCAATTTAAATTTTCAAAG 57.664 29.630 19.91 16.64 0.00 2.77
616 685 1.034292 GCTGGAGCAATCCTTGACCC 61.034 60.000 0.00 0.00 41.59 4.46
667 736 9.868277 TTTAAATGTGAATCCAATGGTATCAAC 57.132 29.630 10.37 6.89 0.00 3.18
672 741 7.901029 TGCTTTTAAATGTGAATCCAATGGTA 58.099 30.769 0.00 0.00 0.00 3.25
674 743 6.875195 ACTGCTTTTAAATGTGAATCCAATGG 59.125 34.615 0.00 0.00 0.00 3.16
696 765 4.566360 CCAAAAAGCACACCACTAAAACTG 59.434 41.667 0.00 0.00 0.00 3.16
702 771 1.698506 CCCCAAAAAGCACACCACTA 58.301 50.000 0.00 0.00 0.00 2.74
704 774 1.227527 GCCCCAAAAAGCACACCAC 60.228 57.895 0.00 0.00 0.00 4.16
711 781 2.031012 GGCTGTGCCCCAAAAAGC 59.969 61.111 0.00 0.00 44.06 3.51
724 797 2.037511 ACAACAATTTCACCATGGGCTG 59.962 45.455 18.09 6.33 0.00 4.85
761 834 5.319043 TCTTTTTAACTCCCACTGTCCAT 57.681 39.130 0.00 0.00 0.00 3.41
803 879 9.046296 TCAGAAGTCTCAGTTATTTTGTCTTTC 57.954 33.333 0.00 0.00 0.00 2.62
821 897 7.139392 GGTCACCACTTAAAAATTCAGAAGTC 58.861 38.462 0.00 0.00 29.73 3.01
846 922 1.480545 GGGGGATGGTTCCAAATTTCG 59.519 52.381 0.00 0.00 44.60 3.46
865 941 3.149981 GGAGGGAAGAGACAAACAAAGG 58.850 50.000 0.00 0.00 0.00 3.11
866 942 4.092116 AGGAGGGAAGAGACAAACAAAG 57.908 45.455 0.00 0.00 0.00 2.77
867 943 5.640158 TTAGGAGGGAAGAGACAAACAAA 57.360 39.130 0.00 0.00 0.00 2.83
869 945 4.225267 GGATTAGGAGGGAAGAGACAAACA 59.775 45.833 0.00 0.00 0.00 2.83
870 946 4.225267 TGGATTAGGAGGGAAGAGACAAAC 59.775 45.833 0.00 0.00 0.00 2.93
905 992 9.551734 GGGTTTTGATAAGGTTATATACTCGTT 57.448 33.333 0.00 0.00 0.00 3.85
908 995 9.722184 GAGGGGTTTTGATAAGGTTATATACTC 57.278 37.037 0.00 0.00 0.00 2.59
1035 1172 0.252103 AGCCGGTGAAGTAGGAGGAA 60.252 55.000 1.90 0.00 0.00 3.36
1324 1461 4.593864 GGCCGGGTCGATCAGCTC 62.594 72.222 2.18 0.00 0.00 4.09
1384 1533 2.210116 CCAAGAACAACAGCTACACGT 58.790 47.619 0.00 0.00 0.00 4.49
1387 1536 2.571212 CACCCAAGAACAACAGCTACA 58.429 47.619 0.00 0.00 0.00 2.74
1401 1550 2.281900 GCAACTACCGCCACCCAA 60.282 61.111 0.00 0.00 0.00 4.12
1483 1632 2.493675 CTCGAGAGGGAGTCACATTTGA 59.506 50.000 6.58 0.00 0.00 2.69
1528 1686 1.445066 CGATCGGATCATCGCAGGG 60.445 63.158 17.53 0.00 39.32 4.45
1533 1691 1.709203 GTTCGTTCGATCGGATCATCG 59.291 52.381 16.41 16.22 45.91 3.84
1550 1708 1.257155 GTGGTCACAACTCGTTCGTTC 59.743 52.381 0.00 0.00 0.00 3.95
1551 1709 1.283736 GTGGTCACAACTCGTTCGTT 58.716 50.000 0.00 0.00 0.00 3.85
1552 1710 0.868602 CGTGGTCACAACTCGTTCGT 60.869 55.000 1.90 0.00 0.00 3.85
1553 1711 1.844003 CGTGGTCACAACTCGTTCG 59.156 57.895 1.90 0.00 0.00 3.95
1596 1756 3.266964 CCACTGTTCACATGGCCG 58.733 61.111 0.00 0.00 0.00 6.13
