Multiple sequence alignment - TraesCS3A01G231400

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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 TraesCS3A01G231400 chr3A 100.000 5126 0 0 1 5126 431826516 431821391 0.000000e+00 9467.0
1 TraesCS3A01G231400 chr3A 85.574 305 29 6 4496 4790 57958855 57958556 6.450000e-79 305.0
2 TraesCS3A01G231400 chr3A 81.343 134 15 7 4997 5121 510303105 510302973 3.270000e-17 100.0
3 TraesCS3A01G231400 chr3A 95.455 44 2 0 4305 4348 737434411 737434368 2.560000e-08 71.3
4 TraesCS3A01G231400 chr3B 93.456 4340 191 47 1 4292 418456824 418452530 0.000000e+00 6355.0
5 TraesCS3A01G231400 chr3B 96.479 284 9 1 4346 4629 418452534 418452252 7.770000e-128 468.0
6 TraesCS3A01G231400 chr3B 86.885 61 4 2 4288 4348 280109126 280109182 1.190000e-06 65.8
7 TraesCS3A01G231400 chr3D 94.354 4056 168 37 186 4203 302926164 302930196 0.000000e+00 6165.0
8 TraesCS3A01G231400 chr3D 88.243 757 55 13 323 1078 302924294 302925017 0.000000e+00 874.0
9 TraesCS3A01G231400 chr3D 91.511 483 12 3 4201 4658 302930299 302930777 5.600000e-179 638.0
10 TraesCS3A01G231400 chr3D 96.310 271 9 1 4857 5126 302931282 302931552 1.310000e-120 444.0
11 TraesCS3A01G231400 chr3D 97.573 206 3 1 4657 4860 302930956 302931161 8.170000e-93 351.0
12 TraesCS3A01G231400 chr4A 84.706 255 28 9 4527 4774 718620600 718620350 1.430000e-60 244.0
13 TraesCS3A01G231400 chr7D 84.047 257 29 8 4525 4774 582600132 582600383 2.390000e-58 237.0
14 TraesCS3A01G231400 chr7D 88.750 160 10 3 1808 1966 34757018 34756866 6.780000e-44 189.0
15 TraesCS3A01G231400 chr1D 83.784 259 31 9 4523 4774 202027776 202027522 8.580000e-58 235.0
16 TraesCS3A01G231400 chr7B 83.721 258 29 10 4525 4774 34217005 34217257 1.110000e-56 231.0
17 TraesCS3A01G231400 chrUn 80.968 310 40 11 4497 4792 79467323 79467627 1.440000e-55 228.0
18 TraesCS3A01G231400 chr5D 83.268 257 33 8 4525 4774 319212412 319212665 1.440000e-55 228.0
19 TraesCS3A01G231400 chr5D 88.272 162 11 6 1806 1966 211983681 211983835 2.440000e-43 187.0
20 TraesCS3A01G231400 chr1A 90.062 161 9 5 1808 1967 155857706 155857860 8.700000e-48 202.0
21 TraesCS3A01G231400 chr1A 91.935 62 4 1 1 62 42112572 42112512 9.140000e-13 86.1
22 TraesCS3A01G231400 chr6D 87.425 167 13 5 1804 1968 303059849 303060009 8.760000e-43 185.0
23 TraesCS3A01G231400 chr6D 100.000 30 0 0 3422 3451 30290016 30289987 7.170000e-04 56.5
24 TraesCS3A01G231400 chr5A 88.344 163 7 7 1806 1966 275094840 275094992 8.760000e-43 185.0
25 TraesCS3A01G231400 chr5A 95.349 43 2 0 4308 4350 48828288 48828246 9.210000e-08 69.4
26 TraesCS3A01G231400 chr5B 87.730 163 11 6 1806 1966 225521534 225521689 1.130000e-41 182.0
27 TraesCS3A01G231400 chr5B 91.781 73 4 2 4289 4359 501472165 501472093 3.270000e-17 100.0
28 TraesCS3A01G231400 chr7A 87.500 160 12 4 1808 1966 421785006 421785158 1.470000e-40 178.0
29 TraesCS3A01G231400 chr1B 80.368 163 24 6 4972 5126 599589146 599589308 3.240000e-22 117.0
30 TraesCS3A01G231400 chr1B 94.444 36 2 0 487 522 663011199 663011234 7.170000e-04 56.5
31 TraesCS3A01G231400 chr4B 100.000 31 0 0 3422 3452 25710911 25710941 1.990000e-04 58.4
32 TraesCS3A01G231400 chr2D 94.595 37 1 1 4277 4312 175820797 175820833 7.170000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G231400 chr3A 431821391 431826516 5125 True 9467.0 9467 100.0000 1 5126 1 chr3A.!!$R2 5125
1 TraesCS3A01G231400 chr3B 418452252 418456824 4572 True 3411.5 6355 94.9675 1 4629 2 chr3B.!!$R1 4628
2 TraesCS3A01G231400 chr3D 302924294 302931552 7258 False 1694.4 6165 93.5982 186 5126 5 chr3D.!!$F1 4940

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
92 93 0.658897 CACTTTTGCGTACCGTGGTT 59.341 50.0 0.0 0.0 0.00 3.67 F
118 119 0.678950 TGACTGAATCCGCACAGACA 59.321 50.0 0.0 0.0 36.75 3.41 F
186 187 0.758734 CCCTTGTCCTCACACTGTCA 59.241 55.0 0.0 0.0 29.76 3.58 F
1783 3525 0.822121 GGATCATACCGCCCAAACCC 60.822 60.0 0.0 0.0 0.00 4.11 F
3015 4763 0.178998 CATGGGGCATCTCCTCCTTG 60.179 60.0 0.0 0.0 32.90 3.61 F
3017 4765 0.327867 TGGGGCATCTCCTCCTTGAT 60.328 55.0 0.0 0.0 32.90 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 3101 1.325640 CACATCACATTTCGGCTCTCG 59.674 52.381 0.00 0.0 40.90 4.04 R
1404 3145 2.404559 TCCCACCATTATAGCCTTCGT 58.595 47.619 0.00 0.0 0.00 3.85 R
2034 3777 2.615912 GCAATCTAGGTGAATGAGTGGC 59.384 50.000 0.00 0.0 0.00 5.01 R
3706 5457 1.064003 TGTGACTACAAGGGGCATGT 58.936 50.000 0.00 0.0 32.88 3.21 R
