Multiple sequence alignment - TraesCS3A01G222000

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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 TraesCS3A01G222000 chr3A 100.000 3107 0 0 1 3107 414203034 414199928 0.000000e+00 5738.0
1 TraesCS3A01G222000 chr3D 95.062 2248 77 19 760 2988 315756913 315754681 0.000000e+00 3506.0
2 TraesCS3A01G222000 chr3D 100.000 54 0 0 1 54 335791818 335791765 1.970000e-17 100.0
3 TraesCS3A01G222000 chr3B 93.559 2391 75 25 752 3107 404622524 404624870 0.000000e+00 3489.0
4 TraesCS3A01G222000 chr3B 86.938 467 46 8 272 732 404621986 404622443 7.690000e-141 510.0
5 TraesCS3A01G222000 chr4B 84.409 186 24 3 438 622 416119080 416119261 8.850000e-41 178.0
6 TraesCS3A01G222000 chr4B 80.676 207 32 6 444 649 39085527 39085328 1.490000e-33 154.0
7 TraesCS3A01G222000 chr5D 85.057 174 22 2 438 611 478597662 478597831 1.150000e-39 174.0
8 TraesCS3A01G222000 chr7D 85.714 168 19 3 444 611 626548455 626548293 4.120000e-39 172.0
9 TraesCS3A01G222000 chr7D 100.000 54 0 0 1 54 494089704 494089651 1.970000e-17 100.0
10 TraesCS3A01G222000 chr4A 85.057 174 21 3 438 611 699937272 699937440 4.120000e-39 172.0
11 TraesCS3A01G222000 chr2B 84.524 168 22 3 438 605 588850926 588850763 2.480000e-36 163.0
12 TraesCS3A01G222000 chrUn 83.929 168 23 3 438 605 51432711 51432548 1.150000e-34 158.0
13 TraesCS3A01G222000 chr5B 83.929 168 23 3 438 605 573978349 573978512 1.150000e-34 158.0
14 TraesCS3A01G222000 chr6D 100.000 54 0 0 1 54 412248498 412248551 1.970000e-17 100.0
15 TraesCS3A01G222000 chr4D 100.000 54 0 0 1 54 75260157 75260104 1.970000e-17 100.0
16 TraesCS3A01G222000 chr4D 100.000 54 0 0 1 54 307311135 307311188 1.970000e-17 100.0
17 TraesCS3A01G222000 chr4D 100.000 54 0 0 1 54 486304898 486304845 1.970000e-17 100.0
18 TraesCS3A01G222000 chr1D 100.000 54 0 0 1 54 302488476 302488529 1.970000e-17 100.0
19 TraesCS3A01G222000 chr1D 100.000 54 0 0 1 54 302495302 302495355 1.970000e-17 100.0
20 TraesCS3A01G222000 chr1B 89.189 74 5 3 1 73 167684060 167684131 4.270000e-14 89.8
21 TraesCS3A01G222000 chr2A 87.500 56 7 0 2986 3041 486891387 486891332 7.190000e-07 65.8
22 TraesCS3A01G222000 chr7A 88.679 53 5 1 2988 3040 146806061 146806010 2.590000e-06 63.9
23 TraesCS3A01G222000 chr7A 94.444 36 0 1 693 726 250219691 250219726 2.000000e-03 54.7


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 TraesCS3A01G222000 chr3A 414199928 414203034 3106 True 5738.0 5738 100.0000 1 3107 1 chr3A.!!$R1 3106
1 TraesCS3A01G222000 chr3D 315754681 315756913 2232 True 3506.0 3506 95.0620 760 2988 1 chr3D.!!$R1 2228
2 TraesCS3A01G222000 chr3B 404621986 404624870 2884 False 1999.5 3489 90.2485 272 3107 2 chr3B.!!$F1 2835

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
19 20 0.178970 AGGGTACGTGGACACACTCT 60.179 55.0 0.00 0.0 45.5 3.24 F
24 25 0.178987 ACGTGGACACACTCTCTCCT 60.179 55.0 3.12 0.0 45.5 3.69 F
819 888 0.250338 AAACTCCACGGCTCCAACTC 60.250 55.0 0.00 0.0 0.0 3.01 F
902 971 0.325933 CCACTCAGCACTCCATTCCA 59.674 55.0 0.00 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1254 1.758514 GGAGAGGGCGGAGATCACA 60.759 63.158 0.00 0.0 0.00 3.58 R
1557 1647 2.478031 CGACTTGTAGGTGATCCTGACG 60.478 54.545 0.00 0.0 44.81 4.35 R
2102 2195 1.314534 TGTTGCCCGGAATGCTCATG 61.315 55.000 0.73 0.0 0.00 3.07 R
2714 2815 1.407989 GGAATGGCTCCACTCCTCAAG 60.408 57.143 9.02 0.0 44.67 3.02 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
17 18 4.613143 AGGGTACGTGGACACACT 57.387 55.556 0.00 0.00 45.50 3.55
18 19 2.348665 AGGGTACGTGGACACACTC 58.651 57.895 0.00 0.00 45.50 3.51
19 20 0.178970 AGGGTACGTGGACACACTCT 60.179 55.000 0.00 0.00 45.50 3.24
20 21 0.243095 GGGTACGTGGACACACTCTC 59.757 60.000 0.00 0.00 45.50 3.20
21 22 1.245732 GGTACGTGGACACACTCTCT 58.754 55.000 0.00 0.00 45.50 3.10
22 23 1.199558 GGTACGTGGACACACTCTCTC 59.800 57.143 0.00 0.00 45.50 3.20
23 24 1.199558 GTACGTGGACACACTCTCTCC 59.800 57.143 0.00 0.00 45.50 3.71
24 25 0.178987 ACGTGGACACACTCTCTCCT 60.179 55.000 3.12 0.00 45.50 3.69
25 26 0.523966 CGTGGACACACTCTCTCCTC 59.476 60.000 3.12 0.00 45.50 3.71
26 27 1.884497 CGTGGACACACTCTCTCCTCT 60.884 57.143 3.12 0.00 45.50 3.69
27 28 1.816224 GTGGACACACTCTCTCCTCTC 59.184 57.143 0.00 0.00 44.29 3.20
28 29 1.091537 GGACACACTCTCTCCTCTCG 58.908 60.000 0.00 0.00 0.00 4.04
29 30 1.612199 GGACACACTCTCTCCTCTCGT 60.612 57.143 0.00 0.00 0.00 4.18
30 31 2.156098 GACACACTCTCTCCTCTCGTT 58.844 52.381 0.00 0.00 0.00 3.85
31 32 1.883275 ACACACTCTCTCCTCTCGTTG 59.117 52.381 0.00 0.00 0.00 4.10
32 33 0.885196 ACACTCTCTCCTCTCGTTGC 59.115 55.000 0.00 0.00 0.00 4.17
33 34 1.173043 CACTCTCTCCTCTCGTTGCT 58.827 55.000 0.00 0.00 0.00 3.91
34 35 2.290387 ACACTCTCTCCTCTCGTTGCTA 60.290 50.000 0.00 0.00 0.00 3.49
35 36 2.948979 CACTCTCTCCTCTCGTTGCTAT 59.051 50.000 0.00 0.00 0.00 2.97
