Multiple sequence alignment - TraesCS5B01G177600

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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 TraesCS5B01G177600 chr5B 100.000 2103 0 0 965 3067 324249405 324247303 0.000000e+00 3884
1 TraesCS5B01G177600 chr5B 100.000 733 0 0 1 733 324250369 324249637 0.000000e+00 1354
2 TraesCS5B01G177600 chr5B 82.258 372 45 10 1554 1925 446996506 446996856 4.970000e-78 302
3 TraesCS5B01G177600 chr5B 97.484 159 4 0 1 159 655024103 655023945 3.900000e-69 272
4 TraesCS5B01G177600 chr5D 92.279 2124 108 27 965 3067 285840496 285838408 0.000000e+00 2963
5 TraesCS5B01G177600 chr5D 96.269 268 5 2 460 723 285840880 285840614 4.700000e-118 435
6 TraesCS5B01G177600 chr5D 81.720 372 47 8 1554 1925 374391717 374392067 1.080000e-74 291
7 TraesCS5B01G177600 chr5D 96.855 159 5 0 1 159 443763158 443763000 1.810000e-67 267
8 TraesCS5B01G177600 chr5D 82.034 295 52 1 1631 1925 279155631 279155338 1.830000e-62 250
9 TraesCS5B01G177600 chr5A 91.460 2096 97 29 965 3029 378272782 378270738 0.000000e+00 2804
10 TraesCS5B01G177600 chr5A 97.133 279 4 1 459 733 378273171 378272893 4.630000e-128 468
11 TraesCS5B01G177600 chr5A 84.859 284 43 0 1642 1925 476225403 476225686 1.390000e-73 287
12 TraesCS5B01G177600 chr4B 95.437 263 10 1 194 454 494016340 494016602 4.730000e-113 418
13 TraesCS5B01G177600 chr6B 94.757 267 12 1 194 458 225863777 225863511 6.120000e-112 414
14 TraesCS5B01G177600 chr1B 94.424 269 12 3 195 461 419190900 419190633 7.910000e-111 411
15 TraesCS5B01G177600 chr1B 85.492 386 48 8 1554 1935 497274563 497274944 2.220000e-106 396
16 TraesCS5B01G177600 chr2A 94.361 266 13 1 194 457 68018624 68018359 1.020000e-109 407
17 TraesCS5B01G177600 chr2A 93.116 276 15 3 193 464 678350888 678350613 4.760000e-108 401
18 TraesCS5B01G177600 chr4A 94.052 269 13 2 194 460 690420792 690421059 3.680000e-109 405
19 TraesCS5B01G177600 chr3A 93.750 272 13 3 194 461 15505305 15505576 3.680000e-109 405
20 TraesCS5B01G177600 chr1D 85.678 391 47 9 1554 1940 372360600 372360985 1.320000e-108 403
21 TraesCS5B01G177600 chr1D 96.296 162 4 2 1 161 407733586 407733746 6.520000e-67 265
22 TraesCS5B01G177600 chr7A 93.141 277 14 5 194 465 430841194 430840918 4.760000e-108 401
23 TraesCS5B01G177600 chr7A 94.297 263 13 1 193 453 599647081 599647343 4.760000e-108 401
24 TraesCS5B01G177600 chr7A 82.171 387 48 5 1554 1940 585356880 585356515 2.300000e-81 313
25 TraesCS5B01G177600 chr7A 84.718 301 45 1 1641 1940 221267240 221266940 1.790000e-77 300
26 TraesCS5B01G177600 chr1A 85.602 382 47 8 1554 1931 471730051 471730428 7.970000e-106 394
27 TraesCS5B01G177600 chr7B 83.463 387 43 8 1554 1940 544481051 544480686 1.050000e-89 340
28 TraesCS5B01G177600 chr7B 85.479 303 43 1 1638 1939 193310900 193311202 6.380000e-82 315
29 TraesCS5B01G177600 chr7D 82.946 387 45 8 1554 1940 512747070 512746705 2.280000e-86 329
30 TraesCS5B01G177600 chr7D 84.718 301 45 1 1641 1940 208223420 208223120 1.790000e-77 300
31 TraesCS5B01G177600 chr7D 98.125 160 3 0 1 160 22649325 22649166 2.330000e-71 279
32 TraesCS5B01G177600 chrUn 97.484 159 4 0 1 159 16207071 16207229 3.900000e-69 272
33 TraesCS5B01G177600 chrUn 97.484 159 4 0 1 159 322212784 322212942 3.900000e-69 272
34 TraesCS5B01G177600 chrUn 97.484 159 4 0 1 159 323318011 323317853 3.900000e-69 272
35 TraesCS5B01G177600 chrUn 97.484 159 4 0 1 159 384284461 384284619 3.900000e-69 272
36 TraesCS5B01G177600 chr6D 97.484 159 4 0 1 159 472371277 472371119 3.900000e-69 272


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 TraesCS5B01G177600 chr5B 324247303 324250369 3066 True 2619 3884 100.0000 1 3067 2 chr5B.!!$R2 3066
1 TraesCS5B01G177600 chr5D 285838408 285840880 2472 True 1699 2963 94.2740 460 3067 2 chr5D.!!$R3 2607
2 TraesCS5B01G177600 chr5A 378270738 378273171 2433 True 1636 2804 94.2965 459 3029 2 chr5A.!!$R1 2570

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
49 50 0.324091 AGAGGGACGGACGTTGGTAT 60.324 55.0 0.0 0.0 0.0 2.73 F