3966 5718 1.494721 TCACCTATCTTGGGGCCATTC 59.505 52.381 4.39 0.0 0.00 2.67 R
4180 5932 1.677576 CATGGCATCTACAATGGCGTT 59.322 47.619 0.00 0.0 46.12 4.84 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
20 21 3.850122 GGGCTTGATTTAGCTTTCGTT 57.150 42.857 0.00 0.00 40.99 3.85
22 23 5.305139 GGGCTTGATTTAGCTTTCGTTTA 57.695 39.130 0.00 0.00 40.99 2.01
24 25 4.786575 GGCTTGATTTAGCTTTCGTTTACG 59.213 41.667 0.00 0.00 40.99 3.18
25 26 5.390145 GGCTTGATTTAGCTTTCGTTTACGA 60.390 40.000 0.03 0.03 42.71 3.43
26 27 5.728507 GCTTGATTTAGCTTTCGTTTACGAG 59.271 40.000 5.06 0.00 42.51 4.18
27 28 6.617953 GCTTGATTTAGCTTTCGTTTACGAGT 60.618 38.462 5.06 0.00 42.51 4.18
28 29 8.039305 GCTTGATTTAGCTTTCGTTTACGAGTT 61.039 37.037 5.06 0.00 42.51 3.01
42 43 9.596677 TCGTTTACGAGTTTATGGTTTATTTTG 57.403 29.630 0.03 0.00 44.22 2.44
43 44 8.842777 CGTTTACGAGTTTATGGTTTATTTTGG 58.157 33.333 0.00 0.00 43.02 3.28
46 47 7.754851 ACGAGTTTATGGTTTATTTTGGACT 57.245 32.000 0.00 0.00 0.00 3.85
47 48 8.173542 ACGAGTTTATGGTTTATTTTGGACTT 57.826 30.769 0.00 0.00 0.00 3.01
48 49 8.635328 ACGAGTTTATGGTTTATTTTGGACTTT 58.365 29.630 0.00 0.00 0.00 2.66
56 57 7.051000 TGGTTTATTTTGGACTTTTTCCCTTG 58.949 34.615 0.00 0.00 45.17 3.61
57 58 7.051623 GGTTTATTTTGGACTTTTTCCCTTGT 58.948 34.615 0.00 0.00 45.17 3.16
58 59 7.011950 GGTTTATTTTGGACTTTTTCCCTTGTG 59.988 37.037 0.00 0.00 45.17 3.33
59 60 5.948742 ATTTTGGACTTTTTCCCTTGTGA 57.051 34.783 0.00 0.00 45.17 3.58
60 61 5.746990 TTTTGGACTTTTTCCCTTGTGAA 57.253 34.783 0.00 0.00 45.17 3.18
61 62 5.746990 TTTGGACTTTTTCCCTTGTGAAA 57.253 34.783 0.00 0.00 45.17 2.69
63 64 5.948742 TGGACTTTTTCCCTTGTGAAATT 57.051 34.783 0.00 0.00 45.17 1.82
64 65 7.425224 TTGGACTTTTTCCCTTGTGAAATTA 57.575 32.000 0.00 0.00 45.17 1.40
65 66 7.610580 TGGACTTTTTCCCTTGTGAAATTAT 57.389 32.000 0.00 0.00 45.17 1.28
66 67 8.713708 TGGACTTTTTCCCTTGTGAAATTATA 57.286 30.769 0.00 0.00 45.17 0.98
67 68 8.581578 TGGACTTTTTCCCTTGTGAAATTATAC 58.418 33.333 0.00 0.00 45.17 1.47
68 69 8.033038 GGACTTTTTCCCTTGTGAAATTATACC 58.967 37.037 0.00 0.00 38.70 2.73
69 70 7.903145 ACTTTTTCCCTTGTGAAATTATACCC 58.097 34.615 0.00 0.00 34.41 3.69
70 71 7.511028 ACTTTTTCCCTTGTGAAATTATACCCA 59.489 33.333 0.00 0.00 34.41 4.51
72 73 8.442660 TTTTCCCTTGTGAAATTATACCCATT 57.557 30.769 0.00 0.00 34.41 3.16
73 74 7.654022 TTCCCTTGTGAAATTATACCCATTC 57.346 36.000 0.00 0.00 0.00 2.67
74 75 6.736581 TCCCTTGTGAAATTATACCCATTCA 58.263 36.000 0.00 0.00 0.00 2.57
81 82 8.185003 GTGAAATTATACCCATTCACTTTTGC 57.815 34.615 9.55 0.00 45.05 3.68
82 83 7.009174 GTGAAATTATACCCATTCACTTTTGCG 59.991 37.037 9.55 0.00 45.05 4.85
84 85 7.633193 AATTATACCCATTCACTTTTGCGTA 57.367 32.000 0.00 0.00 0.00 4.42
87 88 1.135803 CCCATTCACTTTTGCGTACCG 60.136 52.381 0.00 0.00 0.00 4.02
89 90 2.570169 CATTCACTTTTGCGTACCGTG 58.430 47.619 0.00 0.00 0.00 4.94
90 91 0.938713 TTCACTTTTGCGTACCGTGG 59.061 50.000 0.00 0.00 0.00 4.94
92 93 0.658897 CACTTTTGCGTACCGTGGTT 59.341 50.000 0.00 0.00 0.00 3.67
93 94 1.865970 CACTTTTGCGTACCGTGGTTA 59.134 47.619 0.00 0.00 0.00 2.85
94 95 1.866601 ACTTTTGCGTACCGTGGTTAC 59.133 47.619 0.00 0.00 0.00 2.50
95 96 2.137523 CTTTTGCGTACCGTGGTTACT 58.862 47.619 0.00 0.00 0.00 2.24
96 97 3.243704 ACTTTTGCGTACCGTGGTTACTA 60.244 43.478 0.00 0.00 0.00 1.82
97 98 2.634982 TTGCGTACCGTGGTTACTAG 57.365 50.000 0.00 0.00 0.00 2.57
98 99 1.819928 TGCGTACCGTGGTTACTAGA 58.180 50.000 0.00 0.00 0.00 2.43
99 100 2.368439 TGCGTACCGTGGTTACTAGAT 58.632 47.619 0.00 0.00 0.00 1.98
100 101 2.097954 TGCGTACCGTGGTTACTAGATG 59.902 50.000 0.00 0.00 0.00 2.90
101 102 2.355756 GCGTACCGTGGTTACTAGATGA 59.644 50.000 0.00 0.00 0.00 2.92
102 103 3.790123 GCGTACCGTGGTTACTAGATGAC 60.790 52.174 0.00 0.00 0.00 3.06
104 105 4.495349 CGTACCGTGGTTACTAGATGACTG 60.495 50.000 0.00 0.00 0.00 3.51
105 106 3.693807 ACCGTGGTTACTAGATGACTGA 58.306 45.455 0.00 0.00 0.00 3.41
106 107 4.084287 ACCGTGGTTACTAGATGACTGAA 58.916 43.478 0.00 0.00 0.00 3.02
107 108 4.710375 ACCGTGGTTACTAGATGACTGAAT 59.290 41.667 0.00 0.00 0.00 2.57
108 109 5.163540 ACCGTGGTTACTAGATGACTGAATC 60.164 44.000 0.00 0.00 0.00 2.52
109 110 5.282510 CGTGGTTACTAGATGACTGAATCC 58.717 45.833 0.00 0.00 0.00 3.01
110 111 5.282510 GTGGTTACTAGATGACTGAATCCG 58.717 45.833 0.00 0.00 0.00 4.18
111 112 4.202121 TGGTTACTAGATGACTGAATCCGC 60.202 45.833 0.00 0.00 0.00 5.54
112 113 4.202121 GGTTACTAGATGACTGAATCCGCA 60.202 45.833 0.00 0.00 0.00 5.69
