Multiple sequence alignment - TraesCS4D01G132100

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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 TraesCS4D01G132100 chr4D 100.000 4445 0 0 1 4445 118817102 118821546 0.000000e+00 8209.0
1 TraesCS4D01G132100 chr4D 81.657 338 62 0 2412 2749 334155188 334154851 9.410000e-72 281.0
2 TraesCS4D01G132100 chr4A 94.371 3482 94 33 255 3698 454120662 454124079 0.000000e+00 5251.0
3 TraesCS4D01G132100 chr4A 79.070 344 44 18 3667 4002 454124085 454124408 1.250000e-50 211.0
4 TraesCS4D01G132100 chr4B 94.674 3267 101 34 339 3567 181250365 181253596 0.000000e+00 5001.0
5 TraesCS4D01G132100 chr4B 86.829 820 63 24 3659 4445 181254534 181255341 0.000000e+00 874.0
6 TraesCS4D01G132100 chr2B 85.875 2400 271 40 1045 3402 122013695 122016068 0.000000e+00 2492.0
7 TraesCS4D01G132100 chr2B 88.667 150 10 7 114 259 590855770 590855624 4.570000e-40 176.0
8 TraesCS4D01G132100 chr2D 85.726 2396 281 31 1045 3402 78756044 78758416 0.000000e+00 2473.0
9 TraesCS4D01G132100 chr2D 87.075 147 16 2 114 257 169037585 169037731 3.560000e-36 163.0
10 TraesCS4D01G132100 chr2A 86.003 2329 265 37 1096 3390 79172242 79174543 0.000000e+00 2438.0
11 TraesCS4D01G132100 chr2A 79.508 122 16 2 2299 2420 23372915 23372803 1.330000e-10 78.7
12 TraesCS4D01G132100 chr3B 81.006 1869 286 42 1547 3390 612929605 612931429 0.000000e+00 1421.0
13 TraesCS4D01G132100 chr1B 95.871 557 22 1 1309 1864 664770599 664771155 0.000000e+00 900.0
14 TraesCS4D01G132100 chr1B 82.731 249 23 12 2299 2527 645726903 645726655 2.100000e-48 204.0
15 TraesCS4D01G132100 chr1B 92.500 120 8 1 1 120 9560119 9560237 2.130000e-38 171.0
16 TraesCS4D01G132100 chr6B 93.280 372 24 1 1746 2117 141659523 141659153 8.410000e-152 547.0
17 TraesCS4D01G132100 chr6B 93.836 146 9 0 1610 1755 141661068 141660923 2.080000e-53 220.0
18 TraesCS4D01G132100 chr6B 87.248 149 16 3 114 259 127605957 127605809 2.750000e-37 167.0
19 TraesCS4D01G132100 chr6B 85.987 157 18 3 114 267 183753446 183753601 9.890000e-37 165.0
20 TraesCS4D01G132100 chr6B 93.750 64 4 0 2070 2133 141661129 141661066 3.660000e-16 97.1
21 TraesCS4D01G132100 chr7A 89.157 166 18 0 1346 1511 705593853 705593688 1.620000e-49 207.0
22 TraesCS4D01G132100 chr7A 92.000 50 3 1 1756 1804 705593697 705593648 7.980000e-08 69.4
23 TraesCS4D01G132100 chr1D 94.958 119 5 1 1 119 255428475 255428358 7.590000e-43 185.0
24 TraesCS4D01G132100 chr1D 92.562 121 9 0 2 122 154902278 154902158 1.640000e-39 174.0