1645 1805 1.597663 GTCTGTCCTTGTGGTTTGTCG 59.402 52.381 0.00 0.00 34.23 4.35
1690 1850 1.731969 GTGCGCCGAGTTCGTACTT 60.732 57.895 4.18 0.00 39.01 2.24
1691 1851 2.126580 GTGCGCCGAGTTCGTACT 60.127 61.111 4.18 0.00 39.01 2.73
1692 1852 2.126580 AGTGCGCCGAGTTCGTAC 60.127 61.111 4.18 0.00 41.64 3.67
1693 1853 2.177531 GAGTGCGCCGAGTTCGTA 59.822 61.111 4.18 0.00 37.74 3.43
1772 1933 1.000396 CTTTCCCTTCCCTGCCCAG 60.000 63.158 0.00 0.00 0.00 4.45
1777 1938 2.943199 GCACATCTCTTTCCCTTCCCTG 60.943 54.545 0.00 0.00 0.00 4.45
1822 1983 1.880027 AGAAAGCGTCATGTTGTTCCC 59.120 47.619 0.00 0.00 0.00 3.97
1827 1988 5.635280 TCTCTCTAAAGAAAGCGTCATGTTG 59.365 40.000 0.00 0.00 0.00 3.33
1830 1991 7.704472 ACTTATCTCTCTAAAGAAAGCGTCATG 59.296 37.037 0.00 0.00 0.00 3.07
1837 1998 8.465999 TCAGCTCACTTATCTCTCTAAAGAAAG 58.534 37.037 0.00 0.00 0.00 2.62
1841 2002 6.690957 CGTTCAGCTCACTTATCTCTCTAAAG 59.309 42.308 0.00 0.00 0.00 1.85
1846 2007 3.112580 GCGTTCAGCTCACTTATCTCTC 58.887 50.000 0.00 0.00 44.04 3.20
1943 2104 0.179142 GAGCGTAACCGGGACTCTTC 60.179 60.000 6.32 0.00 33.68 2.87
1985 2146 4.021102 ACATTCCATTCCACCGGATATC 57.979 45.455 9.46 0.00 0.00 1.63
2079 2253 1.134521 GGCCACGTCAACATGGATCTA 60.135 52.381 0.00 0.00 38.34 1.98
2086 2260 3.354678 GCAAGGCCACGTCAACAT 58.645 55.556 5.01 0.00 0.00 2.71
2182 2362 1.628846 AGGCACTAGTTACCCAACAGG 59.371 52.381 7.90 0.00 36.02 4.00
2186 2366 1.003118 CAGCAGGCACTAGTTACCCAA 59.997 52.381 7.90 0.00 36.02 4.12
2188 2368 0.107654 CCAGCAGGCACTAGTTACCC 60.108 60.000 7.90 2.53 36.02 3.69
2211 2436 8.649810 AACGAATGTAATCAAACGTTAACATC 57.350 30.769 0.00 2.01 42.31 3.06
2215 2440 8.976471 TCACTAACGAATGTAATCAAACGTTAA 58.024 29.630 0.00 0.00 43.15 2.01
2236 2461 1.278985 CATTGGGCCACAGAGTCACTA 59.721 52.381 5.23 0.00 0.00 2.74
2245 2470 0.396974 GCCTTATCCATTGGGCCACA 60.397 55.000 5.23 0.00 38.77 4.17
2295 2520 0.615331 GTCAACTCTGCTGGGGATCA 59.385 55.000 0.00 0.00 0.00 2.92
2306 2531 3.381590 GGAAACAAAAGGCAGTCAACTCT 59.618 43.478 0.00 0.00 0.00 3.24
2311 2536 0.383949 GCGGAAACAAAAGGCAGTCA 59.616 50.000 0.00 0.00 0.00 3.41
2314 2539 1.006220 GGGCGGAAACAAAAGGCAG 60.006 57.895 0.00 0.00 0.00 4.85
2315 2540 1.456705 AGGGCGGAAACAAAAGGCA 60.457 52.632 0.00 0.00 0.00 4.75
2316 2541 1.179174 AGAGGGCGGAAACAAAAGGC 61.179 55.000 0.00 0.00 0.00 4.35
2317 2542 1.328279 AAGAGGGCGGAAACAAAAGG 58.672 50.000 0.00 0.00 0.00 3.11
2318 2543 3.146847 ACTAAGAGGGCGGAAACAAAAG 58.853 45.455 0.00 0.00 0.00 2.27
2328 2553 4.312443 TCACACTAAAAACTAAGAGGGCG 58.688 43.478 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.