113 114 3.444703 ACTAGATGACTGAATCCGCAC 57.555 47.619 0.00 0.00 0.00 5.34
115 116 2.306341 AGATGACTGAATCCGCACAG 57.694 50.000 0.00 0.00 39.65 3.66
116 117 1.827344 AGATGACTGAATCCGCACAGA 59.173 47.619 0.00 0.00 37.54 3.41
117 118 1.929836 GATGACTGAATCCGCACAGAC 59.070 52.381 0.00 0.00 37.54 3.51
118 119 0.678950 TGACTGAATCCGCACAGACA 59.321 50.000 0.00 0.00 36.75 3.41
119 120 1.337167 TGACTGAATCCGCACAGACAG 60.337 52.381 0.00 0.00 35.00 3.51
121 122 1.344438 ACTGAATCCGCACAGACAGAA 59.656 47.619 0.00 0.00 37.54 3.02
122 123 1.998315 CTGAATCCGCACAGACAGAAG 59.002 52.381 0.00 0.00 36.38 2.85
124 125 2.266554 GAATCCGCACAGACAGAAGAG 58.733 52.381 0.00 0.00 0.00 2.85
126 127 1.328279 TCCGCACAGACAGAAGAGAA 58.672 50.000 0.00 0.00 0.00 2.87
127 128 1.270826 TCCGCACAGACAGAAGAGAAG 59.729 52.381 0.00 0.00 0.00 2.85
128 129 1.000283 CCGCACAGACAGAAGAGAAGT 60.000 52.381 0.00 0.00 0.00 3.01
130 131 3.126831 CGCACAGACAGAAGAGAAGTTT 58.873 45.455 0.00 0.00 0.00 2.66
132 133 4.745125 CGCACAGACAGAAGAGAAGTTTTA 59.255 41.667 0.00 0.00 0.00 1.52
134 135 6.597614 GCACAGACAGAAGAGAAGTTTTATG 58.402 40.000 0.00 0.00 0.00 1.90
135 136 6.348050 GCACAGACAGAAGAGAAGTTTTATGG 60.348 42.308 0.00 0.00 0.00 2.74
136 137 6.148480 CACAGACAGAAGAGAAGTTTTATGGG 59.852 42.308 0.00 0.00 0.00 4.00
138 139 6.593382 CAGACAGAAGAGAAGTTTTATGGGAG 59.407 42.308 0.00 0.00 0.00 4.30
140 141 7.455008 AGACAGAAGAGAAGTTTTATGGGAGTA 59.545 37.037 0.00 0.00 0.00 2.59
141 142 7.387643 ACAGAAGAGAAGTTTTATGGGAGTAC 58.612 38.462 0.00 0.00 0.00 2.73
142 143 6.819146 CAGAAGAGAAGTTTTATGGGAGTACC 59.181 42.308 0.00 0.00 40.81 3.34
156 157 4.518249 GGGAGTACCAATGGAGAAAAGAG 58.482 47.826 6.16 0.00 39.85 2.85
158 159 5.104318 GGGAGTACCAATGGAGAAAAGAGAT 60.104 44.000 6.16 0.00 39.85 2.75
159 160 6.052360 GGAGTACCAATGGAGAAAAGAGATC 58.948 44.000 6.16 0.00 35.97 2.75
160 161 6.352222 GGAGTACCAATGGAGAAAAGAGATCA 60.352 42.308 6.16 0.00 35.97 2.92
161 162 7.020827 AGTACCAATGGAGAAAAGAGATCAA 57.979 36.000 6.16 0.00 0.00 2.57
164 165 6.487828 ACCAATGGAGAAAAGAGATCAATGA 58.512 36.000 6.16 0.00 0.00 2.57
165 166 6.950041 ACCAATGGAGAAAAGAGATCAATGAA 59.050 34.615 6.16 0.00 0.00 2.57
167 168 7.758528 CCAATGGAGAAAAGAGATCAATGAAAC 59.241 37.037 0.00 0.00 0.00 2.78
168 169 6.824305 TGGAGAAAAGAGATCAATGAAACC 57.176 37.500 0.00 0.00 0.00 3.27
169 170 5.711976 TGGAGAAAAGAGATCAATGAAACCC 59.288 40.000 0.00 0.00 0.00 4.11
172 173 7.224522 AGAAAAGAGATCAATGAAACCCTTG 57.775 36.000 0.00 0.00 0.00 3.61
173 174 6.779539 AGAAAAGAGATCAATGAAACCCTTGT 59.220 34.615 0.00 0.00 0.00 3.16
174 175 6.581171 AAAGAGATCAATGAAACCCTTGTC 57.419 37.500 0.00 0.00 0.00 3.18
175 176 4.593956 AGAGATCAATGAAACCCTTGTCC 58.406 43.478 0.00 0.00 0.00 4.02
176 177 4.290722 AGAGATCAATGAAACCCTTGTCCT 59.709 41.667 0.00 0.00 0.00 3.85
177 178 4.593956 AGATCAATGAAACCCTTGTCCTC 58.406 43.478 0.00 0.00 0.00 3.71
179 180 3.486383 TCAATGAAACCCTTGTCCTCAC 58.514 45.455 0.00 0.00 0.00 3.51
180 181 3.117701 TCAATGAAACCCTTGTCCTCACA 60.118 43.478 0.00 0.00 0.00 3.58
181 182 2.341846 TGAAACCCTTGTCCTCACAC 57.658 50.000 0.00 0.00 29.76 3.82
182 183 1.843851 TGAAACCCTTGTCCTCACACT 59.156 47.619 0.00 0.00 29.76 3.55
184 185 1.213296 AACCCTTGTCCTCACACTGT 58.787 50.000 0.00 0.00 29.76 3.55
185 186 0.759346 ACCCTTGTCCTCACACTGTC 59.241 55.000 0.00 0.00 29.76 3.51
186 187 0.758734 CCCTTGTCCTCACACTGTCA 59.241 55.000 0.00 0.00 29.76 3.58
187 188 1.349026 CCCTTGTCCTCACACTGTCAT 59.651 52.381 0.00 0.00 29.76 3.06
188 189 2.420642 CCTTGTCCTCACACTGTCATG 58.579 52.381 0.00 0.00 29.76 3.07
189 190 2.420642 CTTGTCCTCACACTGTCATGG 58.579 52.381 0.00 0.00 29.76 3.66
224 1911 1.203052 GCATGCAAGGCTCAAGCTTAA 59.797 47.619 14.21 0.00 42.67 1.85
225 1912 2.159142 GCATGCAAGGCTCAAGCTTAAT 60.159 45.455 14.21 0.00 42.67 1.40
242 1929 7.848223 AGCTTAATTGCACAATAAAAATCCC 57.152 32.000 0.00 0.00 34.99 3.85
274 1961 2.107378 TCCTAACACATGCTTCCCACAA 59.893 45.455 0.00 0.00 0.00 3.33
276 1963 1.774110 AACACATGCTTCCCACAACA 58.226 45.000 0.00 0.00 0.00 3.33
296 1983 7.064490 CACAACAGTGCTTCCAAAAAGTAAAAT 59.936 33.333 0.00 0.00 0.00 1.82
297 1984 7.064490 ACAACAGTGCTTCCAAAAAGTAAAATG 59.936 33.333 0.00 0.00 0.00 2.32
298 1985 5.523552 ACAGTGCTTCCAAAAAGTAAAATGC 59.476 36.000 0.00 0.00 0.00 3.56
300 1987 5.523552 AGTGCTTCCAAAAAGTAAAATGCAC 59.476 36.000 0.00 0.00 44.76 4.57
302 1989 5.877012 TGCTTCCAAAAAGTAAAATGCACAA 59.123 32.000 0.00 0.00 0.00 3.33