25 TraesCS4D01G132100 chr6D 94.017 117 7 0 1 117 297307614 297307498 1.270000e-40 178.0
26 TraesCS4D01G132100 chr6A 92.562 121 9 0 1 121 215027958 215028078 1.640000e-39 174.0
27 TraesCS4D01G132100 chr6A 93.966 116 4 3 2 117 4577285 4577397 5.910000e-39 172.0
28 TraesCS4D01G132100 chrUn 93.913 115 6 1 2 116 154972252 154972139 5.910000e-39 172.0
29 TraesCS4D01G132100 chrUn 93.913 115 6 1 2 116 155054680 155054567 5.910000e-39 172.0
30 TraesCS4D01G132100 chr5A 91.803 122 10 0 1 122 554944665 554944544 2.130000e-38 171.0
31 TraesCS4D01G132100 chr3A 87.755 147 14 3 114 256 600923094 600923240 7.650000e-38 169.0
32 TraesCS4D01G132100 chr3A 88.732 71 4 1 3880 3946 610548556 610548486 2.850000e-12 84.2
33 TraesCS4D01G132100 chr1A 87.755 147 14 2 114 256 564367386 564367240 7.650000e-38 169.0
34 TraesCS4D01G132100 chr5D 87.671 146 14 3 114 256 528616642 528616786 2.750000e-37 167.0
35 TraesCS4D01G132100 chr7B 86.184 152 17 3 107 256 611908975 611909124 1.280000e-35 161.0
36 TraesCS4D01G132100 chr3D 84.177 158 21 4 114 268 454156507 454156351 2.770000e-32 150.0


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 TraesCS4D01G132100 chr4D 118817102 118821546 4444 False 8209.000000 8209 100.0000 1 4445 1 chr4D.!!$F1 4444
1 TraesCS4D01G132100 chr4A 454120662 454124408 3746 False 2731.000000 5251 86.7205 255 4002 2 chr4A.!!$F1 3747
2 TraesCS4D01G132100 chr4B 181250365 181255341 4976 False 2937.500000 5001 90.7515 339 4445 2 chr4B.!!$F1 4106
3 TraesCS4D01G132100 chr2B 122013695 122016068 2373 False 2492.000000 2492 85.8750 1045 3402 1 chr2B.!!$F1 2357
4 TraesCS4D01G132100 chr2D 78756044 78758416 2372 False 2473.000000 2473 85.7260 1045 3402 1 chr2D.!!$F1 2357
5 TraesCS4D01G132100 chr2A 79172242 79174543 2301 False 2438.000000 2438 86.0030 1096 3390 1 chr2A.!!$F1 2294
6 TraesCS4D01G132100 chr3B 612929605 612931429 1824 False 1421.000000 1421 81.0060 1547 3390 1 chr3B.!!$F1 1843
7 TraesCS4D01G132100 chr1B 664770599 664771155 556 False 900.000000 900 95.8710 1309 1864 1 chr1B.!!$F2 555
8 TraesCS4D01G132100 chr6B 141659153 141661129 1976 True 288.033333 547 93.6220 1610 2133 3 chr6B.!!$R2 523

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
357 358 0.032416 ATCTACGTACACCCCTGCCT 60.032 55.0 0.0 0.0 0.00 4.75 F
874 908 0.401395 AACCCCTCTCCTTCACCACA 60.401 55.0 0.0 0.0 0.00 4.17 F
1967 3440 0.467290 GAGATCCCAGAGAGCCTCGT 60.467 60.0 0.0 0.0 35.36 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 3429 0.251386 TGAGGTTGACGAGGCTCTCT 60.251 55.0 13.5 0.0 0.0 3.10 R
2774 4275 1.081892 CCCACGATTGCAGAGTTGAG 58.918 55.0 0.0 0.0 0.0 3.02 R