106 107 0.388907 GTCGGTGCTTACGTGCCTTA 60.389 55.0 0.0 0.0 0.0 2.69 F
107 108 0.533491 TCGGTGCTTACGTGCCTTAT 59.467 50.0 0.0 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1897 0.394938 TGTGCTTAAAGTCGGAGCCA 59.605 50.000 0.0 0.0 35.59 4.75 R
2047 2073 1.751351 TCTAGAGCAAGACCATGTCGG 59.249 52.381 0.0 0.0 37.67 4.79 R
2081 2117 3.497262 GGACTTCGTACAGGAAACAAAGG 59.503 47.826 0.0 0.0 0.00 3.11 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.351938 CCGCTTCGGTGGTGTCGA 62.352 66.667 0.00 0.00 42.73 4.20
27 28 2.355363 CGCTTCGGTGGTGTCGAA 60.355 61.111 0.00 0.00 43.18 3.71
30 31 3.859221 TTCGGTGGTGTCGAAGGA 58.141 55.556 0.00 0.00 40.99 3.36
31 32 1.663739 TTCGGTGGTGTCGAAGGAG 59.336 57.895 0.00 0.00 40.99 3.69
32 33 0.824595 TTCGGTGGTGTCGAAGGAGA 60.825 55.000 0.00 0.00 40.99 3.71
33 34 1.213013 CGGTGGTGTCGAAGGAGAG 59.787 63.158 0.00 0.00 0.00 3.20
34 35 1.592223 GGTGGTGTCGAAGGAGAGG 59.408 63.158 0.00 0.00 0.00 3.69
35 36 1.592223 GTGGTGTCGAAGGAGAGGG 59.408 63.158 0.00 0.00 0.00 4.30
36 37 0.898789 GTGGTGTCGAAGGAGAGGGA 60.899 60.000 0.00 0.00 0.00 4.20
37 38 0.898789 TGGTGTCGAAGGAGAGGGAC 60.899 60.000 0.00 0.00 0.00 4.46
38 39 1.507174 GTGTCGAAGGAGAGGGACG 59.493 63.158 0.00 0.00 32.17 4.79
39 40 1.677966 TGTCGAAGGAGAGGGACGG 60.678 63.158 0.00 0.00 32.17 4.79
40 41 1.378250 GTCGAAGGAGAGGGACGGA 60.378 63.158 0.00 0.00 0.00 4.69
41 42 1.378250 TCGAAGGAGAGGGACGGAC 60.378 63.158 0.00 0.00 0.00 4.79
42 43 2.762234 CGAAGGAGAGGGACGGACG 61.762 68.421 0.00 0.00 0.00 4.79
43 44 1.678300 GAAGGAGAGGGACGGACGT 60.678 63.158 0.00 0.00 0.00 4.34
44 45 1.228800 AAGGAGAGGGACGGACGTT 60.229 57.895 0.00 0.00 0.00 3.99
45 46 1.533469 AAGGAGAGGGACGGACGTTG 61.533 60.000 0.00 0.00 0.00 4.10
46 47 2.572284 GAGAGGGACGGACGTTGG 59.428 66.667 0.00 0.00 0.00 3.77
47 48 2.203596 AGAGGGACGGACGTTGGT 60.204 61.111 0.00 0.00 0.00 3.67
48 49 0.962356 GAGAGGGACGGACGTTGGTA 60.962 60.000 0.00 0.00 0.00 3.25
49 50 0.324091 AGAGGGACGGACGTTGGTAT 60.324 55.000 0.00 0.00 0.00 2.73
50 51 0.533951 GAGGGACGGACGTTGGTATT 59.466 55.000 0.00 0.00 0.00 1.89
51 52 0.978907 AGGGACGGACGTTGGTATTT 59.021 50.000 0.00 0.00 0.00 1.40
52 53 1.348696 AGGGACGGACGTTGGTATTTT 59.651 47.619 0.00 0.00 0.00 1.82
53 54 1.465777 GGGACGGACGTTGGTATTTTG 59.534 52.381 0.00 0.00 0.00 2.44
54 55 1.135888 GGACGGACGTTGGTATTTTGC 60.136 52.381 0.00 0.00 0.00 3.68
55 56 1.532007 GACGGACGTTGGTATTTTGCA 59.468 47.619 0.00 0.00 0.00 4.08
56 57 2.156098 ACGGACGTTGGTATTTTGCAT 58.844 42.857 0.00 0.00 0.00 3.96
57 58 3.336468 ACGGACGTTGGTATTTTGCATA 58.664 40.909 0.00 0.00 0.00 3.14
58 59 3.372822 ACGGACGTTGGTATTTTGCATAG 59.627 43.478 0.00 0.00 0.00 2.23
59 60 3.242608 CGGACGTTGGTATTTTGCATAGG 60.243 47.826 0.00 0.00 0.00 2.57
60 61 3.942748 GGACGTTGGTATTTTGCATAGGA 59.057 43.478 0.00 0.00 0.00 2.94
61 62 4.578928 GGACGTTGGTATTTTGCATAGGAT 59.421 41.667 0.00 0.00 0.00 3.24
62 63 5.067283 GGACGTTGGTATTTTGCATAGGATT 59.933 40.000 0.00 0.00 0.00 3.01
63 64 6.405397 GGACGTTGGTATTTTGCATAGGATTT 60.405 38.462 0.00 0.00 0.00 2.17
64 65 6.930731 ACGTTGGTATTTTGCATAGGATTTT 58.069 32.000 0.00 0.00 0.00 1.82
65 66 7.033185 ACGTTGGTATTTTGCATAGGATTTTC 58.967 34.615 0.00 0.00 0.00 2.29
66 67 6.475402 CGTTGGTATTTTGCATAGGATTTTCC 59.525 38.462 0.00 0.00 36.58 3.13
83 84 8.341892 GGATTTTCCTATCTTTTCAGTCTTGT 57.658 34.615 0.00 0.00 32.53 3.16
84 85 9.449719 GGATTTTCCTATCTTTTCAGTCTTGTA 57.550 33.333 0.00 0.00 32.53 2.41
87 88 8.792830 TTTCCTATCTTTTCAGTCTTGTATGG 57.207 34.615 0.00 0.00 0.00 2.74
88 89 7.496346 TCCTATCTTTTCAGTCTTGTATGGT 57.504 36.000 0.00 0.00 0.00 3.55
89 90 7.556844 TCCTATCTTTTCAGTCTTGTATGGTC 58.443 38.462 0.00 0.00 0.00 4.02
90 91 6.477033 CCTATCTTTTCAGTCTTGTATGGTCG 59.523 42.308 0.00 0.00 0.00 4.79
91 92 4.566004 TCTTTTCAGTCTTGTATGGTCGG 58.434 43.478 0.00 0.00 0.00 4.79
92 93 4.039973 TCTTTTCAGTCTTGTATGGTCGGT 59.960 41.667 0.00 0.00 0.00 4.69
93 94 3.313012 TTCAGTCTTGTATGGTCGGTG 57.687 47.619 0.00 0.00 0.00 4.94