303 1990 6.183360 TGCTTCCAAAAAGTAAAATGCACAAC 60.183 34.615 0.00 0.00 0.00 3.32
304 1991 5.957910 TCCAAAAAGTAAAATGCACAACG 57.042 34.783 0.00 0.00 0.00 4.10
305 1992 4.806247 TCCAAAAAGTAAAATGCACAACGG 59.194 37.500 0.00 0.00 0.00 4.44
306 1993 4.568760 CCAAAAAGTAAAATGCACAACGGT 59.431 37.500 0.00 0.00 0.00 4.83
379 2091 5.233957 GTGAAAAGCACAAATTTGCCTTT 57.766 34.783 22.08 22.08 46.91 3.11
411 2126 5.888691 TTTTTGGGCTTGTTTTTCCTTTC 57.111 34.783 0.00 0.00 0.00 2.62
415 2130 5.722021 TGGGCTTGTTTTTCCTTTCTATC 57.278 39.130 0.00 0.00 0.00 2.08
416 2131 5.144100 TGGGCTTGTTTTTCCTTTCTATCA 58.856 37.500 0.00 0.00 0.00 2.15
571 2291 8.721019 AAAACGATTTATGATTTGGATGCAAT 57.279 26.923 0.00 0.00 0.00 3.56
592 2312 8.417106 TGCAATGTTCAAGAGGTAAAACATTAA 58.583 29.630 10.85 2.54 45.61 1.40
769 2489 3.526931 TCGATGGAAAAGAGAAGCGAT 57.473 42.857 0.00 0.00 0.00 4.58
793 2514 3.766691 GCCGGCAGGTCGACCTAA 61.767 66.667 35.80 0.00 46.65 2.69
861 2582 2.582498 GCATAGGCGACGCGAACT 60.582 61.111 15.93 8.05 0.00 3.01
876 2597 2.985809 GCGAACTCTATATGCTGCTGAG 59.014 50.000 0.00 3.79 0.00 3.35
908 2629 2.046313 GCATTTGCGCATGCTATACAC 58.954 47.619 24.87 0.00 45.35 2.90
916 2637 1.004610 GCATGCTATACACGTGCACAG 60.005 52.381 17.22 11.24 46.89 3.66
941 2678 5.809562 AGCATGTCACAATTTTGTTTTCGAA 59.190 32.000 0.00 0.00 39.91 3.71
942 2679 6.479660 AGCATGTCACAATTTTGTTTTCGAAT 59.520 30.769 0.00 0.00 39.91 3.34
943 2680 6.787043 GCATGTCACAATTTTGTTTTCGAATC 59.213 34.615 0.00 0.00 39.91 2.52
944 2681 7.516470 GCATGTCACAATTTTGTTTTCGAATCA 60.516 33.333 0.00 0.00 39.91 2.57
945 2682 8.489559 CATGTCACAATTTTGTTTTCGAATCAT 58.510 29.630 0.00 0.00 39.91 2.45
946 2683 8.060020 TGTCACAATTTTGTTTTCGAATCATC 57.940 30.769 0.00 0.00 39.91 2.92
947 2684 7.704047 TGTCACAATTTTGTTTTCGAATCATCA 59.296 29.630 0.00 0.00 39.91 3.07
948 2685 8.702438 GTCACAATTTTGTTTTCGAATCATCAT 58.298 29.630 0.00 0.00 39.91 2.45
949 2686 8.914654 TCACAATTTTGTTTTCGAATCATCATC 58.085 29.630 0.00 0.00 39.91 2.92
950 2687 8.701540 CACAATTTTGTTTTCGAATCATCATCA 58.298 29.630 0.00 0.00 39.91 3.07
951 2688 9.426837 ACAATTTTGTTTTCGAATCATCATCAT 57.573 25.926 0.00 0.00 38.47 2.45
952 2689 9.895894 CAATTTTGTTTTCGAATCATCATCATC 57.104 29.630 0.00 0.00 0.00 2.92
953 2690 9.642327 AATTTTGTTTTCGAATCATCATCATCA 57.358 25.926 0.00 0.00 0.00 3.07
954 2691 8.677871 TTTTGTTTTCGAATCATCATCATCAG 57.322 30.769 0.00 0.00 0.00 2.90
955 2692 6.990341 TGTTTTCGAATCATCATCATCAGT 57.010 33.333 0.00 0.00 0.00 3.41
956 2693 7.008440 TGTTTTCGAATCATCATCATCAGTC 57.992 36.000 0.00 0.00 0.00 3.51
957 2694 6.594937 TGTTTTCGAATCATCATCATCAGTCA 59.405 34.615 0.00 0.00 0.00 3.41
969 2706 0.955178 ATCAGTCATCGTCCTAGCCG 59.045 55.000 0.00 0.00 0.00 5.52
1120 2860 4.214327 CGCCGCTTCCTCCTCCTC 62.214 72.222 0.00 0.00 0.00 3.71
1151 2891 2.044848 TCGCTTCTCCTCTCCGCT 60.045 61.111 0.00 0.00 0.00 5.52
1359 3099 1.028905 TCTCCGTTTGGGCTTGTTTG 58.971 50.000 0.00 0.00 35.24 2.93
1361 3101 1.594021 CCGTTTGGGCTTGTTTGGC 60.594 57.895 0.00 0.00 0.00 4.52
1404 3145 3.868077 CGCTTTTTGTTTTGGTGGATTCA 59.132 39.130 0.00 0.00 0.00 2.57
1595 3336 1.365999 CCGCGTATGCATCTACCCA 59.634 57.895 0.19 0.00 42.97 4.51
1657 3398 4.982701 AGCGCCTTTGCCTTGCCT 62.983 61.111 2.29 0.00 34.65 4.75
1661 3402 2.268076 GCCTTTGCCTTGCCTCGAA 61.268 57.895 0.00 0.00 0.00 3.71
1678 3420 4.624024 CCTCGAACTTGCGTTGTTTAGATA 59.376 41.667 0.00 0.00 32.39 1.98
1771 3513 4.099419 TCAGCTTTGCTAACTCGGATCATA 59.901 41.667 0.00 0.00 36.40 2.15
1783 3525 0.822121 GGATCATACCGCCCAAACCC 60.822 60.000 0.00 0.00 0.00 4.11
1833 3575 8.083828 ACTCGCTCCATTCATAAATATAGGAT 57.916 34.615 0.00 0.00 0.00 3.24
1982 3725 6.651225 GGAGGAGTATTATGTAAACAGGCATC 59.349 42.308 0.00 0.00 0.00 3.91
1996 3739 4.362677 ACAGGCATCCTTAAGTCCTCTAA 58.637 43.478 0.97 0.00 0.00 2.10
2034 3777 6.460676 GCCTATTCATTTGTTCATCCTTCCAG 60.461 42.308 0.00 0.00 0.00 3.86
2056 3799 3.877559 CCACTCATTCACCTAGATTGCA 58.122 45.455 0.00 0.00 0.00 4.08
2124 3867 8.999905 ACCATTTACCTTTTACTAAGTTCCAA 57.000 30.769 0.00 0.00 0.00 3.53
2178 3921 5.045432 AGTTCCGGTGGATTGGTTATCTTAA 60.045 40.000 0.00 0.00 33.53 1.85
2613 4357 9.346005 CGGGGAAACTTGTTAAATATTATAGGT 57.654 33.333 0.00 0.00 0.00 3.08
2681 4425 6.532988 TGTTACAAACTTTGCTTTAAGGGT 57.467 33.333 1.14 0.00 0.00 4.34
2785 4532 5.988310 ACAAAAAGATTGCCATCTCATCA 57.012 34.783 0.00 0.00 39.00 3.07
2793 4540 8.563123 AAGATTGCCATCTCATCATATGTTAG 57.437 34.615 0.00 0.00 39.00 2.34