3917 6347 0.179134 CGAGAACTGGGCTAAGGACG 60.179 60.0 0.0 0.0 0.0 4.79 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
24 25 6.205784 TCTTCTTTTATTTTGGCTTGTCGTG 58.794 36.000 0.00 0.00 0.00 4.35
25 26 5.759506 TCTTTTATTTTGGCTTGTCGTGA 57.240 34.783 0.00 0.00 0.00 4.35
26 27 5.757886 TCTTTTATTTTGGCTTGTCGTGAG 58.242 37.500 0.00 0.00 0.00 3.51
27 28 4.497473 TTTATTTTGGCTTGTCGTGAGG 57.503 40.909 0.00 0.00 0.00 3.86
28 29 2.270352 ATTTTGGCTTGTCGTGAGGA 57.730 45.000 0.00 0.00 0.00 3.71
29 30 1.305201 TTTTGGCTTGTCGTGAGGAC 58.695 50.000 0.00 0.00 46.27 3.85
30 31 0.468226 TTTGGCTTGTCGTGAGGACT 59.532 50.000 6.84 0.00 46.24 3.85
33 34 0.868406 GGCTTGTCGTGAGGACTTTG 59.132 55.000 6.84 0.00 46.24 2.77
36 37 2.286418 GCTTGTCGTGAGGACTTTGTTG 60.286 50.000 6.84 0.00 46.24 3.33
39 40 0.468226 TCGTGAGGACTTTGTTGGCT 59.532 50.000 0.00 0.00 0.00 4.75
41 42 1.680338 GTGAGGACTTTGTTGGCTGT 58.320 50.000 0.00 0.00 0.00 4.40
42 43 1.334869 GTGAGGACTTTGTTGGCTGTG 59.665 52.381 0.00 0.00 0.00 3.66
43 44 1.064758 TGAGGACTTTGTTGGCTGTGT 60.065 47.619 0.00 0.00 0.00 3.72
44 45 1.334869 GAGGACTTTGTTGGCTGTGTG 59.665 52.381 0.00 0.00 0.00 3.82
45 46 0.249031 GGACTTTGTTGGCTGTGTGC 60.249 55.000 0.00 0.00 41.94 4.57
46 47 0.455410 GACTTTGTTGGCTGTGTGCA 59.545 50.000 0.00 0.00 45.15 4.57
47 48 1.067516 GACTTTGTTGGCTGTGTGCAT 59.932 47.619 0.00 0.00 45.15 3.96
49 50 1.338973 CTTTGTTGGCTGTGTGCATCT 59.661 47.619 0.00 0.00 45.15 2.90
50 51 1.401761 TTGTTGGCTGTGTGCATCTT 58.598 45.000 0.00 0.00 45.15 2.40
51 52 2.268762 TGTTGGCTGTGTGCATCTTA 57.731 45.000 0.00 0.00 45.15 2.10
52 53 2.153645 TGTTGGCTGTGTGCATCTTAG 58.846 47.619 0.00 0.00 45.15 2.18
54 55 2.554032 GTTGGCTGTGTGCATCTTAGTT 59.446 45.455 0.00 0.00 45.15 2.24
55 56 3.694043 TGGCTGTGTGCATCTTAGTTA 57.306 42.857 0.00 0.00 45.15 2.24
56 57 4.220693 TGGCTGTGTGCATCTTAGTTAT 57.779 40.909 0.00 0.00 45.15 1.89
57 58 3.940852 TGGCTGTGTGCATCTTAGTTATG 59.059 43.478 0.00 0.00 45.15 1.90
67 68 4.302455 CATCTTAGTTATGCAGAGACCGG 58.698 47.826 0.00 0.00 0.00 5.28
68 69 2.693591 TCTTAGTTATGCAGAGACCGGG 59.306 50.000 6.32 0.00 0.00 5.73
69 70 2.154567 TAGTTATGCAGAGACCGGGT 57.845 50.000 6.32 0.00 0.00 5.28
70 71 0.537188 AGTTATGCAGAGACCGGGTG 59.463 55.000 3.30 0.00 0.00 4.61
71 72 0.249398 GTTATGCAGAGACCGGGTGT 59.751 55.000 3.30 0.00 0.00 4.16
72 73 1.479323 GTTATGCAGAGACCGGGTGTA 59.521 52.381 3.30 0.00 0.00 2.90
73 74 1.855295 TATGCAGAGACCGGGTGTAA 58.145 50.000 3.30 0.00 0.00 2.41
74 75 1.204146 ATGCAGAGACCGGGTGTAAT 58.796 50.000 3.30 0.00 0.00 1.89