94 95 1.067142 TCAGTCTTGTATGGTCGGTGC 60.067 52.381 0.00 0.00 0.00 5.01
95 96 1.066858 CAGTCTTGTATGGTCGGTGCT 60.067 52.381 0.00 0.00 0.00 4.40
96 97 1.623811 AGTCTTGTATGGTCGGTGCTT 59.376 47.619 0.00 0.00 0.00 3.91
97 98 2.829720 AGTCTTGTATGGTCGGTGCTTA 59.170 45.455 0.00 0.00 0.00 3.09
98 99 2.928116 GTCTTGTATGGTCGGTGCTTAC 59.072 50.000 0.00 0.00 0.00 2.34
99 100 1.924524 CTTGTATGGTCGGTGCTTACG 59.075 52.381 0.00 0.00 0.00 3.18
100 101 0.889994 TGTATGGTCGGTGCTTACGT 59.110 50.000 0.00 0.00 0.00 3.57
101 102 1.274596 GTATGGTCGGTGCTTACGTG 58.725 55.000 0.00 0.00 0.00 4.49
102 103 0.458889 TATGGTCGGTGCTTACGTGC 60.459 55.000 0.00 0.00 0.00 5.34
103 104 3.116531 GGTCGGTGCTTACGTGCC 61.117 66.667 0.00 0.00 0.00 5.01
104 105 2.048503 GTCGGTGCTTACGTGCCT 60.049 61.111 0.00 0.00 0.00 4.75
105 106 1.666872 GTCGGTGCTTACGTGCCTT 60.667 57.895 0.00 0.00 0.00 4.35
106 107 0.388907 GTCGGTGCTTACGTGCCTTA 60.389 55.000 0.00 0.00 0.00 2.69
107 108 0.533491 TCGGTGCTTACGTGCCTTAT 59.467 50.000 0.00 0.00 0.00 1.73
108 109 1.750206 TCGGTGCTTACGTGCCTTATA 59.250 47.619 0.00 0.00 0.00 0.98
109 110 2.166050 TCGGTGCTTACGTGCCTTATAA 59.834 45.455 0.00 0.00 0.00 0.98
110 111 2.283351 CGGTGCTTACGTGCCTTATAAC 59.717 50.000 0.00 0.00 0.00 1.89
111 112 3.528532 GGTGCTTACGTGCCTTATAACT 58.471 45.455 0.00 0.00 0.00 2.24
112 113 3.937079 GGTGCTTACGTGCCTTATAACTT 59.063 43.478 0.00 0.00 0.00 2.66
113 114 4.201783 GGTGCTTACGTGCCTTATAACTTG 60.202 45.833 0.00 0.00 0.00 3.16
114 115 4.628333 GTGCTTACGTGCCTTATAACTTGA 59.372 41.667 0.00 0.00 0.00 3.02
115 116 5.293569 GTGCTTACGTGCCTTATAACTTGAT 59.706 40.000 0.00 0.00 0.00 2.57
116 117 5.522460 TGCTTACGTGCCTTATAACTTGATC 59.478 40.000 0.00 0.00 0.00 2.92
117 118 5.753921 GCTTACGTGCCTTATAACTTGATCT 59.246 40.000 0.00 0.00 0.00 2.75
118 119 6.258068 GCTTACGTGCCTTATAACTTGATCTT 59.742 38.462 0.00 0.00 0.00 2.40
119 120 7.201617 GCTTACGTGCCTTATAACTTGATCTTT 60.202 37.037 0.00 0.00 0.00 2.52
120 121 9.309516 CTTACGTGCCTTATAACTTGATCTTTA 57.690 33.333 0.00 0.00 0.00 1.85
121 122 9.826574 TTACGTGCCTTATAACTTGATCTTTAT 57.173 29.630 0.00 0.00 0.00 1.40
122 123 8.732746 ACGTGCCTTATAACTTGATCTTTATT 57.267 30.769 0.00 0.00 0.00 1.40
123 124 9.174166 ACGTGCCTTATAACTTGATCTTTATTT 57.826 29.630 0.00 0.00 0.00 1.40
151 152 5.734855 AAATGAGACACGTATTACCATGC 57.265 39.130 0.00 0.00 0.00 4.06
152 153 3.878160 TGAGACACGTATTACCATGCA 57.122 42.857 0.00 0.00 0.00 3.96
153 154 4.195225 TGAGACACGTATTACCATGCAA 57.805 40.909 0.00 0.00 0.00 4.08
154 155 4.570930 TGAGACACGTATTACCATGCAAA 58.429 39.130 0.00 0.00 0.00 3.68
155 156 4.998033 TGAGACACGTATTACCATGCAAAA 59.002 37.500 0.00 0.00 0.00 2.44
156 157 5.470437 TGAGACACGTATTACCATGCAAAAA 59.530 36.000 0.00 0.00 0.00 1.94
178 179 6.414408 AAAAGTCTCTTAATCTGCGACATG 57.586 37.500 0.00 0.00 0.00 3.21
179 180 3.452474 AGTCTCTTAATCTGCGACATGC 58.548 45.455 0.00 0.00 46.70 4.06
190 191 2.610219 GCGACATGCATGTGTGTTAA 57.390 45.000 35.92 0.00 45.45 2.01
191 192 2.508867 GCGACATGCATGTGTGTTAAG 58.491 47.619 35.92 17.46 45.45 1.85
192 193 2.728846 GCGACATGCATGTGTGTTAAGG 60.729 50.000 35.92 14.66 45.45 2.69
193 194 2.159531 CGACATGCATGTGTGTTAAGGG 60.160 50.000 35.92 9.90 41.95 3.95
194 195 2.819608 GACATGCATGTGTGTTAAGGGT 59.180 45.455 35.92 7.43 41.95 4.34
195 196 4.006989 GACATGCATGTGTGTTAAGGGTA 58.993 43.478 35.92 0.00 41.95 3.69
196 197 3.756434 ACATGCATGTGTGTTAAGGGTAC 59.244 43.478 30.92 0.00 40.03 3.34
197 198 3.780804 TGCATGTGTGTTAAGGGTACT 57.219 42.857 0.00 0.00 0.00 2.73
198 199 3.670625 TGCATGTGTGTTAAGGGTACTC 58.329 45.455 0.00 0.00 0.00 2.59
199 200 3.007635 GCATGTGTGTTAAGGGTACTCC 58.992 50.000 0.00 0.00 0.00 3.85
234 235 8.780846 TTTAGTTCGAATATTAGCTTTGGTCA 57.219 30.769 0.00 0.00 0.00 4.02
235 236 8.780846 TTAGTTCGAATATTAGCTTTGGTCAA 57.219 30.769 0.00 0.00 0.00 3.18
236 237 7.681939 AGTTCGAATATTAGCTTTGGTCAAA 57.318 32.000 0.00 0.00 0.00 2.69
249 250 5.890334 CTTTGGTCAAAGTCAAGCTTTACA 58.110 37.500 13.07 0.00 44.95 2.41