2866 4613 3.710724 TGAAGCCCCATGAATGAAATCA 58.289 40.909 0.00 0.00 0.00 2.57
2967 4715 1.002251 GTACTACTAGCTGCTCTGCCG 60.002 57.143 4.91 0.00 0.00 5.69
3015 4763 0.178998 CATGGGGCATCTCCTCCTTG 60.179 60.000 0.00 0.00 32.90 3.61
3017 4765 0.327867 TGGGGCATCTCCTCCTTGAT 60.328 55.000 0.00 0.00 32.90 2.57
3125 4873 5.139435 TGTGTTCAGGAGTCTAGATTGTG 57.861 43.478 0.00 0.00 0.00 3.33
3167 4915 7.810658 GCATAAGCACTTGCATATTATGTAGT 58.189 34.615 16.74 6.64 45.16 2.73
3258 5009 7.867445 AAGTAGCCGATTGTAATTTGTTTTG 57.133 32.000 0.00 0.00 0.00 2.44
3266 5017 8.547069 CCGATTGTAATTTGTTTTGTGTCAATT 58.453 29.630 0.00 0.00 0.00 2.32
3426 5177 3.271490 TGGGTTAGGCTCTAACCTACTCT 59.729 47.826 28.41 1.17 44.73 3.24
3459 5210 0.892755 TACTTGTCGCGGTTCAGGAT 59.107 50.000 6.13 0.00 0.00 3.24
3509 5260 6.257193 GGTTCTAACTATTTACCCATGTGACG 59.743 42.308 0.00 0.00 0.00 4.35
3573 5324 7.756722 CCACTCTAAAATCATCAAAACACCATC 59.243 37.037 0.00 0.00 0.00 3.51
3706 5457 6.891361 ACCAATTGTCTCATTAATGATGTCCA 59.109 34.615 18.26 9.77 36.02 4.02
3711 5462 5.297527 TGTCTCATTAATGATGTCCACATGC 59.702 40.000 18.26 2.09 36.57 4.06
3886 5637 6.369615 GCATTTGGAATTATGTTCAGCTTTGT 59.630 34.615 0.00 0.00 0.00 2.83
3966 5718 3.670625 TCTGTTTCTTGGTAACGATGGG 58.329 45.455 0.00 0.00 42.51 4.00
4016 5768 2.876550 GCGTTGGGTACTTCTGAAAGTT 59.123 45.455 0.00 0.00 43.28 2.66
4017 5769 3.303791 GCGTTGGGTACTTCTGAAAGTTG 60.304 47.826 0.00 0.00 43.28 3.16
4059 5811 3.426615 AGAACTGAGACTGAGGTACTGG 58.573 50.000 0.00 0.00 41.55 4.00
4180 5932 6.716628 ACATTCCTGTCTTCATTAAGCTTTCA 59.283 34.615 3.20 0.00 32.36 2.69
4310 6167 6.875076 TGTACTCCCTCTGTAAAGAAATAGC 58.125 40.000 0.00 0.00 0.00 2.97
4490 6372 1.344438 CACGCTGCTAATCCCTCCATA 59.656 52.381 0.00 0.00 0.00 2.74
4508 6390 8.487028 CCCTCCATACATAAATATACTTCCTCC 58.513 40.741 0.00 0.00 0.00 4.30
4698 6762 8.905660 ATTCCTGTGATGAGAGAGAATTATTG 57.094 34.615 0.00 0.00 0.00 1.90
4791 6855 6.183361 TGTTCACTTATTTGAGGACAGAGGAA 60.183 38.462 0.00 0.00 0.00 3.36
4933 7122 9.570468 ACATGAGATGTATGCTAGAAAAATCAT 57.430 29.630 0.00 0.00 42.78 2.45
4992 7181 2.567169 CAATAGGGCATATCGGAGACCA 59.433 50.000 0.00 0.00 42.51 4.02
4998 7187 2.354203 GGCATATCGGAGACCAAGATCC 60.354 54.545 0.00 0.00 42.51 3.36
5111 7300 8.690203 TCTGTCTGTAAAATTTGAGGATGAAA 57.310 30.769 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.842777 CCAAAATAAACCATAAACTCGTAAACG 58.157 33.333 0.00 0.00 41.45 3.60
20 21 9.287373 AGTCCAAAATAAACCATAAACTCGTAA 57.713 29.630 0.00 0.00 0.00 3.18
22 23 7.754851 AGTCCAAAATAAACCATAAACTCGT 57.245 32.000 0.00 0.00 0.00 4.18
43 44 8.033038 GGGTATAATTTCACAAGGGAAAAAGTC 58.967 37.037 1.11 0.00 39.94 3.01
46 47 7.857404 TGGGTATAATTTCACAAGGGAAAAA 57.143 32.000 1.11 0.00 39.94 1.94
47 48 8.442660 AATGGGTATAATTTCACAAGGGAAAA 57.557 30.769 1.11 0.00 39.94 2.29
48 49 7.676043 TGAATGGGTATAATTTCACAAGGGAAA 59.324 33.333 0.00 0.00 40.72 3.13
50 51 6.605594 GTGAATGGGTATAATTTCACAAGGGA 59.394 38.462 9.16 0.00 44.56 4.20
51 52 6.607198 AGTGAATGGGTATAATTTCACAAGGG 59.393 38.462 14.79 0.00 46.51 3.95
52 53 7.645058 AGTGAATGGGTATAATTTCACAAGG 57.355 36.000 14.79 0.00 46.51 3.61
56 57 7.009174 CGCAAAAGTGAATGGGTATAATTTCAC 59.991 37.037 6.55 6.55 45.18 3.18
57 58 7.032580 CGCAAAAGTGAATGGGTATAATTTCA 58.967 34.615 0.00 0.00 0.00 2.69
58 59 7.033185 ACGCAAAAGTGAATGGGTATAATTTC 58.967 34.615 0.00 0.00 40.43 2.17
59 60 6.930731 ACGCAAAAGTGAATGGGTATAATTT 58.069 32.000 0.00 0.00 40.43 1.82
60 61 6.524101 ACGCAAAAGTGAATGGGTATAATT 57.476 33.333 0.00 0.00 40.43 1.40
61 62 6.038936 GGTACGCAAAAGTGAATGGGTATAAT 59.961 38.462 6.07 0.00 43.77 1.28
63 64 4.877251 GGTACGCAAAAGTGAATGGGTATA 59.123 41.667 6.07 0.00 43.77 1.47
64 65 3.692593 GGTACGCAAAAGTGAATGGGTAT 59.307 43.478 6.07 0.00 43.77 2.73
65 66 3.075884 GGTACGCAAAAGTGAATGGGTA 58.924 45.455 0.00 0.00 42.01 3.69
66 67 1.883926 GGTACGCAAAAGTGAATGGGT 59.116 47.619 0.00 0.00 43.88 4.51
67 68 2.629639 GGTACGCAAAAGTGAATGGG 57.370 50.000 0.00 0.00 35.78 4.00
82 83 4.637534 TCAGTCATCTAGTAACCACGGTAC 59.362 45.833 0.00 0.00 0.00 3.34
84 85 3.693807 TCAGTCATCTAGTAACCACGGT 58.306 45.455 0.00 0.00 0.00 4.83
87 88 5.282510 CGGATTCAGTCATCTAGTAACCAC 58.717 45.833 0.00 0.00 0.00 4.16
89 90 4.202121 TGCGGATTCAGTCATCTAGTAACC 60.202 45.833 0.00 0.00 0.00 2.85
90 91 4.740695 GTGCGGATTCAGTCATCTAGTAAC 59.259 45.833 0.00 0.00 0.00 2.50
92 93 3.951680 TGTGCGGATTCAGTCATCTAGTA 59.048 43.478 0.00 0.00 0.00 1.82
93 94 2.760650 TGTGCGGATTCAGTCATCTAGT 59.239 45.455 0.00 0.00 0.00 2.57