75 76 0.249120 TGCAGAGACCGGGTGTAATG 59.751 55.000 3.30 4.42 0.00 1.90
76 77 0.535335 GCAGAGACCGGGTGTAATGA 59.465 55.000 3.30 0.00 0.00 2.57
77 78 1.139058 GCAGAGACCGGGTGTAATGAT 59.861 52.381 3.30 0.00 0.00 2.45
78 79 2.420129 GCAGAGACCGGGTGTAATGATT 60.420 50.000 3.30 0.00 0.00 2.57
79 80 3.181469 GCAGAGACCGGGTGTAATGATTA 60.181 47.826 3.30 0.00 0.00 1.75
80 81 4.682320 GCAGAGACCGGGTGTAATGATTAA 60.682 45.833 3.30 0.00 0.00 1.40
81 82 5.424757 CAGAGACCGGGTGTAATGATTAAA 58.575 41.667 3.30 0.00 0.00 1.52
82 83 5.293569 CAGAGACCGGGTGTAATGATTAAAC 59.706 44.000 3.30 0.00 0.00 2.01
83 84 4.520179 AGACCGGGTGTAATGATTAAACC 58.480 43.478 14.90 14.90 41.91 3.27
84 85 4.226620 AGACCGGGTGTAATGATTAAACCT 59.773 41.667 20.81 4.76 42.23 3.50
85 86 4.925836 ACCGGGTGTAATGATTAAACCTT 58.074 39.130 20.81 6.34 42.23 3.50
86 87 5.326900 ACCGGGTGTAATGATTAAACCTTT 58.673 37.500 20.81 6.04 42.23 3.11
87 88 5.776208 ACCGGGTGTAATGATTAAACCTTTT 59.224 36.000 20.81 5.74 42.23 2.27
88 89 6.947158 ACCGGGTGTAATGATTAAACCTTTTA 59.053 34.615 20.81 0.00 42.23 1.52
89 90 7.450944 ACCGGGTGTAATGATTAAACCTTTTAA 59.549 33.333 20.81 0.00 42.23 1.52
90 91 7.971722 CCGGGTGTAATGATTAAACCTTTTAAG 59.028 37.037 20.81 8.35 42.23 1.85
91 92 8.517056 CGGGTGTAATGATTAAACCTTTTAAGT 58.483 33.333 20.81 0.00 42.23 2.24
102 103 8.969121 TTAAACCTTTTAAGTAATAAAGCGCC 57.031 30.769 2.29 0.00 35.03 6.53
103 104 5.571784 ACCTTTTAAGTAATAAAGCGCCC 57.428 39.130 2.29 0.00 35.03 6.13
104 105 5.258841 ACCTTTTAAGTAATAAAGCGCCCT 58.741 37.500 2.29 0.00 35.03 5.19
105 106 5.713389 ACCTTTTAAGTAATAAAGCGCCCTT 59.287 36.000 2.29 0.00 35.03 3.95
106 107 6.209986 ACCTTTTAAGTAATAAAGCGCCCTTT 59.790 34.615 2.29 0.94 43.43 3.11
107 108 7.094631 CCTTTTAAGTAATAAAGCGCCCTTTT 58.905 34.615 2.29 0.06 41.37 2.27
108 109 7.274904 CCTTTTAAGTAATAAAGCGCCCTTTTC 59.725 37.037 2.29 0.00 41.37 2.29
109 110 4.713824 AAGTAATAAAGCGCCCTTTTCC 57.286 40.909 2.29 0.00 41.37 3.13
110 111 2.681344 AGTAATAAAGCGCCCTTTTCCG 59.319 45.455 2.29 0.00 41.37 4.30
116 117 4.985845 CGCCCTTTTCCGCAAAAT 57.014 50.000 0.00 0.00 30.91 1.82
118 119 2.577449 CGCCCTTTTCCGCAAAATAT 57.423 45.000 0.00 0.00 30.91 1.28
119 120 3.701532 CGCCCTTTTCCGCAAAATATA 57.298 42.857 0.00 0.00 30.91 0.86
120 121 4.035278 CGCCCTTTTCCGCAAAATATAA 57.965 40.909 0.00 0.00 30.91 0.98
121 122 3.794564 CGCCCTTTTCCGCAAAATATAAC 59.205 43.478 0.00 0.00 30.91 1.89
122 123 4.439563 CGCCCTTTTCCGCAAAATATAACT 60.440 41.667 0.00 0.00 30.91 2.24
123 124 5.041287 GCCCTTTTCCGCAAAATATAACTC 58.959 41.667 0.00 0.00 30.91 3.01