36 37 2.948979 ACTCTCTCCTCTCGTTGCTATG 59.051 50.000 0.00 0.00 0.00 2.23
37 38 1.678627 TCTCTCCTCTCGTTGCTATGC 59.321 52.381 0.00 0.00 0.00 3.14
38 39 1.406898 CTCTCCTCTCGTTGCTATGCA 59.593 52.381 0.00 0.00 36.47 3.96
39 40 2.034878 TCTCCTCTCGTTGCTATGCAT 58.965 47.619 3.79 3.79 38.76 3.96
40 41 2.035193 TCTCCTCTCGTTGCTATGCATC 59.965 50.000 0.19 0.00 38.76 3.91
41 42 1.756538 TCCTCTCGTTGCTATGCATCA 59.243 47.619 0.19 0.00 38.76 3.07
42 43 1.863454 CCTCTCGTTGCTATGCATCAC 59.137 52.381 0.19 0.00 38.76 3.06
43 44 1.863454 CTCTCGTTGCTATGCATCACC 59.137 52.381 0.19 0.00 38.76 4.02
44 45 1.206849 TCTCGTTGCTATGCATCACCA 59.793 47.619 0.19 0.00 38.76 4.17
45 46 2.158914 TCTCGTTGCTATGCATCACCAT 60.159 45.455 0.19 0.00 38.76 3.55
46 47 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
47 48 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
48 49 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
49 50 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
50 51 2.786777 TGCTATGCATCACCATGATCC 58.213 47.619 0.19 0.00 34.28 3.36
51 52 2.374170 TGCTATGCATCACCATGATCCT 59.626 45.455 0.19 0.00 34.28 3.24
52 53 2.747989 GCTATGCATCACCATGATCCTG 59.252 50.000 0.19 0.00 34.28 3.86
53 54 3.809678 GCTATGCATCACCATGATCCTGT 60.810 47.826 0.19 0.00 34.28 4.00
54 55 4.564199 GCTATGCATCACCATGATCCTGTA 60.564 45.833 0.19 0.00 34.28 2.74
55 56 4.652679 ATGCATCACCATGATCCTGTAT 57.347 40.909 0.00 0.00 34.28 2.29
56 57 5.767277 ATGCATCACCATGATCCTGTATA 57.233 39.130 0.00 0.00 34.28 1.47
57 58 5.156608 TGCATCACCATGATCCTGTATAG 57.843 43.478 0.00 0.00 34.28 1.31
58 59 3.937706 GCATCACCATGATCCTGTATAGC 59.062 47.826 0.00 0.00 34.28 2.97
59 60 4.323333 GCATCACCATGATCCTGTATAGCT 60.323 45.833 0.00 0.00 34.28 3.32
60 61 5.802465 CATCACCATGATCCTGTATAGCTT 58.198 41.667 0.00 0.00 34.28 3.74
61 62 6.575056 GCATCACCATGATCCTGTATAGCTTA 60.575 42.308 0.00 0.00 34.28 3.09
62 63 7.563020 CATCACCATGATCCTGTATAGCTTAT 58.437 38.462 0.00 0.00 34.28 1.73
63 64 6.939622 TCACCATGATCCTGTATAGCTTATG 58.060 40.000 0.00 0.00 0.00 1.90
64 65 6.070596 TCACCATGATCCTGTATAGCTTATGG 60.071 42.308 0.00 0.00 38.71 2.74
65 66 5.787494 ACCATGATCCTGTATAGCTTATGGT 59.213 40.000 0.00 0.00 40.49 3.55
66 67 6.959954 ACCATGATCCTGTATAGCTTATGGTA 59.040 38.462 11.99 0.00 42.69 3.25
67 68 7.625280 ACCATGATCCTGTATAGCTTATGGTAT 59.375 37.037 11.99 5.74 42.69 2.73
68 69 7.930325 CCATGATCCTGTATAGCTTATGGTATG 59.070 40.741 9.85 0.00 37.44 2.39
69 70 8.699130 CATGATCCTGTATAGCTTATGGTATGA 58.301 37.037 9.85 0.88 37.44 2.15
70 71 8.844865 TGATCCTGTATAGCTTATGGTATGAT 57.155 34.615 9.85 4.91 37.44 2.45
71 72 9.271921 TGATCCTGTATAGCTTATGGTATGATT 57.728 33.333 9.85 0.00 37.44 2.57
74 75 8.251026 TCCTGTATAGCTTATGGTATGATTTCG 58.749 37.037 9.85 0.00 37.44 3.46
75 76 8.035394 CCTGTATAGCTTATGGTATGATTTCGT 58.965 37.037 9.85 0.00 37.44 3.85
76 77 8.981724 TGTATAGCTTATGGTATGATTTCGTC 57.018 34.615 9.85 0.00 37.44 4.20
77 78 8.581578 TGTATAGCTTATGGTATGATTTCGTCA 58.418 33.333 9.85 0.00 42.06 4.35
107 108 9.921637 ACCATAATAAACAAAATTGACACGAAT 57.078 25.926 0.00 0.00 0.00 3.34
114 115 8.873242 AAACAAAATTGACACGAATTTGAAAC 57.127 26.923 0.00 0.00 36.01 2.78
115 116 6.999456 ACAAAATTGACACGAATTTGAAACC 58.001 32.000 0.00 0.00 36.01 3.27
116 117 5.881637 AAATTGACACGAATTTGAAACCG 57.118 34.783 0.00 0.95 34.84 4.44
117 118 4.822036 ATTGACACGAATTTGAAACCGA 57.178 36.364 0.00 0.00 0.00 4.69
118 119 3.595709 TGACACGAATTTGAAACCGAC 57.404 42.857 0.00 1.87 0.00 4.79
119 120 2.288458 TGACACGAATTTGAAACCGACC 59.712 45.455 0.00 0.00 0.00 4.79
120 121 2.546789 GACACGAATTTGAAACCGACCT 59.453 45.455 0.00 0.00 0.00 3.85
121 122 3.731089 ACACGAATTTGAAACCGACCTA 58.269 40.909 0.00 0.00 0.00 3.08
122 123 4.128643 ACACGAATTTGAAACCGACCTAA 58.871 39.130 0.00 0.00 0.00 2.69
123 124 4.758165 ACACGAATTTGAAACCGACCTAAT 59.242 37.500 0.00 0.00 0.00 1.73
124 125 5.933463 ACACGAATTTGAAACCGACCTAATA 59.067 36.000 0.00 0.00 0.00 0.98
125 126 6.427547 ACACGAATTTGAAACCGACCTAATAA 59.572 34.615 0.00 0.00 0.00 1.40
126 127 7.120138 ACACGAATTTGAAACCGACCTAATAAT 59.880 33.333 0.00 0.00 0.00 1.28
127 128 8.605746 CACGAATTTGAAACCGACCTAATAATA 58.394 33.333 0.00 0.00 0.00 0.98
128 129 9.165035 ACGAATTTGAAACCGACCTAATAATAA 57.835 29.630 0.00 0.00 0.00 1.40
200 201 2.594131 CATGGATCATGCCTTGATGGT 58.406 47.619 4.13 0.00 45.29 3.55
201 202 2.832643 TGGATCATGCCTTGATGGTT 57.167 45.000 4.13 0.00 45.29 3.67
202 203 3.949586 TGGATCATGCCTTGATGGTTA 57.050 42.857 4.13 0.00 45.29 2.85
203 204 4.458256 TGGATCATGCCTTGATGGTTAT 57.542 40.909 4.13 0.00 45.29 1.89
204 205 4.146564 TGGATCATGCCTTGATGGTTATG 58.853 43.478 4.13 0.00 45.29 1.90
205 206 3.508793 GGATCATGCCTTGATGGTTATGG 59.491 47.826 4.13 0.00 45.29 2.74
206 207 3.949586 TCATGCCTTGATGGTTATGGA 57.050 42.857 0.00 0.00 38.35 3.41
207 208 3.554934 TCATGCCTTGATGGTTATGGAC 58.445 45.455 0.00 0.00 38.35 4.02
208 209 2.036958 TGCCTTGATGGTTATGGACG 57.963 50.000 0.00 0.00 38.35 4.79