250 251 5.906113 TTGGTCAAAGTCAAGCTTTACAA 57.094 34.783 13.07 0.00 44.95 2.41
251 252 5.906113 TGGTCAAAGTCAAGCTTTACAAA 57.094 34.783 13.07 0.00 44.95 2.83
252 253 6.463995 TGGTCAAAGTCAAGCTTTACAAAT 57.536 33.333 13.07 0.00 44.95 2.32
253 254 6.872920 TGGTCAAAGTCAAGCTTTACAAATT 58.127 32.000 13.07 2.76 44.95 1.82
254 255 7.327214 TGGTCAAAGTCAAGCTTTACAAATTT 58.673 30.769 13.07 2.67 44.95 1.82
255 256 7.821846 TGGTCAAAGTCAAGCTTTACAAATTTT 59.178 29.630 13.07 2.34 44.95 1.82
256 257 8.116136 GGTCAAAGTCAAGCTTTACAAATTTTG 58.884 33.333 13.07 13.14 44.95 2.44
257 258 8.868916 GTCAAAGTCAAGCTTTACAAATTTTGA 58.131 29.630 15.81 16.09 44.95 2.69
258 259 8.868916 TCAAAGTCAAGCTTTACAAATTTTGAC 58.131 29.630 15.81 16.10 44.95 3.18
259 260 7.770801 AAGTCAAGCTTTACAAATTTTGACC 57.229 32.000 15.81 0.01 39.43 4.02
260 261 6.872920 AGTCAAGCTTTACAAATTTTGACCA 58.127 32.000 15.81 0.00 39.43 4.02
261 262 7.327214 AGTCAAGCTTTACAAATTTTGACCAA 58.673 30.769 15.81 4.27 39.43 3.67
262 263 7.492344 AGTCAAGCTTTACAAATTTTGACCAAG 59.508 33.333 15.81 13.34 39.43 3.61
263 264 7.277760 GTCAAGCTTTACAAATTTTGACCAAGT 59.722 33.333 15.81 0.00 36.35 3.16
264 265 7.821846 TCAAGCTTTACAAATTTTGACCAAGTT 59.178 29.630 15.81 8.95 0.00 2.66
265 266 8.450180 CAAGCTTTACAAATTTTGACCAAGTTT 58.550 29.630 15.81 13.28 0.00 2.66
266 267 9.660180 AAGCTTTACAAATTTTGACCAAGTTTA 57.340 25.926 15.81 0.00 0.00 2.01
267 268 9.830975 AGCTTTACAAATTTTGACCAAGTTTAT 57.169 25.926 15.81 0.00 0.00 1.40
273 274 9.606631 ACAAATTTTGACCAAGTTTATAAGCAA 57.393 25.926 15.81 0.00 0.00 3.91
420 421 9.807649 TTACGAAGTTTGACTTTAGTTAACTCT 57.192 29.630 12.39 0.00 37.78 3.24
422 423 9.807649 ACGAAGTTTGACTTTAGTTAACTCTAA 57.192 29.630 12.39 7.12 37.78 2.10
447 448 5.873179 TGCAGAGTAAATAAAAACGGAGG 57.127 39.130 0.00 0.00 0.00 4.30
448 449 4.698304 TGCAGAGTAAATAAAAACGGAGGG 59.302 41.667 0.00 0.00 0.00 4.30
449 450 4.939439 GCAGAGTAAATAAAAACGGAGGGA 59.061 41.667 0.00 0.00 0.00 4.20
450 451 5.064834 GCAGAGTAAATAAAAACGGAGGGAG 59.935 44.000 0.00 0.00 0.00 4.30
451 452 6.171213 CAGAGTAAATAAAAACGGAGGGAGT 58.829 40.000 0.00 0.00 0.00 3.85
452 453 7.325694 CAGAGTAAATAAAAACGGAGGGAGTA 58.674 38.462 0.00 0.00 0.00 2.59
453 454 7.985752 CAGAGTAAATAAAAACGGAGGGAGTAT 59.014 37.037 0.00 0.00 0.00 2.12
454 455 9.205513 AGAGTAAATAAAAACGGAGGGAGTATA 57.794 33.333 0.00 0.00 0.00 1.47
455 456 9.993454 GAGTAAATAAAAACGGAGGGAGTATAT 57.007 33.333 0.00 0.00 0.00 0.86
540 541 7.136822 ACCAATCATTCACTATACTTAGCCA 57.863 36.000 0.00 0.00 0.00 4.75
605 610 2.854032 CCCCACCCACAGACCAGT 60.854 66.667 0.00 0.00 0.00 4.00
991 996 2.265739 GCGGCACTGAGGATGACA 59.734 61.111 0.00 0.00 0.00 3.58
1071 1076 4.742649 TCCTCGGCGTGCTCCTCT 62.743 66.667 6.85 0.00 0.00 3.69
1128 1133 1.152546 GCCCTGGTTCAACCCAAGT 60.153 57.895 3.42 0.00 37.50 3.16
1152 1157 1.815421 CTACCATGGCTGTGGCGTC 60.815 63.158 13.04 0.00 43.27 5.19
1462 1479 3.241995 GGTAACACGATGATCTTTGTCGC 60.242 47.826 0.00 0.00 38.85 5.19
1486 1503 4.201910 ACGTACATCATTTAATGCACTGGC 60.202 41.667 0.00 0.00 41.68 4.85
1524 1550 4.035017 GTGTGTGTTCAAAGTACATGTGC 58.965 43.478 9.11 7.34 0.00 4.57
1551 1577 3.993535 GCTTCTGGCTGTTCCCTG 58.006 61.111 0.00 0.00 38.06 4.45
1552 1578 2.338785 GCTTCTGGCTGTTCCCTGC 61.339 63.158 0.00 0.00 38.06 4.85
1871 1897 1.595382 GCTGTGGTTCTGCGTCTGT 60.595 57.895 0.00 0.00 0.00 3.41
1883 1909 1.006102 CGTCTGTGGCTCCGACTTT 60.006 57.895 8.99 0.00 0.00 2.66
2072 2098 3.324846 ACATGGTCTTGCTCTAGACAACA 59.675 43.478 12.14 4.15 45.07 3.33
2076 2105 4.587262 TGGTCTTGCTCTAGACAACAACTA 59.413 41.667 12.14 0.00 45.07 2.24
2081 2117 7.326547 GTCTTGCTCTAGACAACAACTACTTAC 59.673 40.741 6.60 0.00 43.23 2.34
2089 2125 7.933215 AGACAACAACTACTTACCTTTGTTT 57.067 32.000 0.00 0.00 39.56 2.83
2099 2135 5.673514 ACTTACCTTTGTTTCCTGTACGAA 58.326 37.500 0.00 0.00 0.00 3.85
2103 2139 3.497262 CCTTTGTTTCCTGTACGAAGTCC 59.503 47.826 0.00 0.00 43.93 3.85
2128 2165 8.795786 CTAGTTAGTACTAGTCCACTACGTAG 57.204 42.308 20.97 20.97 45.82 3.51