124 125 5.163550 GCCCTTTTCCGCAAAATATAACTCT 60.164 40.000 0.00 0.00 30.91 3.24
125 126 6.627287 GCCCTTTTCCGCAAAATATAACTCTT 60.627 38.462 0.00 0.00 30.91 2.85
126 127 7.320399 CCCTTTTCCGCAAAATATAACTCTTT 58.680 34.615 0.00 0.00 30.91 2.52
127 128 7.817478 CCCTTTTCCGCAAAATATAACTCTTTT 59.183 33.333 0.00 0.00 30.91 2.27
128 129 9.203421 CCTTTTCCGCAAAATATAACTCTTTTT 57.797 29.630 0.00 0.00 30.91 1.94
133 134 9.661563 TCCGCAAAATATAACTCTTTTTAGAGA 57.338 29.630 9.03 0.00 39.14 3.10
181 182 9.947669 GATGTATACAGACGTATTTTAGAGTGT 57.052 33.333 11.91 0.00 39.17 3.55
188 189 8.737175 ACAGACGTATTTTAGAGTGTAGATTCA 58.263 33.333 0.00 0.00 0.00 2.57
189 190 9.737427 CAGACGTATTTTAGAGTGTAGATTCAT 57.263 33.333 0.00 0.00 0.00 2.57
201 202 9.606631 AGAGTGTAGATTCATTCATTTTACTCC 57.393 33.333 0.00 0.00 32.34 3.85
202 203 8.425577 AGTGTAGATTCATTCATTTTACTCCG 57.574 34.615 0.00 0.00 0.00 4.63
203 204 8.041323 AGTGTAGATTCATTCATTTTACTCCGT 58.959 33.333 0.00 0.00 0.00 4.69
204 205 9.309516 GTGTAGATTCATTCATTTTACTCCGTA 57.690 33.333 0.00 0.00 0.00 4.02
207 208 8.964476 AGATTCATTCATTTTACTCCGTATGT 57.036 30.769 0.00 0.00 0.00 2.29
210 211 9.832445 ATTCATTCATTTTACTCCGTATGTAGT 57.168 29.630 0.00 0.00 0.00 2.73
211 212 8.867112 TCATTCATTTTACTCCGTATGTAGTC 57.133 34.615 0.00 0.00 0.00 2.59
212 213 7.924412 TCATTCATTTTACTCCGTATGTAGTCC 59.076 37.037 0.00 0.00 0.00 3.85
213 214 6.778834 TCATTTTACTCCGTATGTAGTCCA 57.221 37.500 0.00 0.00 0.00 4.02
214 215 7.356089 TCATTTTACTCCGTATGTAGTCCAT 57.644 36.000 0.00 0.00 37.58 3.41
215 216 8.467963 TCATTTTACTCCGTATGTAGTCCATA 57.532 34.615 0.00 0.00 34.86 2.74
216 217 9.085645 TCATTTTACTCCGTATGTAGTCCATAT 57.914 33.333 0.00 0.00 38.29 1.78
217 218 9.706691 CATTTTACTCCGTATGTAGTCCATATT 57.293 33.333 0.00 0.00 38.29 1.28
218 219 9.706691 ATTTTACTCCGTATGTAGTCCATATTG 57.293 33.333 0.00 0.00 38.29 1.90
219 220 8.467963 TTTACTCCGTATGTAGTCCATATTGA 57.532 34.615 0.00 0.00 38.29 2.57
220 221 6.971726 ACTCCGTATGTAGTCCATATTGAA 57.028 37.500 0.00 0.00 38.29 2.69
221 222 7.356089 ACTCCGTATGTAGTCCATATTGAAA 57.644 36.000 0.00 0.00 38.29 2.69
222 223 7.788026 ACTCCGTATGTAGTCCATATTGAAAA 58.212 34.615 0.00 0.00 38.29 2.29
223 224 7.709613 ACTCCGTATGTAGTCCATATTGAAAAC 59.290 37.037 0.00 0.00 38.29 2.43
224 225 7.788026 TCCGTATGTAGTCCATATTGAAAACT 58.212 34.615 0.00 0.00 38.29 2.66
225 226 7.924412 TCCGTATGTAGTCCATATTGAAAACTC 59.076 37.037 0.00 0.00 38.29 3.01
226 227 7.926555 CCGTATGTAGTCCATATTGAAAACTCT 59.073 37.037 0.00 0.00 38.29 3.24