209 210 1.557371 TGCCTTGATGGTTATGGACGA 59.443 47.619 0.00 0.00 38.35 4.20
210 211 2.213499 GCCTTGATGGTTATGGACGAG 58.787 52.381 0.00 0.00 38.35 4.18
211 212 2.213499 CCTTGATGGTTATGGACGAGC 58.787 52.381 0.00 0.00 0.00 5.03
212 213 2.158900 CCTTGATGGTTATGGACGAGCT 60.159 50.000 0.00 0.00 0.00 4.09
213 214 3.535561 CTTGATGGTTATGGACGAGCTT 58.464 45.455 0.00 0.00 0.00 3.74
214 215 4.442893 CCTTGATGGTTATGGACGAGCTTA 60.443 45.833 0.00 0.00 0.00 3.09
215 216 4.322080 TGATGGTTATGGACGAGCTTAG 57.678 45.455 0.00 0.00 0.00 2.18
216 217 3.704566 TGATGGTTATGGACGAGCTTAGT 59.295 43.478 0.00 0.00 0.00 2.24
217 218 4.891168 TGATGGTTATGGACGAGCTTAGTA 59.109 41.667 0.00 0.00 0.00 1.82
218 219 5.538813 TGATGGTTATGGACGAGCTTAGTAT 59.461 40.000 0.00 0.00 0.00 2.12
219 220 5.196341 TGGTTATGGACGAGCTTAGTATG 57.804 43.478 0.00 0.00 0.00 2.39
220 221 4.647853 TGGTTATGGACGAGCTTAGTATGT 59.352 41.667 0.00 0.00 0.00 2.29
221 222 5.128171 TGGTTATGGACGAGCTTAGTATGTT 59.872 40.000 0.00 0.00 0.00 2.71
222 223 6.047231 GGTTATGGACGAGCTTAGTATGTTT 58.953 40.000 0.00 0.00 0.00 2.83
223 224 6.537660 GGTTATGGACGAGCTTAGTATGTTTT 59.462 38.462 0.00 0.00 0.00 2.43
224 225 7.065443 GGTTATGGACGAGCTTAGTATGTTTTT 59.935 37.037 0.00 0.00 0.00 1.94
225 226 9.090692 GTTATGGACGAGCTTAGTATGTTTTTA 57.909 33.333 0.00 0.00 0.00 1.52
226 227 9.656040 TTATGGACGAGCTTAGTATGTTTTTAA 57.344 29.630 0.00 0.00 0.00 1.52
227 228 7.591006 TGGACGAGCTTAGTATGTTTTTAAG 57.409 36.000 0.00 0.00 0.00 1.85
228 229 7.380536 TGGACGAGCTTAGTATGTTTTTAAGA 58.619 34.615 0.00 0.00 0.00 2.10
229 230 7.544566 TGGACGAGCTTAGTATGTTTTTAAGAG 59.455 37.037 0.00 0.00 0.00 2.85
230 231 7.758528 GGACGAGCTTAGTATGTTTTTAAGAGA 59.241 37.037 0.00 0.00 0.00 3.10
231 232 9.136952 GACGAGCTTAGTATGTTTTTAAGAGAA 57.863 33.333 0.00 0.00 0.00 2.87
232 233 9.485206 ACGAGCTTAGTATGTTTTTAAGAGAAA 57.515 29.630 0.00 0.00 0.00 2.52
262 263 8.931385 ATACATTACAAGAAAAATGGATGTGC 57.069 30.769 0.00 0.00 35.71 4.57
263 264 6.996509 ACATTACAAGAAAAATGGATGTGCT 58.003 32.000 0.00 0.00 37.40 4.40
264 265 7.092716 ACATTACAAGAAAAATGGATGTGCTC 58.907 34.615 0.00 0.00 37.40 4.26
265 266 6.647334 TTACAAGAAAAATGGATGTGCTCA 57.353 33.333 0.00 0.00 0.00 4.26
266 267 5.130292 ACAAGAAAAATGGATGTGCTCAG 57.870 39.130 0.00 0.00 0.00 3.35
267 268 3.863142 AGAAAAATGGATGTGCTCAGC 57.137 42.857 0.00 0.00 0.00 4.26
268 269 2.163010 AGAAAAATGGATGTGCTCAGCG 59.837 45.455 0.00 0.00 0.00 5.18
269 270 0.813184 AAAATGGATGTGCTCAGCGG 59.187 50.000 0.00 0.00 0.00 5.52
270 271 1.033746 AAATGGATGTGCTCAGCGGG 61.034 55.000 0.00 0.00 0.00 6.13
271 272 1.913951 AATGGATGTGCTCAGCGGGA 61.914 55.000 0.00 0.00 0.00 5.14
272 273 1.913951 ATGGATGTGCTCAGCGGGAA 61.914 55.000 0.00 0.00 0.00 3.97
273 274 1.377202 GGATGTGCTCAGCGGGAAA 60.377 57.895 0.00 0.00 0.00 3.13
274 275 0.960364 GGATGTGCTCAGCGGGAAAA 60.960 55.000 0.00 0.00 0.00 2.29
275 276 0.881118 GATGTGCTCAGCGGGAAAAA 59.119 50.000 0.00 0.00 0.00 1.94
276 277 1.474077 GATGTGCTCAGCGGGAAAAAT 59.526 47.619 0.00 0.00 0.00 1.82
277 278 2.192664 TGTGCTCAGCGGGAAAAATA 57.807 45.000 0.00 0.00 0.00 1.40
286 287 2.026262 AGCGGGAAAAATAGCTCCTTGA 60.026 45.455 0.00 0.00 34.48 3.02
291 292 5.619981 CGGGAAAAATAGCTCCTTGAACAAG 60.620 44.000 7.49 7.49 38.14 3.16
304 305 9.045223 GCTCCTTGAACAAGAAAAATTACATTT 57.955 29.630 14.99 0.00 40.79 2.32
321 322 9.905713 AATTACATTTCTCTCCATAGCTGTAAA 57.094 29.630 0.00 0.00 33.20 2.01
324 325 6.820656 ACATTTCTCTCCATAGCTGTAAAGTG 59.179 38.462 0.00 0.00 0.00 3.16
325 326 5.344743 TTCTCTCCATAGCTGTAAAGTGG 57.655 43.478 0.00 0.00 0.00 4.00
326 327 3.706594 TCTCTCCATAGCTGTAAAGTGGG 59.293 47.826 0.00 0.00 0.00 4.61
336 341 3.684697 GCTGTAAAGTGGGTAGGGGAATC 60.685 52.174 0.00 0.00 0.00 2.52
337 342 3.780850 CTGTAAAGTGGGTAGGGGAATCT 59.219 47.826 0.00 0.00 0.00 2.40
356 361 0.537143 TGAGCGATTGGTTGGTGCTT 60.537 50.000 0.00 0.00 35.73 3.91
365 370 5.616866 CGATTGGTTGGTGCTTACAAACTAG 60.617 44.000 5.50 0.00 36.51 2.57
373 378 5.221641 TGGTGCTTACAAACTAGACACTGAT 60.222 40.000 0.00 0.00 0.00 2.90
374 379 5.348997 GGTGCTTACAAACTAGACACTGATC 59.651 44.000 0.00 0.00 0.00 2.92
376 381 7.313646 GTGCTTACAAACTAGACACTGATCTA 58.686 38.462 0.00 0.00 0.00 1.98
400 405 5.165911 CACCATATGCATGTTGAGAGAAC 57.834 43.478 10.16 0.00 26.15 3.01
425 430 5.546499 TGTTAGTAGTGGGGATCAACTTCTT 59.454 40.000 0.00 0.00 0.00 2.52
428 433 6.697641 AGTAGTGGGGATCAACTTCTTAAA 57.302 37.500 0.00 0.00 0.00 1.52
429 434 7.086685 AGTAGTGGGGATCAACTTCTTAAAA 57.913 36.000 0.00 0.00 0.00 1.52
430 435 7.523415 AGTAGTGGGGATCAACTTCTTAAAAA 58.477 34.615 0.00 0.00 0.00 1.94
431 436 6.650427 AGTGGGGATCAACTTCTTAAAAAC 57.350 37.500 0.00 0.00 0.00 2.43
432 437 6.133356 AGTGGGGATCAACTTCTTAAAAACA 58.867 36.000 0.00 0.00 0.00 2.83
433 438 6.040504 AGTGGGGATCAACTTCTTAAAAACAC 59.959 38.462 0.00 0.00 0.00 3.32