2130 2167 6.381420 AGTTAGTACTAGTCCACTACGTAGGA 59.619 42.308 25.63 13.13 31.21 2.94
2169 2208 4.679373 TTAGTTTGCATTGCTTCCCAAA 57.321 36.364 10.49 0.00 36.92 3.28
2170 2209 3.557228 AGTTTGCATTGCTTCCCAAAA 57.443 38.095 10.49 0.00 36.92 2.44
2190 2229 6.529125 CCAAAACAAGTGCATCATCATTAGTC 59.471 38.462 0.00 0.00 0.00 2.59
2311 2350 4.128925 AGTACGTACGGTCAGAGTCATA 57.871 45.455 21.06 0.00 0.00 2.15
2313 2352 1.662629 ACGTACGGTCAGAGTCATACG 59.337 52.381 21.06 0.00 40.81 3.06
2369 2408 5.060506 TGGTCACTTCATGTATTTGTCGTT 58.939 37.500 0.00 0.00 0.00 3.85
2383 2422 7.658167 TGTATTTGTCGTTTGGTCTTTATCTGA 59.342 33.333 0.00 0.00 0.00 3.27
2436 2475 0.299895 GTGCATGCGTCAAGATCGAG 59.700 55.000 14.09 0.00 0.00 4.04
2437 2476 0.108662 TGCATGCGTCAAGATCGAGT 60.109 50.000 14.09 0.00 0.00 4.18
2438 2477 1.134175 TGCATGCGTCAAGATCGAGTA 59.866 47.619 14.09 0.00 0.00 2.59
2439 2478 1.518929 GCATGCGTCAAGATCGAGTAC 59.481 52.381 0.00 0.00 0.00 2.73
2460 2499 7.102346 AGTACGTACTACAAAAGAGCTAGAGA 58.898 38.462 26.36 0.00 34.13 3.10
2467 2506 7.346471 ACTACAAAAGAGCTAGAGAGAGAGAT 58.654 38.462 0.00 0.00 0.00 2.75
2481 2520 0.259938 AGAGATGGGGTGCCATTTCC 59.740 55.000 0.00 0.00 33.49 3.13
2491 2530 3.356290 GGTGCCATTTCCATCTTACTGT 58.644 45.455 0.00 0.00 0.00 3.55
2504 2543 6.491745 TCCATCTTACTGTGTTTATTTTGGCA 59.508 34.615 0.00 0.00 0.00 4.92
2506 2545 5.753744 TCTTACTGTGTTTATTTTGGCACG 58.246 37.500 0.00 0.00 34.86 5.34
2508 2547 2.035321 ACTGTGTTTATTTTGGCACGGG 59.965 45.455 0.00 0.00 41.16 5.28
2663 2703 0.460311 TTTTCCTCGATCGGCTCCTC 59.540 55.000 16.41 0.00 0.00 3.71
2672 2712 2.838748 ATCGGCTCCTCGACACCAGA 62.839 60.000 0.00 0.00 42.21 3.86
2819 2859 1.694639 GCTCTCAAATGCAACAGCAC 58.305 50.000 0.00 0.00 41.80 4.40
2832 2872 2.586258 ACAGCACGTGATCCATCTAC 57.414 50.000 22.23 0.00 0.00 2.59
2833 2873 1.202302 ACAGCACGTGATCCATCTACG 60.202 52.381 22.23 0.07 42.98 3.51
2913 2960 1.454847 GGCGGGGGCACATTATGAA 60.455 57.895 0.00 0.00 0.00 2.57
2919 2966 3.691118 CGGGGGCACATTATGAAGATATG 59.309 47.826 0.00 0.00 0.00 1.78
2920 2967 4.019174 GGGGGCACATTATGAAGATATGG 58.981 47.826 0.00 0.00 0.00 2.74
2961 3008 1.264288 GGAGAAGCGTTTGACCAACAG 59.736 52.381 0.00 0.00 34.68 3.16
2964 3011 2.097466 AGAAGCGTTTGACCAACAGTTG 59.903 45.455 6.28 6.28 34.68 3.16
2981 3028 9.716507 CCAACAGTTGCACTATTAATATGTAAC 57.283 33.333 19.24 19.24 38.69 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.737172 CCGAAGCGGCCACCAAAG 61.737 66.667 2.24 0.00 41.17 2.77
10 11 2.355363 TTCGACACCACCGAAGCG 60.355 61.111 0.00 0.00 40.56 4.68
13 14 0.824595 TCTCCTTCGACACCACCGAA 60.825 55.000 0.00 0.00 42.79 4.30
14 15 1.228337 TCTCCTTCGACACCACCGA 60.228 57.895 0.00 0.00 0.00 4.69
15 16 1.213013 CTCTCCTTCGACACCACCG 59.787 63.158 0.00 0.00 0.00 4.94
16 17 1.592223 CCTCTCCTTCGACACCACC 59.408 63.158 0.00 0.00 0.00 4.61
17 18 0.898789 TCCCTCTCCTTCGACACCAC 60.899 60.000 0.00 0.00 0.00 4.16
18 19 0.898789 GTCCCTCTCCTTCGACACCA 60.899 60.000 0.00 0.00 0.00 4.17
19 20 1.891616 GTCCCTCTCCTTCGACACC 59.108 63.158 0.00 0.00 0.00 4.16
20 21 1.507174 CGTCCCTCTCCTTCGACAC 59.493 63.158 0.00 0.00 0.00 3.67
21 22 1.677966 CCGTCCCTCTCCTTCGACA 60.678 63.158 0.00 0.00 0.00 4.35
22 23 1.378250 TCCGTCCCTCTCCTTCGAC 60.378 63.158 0.00 0.00 0.00 4.20
23 24 1.378250 GTCCGTCCCTCTCCTTCGA 60.378 63.158 0.00 0.00 0.00 3.71
24 25 2.762234 CGTCCGTCCCTCTCCTTCG 61.762 68.421 0.00 0.00 0.00 3.79
25 26 1.249469 AACGTCCGTCCCTCTCCTTC 61.249 60.000 0.00 0.00 0.00 3.46
26 27 1.228800 AACGTCCGTCCCTCTCCTT 60.229 57.895 0.00 0.00 0.00 3.36
27 28 1.977544 CAACGTCCGTCCCTCTCCT 60.978 63.158 0.00 0.00 0.00 3.69
28 29 2.572284 CAACGTCCGTCCCTCTCC 59.428 66.667 0.00 0.00 0.00 3.71
29 30 0.962356 TACCAACGTCCGTCCCTCTC 60.962 60.000 0.00 0.00 0.00 3.20
30 31 0.324091 ATACCAACGTCCGTCCCTCT 60.324 55.000 0.00 0.00 0.00 3.69
31 32 0.533951 AATACCAACGTCCGTCCCTC 59.466 55.000 0.00 0.00 0.00 4.30
32 33 0.978907 AAATACCAACGTCCGTCCCT 59.021 50.000 0.00 0.00 0.00 4.20
33 34 1.465777 CAAAATACCAACGTCCGTCCC 59.534 52.381 0.00 0.00 0.00 4.46