227 228 9.961265 CGTATGTAGTCCATATTGAAAACTCTA 57.039 33.333 0.00 0.00 38.29 2.43
233 234 8.794335 AGTCCATATTGAAAACTCTAAAGACC 57.206 34.615 0.00 0.00 0.00 3.85
234 235 8.606830 AGTCCATATTGAAAACTCTAAAGACCT 58.393 33.333 0.00 0.00 0.00 3.85
235 236 9.886132 GTCCATATTGAAAACTCTAAAGACCTA 57.114 33.333 0.00 0.00 0.00 3.08
244 245 9.418839 GAAAACTCTAAAGACCTATACCTAGGA 57.581 37.037 17.98 0.00 46.66 2.94
245 246 9.779951 AAAACTCTAAAGACCTATACCTAGGAA 57.220 33.333 17.98 0.00 46.66 3.36
246 247 8.765488 AACTCTAAAGACCTATACCTAGGAAC 57.235 38.462 17.98 0.00 46.66 3.62
247 248 6.997476 ACTCTAAAGACCTATACCTAGGAACG 59.003 42.308 17.98 0.34 46.66 3.95
248 249 6.302269 TCTAAAGACCTATACCTAGGAACGG 58.698 44.000 17.98 12.21 46.66 4.44
249 250 3.522392 AGACCTATACCTAGGAACGGG 57.478 52.381 17.98 14.03 46.66 5.28
250 251 2.109657 AGACCTATACCTAGGAACGGGG 59.890 54.545 17.98 12.64 46.66 5.73
251 252 1.148656 ACCTATACCTAGGAACGGGGG 59.851 57.143 17.98 11.60 46.66 5.40
252 253 1.430464 CCTATACCTAGGAACGGGGGA 59.570 57.143 17.98 0.00 46.66 4.81
253 254 2.557005 CCTATACCTAGGAACGGGGGAG 60.557 59.091 17.98 0.89 46.66 4.30
283 284 4.577677 TGCATGGGGTGTGCGTGT 62.578 61.111 0.00 0.00 45.37 4.49
284 285 4.041917 GCATGGGGTGTGCGTGTG 62.042 66.667 0.00 0.00 32.29 3.82
285 286 2.281414 CATGGGGTGTGCGTGTGA 60.281 61.111 0.00 0.00 0.00 3.58
286 287 1.675310 CATGGGGTGTGCGTGTGAT 60.675 57.895 0.00 0.00 0.00 3.06
287 288 1.675310 ATGGGGTGTGCGTGTGATG 60.675 57.895 0.00 0.00 0.00 3.07
288 289 2.031919 GGGGTGTGCGTGTGATGA 59.968 61.111 0.00 0.00 0.00 2.92
289 290 1.377202 GGGGTGTGCGTGTGATGAT 60.377 57.895 0.00 0.00 0.00 2.45
290 291 1.647545 GGGGTGTGCGTGTGATGATG 61.648 60.000 0.00 0.00 0.00 3.07
291 292 0.673333 GGGTGTGCGTGTGATGATGA 60.673 55.000 0.00 0.00 0.00 2.92
292 293 1.372582 GGTGTGCGTGTGATGATGAT 58.627 50.000 0.00 0.00 0.00 2.45
310 311 6.122277 TGATGATGATGATGATGATGATGGG 58.878 40.000 0.00 0.00 0.00 4.00
329 330 5.290493 TGGGTGTGGATAATGACTGATAC 57.710 43.478 0.00 0.00 0.00 2.24
330 331 4.968719 TGGGTGTGGATAATGACTGATACT 59.031 41.667 0.00 0.00 0.00 2.12
331 332 6.140377 TGGGTGTGGATAATGACTGATACTA 58.860 40.000 0.00 0.00 0.00 1.82
354 355 0.821517 TGCATCTACGTACACCCCTG 59.178 55.000 0.00 0.00 0.00 4.45
355 356 0.529992 GCATCTACGTACACCCCTGC 60.530 60.000 0.00 0.00 0.00 4.85
356 357 0.104304 CATCTACGTACACCCCTGCC 59.896 60.000 0.00 0.00 0.00 4.85
357 358 0.032416 ATCTACGTACACCCCTGCCT 60.032 55.000 0.00 0.00 0.00 4.75
377 378 6.092092 TGCCTCATCAAAACGAAAATGTATG 58.908 36.000 0.00 0.00 0.00 2.39