434 439 5.894393 TGGGGATCAACTTCTTAAAAACACA 59.106 36.000 0.00 0.00 0.00 3.72
452 457 4.836825 ACACAGGATGACTACTTGAATGG 58.163 43.478 0.00 0.00 39.69 3.16
458 463 6.207417 CAGGATGACTACTTGAATGGTTGTTT 59.793 38.462 0.00 0.00 39.69 2.83
460 465 5.181690 TGACTACTTGAATGGTTGTTTGC 57.818 39.130 0.00 0.00 0.00 3.68
468 473 3.703556 TGAATGGTTGTTTGCCTCAAGAA 59.296 39.130 0.00 0.00 0.00 2.52
474 479 7.531857 TGGTTGTTTGCCTCAAGAAATATAA 57.468 32.000 0.00 0.00 0.00 0.98
576 581 9.561069 GGTATGGAAAGTTCATATCATAACAGT 57.439 33.333 0.00 0.00 30.72 3.55
581 586 9.774742 GGAAAGTTCATATCATAACAGTGAAAC 57.225 33.333 0.00 0.00 31.38 2.78
582 587 9.774742 GAAAGTTCATATCATAACAGTGAAACC 57.225 33.333 0.00 0.00 37.80 3.27
583 588 9.520515 AAAGTTCATATCATAACAGTGAAACCT 57.479 29.630 0.00 0.00 37.80 3.50
600 605 9.362151 AGTGAAACCTAGAAACCATAAAAATCA 57.638 29.630 0.00 0.00 37.80 2.57
637 642 6.900568 TTTGGTTTTAGAATGCACAAAGTG 57.099 33.333 0.00 0.00 36.51 3.16
646 652 6.822667 AGAATGCACAAAGTGATCATTACA 57.177 33.333 0.00 0.00 35.23 2.41
676 682 3.941629 ACCCAAGGATCCATAAGCTAGA 58.058 45.455 15.82 0.00 0.00 2.43
677 683 4.507342 ACCCAAGGATCCATAAGCTAGAT 58.493 43.478 15.82 0.00 0.00 1.98
708 714 5.463499 AAGAAATTTTGTTCCGTTGCAAC 57.537 34.783 19.89 19.89 0.00 4.17
819 888 0.250338 AAACTCCACGGCTCCAACTC 60.250 55.000 0.00 0.00 0.00 3.01
820 889 1.407656 AACTCCACGGCTCCAACTCA 61.408 55.000 0.00 0.00 0.00 3.41
821 890 1.371183 CTCCACGGCTCCAACTCAA 59.629 57.895 0.00 0.00 0.00 3.02
852 921 1.633945 GATAAGTATTGGGCCGGGGAT 59.366 52.381 2.18 0.00 0.00 3.85
900 969 0.326264 ACCCACTCAGCACTCCATTC 59.674 55.000 0.00 0.00 0.00 2.67
901 970 0.393537 CCCACTCAGCACTCCATTCC 60.394 60.000 0.00 0.00 0.00 3.01
902 971 0.325933 CCACTCAGCACTCCATTCCA 59.674 55.000 0.00 0.00 0.00 3.53
903 972 1.064906 CCACTCAGCACTCCATTCCAT 60.065 52.381 0.00 0.00 0.00 3.41
904 973 2.619849 CCACTCAGCACTCCATTCCATT 60.620 50.000 0.00 0.00 0.00 3.16
914 983 4.082125 ACTCCATTCCATTGTCCAACTTC 58.918 43.478 0.00 0.00 0.00 3.01
928 997 2.762327 CCAACTTCCATCCATTTCCCAG 59.238 50.000 0.00 0.00 0.00 4.45
1164 1254 2.115266 CCGACCAACCCCAAAGCT 59.885 61.111 0.00 0.00 0.00 3.74
1254 1344 1.522355 CACCGCCGAGCATCTCAAT 60.522 57.895 0.00 0.00 0.00 2.57
1557 1647 2.227968 CTGACGCTGCCGCTTACAAC 62.228 60.000 0.00 0.00 38.22 3.32
1734 1824 2.170607 GGAGGTATACAGGAGCTTGCAA 59.829 50.000 5.01 0.00 0.00 4.08
2232 2330 7.066284 AGACACTCATACATAGTTTTTGGATGC 59.934 37.037 0.00 0.00 35.71 3.91
2274 2372 7.476540 ACGATCCATAGCCTATATTTGTGTA 57.523 36.000 0.00 0.00 0.00 2.90
2360 2458 8.280497 CCTATATTGGTAGTTGAATTTACACGC 58.720 37.037 0.00 0.00 0.00 5.34
2481 2580 3.374988 CAGTTCACTGCTGAAGAACAACA 59.625 43.478 23.69 0.00 43.00 3.33
2595 2694 0.530744 TGCAGGCTCGTACTAACTGG 59.469 55.000 0.00 0.00 0.00 4.00
2634 2733 1.164411 TGGTTTGCCAGCTAATGTCG 58.836 50.000 0.00 0.00 40.46 4.35
2669 2769 0.669318 CCTAGCACTTTGGCGAACGA 60.669 55.000 0.00 0.00 39.27 3.85
2679 2779 3.740044 TTGGCGAACGATGAGAATTTC 57.260 42.857 0.00 0.00 0.00 2.17
2700 2801 9.736023 AATTTCAGAGAAATTGTACAGAAACAC 57.264 29.630 14.81 0.00 0.00 3.32
2701 2802 6.525121 TCAGAGAAATTGTACAGAAACACG 57.475 37.500 0.00 0.00 0.00 4.49
2714 2815 4.088648 CAGAAACACGTGTTCAACTCAAC 58.911 43.478 32.36 15.87 37.25 3.18
2775 2876 2.842188 ATTGCGAGGAATGCCCAGCA 62.842 55.000 5.65 5.65 44.89 4.41
2924 3025 9.099454 GTAATGGTTTCATTTTTGTGTTTGGTA 57.901 29.630 0.00 0.00 42.90 3.25
2968 3069 3.237746 TGATTCAGCCTCATCCCTAGAG 58.762 50.000 0.00 0.00 0.00 2.43
2969 3070 3.116977 TGATTCAGCCTCATCCCTAGAGA 60.117 47.826 0.00 0.00 35.09 3.10
2972 3073 4.749048 TCAGCCTCATCCCTAGAGAATA 57.251 45.455 0.00 0.00 35.09 1.75
2973 3074 5.282436 TCAGCCTCATCCCTAGAGAATAT 57.718 43.478 0.00 0.00 35.09 1.28
2975 3076 4.161942 CAGCCTCATCCCTAGAGAATATGG 59.838 50.000 0.00 0.00 35.09 2.74
2977 3078 4.693420 CCTCATCCCTAGAGAATATGGGT 58.307 47.826 0.00 0.00 40.48 4.51
2978 3079 4.469227 CCTCATCCCTAGAGAATATGGGTG 59.531 50.000 0.00 0.00 40.48 4.61
2979 3080 5.090139 CTCATCCCTAGAGAATATGGGTGT 58.910 45.833 0.00 0.00 40.48 4.16
2980 3081 4.840680 TCATCCCTAGAGAATATGGGTGTG 59.159 45.833 0.00 0.00 40.48 3.82
2983 3084 5.476983 TCCCTAGAGAATATGGGTGTGAAT 58.523 41.667 0.00 0.00 40.48 2.57
2984 3085 6.630131 TCCCTAGAGAATATGGGTGTGAATA 58.370 40.000 0.00 0.00 40.48 1.75
2985 3086 7.256399 TCCCTAGAGAATATGGGTGTGAATAT 58.744 38.462 0.00 0.00 40.48 1.28
2986 3087 8.406643 TCCCTAGAGAATATGGGTGTGAATATA 58.593 37.037 0.00 0.00 40.48 0.86
2987 3088 9.218525 CCCTAGAGAATATGGGTGTGAATATAT 57.781 37.037 0.00 0.00 35.13 0.86
2995 3096 5.468540 TGGGTGTGAATATATTCTCTCCG 57.531 43.478 26.63 0.00 41.33 4.63
2997 3098 5.365605 TGGGTGTGAATATATTCTCTCCGTT 59.634 40.000 26.63 0.00 41.33 4.44
2998 3099 5.927115 GGGTGTGAATATATTCTCTCCGTTC 59.073 44.000 26.63 17.16 41.33 3.95
3001 3102 7.039923 GGTGTGAATATATTCTCTCCGTTCCTA 60.040 40.741 22.88 4.49 35.56 2.94