34 35 1.135888 GCAAAATACCAACGTCCGTCC 60.136 52.381 0.00 0.00 0.00 4.79
35 36 1.532007 TGCAAAATACCAACGTCCGTC 59.468 47.619 0.00 0.00 0.00 4.79
36 37 1.595466 TGCAAAATACCAACGTCCGT 58.405 45.000 0.00 0.00 0.00 4.69
37 38 2.911819 ATGCAAAATACCAACGTCCG 57.088 45.000 0.00 0.00 0.00 4.79
38 39 3.942748 TCCTATGCAAAATACCAACGTCC 59.057 43.478 0.00 0.00 0.00 4.79
39 40 5.751243 ATCCTATGCAAAATACCAACGTC 57.249 39.130 0.00 0.00 0.00 4.34
40 41 6.524101 AAATCCTATGCAAAATACCAACGT 57.476 33.333 0.00 0.00 0.00 3.99
41 42 6.475402 GGAAAATCCTATGCAAAATACCAACG 59.525 38.462 0.00 0.00 32.53 4.10
42 43 7.770801 GGAAAATCCTATGCAAAATACCAAC 57.229 36.000 0.00 0.00 32.53 3.77
58 59 8.341892 ACAAGACTGAAAAGATAGGAAAATCC 57.658 34.615 0.00 0.00 36.58 3.01
61 62 9.231297 CCATACAAGACTGAAAAGATAGGAAAA 57.769 33.333 0.00 0.00 0.00 2.29
62 63 8.383175 ACCATACAAGACTGAAAAGATAGGAAA 58.617 33.333 0.00 0.00 0.00 3.13
63 64 7.918076 ACCATACAAGACTGAAAAGATAGGAA 58.082 34.615 0.00 0.00 0.00 3.36
64 65 7.496346 ACCATACAAGACTGAAAAGATAGGA 57.504 36.000 0.00 0.00 0.00 2.94
65 66 6.477033 CGACCATACAAGACTGAAAAGATAGG 59.523 42.308 0.00 0.00 0.00 2.57
66 67 6.477033 CCGACCATACAAGACTGAAAAGATAG 59.523 42.308 0.00 0.00 0.00 2.08
67 68 6.070995 ACCGACCATACAAGACTGAAAAGATA 60.071 38.462 0.00 0.00 0.00 1.98
68 69 5.178797 CCGACCATACAAGACTGAAAAGAT 58.821 41.667 0.00 0.00 0.00 2.40
69 70 4.039973 ACCGACCATACAAGACTGAAAAGA 59.960 41.667 0.00 0.00 0.00 2.52
70 71 4.152402 CACCGACCATACAAGACTGAAAAG 59.848 45.833 0.00 0.00 0.00 2.27
71 72 4.062293 CACCGACCATACAAGACTGAAAA 58.938 43.478 0.00 0.00 0.00 2.29
72 73 3.659786 CACCGACCATACAAGACTGAAA 58.340 45.455 0.00 0.00 0.00 2.69
73 74 2.611971 GCACCGACCATACAAGACTGAA 60.612 50.000 0.00 0.00 0.00 3.02
74 75 1.067142 GCACCGACCATACAAGACTGA 60.067 52.381 0.00 0.00 0.00 3.41
75 76 1.066858 AGCACCGACCATACAAGACTG 60.067 52.381 0.00 0.00 0.00 3.51
76 77 1.267121 AGCACCGACCATACAAGACT 58.733 50.000 0.00 0.00 0.00 3.24
77 78 2.094762 AAGCACCGACCATACAAGAC 57.905 50.000 0.00 0.00 0.00 3.01
78 79 2.416296 CGTAAGCACCGACCATACAAGA 60.416 50.000 0.00 0.00 0.00 3.02
79 80 1.924524 CGTAAGCACCGACCATACAAG 59.075 52.381 0.00 0.00 0.00 3.16
80 81 1.273048 ACGTAAGCACCGACCATACAA 59.727 47.619 0.00 0.00 45.62 2.41
81 82 0.889994 ACGTAAGCACCGACCATACA 59.110 50.000 0.00 0.00 45.62 2.29
82 83 1.274596 CACGTAAGCACCGACCATAC 58.725 55.000 0.00 0.00 45.62 2.39
83 84 0.458889 GCACGTAAGCACCGACCATA 60.459 55.000 0.00 0.00 45.62 2.74
84 85 1.740296 GCACGTAAGCACCGACCAT 60.740 57.895 0.00 0.00 45.62 3.55
85 86 2.356553 GCACGTAAGCACCGACCA 60.357 61.111 0.00 0.00 45.62 4.02
86 87 3.116531 GGCACGTAAGCACCGACC 61.117 66.667 0.00 0.00 45.62 4.79
87 88 0.388907 TAAGGCACGTAAGCACCGAC 60.389 55.000 0.00 0.00 45.62 4.79
88 89 0.533491 ATAAGGCACGTAAGCACCGA 59.467 50.000 0.00 0.00 45.62 4.69
89 90 2.212869 TATAAGGCACGTAAGCACCG 57.787 50.000 0.00 0.00 45.62 4.94
90 91 3.528532 AGTTATAAGGCACGTAAGCACC 58.471 45.455 0.00 0.00 45.62 5.01
91 92 4.628333 TCAAGTTATAAGGCACGTAAGCAC 59.372 41.667 0.00 0.00 45.62 4.40
92 93 4.823157 TCAAGTTATAAGGCACGTAAGCA 58.177 39.130 0.00 0.00 45.62 3.91
93 94 5.753921 AGATCAAGTTATAAGGCACGTAAGC 59.246 40.000 0.00 0.00 45.62 3.09
95 96 9.826574 ATAAAGATCAAGTTATAAGGCACGTAA 57.173 29.630 0.00 0.00 0.00 3.18
96 97 9.826574 AATAAAGATCAAGTTATAAGGCACGTA 57.173 29.630 0.00 0.00 0.00 3.57
97 98 8.732746 AATAAAGATCAAGTTATAAGGCACGT 57.267 30.769 0.00 0.00 0.00 4.49
125 126 9.151471 GCATGGTAATACGTGTCTCATTTATAT 57.849 33.333 0.00 0.00 0.00 0.86
126 127 8.145122 TGCATGGTAATACGTGTCTCATTTATA 58.855 33.333 0.00 0.00 0.00 0.98
127 128 6.989759 TGCATGGTAATACGTGTCTCATTTAT 59.010 34.615 0.00 0.00 0.00 1.40
128 129 6.342111 TGCATGGTAATACGTGTCTCATTTA 58.658 36.000 0.00 0.00 0.00 1.40
129 130 5.182487 TGCATGGTAATACGTGTCTCATTT 58.818 37.500 0.00 0.00 0.00 2.32
130 131 4.765273 TGCATGGTAATACGTGTCTCATT 58.235 39.130 0.00 0.00 0.00 2.57
131 132 4.400529 TGCATGGTAATACGTGTCTCAT 57.599 40.909 0.00 0.00 0.00 2.90