94 95 3.067320 TCTGTGCGGATTCAGTCATCTAG 59.933 47.826 0.00 0.00 33.89 2.43
95 96 3.023832 TCTGTGCGGATTCAGTCATCTA 58.976 45.455 0.00 0.00 33.89 1.98
96 97 1.827344 TCTGTGCGGATTCAGTCATCT 59.173 47.619 0.00 0.00 33.89 2.90
97 98 1.929836 GTCTGTGCGGATTCAGTCATC 59.070 52.381 0.00 0.00 33.89 2.92
98 99 1.276138 TGTCTGTGCGGATTCAGTCAT 59.724 47.619 0.00 0.00 33.89 3.06
99 100 0.678950 TGTCTGTGCGGATTCAGTCA 59.321 50.000 0.00 0.00 33.89 3.41
100 101 1.067565 TCTGTCTGTGCGGATTCAGTC 60.068 52.381 0.00 0.00 33.89 3.51
101 102 0.969149 TCTGTCTGTGCGGATTCAGT 59.031 50.000 0.00 0.00 33.89 3.41
102 103 1.998315 CTTCTGTCTGTGCGGATTCAG 59.002 52.381 0.00 0.00 0.00 3.02
104 105 2.094494 TCTCTTCTGTCTGTGCGGATTC 60.094 50.000 0.00 0.00 0.00 2.52
105 106 1.895798 TCTCTTCTGTCTGTGCGGATT 59.104 47.619 0.00 0.00 0.00 3.01
106 107 1.550327 TCTCTTCTGTCTGTGCGGAT 58.450 50.000 0.00 0.00 0.00 4.18
107 108 1.270826 CTTCTCTTCTGTCTGTGCGGA 59.729 52.381 0.00 0.00 0.00 5.54
108 109 1.000283 ACTTCTCTTCTGTCTGTGCGG 60.000 52.381 0.00 0.00 0.00 5.69
109 110 2.430546 ACTTCTCTTCTGTCTGTGCG 57.569 50.000 0.00 0.00 0.00 5.34
110 111 6.348050 CCATAAAACTTCTCTTCTGTCTGTGC 60.348 42.308 0.00 0.00 0.00 4.57
111 112 6.148480 CCCATAAAACTTCTCTTCTGTCTGTG 59.852 42.308 0.00 0.00 0.00 3.66
112 113 6.043243 TCCCATAAAACTTCTCTTCTGTCTGT 59.957 38.462 0.00 0.00 0.00 3.41
113 114 6.467677 TCCCATAAAACTTCTCTTCTGTCTG 58.532 40.000 0.00 0.00 0.00 3.51
115 116 6.468543 ACTCCCATAAAACTTCTCTTCTGTC 58.531 40.000 0.00 0.00 0.00 3.51
116 117 6.441088 ACTCCCATAAAACTTCTCTTCTGT 57.559 37.500 0.00 0.00 0.00 3.41
117 118 6.819146 GGTACTCCCATAAAACTTCTCTTCTG 59.181 42.308 0.00 0.00 0.00 3.02
118 119 6.500751 TGGTACTCCCATAAAACTTCTCTTCT 59.499 38.462 0.00 0.00 38.72 2.85
119 120 6.708285 TGGTACTCCCATAAAACTTCTCTTC 58.292 40.000 0.00 0.00 38.72 2.87
121 122 6.697641 TTGGTACTCCCATAAAACTTCTCT 57.302 37.500 0.00 0.00 44.74 3.10
122 123 6.318900 CCATTGGTACTCCCATAAAACTTCTC 59.681 42.308 0.00 0.00 44.74 2.87
124 125 6.184789 TCCATTGGTACTCCCATAAAACTTC 58.815 40.000 1.86 0.00 44.74 3.01
126 127 5.491078 TCTCCATTGGTACTCCCATAAAACT 59.509 40.000 1.86 0.00 44.74 2.66
127 128 5.751586 TCTCCATTGGTACTCCCATAAAAC 58.248 41.667 1.86 0.00 44.74 2.43
128 129 6.395780 TTCTCCATTGGTACTCCCATAAAA 57.604 37.500 1.86 0.00 44.74 1.52
130 131 6.216662 TCTTTTCTCCATTGGTACTCCCATAA 59.783 38.462 1.86 0.00 44.74 1.90
132 133 4.540099 TCTTTTCTCCATTGGTACTCCCAT 59.460 41.667 1.86 0.00 44.74 4.00
134 135 4.225267 TCTCTTTTCTCCATTGGTACTCCC 59.775 45.833 1.86 0.00 0.00 4.30
135 136 5.422214 TCTCTTTTCTCCATTGGTACTCC 57.578 43.478 1.86 0.00 0.00 3.85
136 137 6.644347 TGATCTCTTTTCTCCATTGGTACTC 58.356 40.000 1.86 0.00 0.00 2.59
138 139 7.554118 TCATTGATCTCTTTTCTCCATTGGTAC 59.446 37.037 1.86 0.00 0.00 3.34
140 141 6.487828 TCATTGATCTCTTTTCTCCATTGGT 58.512 36.000 1.86 0.00 0.00 3.67
141 142 7.400599 TTCATTGATCTCTTTTCTCCATTGG 57.599 36.000 0.00 0.00 0.00 3.16
142 143 7.758528 GGTTTCATTGATCTCTTTTCTCCATTG 59.241 37.037 0.00 0.00 0.00 2.82
143 144 7.093596 GGGTTTCATTGATCTCTTTTCTCCATT 60.094 37.037 0.00 0.00 0.00 3.16
144 145 6.379417 GGGTTTCATTGATCTCTTTTCTCCAT 59.621 38.462 0.00 0.00 0.00 3.41
146 147 5.948758 AGGGTTTCATTGATCTCTTTTCTCC 59.051 40.000 0.00 0.00 0.00 3.71
147 148 7.040132 ACAAGGGTTTCATTGATCTCTTTTCTC 60.040 37.037 0.00 0.00 37.99 2.87
149 150 6.986250 ACAAGGGTTTCATTGATCTCTTTTC 58.014 36.000 0.00 0.00 37.99 2.29
151 152 5.478332 GGACAAGGGTTTCATTGATCTCTTT 59.522 40.000 0.00 0.00 37.99 2.52
152 153 5.012893 GGACAAGGGTTTCATTGATCTCTT 58.987 41.667 0.00 0.00 37.99 2.85
153 154 4.290722 AGGACAAGGGTTTCATTGATCTCT 59.709 41.667 0.00 0.00 37.99 3.10
154 155 4.593956 AGGACAAGGGTTTCATTGATCTC 58.406 43.478 0.00 0.00 37.99 2.75
156 157 4.156739 GTGAGGACAAGGGTTTCATTGATC 59.843 45.833 0.00 0.00 37.99 2.92
158 159 3.117701 TGTGAGGACAAGGGTTTCATTGA 60.118 43.478 0.00 0.00 37.99 2.57
159 160 3.004734 GTGTGAGGACAAGGGTTTCATTG 59.995 47.826 0.00 0.00 40.17 2.82
160 161 3.117512 AGTGTGAGGACAAGGGTTTCATT 60.118 43.478 0.00 0.00 32.49 2.57
161 162 2.443255 AGTGTGAGGACAAGGGTTTCAT 59.557 45.455 0.00 0.00 32.49 2.57
164 165 1.564348 ACAGTGTGAGGACAAGGGTTT 59.436 47.619 0.00 0.00 32.49 3.27
165 166 1.141053 GACAGTGTGAGGACAAGGGTT 59.859 52.381 0.00 0.00 32.49 4.11
167 168 0.758734 TGACAGTGTGAGGACAAGGG 59.241 55.000 0.00 0.00 32.49 3.95
168 169 2.420642 CATGACAGTGTGAGGACAAGG 58.579 52.381 0.00 0.00 32.49 3.61