3015 3116 9.632807 CTCTCCGTTCCTAAATATAAATCTCTG 57.367 37.037 0.00 0.00 0.00 3.35
3016 3117 9.144298 TCTCCGTTCCTAAATATAAATCTCTGT 57.856 33.333 0.00 0.00 0.00 3.41
3035 3136 7.156000 TCTCTGTAGAGATTCCACTATAGACG 58.844 42.308 6.78 0.00 45.48 4.18
3036 3137 7.015389 TCTCTGTAGAGATTCCACTATAGACGA 59.985 40.741 6.78 0.00 45.48 4.20
3037 3138 6.930164 TCTGTAGAGATTCCACTATAGACGAC 59.070 42.308 6.78 0.00 33.97 4.34
3038 3139 6.589135 TGTAGAGATTCCACTATAGACGACA 58.411 40.000 6.78 0.00 0.00 4.35
3039 3140 7.225011 TGTAGAGATTCCACTATAGACGACAT 58.775 38.462 6.78 0.00 0.00 3.06
3041 3142 9.217278 GTAGAGATTCCACTATAGACGACATAA 57.783 37.037 6.78 0.00 0.00 1.90
3042 3143 8.330466 AGAGATTCCACTATAGACGACATAAG 57.670 38.462 6.78 0.00 0.00 1.73
3043 3144 7.940137 AGAGATTCCACTATAGACGACATAAGT 59.060 37.037 6.78 0.00 0.00 2.24
3044 3145 8.101654 AGATTCCACTATAGACGACATAAGTC 57.898 38.462 6.78 0.00 41.46 3.01
3045 3146 7.720074 AGATTCCACTATAGACGACATAAGTCA 59.280 37.037 6.78 0.00 45.23 3.41
3046 3147 7.634671 TTCCACTATAGACGACATAAGTCAA 57.365 36.000 6.78 0.00 45.23 3.18
3047 3148 7.260558 TCCACTATAGACGACATAAGTCAAG 57.739 40.000 6.78 0.00 45.23 3.02
3063 3164 2.096496 GTCAAGAATCATCAACCGGCAG 59.904 50.000 0.00 0.00 0.00 4.85
3076 3177 2.482374 GGCAGACGCATCAAGCAC 59.518 61.111 0.00 0.00 46.13 4.40
3080 3181 0.870393 CAGACGCATCAAGCACAAGT 59.130 50.000 0.00 0.00 46.13 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.243095 GAGAGTGTGTCCACGTACCC 59.757 60.000 0.00 0.00 46.56 3.69
2 3 1.199558 GAGAGAGTGTGTCCACGTACC 59.800 57.143 0.00 0.00 46.56 3.34
3 4 1.199558 GGAGAGAGTGTGTCCACGTAC 59.800 57.143 0.00 0.00 46.56 3.67
4 5 1.073444 AGGAGAGAGTGTGTCCACGTA 59.927 52.381 6.22 0.00 46.56 3.57
5 6 0.178987 AGGAGAGAGTGTGTCCACGT 60.179 55.000 6.22 0.00 46.56 4.49
6 7 0.523966 GAGGAGAGAGTGTGTCCACG 59.476 60.000 6.22 0.00 46.56 4.94
8 9 1.611936 CGAGAGGAGAGAGTGTGTCCA 60.612 57.143 6.22 0.00 41.41 4.02
9 10 1.091537 CGAGAGGAGAGAGTGTGTCC 58.908 60.000 0.00 0.00 39.04 4.02
10 11 1.816074 ACGAGAGGAGAGAGTGTGTC 58.184 55.000 0.00 0.00 0.00 3.67
11 12 1.883275 CAACGAGAGGAGAGAGTGTGT 59.117 52.381 0.00 0.00 0.00 3.72
12 13 1.402194 GCAACGAGAGGAGAGAGTGTG 60.402 57.143 0.00 0.00 0.00 3.82
13 14 0.885196 GCAACGAGAGGAGAGAGTGT 59.115 55.000 0.00 0.00 0.00 3.55
14 15 1.173043 AGCAACGAGAGGAGAGAGTG 58.827 55.000 0.00 0.00 0.00 3.51
15 16 2.791347 TAGCAACGAGAGGAGAGAGT 57.209 50.000 0.00 0.00 0.00 3.24
16 17 2.287547 GCATAGCAACGAGAGGAGAGAG 60.288 54.545 0.00 0.00 0.00 3.20
17 18 1.678627 GCATAGCAACGAGAGGAGAGA 59.321 52.381 0.00 0.00 0.00 3.10
18 19 1.406898 TGCATAGCAACGAGAGGAGAG 59.593 52.381 0.00 0.00 34.76 3.20
19 20 1.474330 TGCATAGCAACGAGAGGAGA 58.526 50.000 0.00 0.00 34.76 3.71
20 21 2.223900 TGATGCATAGCAACGAGAGGAG 60.224 50.000 0.00 0.00 43.62 3.69
21 22 1.756538 TGATGCATAGCAACGAGAGGA 59.243 47.619 0.00 0.00 43.62 3.71
22 23 1.863454 GTGATGCATAGCAACGAGAGG 59.137 52.381 0.00 0.00 43.62 3.69
23 24 1.863454 GGTGATGCATAGCAACGAGAG 59.137 52.381 0.00 0.00 43.62 3.20
24 25 1.206849 TGGTGATGCATAGCAACGAGA 59.793 47.619 0.00 0.00 43.62 4.04
25 26 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
26 27 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
27 28 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
28 29 3.057736 GGATCATGGTGATGCATAGCAAC 60.058 47.826 0.00 0.00 43.55 4.17
29 30 3.151554 GGATCATGGTGATGCATAGCAA 58.848 45.455 0.00 0.00 43.55 3.91
30 31 2.374170 AGGATCATGGTGATGCATAGCA 59.626 45.455 12.83 4.86 46.03 3.49
31 32 2.747989 CAGGATCATGGTGATGCATAGC 59.252 50.000 12.83 0.00 46.03 2.97
32 33 4.017177 ACAGGATCATGGTGATGCATAG 57.983 45.455 12.66 5.87 46.03 2.23
33 34 5.767277 ATACAGGATCATGGTGATGCATA 57.233 39.130 12.66 6.20 46.03 3.14
34 35 4.652679 ATACAGGATCATGGTGATGCAT 57.347 40.909 12.66 0.00 46.03 3.96
35 36 4.564199 GCTATACAGGATCATGGTGATGCA 60.564 45.833 12.66 0.00 46.03 3.96
36 37 3.937706 GCTATACAGGATCATGGTGATGC 59.062 47.826 12.66 5.71 44.29 3.91
37 38 5.417754 AGCTATACAGGATCATGGTGATG 57.582 43.478 12.66 0.00 37.20 3.07
38 39 7.365384 CCATAAGCTATACAGGATCATGGTGAT 60.365 40.741 12.66 4.79 40.34 3.06
39 40 6.070596 CCATAAGCTATACAGGATCATGGTGA 60.071 42.308 12.66 0.00 0.00 4.02
40 41 6.111382 CCATAAGCTATACAGGATCATGGTG 58.889 44.000 12.66 0.04 0.00 4.17
41 42 5.787494 ACCATAAGCTATACAGGATCATGGT 59.213 40.000 12.66 6.24 38.97 3.55
42 43 6.305272 ACCATAAGCTATACAGGATCATGG 57.695 41.667 12.66 5.61 37.12 3.66
43 44 8.699130 TCATACCATAAGCTATACAGGATCATG 58.301 37.037 5.68 5.68 0.00 3.07
44 45 8.844865 TCATACCATAAGCTATACAGGATCAT 57.155 34.615 0.00 0.00 0.00 2.45
45 46 8.844865 ATCATACCATAAGCTATACAGGATCA 57.155 34.615 0.00 0.00 0.00 2.92
48 49 8.251026 CGAAATCATACCATAAGCTATACAGGA 58.749 37.037 0.00 0.00 0.00 3.86
49 50 8.035394 ACGAAATCATACCATAAGCTATACAGG 58.965 37.037 0.00 0.00 0.00 4.00
50 51 8.988064 ACGAAATCATACCATAAGCTATACAG 57.012 34.615 0.00 0.00 0.00 2.74