132 133 3.878160 TGCATGGTAATACGTGTCTCA 57.122 42.857 0.00 0.00 0.00 3.27
133 134 5.539582 TTTTGCATGGTAATACGTGTCTC 57.460 39.130 0.00 0.00 0.00 3.36
134 135 5.950758 TTTTTGCATGGTAATACGTGTCT 57.049 34.783 0.00 0.00 0.00 3.41
154 155 6.621596 GCATGTCGCAGATTAAGAGACTTTTT 60.622 38.462 0.00 0.00 40.67 1.94
155 156 5.163814 GCATGTCGCAGATTAAGAGACTTTT 60.164 40.000 0.00 0.00 40.67 2.27
156 157 4.331168 GCATGTCGCAGATTAAGAGACTTT 59.669 41.667 0.00 0.00 40.67 2.66
157 158 3.868077 GCATGTCGCAGATTAAGAGACTT 59.132 43.478 0.00 0.00 40.67 3.01
158 159 3.452474 GCATGTCGCAGATTAAGAGACT 58.548 45.455 0.00 0.00 40.67 3.24
159 160 3.850657 GCATGTCGCAGATTAAGAGAC 57.149 47.619 0.00 0.00 40.67 3.36
171 172 2.508867 CTTAACACACATGCATGTCGC 58.491 47.619 29.23 0.00 39.39 5.19
172 173 2.159531 CCCTTAACACACATGCATGTCG 60.160 50.000 29.23 23.67 39.39 4.35
173 174 2.819608 ACCCTTAACACACATGCATGTC 59.180 45.455 29.23 0.00 39.39 3.06
174 175 2.875296 ACCCTTAACACACATGCATGT 58.125 42.857 26.61 26.61 42.84 3.21
175 176 4.009675 AGTACCCTTAACACACATGCATG 58.990 43.478 25.09 25.09 0.00 4.06
176 177 4.261801 GAGTACCCTTAACACACATGCAT 58.738 43.478 0.00 0.00 0.00 3.96
177 178 3.558321 GGAGTACCCTTAACACACATGCA 60.558 47.826 0.00 0.00 0.00 3.96
178 179 3.007635 GGAGTACCCTTAACACACATGC 58.992 50.000 0.00 0.00 0.00 4.06
208 209 9.221933 TGACCAAAGCTAATATTCGAACTAAAA 57.778 29.630 0.00 0.00 0.00 1.52
209 210 8.780846 TGACCAAAGCTAATATTCGAACTAAA 57.219 30.769 0.00 0.00 0.00 1.85
210 211 8.780846 TTGACCAAAGCTAATATTCGAACTAA 57.219 30.769 0.00 0.00 0.00 2.24
211 212 8.780846 TTTGACCAAAGCTAATATTCGAACTA 57.219 30.769 0.00 0.00 0.00 2.24
212 213 7.681939 TTTGACCAAAGCTAATATTCGAACT 57.318 32.000 0.00 0.00 0.00 3.01
213 214 7.954906 CTTTGACCAAAGCTAATATTCGAAC 57.045 36.000 0.00 0.00 40.94 3.95
235 236 7.327214 TGGTCAAAATTTGTAAAGCTTGACTT 58.673 30.769 15.19 0.00 40.12 3.01
236 237 6.872920 TGGTCAAAATTTGTAAAGCTTGACT 58.127 32.000 15.19 0.00 40.12 3.41
237 238 7.277760 ACTTGGTCAAAATTTGTAAAGCTTGAC 59.722 33.333 7.04 7.04 39.84 3.18
238 239 7.327214 ACTTGGTCAAAATTTGTAAAGCTTGA 58.673 30.769 0.00 0.00 0.00 3.02
239 240 7.538303 ACTTGGTCAAAATTTGTAAAGCTTG 57.462 32.000 0.00 0.00 0.00 4.01
240 241 8.560355 AAACTTGGTCAAAATTTGTAAAGCTT 57.440 26.923 5.56 0.00 0.00 3.74
241 242 9.830975 ATAAACTTGGTCAAAATTTGTAAAGCT 57.169 25.926 5.56 0.00 0.00 3.74
247 248 9.606631 TTGCTTATAAACTTGGTCAAAATTTGT 57.393 25.926 5.56 0.00 0.00 2.83
394 395 9.807649 AGAGTTAACTAAAGTCAAACTTCGTAA 57.192 29.630 8.42 0.00 37.47 3.18
396 397 9.807649 TTAGAGTTAACTAAAGTCAAACTTCGT 57.192 29.630 8.42 0.00 37.47 3.85
421 422 8.621286 CCTCCGTTTTTATTTACTCTGCATATT 58.379 33.333 0.00 0.00 0.00 1.28
422 423 7.228706 CCCTCCGTTTTTATTTACTCTGCATAT 59.771 37.037 0.00 0.00 0.00 1.78
423 424 6.540914 CCCTCCGTTTTTATTTACTCTGCATA 59.459 38.462 0.00 0.00 0.00 3.14
424 425 5.357032 CCCTCCGTTTTTATTTACTCTGCAT 59.643 40.000 0.00 0.00 0.00 3.96
425 426 4.698304 CCCTCCGTTTTTATTTACTCTGCA 59.302 41.667 0.00 0.00 0.00 4.41
426 427 4.939439 TCCCTCCGTTTTTATTTACTCTGC 59.061 41.667 0.00 0.00 0.00 4.26
427 428 6.171213 ACTCCCTCCGTTTTTATTTACTCTG 58.829 40.000 0.00 0.00 0.00 3.35
428 429 6.370186 ACTCCCTCCGTTTTTATTTACTCT 57.630 37.500 0.00 0.00 0.00 3.24
429 430 9.993454 ATATACTCCCTCCGTTTTTATTTACTC 57.007 33.333 0.00 0.00 0.00 2.59
436 437 8.514594 CGTATGTATATACTCCCTCCGTTTTTA 58.485 37.037 13.89 0.00 37.58 1.52
437 438 7.014615 ACGTATGTATATACTCCCTCCGTTTTT 59.985 37.037 13.89 0.00 37.58 1.94
438 439 6.491403 ACGTATGTATATACTCCCTCCGTTTT 59.509 38.462 13.89 0.00 37.58 2.43
439 440 6.006449 ACGTATGTATATACTCCCTCCGTTT 58.994 40.000 13.89 0.00 37.58 3.60
440 441 5.564550 ACGTATGTATATACTCCCTCCGTT 58.435 41.667 13.89 0.00 37.58 4.44
441 442 5.171339 ACGTATGTATATACTCCCTCCGT 57.829 43.478 13.89 10.00 37.58 4.69
442 443 5.757320 CCTACGTATGTATATACTCCCTCCG 59.243 48.000 13.89 9.47 37.58 4.63
443 444 6.060788 CCCTACGTATGTATATACTCCCTCC 58.939 48.000 13.89 0.00 37.58 4.30