169 170 2.224378 ACCATGACAGTGTGAGGACAAG 60.224 50.000 0.00 0.00 32.49 3.16
172 173 2.550830 AACCATGACAGTGTGAGGAC 57.449 50.000 0.00 0.00 0.00 3.85
173 174 3.576078 AAAACCATGACAGTGTGAGGA 57.424 42.857 0.00 0.00 0.00 3.71
174 175 4.133820 TGTAAAACCATGACAGTGTGAGG 58.866 43.478 0.00 1.73 0.00 3.86
175 176 5.056480 TCTGTAAAACCATGACAGTGTGAG 58.944 41.667 0.00 0.00 41.14 3.51
176 177 5.029807 TCTGTAAAACCATGACAGTGTGA 57.970 39.130 0.00 0.00 41.14 3.58
177 178 5.056480 TCTCTGTAAAACCATGACAGTGTG 58.944 41.667 0.00 0.00 41.14 3.82
179 180 6.348786 CCAATCTCTGTAAAACCATGACAGTG 60.349 42.308 10.33 8.63 41.14 3.66
180 181 5.707298 CCAATCTCTGTAAAACCATGACAGT 59.293 40.000 10.33 0.00 41.14 3.55
181 182 5.392380 GCCAATCTCTGTAAAACCATGACAG 60.392 44.000 5.37 5.37 41.62 3.51
182 183 4.458989 GCCAATCTCTGTAAAACCATGACA 59.541 41.667 0.00 0.00 0.00 3.58
184 185 4.661222 TGCCAATCTCTGTAAAACCATGA 58.339 39.130 0.00 0.00 0.00 3.07
185 186 5.345702 CATGCCAATCTCTGTAAAACCATG 58.654 41.667 0.00 0.00 0.00 3.66
186 187 4.142093 GCATGCCAATCTCTGTAAAACCAT 60.142 41.667 6.36 0.00 0.00 3.55
187 188 3.193267 GCATGCCAATCTCTGTAAAACCA 59.807 43.478 6.36 0.00 0.00 3.67
188 189 3.193267 TGCATGCCAATCTCTGTAAAACC 59.807 43.478 16.68 0.00 0.00 3.27
189 190 4.439305 TGCATGCCAATCTCTGTAAAAC 57.561 40.909 16.68 0.00 0.00 2.43
224 1911 5.167845 GTCACGGGATTTTTATTGTGCAAT 58.832 37.500 0.00 2.83 34.93 3.56
225 1912 4.038042 TGTCACGGGATTTTTATTGTGCAA 59.962 37.500 0.00 0.00 0.00 4.08
242 1929 4.494690 GCATGTGTTAGGATCAATGTCACG 60.495 45.833 0.00 0.00 0.00 4.35
274 1961 5.523552 GCATTTTACTTTTTGGAAGCACTGT 59.476 36.000 0.00 0.00 0.00 3.55
276 1963 5.523552 GTGCATTTTACTTTTTGGAAGCACT 59.476 36.000 0.00 0.00 43.62 4.40
298 1985 2.842208 TCTGAAAAAGCACCGTTGTG 57.158 45.000 0.00 0.00 45.65 3.33
300 1987 3.547468 CACTTTCTGAAAAAGCACCGTTG 59.453 43.478 4.18 0.00 0.00 4.10
302 1989 3.013921 TCACTTTCTGAAAAAGCACCGT 58.986 40.909 4.18 0.00 0.00 4.83
303 1990 3.691049 TCACTTTCTGAAAAAGCACCG 57.309 42.857 4.18 0.00 0.00 4.94
304 1991 5.289434 CACTTTCACTTTCTGAAAAAGCACC 59.711 40.000 4.18 0.00 46.20 5.01
305 1992 6.092748 TCACTTTCACTTTCTGAAAAAGCAC 58.907 36.000 4.18 0.00 46.20 4.40
306 1993 6.266168 TCACTTTCACTTTCTGAAAAAGCA 57.734 33.333 4.18 0.00 46.20 3.91
307 1994 7.581011 TTTCACTTTCACTTTCTGAAAAAGC 57.419 32.000 4.18 0.00 46.20 3.51
308 1995 8.650714 CCTTTTCACTTTCACTTTCTGAAAAAG 58.349 33.333 4.18 7.38 46.20 2.27
309 1996 8.147704 ACCTTTTCACTTTCACTTTCTGAAAAA 58.852 29.630 4.18 0.00 46.20 1.94
333 2045 2.046604 GGGAAGCACACCGGTACC 60.047 66.667 6.87 0.16 0.00 3.34
364 2076 3.627123 AGAAACCAAAGGCAAATTTGTGC 59.373 39.130 19.03 6.81 44.14 4.57
394 2106 5.722021 TGATAGAAAGGAAAAACAAGCCC 57.278 39.130 0.00 0.00 0.00 5.19
395 2107 8.607441 AAATTGATAGAAAGGAAAAACAAGCC 57.393 30.769 0.00 0.00 0.00 4.35
396 2108 9.481340 AGAAATTGATAGAAAGGAAAAACAAGC 57.519 29.630 0.00 0.00 0.00 4.01
647 2367 3.595173 TGATAAGTAACGCACTGCATGT 58.405 40.909 1.11 0.00 37.63 3.21
755 2475 5.506181 GGCAATCTTATCGCTTCTCTTTTC 58.494 41.667 0.00 0.00 0.00 2.29
769 2489 1.153449 CGACCTGCCGGCAATCTTA 60.153 57.895 32.09 6.08 0.00 2.10
793 2514 5.243060 CCCATTTTCTTTCCTTCTTAACGGT 59.757 40.000 0.00 0.00 0.00 4.83
861 2582 1.543358 CCGCTCTCAGCAGCATATAGA 59.457 52.381 0.00 0.00 42.58 1.98
876 2597 2.574322 CGCAAATGCAATATACCGCTC 58.426 47.619 6.18 0.00 42.21 5.03
916 2637 5.458452 TCGAAAACAAAATTGTGACATGCTC 59.542 36.000 1.62 0.00 41.31 4.26
941 2678 4.527427 AGGACGATGACTGATGATGATGAT 59.473 41.667 0.00 0.00 0.00 2.45
942 2679 3.893813 AGGACGATGACTGATGATGATGA 59.106 43.478 0.00 0.00 0.00 2.92
943 2680 4.254402 AGGACGATGACTGATGATGATG 57.746 45.455 0.00 0.00 0.00 3.07
944 2681 4.082300 GCTAGGACGATGACTGATGATGAT 60.082 45.833 0.00 0.00 0.00 2.45
945 2682 3.254411 GCTAGGACGATGACTGATGATGA 59.746 47.826 0.00 0.00 0.00 2.92
946 2683 3.573598 GCTAGGACGATGACTGATGATG 58.426 50.000 0.00 0.00 0.00 3.07
947 2684 2.560542 GGCTAGGACGATGACTGATGAT 59.439 50.000 0.00 0.00 0.00 2.45
948 2685 1.957177 GGCTAGGACGATGACTGATGA 59.043 52.381 0.00 0.00 0.00 2.92
949 2686 1.335415 CGGCTAGGACGATGACTGATG 60.335 57.143 0.00 0.00 35.20 3.07
950 2687 0.955178 CGGCTAGGACGATGACTGAT 59.045 55.000 0.00 0.00 35.20 2.90
951 2688 1.101635 CCGGCTAGGACGATGACTGA 61.102 60.000 0.00 0.00 45.00 3.41
952 2689 1.360551 CCGGCTAGGACGATGACTG 59.639 63.158 0.00 0.00 45.00 3.51
953 2690 2.491022 GCCGGCTAGGACGATGACT 61.491 63.158 22.15 0.00 45.00 3.41