51 52 8.581578 TGACGAAATCATACCATAAGCTATACA 58.418 33.333 0.00 0.00 29.99 2.29
52 53 8.981724 TGACGAAATCATACCATAAGCTATAC 57.018 34.615 0.00 0.00 29.99 1.47
81 82 9.921637 ATTCGTGTCAATTTTGTTTATTATGGT 57.078 25.926 0.00 0.00 0.00 3.55
88 89 9.959775 GTTTCAAATTCGTGTCAATTTTGTTTA 57.040 25.926 0.00 0.00 34.37 2.01
89 90 7.960195 GGTTTCAAATTCGTGTCAATTTTGTTT 59.040 29.630 0.00 0.00 34.37 2.83
90 91 7.460296 GGTTTCAAATTCGTGTCAATTTTGTT 58.540 30.769 0.00 0.00 34.37 2.83
91 92 6.237701 CGGTTTCAAATTCGTGTCAATTTTGT 60.238 34.615 0.00 0.00 34.37 2.83
92 93 6.020281 TCGGTTTCAAATTCGTGTCAATTTTG 60.020 34.615 0.00 0.00 34.37 2.44
93 94 6.020201 GTCGGTTTCAAATTCGTGTCAATTTT 60.020 34.615 0.00 0.00 34.37 1.82
94 95 5.457473 GTCGGTTTCAAATTCGTGTCAATTT 59.543 36.000 0.00 0.00 36.57 1.82
95 96 4.973663 GTCGGTTTCAAATTCGTGTCAATT 59.026 37.500 0.00 0.00 0.00 2.32
96 97 4.533222 GTCGGTTTCAAATTCGTGTCAAT 58.467 39.130 0.00 0.00 0.00 2.57
97 98 3.242804 GGTCGGTTTCAAATTCGTGTCAA 60.243 43.478 0.00 0.00 0.00 3.18
98 99 2.288458 GGTCGGTTTCAAATTCGTGTCA 59.712 45.455 0.00 0.00 0.00 3.58
99 100 2.546789 AGGTCGGTTTCAAATTCGTGTC 59.453 45.455 0.00 0.00 0.00 3.67
100 101 2.567985 AGGTCGGTTTCAAATTCGTGT 58.432 42.857 0.00 0.00 0.00 4.49
101 102 4.735662 TTAGGTCGGTTTCAAATTCGTG 57.264 40.909 0.00 0.00 0.00 4.35
102 103 7.619964 ATTATTAGGTCGGTTTCAAATTCGT 57.380 32.000 0.00 0.00 0.00 3.85
180 181 2.594131 ACCATCAAGGCATGATCCATG 58.406 47.619 1.56 2.77 45.91 3.66
181 182 3.323774 AACCATCAAGGCATGATCCAT 57.676 42.857 1.56 0.00 45.91 3.41
182 183 2.832643 AACCATCAAGGCATGATCCA 57.167 45.000 1.56 0.00 45.91 3.41
183 184 3.508793 CCATAACCATCAAGGCATGATCC 59.491 47.826 1.56 0.00 45.91 3.36
184 185 4.217118 GTCCATAACCATCAAGGCATGATC 59.783 45.833 1.56 0.00 45.91 2.92
186 187 3.554934 GTCCATAACCATCAAGGCATGA 58.445 45.455 0.00 0.00 43.14 3.07
187 188 2.291465 CGTCCATAACCATCAAGGCATG 59.709 50.000 0.00 0.00 43.14 4.06
188 189 2.172505 TCGTCCATAACCATCAAGGCAT 59.827 45.455 0.00 0.00 43.14 4.40
189 190 1.557371 TCGTCCATAACCATCAAGGCA 59.443 47.619 0.00 0.00 43.14 4.75
190 191 2.213499 CTCGTCCATAACCATCAAGGC 58.787 52.381 0.00 0.00 43.14 4.35
191 192 2.158900 AGCTCGTCCATAACCATCAAGG 60.159 50.000 0.00 0.00 45.67 3.61
192 193 3.185246 AGCTCGTCCATAACCATCAAG 57.815 47.619 0.00 0.00 0.00 3.02
193 194 3.627395 AAGCTCGTCCATAACCATCAA 57.373 42.857 0.00 0.00 0.00 2.57
194 195 3.704566 ACTAAGCTCGTCCATAACCATCA 59.295 43.478 0.00 0.00 0.00 3.07
195 196 4.323553 ACTAAGCTCGTCCATAACCATC 57.676 45.455 0.00 0.00 0.00 3.51
196 197 5.304614 ACATACTAAGCTCGTCCATAACCAT 59.695 40.000 0.00 0.00 0.00 3.55
197 198 4.647853 ACATACTAAGCTCGTCCATAACCA 59.352 41.667 0.00 0.00 0.00 3.67
198 199 5.197682 ACATACTAAGCTCGTCCATAACC 57.802 43.478 0.00 0.00 0.00 2.85
199 200 7.535489 AAAACATACTAAGCTCGTCCATAAC 57.465 36.000 0.00 0.00 0.00 1.89
200 201 9.656040 TTAAAAACATACTAAGCTCGTCCATAA 57.344 29.630 0.00 0.00 0.00 1.90
201 202 9.309516 CTTAAAAACATACTAAGCTCGTCCATA 57.690 33.333 0.00 0.00 0.00 2.74
202 203 8.038944 TCTTAAAAACATACTAAGCTCGTCCAT 58.961 33.333 0.00 0.00 0.00 3.41
203 204 7.380536 TCTTAAAAACATACTAAGCTCGTCCA 58.619 34.615 0.00 0.00 0.00 4.02
204 205 7.758528 TCTCTTAAAAACATACTAAGCTCGTCC 59.241 37.037 0.00 0.00 0.00 4.79
205 206 8.684973 TCTCTTAAAAACATACTAAGCTCGTC 57.315 34.615 0.00 0.00 0.00 4.20
206 207 9.485206 TTTCTCTTAAAAACATACTAAGCTCGT 57.515 29.630 0.00 0.00 0.00 4.18
236 237 9.023967 GCACATCCATTTTTCTTGTAATGTATC 57.976 33.333 0.00 0.00 31.38 2.24
237 238 8.752187 AGCACATCCATTTTTCTTGTAATGTAT 58.248 29.630 0.00 0.00 31.38 2.29
238 239 8.121305 AGCACATCCATTTTTCTTGTAATGTA 57.879 30.769 0.00 0.00 31.38 2.29
239 240 6.996509 AGCACATCCATTTTTCTTGTAATGT 58.003 32.000 0.00 0.00 31.38 2.71
240 241 7.092079 TGAGCACATCCATTTTTCTTGTAATG 58.908 34.615 0.00 0.00 0.00 1.90
241 242 7.230849 TGAGCACATCCATTTTTCTTGTAAT 57.769 32.000 0.00 0.00 0.00 1.89
242 243 6.647334 TGAGCACATCCATTTTTCTTGTAA 57.353 33.333 0.00 0.00 0.00 2.41
243 244 5.335897 GCTGAGCACATCCATTTTTCTTGTA 60.336 40.000 0.00 0.00 0.00 2.41
244 245 4.560108 GCTGAGCACATCCATTTTTCTTGT 60.560 41.667 0.00 0.00 0.00 3.16
245 246 3.924686 GCTGAGCACATCCATTTTTCTTG 59.075 43.478 0.00 0.00 0.00 3.02
246 247 3.366679 CGCTGAGCACATCCATTTTTCTT 60.367 43.478 4.88 0.00 0.00 2.52
247 248 2.163010 CGCTGAGCACATCCATTTTTCT 59.837 45.455 4.88 0.00 0.00 2.52
248 249 2.523015 CGCTGAGCACATCCATTTTTC 58.477 47.619 4.88 0.00 0.00 2.29
249 250 1.203052 CCGCTGAGCACATCCATTTTT 59.797 47.619 4.88 0.00 0.00 1.94
250 251 0.813184 CCGCTGAGCACATCCATTTT 59.187 50.000 4.88 0.00 0.00 1.82
251 252 1.033746 CCCGCTGAGCACATCCATTT 61.034 55.000 4.88 0.00 0.00 2.32
252 253 1.452651 CCCGCTGAGCACATCCATT 60.453 57.895 4.88 0.00 0.00 3.16
253 254 1.913951 TTCCCGCTGAGCACATCCAT 61.914 55.000 4.88 0.00 0.00 3.41
254 255 2.123248 TTTCCCGCTGAGCACATCCA 62.123 55.000 4.88 0.00 0.00 3.41