444 445 6.657875 ACCCTACGTATGTATATACTCCCTC 58.342 44.000 13.89 0.67 37.58 4.30
445 446 6.649041 ACCCTACGTATGTATATACTCCCT 57.351 41.667 13.89 0.00 37.58 4.20
446 447 6.768381 GGTACCCTACGTATGTATATACTCCC 59.232 46.154 13.89 1.22 37.58 4.30
447 448 7.569240 AGGTACCCTACGTATGTATATACTCC 58.431 42.308 8.74 1.54 33.22 3.85
540 541 1.306568 GGAGAGAGACAGGGGGCTT 60.307 63.158 0.00 0.00 0.00 4.35
991 996 0.548682 AGGAGGAGCATGGACTGGTT 60.549 55.000 0.00 0.00 35.19 3.67
1168 1179 1.103398 AACAAGAAGCTGCCGTTGCT 61.103 50.000 0.00 0.00 43.32 3.91
1172 1183 1.148273 TGGAACAAGAAGCTGCCGT 59.852 52.632 0.00 0.00 31.92 5.68
1462 1479 5.265477 CCAGTGCATTAAATGATGTACGTG 58.735 41.667 0.00 0.00 44.25 4.49
1486 1503 1.221466 ACACACGTTGATCTGCACCG 61.221 55.000 0.00 0.00 38.49 4.94
1544 1570 0.815213 TATGCATCTGCGCAGGGAAC 60.815 55.000 35.36 22.34 46.99 3.62
1551 1577 1.577922 CCCACATATGCATCTGCGC 59.422 57.895 11.70 0.00 45.83 6.09
1552 1578 1.239296 CCCCCACATATGCATCTGCG 61.239 60.000 11.70 2.71 45.83 5.18
1659 1685 3.049674 GCAGCAGTAGCACGGCAA 61.050 61.111 12.18 0.00 41.80 4.52
1685 1711 1.024579 GGTCGATGTTGTTCCGGCAT 61.025 55.000 0.00 0.00 0.00 4.40
1871 1897 0.394938 TGTGCTTAAAGTCGGAGCCA 59.605 50.000 0.00 0.00 35.59 4.75
1946 1972 2.438975 ACGGCCACGGACTCGATA 60.439 61.111 2.24 0.00 46.48 2.92
2047 2073 1.751351 TCTAGAGCAAGACCATGTCGG 59.249 52.381 0.00 0.00 37.67 4.79
2072 2098 6.703165 CGTACAGGAAACAAAGGTAAGTAGTT 59.297 38.462 0.00 0.00 0.00 2.24
2076 2105 5.280654 TCGTACAGGAAACAAAGGTAAGT 57.719 39.130 0.00 0.00 0.00 2.24
2081 2117 3.497262 GGACTTCGTACAGGAAACAAAGG 59.503 47.826 0.00 0.00 0.00 3.11
2089 2125 5.171339 ACTAACTAGGACTTCGTACAGGA 57.829 43.478 0.00 0.00 0.00 3.86
2125 2162 4.702831 ACCTAGAAGCTACGTACTCCTAC 58.297 47.826 0.00 0.00 0.00 3.18
2128 2165 4.979943 AAACCTAGAAGCTACGTACTCC 57.020 45.455 0.00 0.00 0.00 3.85
2130 2167 7.311408 CAAACTAAACCTAGAAGCTACGTACT 58.689 38.462 0.00 0.00 0.00 2.73
2169 2208 4.333649 CGGACTAATGATGATGCACTTGTT 59.666 41.667 0.00 0.00 0.00 2.83
2170 2209 3.873361 CGGACTAATGATGATGCACTTGT 59.127 43.478 0.00 0.00 0.00 3.16
2190 2229 1.376424 ATGCAAGCACTCTGGACGG 60.376 57.895 0.00 0.00 0.00 4.79
2313 2352 1.267261 CTACCACATCTCGGTCGATCC 59.733 57.143 0.00 0.00 37.99 3.36
2369 2408 7.179338 AGAGCTTTAGACTCAGATAAAGACCAA 59.821 37.037 14.56 0.00 40.06 3.67
2383 2422 5.304614 TGAAACAGTGGTAGAGCTTTAGACT 59.695 40.000 0.00 0.00 0.00 3.24
2436 2475 7.277539 TCTCTCTAGCTCTTTTGTAGTACGTAC 59.722 40.741 18.10 18.10 0.00 3.67
2437 2476 7.326454 TCTCTCTAGCTCTTTTGTAGTACGTA 58.674 38.462 0.00 0.00 0.00 3.57
2438 2477 6.171921 TCTCTCTAGCTCTTTTGTAGTACGT 58.828 40.000 0.00 0.00 0.00 3.57
2439 2478 6.535865 TCTCTCTCTAGCTCTTTTGTAGTACG 59.464 42.308 0.00 0.00 0.00 3.67
2481 2520 6.305399 CGTGCCAAAATAAACACAGTAAGATG 59.695 38.462 0.00 0.00 33.23 2.90
2491 2530 3.637229 TCTTTCCCGTGCCAAAATAAACA 59.363 39.130 0.00 0.00 0.00 2.83
2504 2543 3.118149 ACAGTGGTAAAACTCTTTCCCGT 60.118 43.478 0.00 0.00 0.00 5.28
2506 2545 3.568430 CCACAGTGGTAAAACTCTTTCCC 59.432 47.826 11.99 0.00 31.35 3.97
2663 2703 0.037232 GGAGAAAGGGTCTGGTGTCG 60.037 60.000 0.00 0.00 36.41 4.35
2672 2712 1.439543 AGACAAGCAGGAGAAAGGGT 58.560 50.000 0.00 0.00 0.00 4.34
2799 2839 0.239082 TGCTGTTGCATTTGAGAGCG 59.761 50.000 1.37 0.00 45.31 5.03
2819 2859 8.348983 ACTAAATAAAACGTAGATGGATCACG 57.651 34.615 0.00 0.00 37.35 4.35
2870 2916 7.547370 CCAAAATGCCGGTTCAGATTTTATTTA 59.453 33.333 1.90 0.00 0.00 1.40
2874 2920 4.815269 CCAAAATGCCGGTTCAGATTTTA 58.185 39.130 1.90 0.00 0.00 1.52
2875 2921 3.663025 CCAAAATGCCGGTTCAGATTTT 58.337 40.909 1.90 4.12 0.00 1.82
2876 2922 2.612721 GCCAAAATGCCGGTTCAGATTT 60.613 45.455 1.90 0.00 0.00 2.17
2877 2923 1.066929 GCCAAAATGCCGGTTCAGATT 60.067 47.619 1.90 0.00 0.00 2.40
2898 2945 4.019174 CCATATCTTCATAATGTGCCCCC 58.981 47.826 0.00 0.00 0.00 5.40
2913 2960 6.609212 ACGAGGACTAATATGCATCCATATCT 59.391 38.462 0.19 0.00 42.40 1.98


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

AutoCloner maintained by Alex Coulton.