954 2691 2.027751 GCCGGCTAGGACGATGAC 59.972 66.667 22.15 0.00 45.00 3.06
955 2692 3.592814 CGCCGGCTAGGACGATGA 61.593 66.667 26.68 0.00 45.00 2.92
956 2693 4.647615 CCGCCGGCTAGGACGATG 62.648 72.222 26.68 4.88 45.00 3.84
980 2717 3.292159 GTTGCGTCCGGGGCTTTT 61.292 61.111 17.36 0.00 0.00 2.27
1002 2739 2.029918 CCTGTGCAAAGCCCTAGTTTTC 60.030 50.000 0.00 0.00 0.00 2.29
1118 2858 4.856607 GACGAAGCGGCGGGAGAG 62.857 72.222 9.78 0.00 35.12 3.20
1136 2876 1.326951 AAGGAGCGGAGAGGAGAAGC 61.327 60.000 0.00 0.00 0.00 3.86
1151 2891 4.308458 CGCGGTGGTGGACAAGGA 62.308 66.667 0.00 0.00 0.00 3.36
1361 3101 1.325640 CACATCACATTTCGGCTCTCG 59.674 52.381 0.00 0.00 40.90 4.04
1404 3145 2.404559 TCCCACCATTATAGCCTTCGT 58.595 47.619 0.00 0.00 0.00 3.85
1678 3420 6.771749 TCAAAATTGCATCCAACAAAAGGAAT 59.228 30.769 0.00 0.00 38.93 3.01
1934 3677 7.581476 TCCGTTCACAAATAGAAGATGTTTTC 58.419 34.615 0.00 0.00 0.00 2.29
1982 3725 6.872020 TGAAAACGACATTAGAGGACTTAAGG 59.128 38.462 7.53 0.00 0.00 2.69
1996 3739 6.515272 AATGAATAGGCTTGAAAACGACAT 57.485 33.333 0.00 0.00 0.00 3.06
2034 3777 2.615912 GCAATCTAGGTGAATGAGTGGC 59.384 50.000 0.00 0.00 0.00 5.01
2056 3799 8.160106 ACCAAGAGAATCAAGTACTCAGATTTT 58.840 33.333 18.92 15.24 37.82 1.82
2124 3867 5.482175 ACAGTGCTCTCTAACTTCCACTAAT 59.518 40.000 0.00 0.00 32.76 1.73
2178 3921 6.374333 ACGCATATTCAGTTTCCAACTACAAT 59.626 34.615 0.00 0.00 40.46 2.71
2501 4245 8.352942 GGCTGAAAACAAATAATGGAGGTATAG 58.647 37.037 0.00 0.00 0.00 1.31
2502 4246 8.058847 AGGCTGAAAACAAATAATGGAGGTATA 58.941 33.333 0.00 0.00 0.00 1.47
2511 4255 9.077885 TCTAAGACAAGGCTGAAAACAAATAAT 57.922 29.630 0.00 0.00 0.00 1.28
2738 4482 3.116746 AGAACAAAAGTGGGGGAAGGAAT 60.117 43.478 0.00 0.00 0.00 3.01
2833 4580 6.777782 TCATGGGGCTTCAAAAATGTATTTT 58.222 32.000 0.00 0.00 41.40 1.82
2837 4584 5.483231 TCATTCATGGGGCTTCAAAAATGTA 59.517 36.000 0.00 0.00 30.93 2.29
2844 4591 4.081531 GTGATTTCATTCATGGGGCTTCAA 60.082 41.667 0.00 0.00 0.00 2.69
2881 4628 4.891756 CCAGATAGTGGGAATGCAGAAAAT 59.108 41.667 0.00 0.00 43.63 1.82
2967 4715 6.486657 TGAAGATGGCTGTTATATAGGTTTGC 59.513 38.462 0.00 0.00 0.00 3.68
3015 4763 6.773976 TTGAAACATTGGGAAGTATGGATC 57.226 37.500 0.00 0.00 0.00 3.36
3017 4765 5.048364 CGTTTGAAACATTGGGAAGTATGGA 60.048 40.000 8.93 0.00 0.00 3.41
3125 4873 3.855689 ATGCAGTTGGTATTTCAGTGC 57.144 42.857 0.00 0.00 0.00 4.40
3239 4987 5.460419 TGACACAAAACAAATTACAATCGGC 59.540 36.000 0.00 0.00 0.00 5.54
3240 4988 7.456684 TTGACACAAAACAAATTACAATCGG 57.543 32.000 0.00 0.00 0.00 4.18
3258 5009 9.532697 GCAATGATTTGATGTTTTAATTGACAC 57.467 29.630 0.00 0.00 34.60 3.67
3277 5028 9.736414 ATCAATACAGCTCTATTTAGCAATGAT 57.264 29.630 0.00 0.00 45.30 2.45
3459 5210 3.958798 GCAGTAGTAACATACTCCCTCCA 59.041 47.826 0.00 0.00 40.14 3.86
3706 5457 1.064003 TGTGACTACAAGGGGCATGT 58.936 50.000 0.00 0.00 32.88 3.21
3711 5462 4.576463 GCTTATCAATGTGACTACAAGGGG 59.424 45.833 0.00 0.00 40.84 4.79
3787 5538 5.120399 ACATAATTCCAAATGCCATGCAAG 58.880 37.500 0.00 0.00 43.62 4.01
3886 5637 3.002038 ACCAAAACCTAAACACGGTCA 57.998 42.857 0.00 0.00 32.46 4.02
3966 5718 1.494721 TCACCTATCTTGGGGCCATTC 59.505 52.381 4.39 0.00 0.00 2.67
4016 5768 3.164268 CAAATGGATTCTGTTGGACCCA 58.836 45.455 0.00 0.00 0.00 4.51
4017 5769 3.430453 TCAAATGGATTCTGTTGGACCC 58.570 45.455 0.00 0.00 0.00 4.46
4027 5779 6.169094 TCAGTCTCAGTTCTCAAATGGATTC 58.831 40.000 0.00 0.00 0.00 2.52
4180 5932 1.677576 CATGGCATCTACAATGGCGTT 59.322 47.619 0.00 0.00 46.12 4.84
4227 6084 6.567891 GCATTGTACTCCAACCAGAGTTAAAC 60.568 42.308 0.00 0.00 44.83 2.01
4310 6167 8.958175 AGAGAAATATAAGAGCGTTTAGATCG 57.042 34.615 0.00 0.00 40.85 3.69
4334 6216 7.184067 ACTGTAAAAAGTACTCCCTCCATAG 57.816 40.000 0.00 0.00 0.00 2.23
4490 6372 6.781014 TGAGGACGGAGGAAGTATATTTATGT 59.219 38.462 0.00 0.00 0.00 2.29
4585 6467 7.216494 GGAGGAAATTAAAGAGGAGAGAGATG 58.784 42.308 0.00 0.00 0.00 2.90
4718 6782 9.240734 ACAAAAGAATGCTTCTATCTTCTCAAT 57.759 29.630 0.00 0.00 39.61 2.57
4907 7096 8.969260 TGATTTTTCTAGCATACATCTCATGT 57.031 30.769 0.00 0.00 46.92 3.21
4933 7122 9.542462 CATATTCGAAAGGAGTTTCCAATAGTA 57.458 33.333 0.00 0.00 38.40 1.82
4992 7181 4.821532 AATAAAGGCCTCCATGGATCTT 57.178 40.909 16.63 15.79 38.35 2.40
4998 7187 7.607223 TGAATTTTTCAAATAAAGGCCTCCATG 59.393 33.333 5.23 1.29 36.59 3.66


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

AutoCloner maintained by Alex Coulton.