255 256 0.960364 TTTTCCCGCTGAGCACATCC 60.960 55.000 4.88 0.00 0.00 3.51
256 257 0.881118 TTTTTCCCGCTGAGCACATC 59.119 50.000 4.88 0.00 0.00 3.06
257 258 1.549203 ATTTTTCCCGCTGAGCACAT 58.451 45.000 4.88 0.00 0.00 3.21
258 259 2.083774 CTATTTTTCCCGCTGAGCACA 58.916 47.619 4.88 0.00 0.00 4.57
259 260 1.202188 GCTATTTTTCCCGCTGAGCAC 60.202 52.381 4.88 0.00 0.00 4.40
260 261 1.094785 GCTATTTTTCCCGCTGAGCA 58.905 50.000 4.88 0.00 0.00 4.26
261 262 1.332065 GAGCTATTTTTCCCGCTGAGC 59.668 52.381 0.00 0.00 31.96 4.26
262 263 1.943340 GGAGCTATTTTTCCCGCTGAG 59.057 52.381 0.00 0.00 31.96 3.35
263 264 1.559682 AGGAGCTATTTTTCCCGCTGA 59.440 47.619 0.00 0.00 33.83 4.26
264 265 2.044123 AGGAGCTATTTTTCCCGCTG 57.956 50.000 0.00 0.00 33.83 5.18
265 266 2.026262 TCAAGGAGCTATTTTTCCCGCT 60.026 45.455 0.00 0.00 33.83 5.52
266 267 2.365582 TCAAGGAGCTATTTTTCCCGC 58.634 47.619 0.00 0.00 33.83 6.13
267 268 3.756434 TGTTCAAGGAGCTATTTTTCCCG 59.244 43.478 0.00 0.00 33.83 5.14
268 269 5.476945 TCTTGTTCAAGGAGCTATTTTTCCC 59.523 40.000 11.82 0.00 33.83 3.97
269 270 6.575162 TCTTGTTCAAGGAGCTATTTTTCC 57.425 37.500 11.82 0.00 0.00 3.13
270 271 8.871686 TTTTCTTGTTCAAGGAGCTATTTTTC 57.128 30.769 11.82 0.00 0.00 2.29
271 272 9.836864 ATTTTTCTTGTTCAAGGAGCTATTTTT 57.163 25.926 11.82 0.00 0.00 1.94
272 273 9.836864 AATTTTTCTTGTTCAAGGAGCTATTTT 57.163 25.926 11.82 0.00 0.00 1.82
274 275 9.914131 GTAATTTTTCTTGTTCAAGGAGCTATT 57.086 29.630 11.82 7.26 0.00 1.73
275 276 9.077885 TGTAATTTTTCTTGTTCAAGGAGCTAT 57.922 29.630 11.82 0.00 0.00 2.97
276 277 8.458573 TGTAATTTTTCTTGTTCAAGGAGCTA 57.541 30.769 11.82 0.00 0.00 3.32
277 278 7.346751 TGTAATTTTTCTTGTTCAAGGAGCT 57.653 32.000 11.82 0.00 0.00 4.09
304 305 3.706594 CCCACTTTACAGCTATGGAGAGA 59.293 47.826 0.00 0.00 31.69 3.10
315 316 3.780850 AGATTCCCCTACCCACTTTACAG 59.219 47.826 0.00 0.00 0.00 2.74
321 322 1.972207 GCTCAGATTCCCCTACCCACT 60.972 57.143 0.00 0.00 0.00 4.00
324 325 0.759436 TCGCTCAGATTCCCCTACCC 60.759 60.000 0.00 0.00 0.00 3.69
325 326 1.343069 ATCGCTCAGATTCCCCTACC 58.657 55.000 0.00 0.00 35.73 3.18
326 327 2.548920 CCAATCGCTCAGATTCCCCTAC 60.549 54.545 0.00 0.00 45.95 3.18
336 341 0.957395 AGCACCAACCAATCGCTCAG 60.957 55.000 0.00 0.00 0.00 3.35
337 342 0.537143 AAGCACCAACCAATCGCTCA 60.537 50.000 0.00 0.00 31.17 4.26
356 361 6.127703 GGTGCTAGATCAGTGTCTAGTTTGTA 60.128 42.308 20.99 8.60 46.08 2.41
395 400 4.710375 TGATCCCCACTACTAACAGTTCTC 59.290 45.833 0.00 0.00 0.00 2.87
397 402 5.046520 AGTTGATCCCCACTACTAACAGTTC 60.047 44.000 0.00 0.00 0.00 3.01
400 405 5.187967 AGAAGTTGATCCCCACTACTAACAG 59.812 44.000 0.00 0.00 0.00 3.16
425 430 8.783093 CATTCAAGTAGTCATCCTGTGTTTTTA 58.217 33.333 0.00 0.00 0.00 1.52
428 433 5.707298 CCATTCAAGTAGTCATCCTGTGTTT 59.293 40.000 0.00 0.00 0.00 2.83
429 434 5.221925 ACCATTCAAGTAGTCATCCTGTGTT 60.222 40.000 0.00 0.00 0.00 3.32
430 435 4.287067 ACCATTCAAGTAGTCATCCTGTGT 59.713 41.667 0.00 0.00 0.00 3.72
431 436 4.836825 ACCATTCAAGTAGTCATCCTGTG 58.163 43.478 0.00 0.00 0.00 3.66
432 437 5.221925 ACAACCATTCAAGTAGTCATCCTGT 60.222 40.000 0.00 0.00 0.00 4.00
433 438 5.248640 ACAACCATTCAAGTAGTCATCCTG 58.751 41.667 0.00 0.00 0.00 3.86
434 439 5.505181 ACAACCATTCAAGTAGTCATCCT 57.495 39.130 0.00 0.00 0.00 3.24
549 554 9.559732 CTGTTATGATATGAACTTTCCATACCA 57.440 33.333 0.00 0.00 30.26 3.25
557 562 9.520515 AGGTTTCACTGTTATGATATGAACTTT 57.479 29.630 0.00 0.00 0.00 2.66
573 578 9.626045 GATTTTTATGGTTTCTAGGTTTCACTG 57.374 33.333 0.00 0.00 0.00 3.66
608 613 5.988561 TGTGCATTCTAAAACCAAATTGACC 59.011 36.000 0.00 0.00 0.00 4.02
612 617 7.768120 TCACTTTGTGCATTCTAAAACCAAATT 59.232 29.630 0.00 0.00 32.98 1.82
613 618 7.271511 TCACTTTGTGCATTCTAAAACCAAAT 58.728 30.769 0.00 0.00 32.98 2.32
637 642 5.070770 TGGGTTGCAACATTGTAATGATC 57.929 39.130 29.55 8.53 39.67 2.92
646 652 1.901833 GGATCCTTGGGTTGCAACATT 59.098 47.619 29.55 6.84 0.00 2.71
676 682 8.966868 ACGGAACAAAATTTCTTCCATGTATAT 58.033 29.630 20.05 0.00 34.20 0.86
677 683 8.343168 ACGGAACAAAATTTCTTCCATGTATA 57.657 30.769 20.05 0.00 34.20 1.47
708 714 3.414549 AAAAGCAAATATACCCGTGCG 57.585 42.857 0.00 0.00 41.90 5.34
798 867 0.534203 GTTGGAGCCGTGGAGTTTGA 60.534 55.000 0.00 0.00 0.00 2.69
819 888 2.781681 ACTTATCCTTCACCCCGTTG 57.218 50.000 0.00 0.00 0.00 4.10
820 889 4.384868 CCAATACTTATCCTTCACCCCGTT 60.385 45.833 0.00 0.00 0.00 4.44
821 890 3.135895 CCAATACTTATCCTTCACCCCGT 59.864 47.826 0.00 0.00 0.00 5.28
852 921 2.036572 GTTGGAATCCCGGGCCAA 59.963 61.111 23.00 23.00 39.23 4.52
900 969 2.806434 TGGATGGAAGTTGGACAATGG 58.194 47.619 0.00 0.00 0.00 3.16
901 970 5.410355 AAATGGATGGAAGTTGGACAATG 57.590 39.130 0.00 0.00 0.00 2.82
902 971 4.467438 GGAAATGGATGGAAGTTGGACAAT 59.533 41.667 0.00 0.00 0.00 2.71
903 972 3.831911 GGAAATGGATGGAAGTTGGACAA 59.168 43.478 0.00 0.00 0.00 3.18
904 973 3.430453 GGAAATGGATGGAAGTTGGACA 58.570 45.455 0.00 0.00 0.00 4.02
914 983 2.954318 GTGTCATCTGGGAAATGGATGG 59.046 50.000 0.00 0.00 37.85 3.51
928 997 0.460284 ACTCGGCGGATTGTGTCATC 60.460 55.000 7.21 0.00 0.00 2.92
1026 1116 3.695606 GTGGAGAGCAGGCGGTGA 61.696 66.667 0.00 0.00 0.00 4.02
1164 1254 1.758514 GGAGAGGGCGGAGATCACA 60.759 63.158 0.00 0.00 0.00 3.58
1557 1647 2.478031 CGACTTGTAGGTGATCCTGACG 60.478 54.545 0.00 0.00 44.81 4.35
1734 1824 4.806339 CCCTCCGCCCCCTTCTCT 62.806 72.222 0.00 0.00 0.00 3.10
2102 2195 1.314534 TGTTGCCCGGAATGCTCATG 61.315 55.000 0.73 0.00 0.00 3.07
2186 2279 9.574516 AGTGTCTATTGTAACCTCAGAAAAATT 57.425 29.630 0.00 0.00 0.00 1.82
2187 2280 9.220767 GAGTGTCTATTGTAACCTCAGAAAAAT 57.779 33.333 0.00 0.00 0.00 1.82
2274 2372 1.525995 CGGCAGTTGGACAACAGGT 60.526 57.895 16.58 0.00 43.47 4.00
2360 2458 3.961182 CGAAAGCAAATCCATCATGAGG 58.039 45.455 0.09 0.00 0.00 3.86
2554 2653 1.909700 TTCCTGAATGTGGTCTTGGC 58.090 50.000 0.00 0.00 0.00 4.52
2595 2694 4.219725 ACCAAACCAGCAACCATTATGTAC 59.780 41.667 0.00 0.00 0.00 2.90
2669 2769 9.730705 TCTGTACAATTTCTCTGAAATTCTCAT 57.269 29.630 13.35 5.13 32.14 2.90
2679 2779 6.129393 CACGTGTTTCTGTACAATTTCTCTG 58.871 40.000 7.58 0.00 0.00 3.35
2700 2801 3.194861 TCCTCAAGTTGAGTTGAACACG 58.805 45.455 27.07 12.28 42.80 4.49
2701 2802 4.034510 CACTCCTCAAGTTGAGTTGAACAC 59.965 45.833 27.07 0.00 42.80 3.32
2714 2815 1.407989 GGAATGGCTCCACTCCTCAAG 60.408 57.143 9.02 0.00 44.67 3.02
2754 2855 1.450531 CTGGGCATTCCTCGCAATCC 61.451 60.000 0.00 0.00 36.20 3.01
2775 2876 2.881403 GCACACCCTCCATGATTCAGTT 60.881 50.000 0.00 0.00 0.00 3.16
2909 3010 8.383175 TCTATCTCTCCTACCAAACACAAAAAT 58.617 33.333 0.00 0.00 0.00 1.82
2924 3025 6.791466 TCAAATCCATTCCATCTATCTCTCCT 59.209 38.462 0.00 0.00 0.00 3.69
2968 3069 9.606631 GGAGAGAATATATTCACACCCATATTC 57.393 37.037 24.00 10.80 39.23 1.75
2969 3070 8.260818 CGGAGAGAATATATTCACACCCATATT 58.739 37.037 24.00 2.77 39.23 1.28
2972 3073 5.544176 ACGGAGAGAATATATTCACACCCAT 59.456 40.000 24.00 13.74 39.23 4.00
2973 3074 4.899457 ACGGAGAGAATATATTCACACCCA 59.101 41.667 24.00 0.00 39.23 4.51
2975 3076 5.927115 GGAACGGAGAGAATATATTCACACC 59.073 44.000 24.00 22.52 39.23 4.16
2977 3078 6.978674 AGGAACGGAGAGAATATATTCACA 57.021 37.500 24.00 0.00 39.23 3.58
2978 3079 9.930693 ATTTAGGAACGGAGAGAATATATTCAC 57.069 33.333 24.00 18.67 39.23 3.18
2989 3090 9.632807 CAGAGATTTATATTTAGGAACGGAGAG 57.367 37.037 0.00 0.00 0.00 3.20
3011 3112 7.117236 GTCGTCTATAGTGGAATCTCTACAGAG 59.883 44.444 0.00 0.00 43.36 3.35
3012 3113 6.930164 GTCGTCTATAGTGGAATCTCTACAGA 59.070 42.308 0.00 0.00 29.47 3.41
3013 3114 6.706716 TGTCGTCTATAGTGGAATCTCTACAG 59.293 42.308 0.00 0.00 29.47 2.74
3015 3116 7.675962 ATGTCGTCTATAGTGGAATCTCTAC 57.324 40.000 0.00 0.00 0.00 2.59
3016 3117 9.438228 CTTATGTCGTCTATAGTGGAATCTCTA 57.562 37.037 0.00 0.00 0.00 2.43
3017 3118 7.940137 ACTTATGTCGTCTATAGTGGAATCTCT 59.060 37.037 0.00 0.00 0.00 3.10
3018 3119 8.101654 ACTTATGTCGTCTATAGTGGAATCTC 57.898 38.462 0.00 0.00 0.00 2.75
3019 3120 7.720074 TGACTTATGTCGTCTATAGTGGAATCT 59.280 37.037 0.00 0.00 45.70 2.40
3020 3121 7.872881 TGACTTATGTCGTCTATAGTGGAATC 58.127 38.462 0.00 0.00 45.70 2.52
3021 3122 7.818997 TGACTTATGTCGTCTATAGTGGAAT 57.181 36.000 0.00 0.00 45.70 3.01
3022 3123 7.555195 TCTTGACTTATGTCGTCTATAGTGGAA 59.445 37.037 0.00 0.00 45.70 3.53
3023 3124 7.052248 TCTTGACTTATGTCGTCTATAGTGGA 58.948 38.462 0.00 0.00 45.70 4.02
3024 3125 7.260558 TCTTGACTTATGTCGTCTATAGTGG 57.739 40.000 0.00 0.00 45.70 4.00
3030 3131 7.996385 TGATGATTCTTGACTTATGTCGTCTA 58.004 34.615 4.48 0.00 45.70 2.59
3032 3133 7.394872 GTTGATGATTCTTGACTTATGTCGTC 58.605 38.462 4.48 0.00 45.70 4.20
3034 3135 6.508563 CGGTTGATGATTCTTGACTTATGTCG 60.509 42.308 4.48 0.00 45.70 4.35
3035 3136 6.238211 CCGGTTGATGATTCTTGACTTATGTC 60.238 42.308 0.00 1.85 43.20 3.06
3036 3137 5.586243 CCGGTTGATGATTCTTGACTTATGT 59.414 40.000 0.00 0.00 0.00 2.29
3037 3138 5.504665 GCCGGTTGATGATTCTTGACTTATG 60.505 44.000 1.90 0.00 0.00 1.90
3038 3139 4.576463 GCCGGTTGATGATTCTTGACTTAT 59.424 41.667 1.90 0.00 0.00 1.73
3039 3140 3.938963 GCCGGTTGATGATTCTTGACTTA 59.061 43.478 1.90 0.00 0.00 2.24
3041 3142 2.290260 TGCCGGTTGATGATTCTTGACT 60.290 45.455 1.90 0.00 0.00 3.41
3042 3143 2.083774 TGCCGGTTGATGATTCTTGAC 58.916 47.619 1.90 0.00 0.00 3.18
3043 3144 2.027285 TCTGCCGGTTGATGATTCTTGA 60.027 45.455 1.90 0.00 0.00 3.02
3044 3145 2.096496 GTCTGCCGGTTGATGATTCTTG 59.904 50.000 1.90 0.00 0.00 3.02
3045 3146 2.359900 GTCTGCCGGTTGATGATTCTT 58.640 47.619 1.90 0.00 0.00 2.52
3046 3147 1.740380 CGTCTGCCGGTTGATGATTCT 60.740 52.381 1.90 0.00 0.00 2.40
3047 3148 0.652592 CGTCTGCCGGTTGATGATTC 59.347 55.000 1.90 0.00 0.00 2.52
3063 3164 0.867746 TGACTTGTGCTTGATGCGTC 59.132 50.000 0.00 0.00 46.63 5.19


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

AutoCloner maintained by Alex Coulton.