413 414 7.042725 GCAGTAGAGTTGTATGATCGCAAAATA 60.043 37.037 0.00 0.00 0.00 1.40
471 476 3.120130 GGTACGAAATCCACGATGCAAAA 60.120 43.478 0.00 0.00 34.70 2.44
597 606 1.081840 GAAGCAAACAGAGGTGCGC 60.082 57.895 0.00 0.00 45.62 6.09
627 636 2.983592 GTTTGTGGGCCCGAGTGG 60.984 66.667 19.37 0.00 37.09 4.00
636 645 2.983592 CCCGAGTGGCCAAACACC 60.984 66.667 7.24 0.00 42.28 4.16
637 646 2.113139 CCGAGTGGCCAAACACCT 59.887 61.111 7.24 0.00 42.28 4.00
638 647 2.260869 CCGAGTGGCCAAACACCTG 61.261 63.158 7.24 0.00 42.28 4.00
639 648 2.260869 CGAGTGGCCAAACACCTGG 61.261 63.158 7.24 0.00 42.28 4.45
642 651 1.152756 GTGGCCAAACACCTGGACT 60.153 57.895 7.24 0.00 45.80 3.85
671 680 0.613292 TGGAGCCTGTCTCTGTCTCC 60.613 60.000 0.00 0.00 42.67 3.71
853 880 3.387947 CCGTTGCCTCCCGTACCT 61.388 66.667 0.00 0.00 0.00 3.08
874 908 0.401395 AACCCCTCTCCTTCACCACA 60.401 55.000 0.00 0.00 0.00 4.17
878 912 1.638529 CCTCTCCTTCACCACACTCT 58.361 55.000 0.00 0.00 0.00 3.24
880 914 1.201181 CTCTCCTTCACCACACTCTCG 59.799 57.143 0.00 0.00 0.00 4.04
882 916 0.827925 TCCTTCACCACACTCTCGCT 60.828 55.000 0.00 0.00 0.00 4.93
884 918 0.730834 CTTCACCACACTCTCGCTCG 60.731 60.000 0.00 0.00 0.00 5.03
885 919 2.749110 TTCACCACACTCTCGCTCGC 62.749 60.000 0.00 0.00 0.00 5.03
887 921 4.056125 CCACACTCTCGCTCGCCA 62.056 66.667 0.00 0.00 0.00 5.69
888 922 2.505777 CACACTCTCGCTCGCCAG 60.506 66.667 0.00 0.00 0.00 4.85
889 923 4.427661 ACACTCTCGCTCGCCAGC 62.428 66.667 0.00 0.00 42.96 4.85
890 924 4.127040 CACTCTCGCTCGCCAGCT 62.127 66.667 0.79 0.00 44.40 4.24
891 925 2.438614 ACTCTCGCTCGCCAGCTA 60.439 61.111 0.79 0.00 44.40 3.32
892 926 2.025441 CTCTCGCTCGCCAGCTAC 59.975 66.667 0.79 0.00 44.40 3.58
893 927 2.750237 TCTCGCTCGCCAGCTACA 60.750 61.111 0.79 0.00 44.40 2.74
913 953 2.125753 CTCCCACACTCGCAGCTC 60.126 66.667 0.00 0.00 0.00 4.09
948 988 3.544684 CTCGAATCCATTCCATCCACAA 58.455 45.455 0.00 0.00 33.28 3.33
957 997 4.264253 CATTCCATCCACAACTAAGCTCA 58.736 43.478 0.00 0.00 0.00 4.26
967 1007 5.181009 CACAACTAAGCTCATCCTGATTCA 58.819 41.667 0.00 0.00 0.00 2.57
1751 3224 3.817647 GAGCGGAAATTAGAAGCCATCAT 59.182 43.478 0.00 0.00 0.00 2.45
1956 3429 2.519541 CTCGCCGGAGAGATCCCA 60.520 66.667 29.23 0.00 43.27 4.37
1967 3440 0.467290 GAGATCCCAGAGAGCCTCGT 60.467 60.000 0.00 0.00 35.36 4.18
2400 3885 2.636412 CGAGAAGCCAGGGACGTCA 61.636 63.158 18.91 0.00 0.00 4.35
2753 4238 1.569479 GCCTTCTTGCACGGTGAGAC 61.569 60.000 13.29 0.00 0.00 3.36
2774 4275 5.703130 AGACTGTTAATCCTTTGAGCTGAAC 59.297 40.000 0.00 0.00 0.00 3.18
2803 4304 1.812571 GCAATCGTGGGTTCTGACATT 59.187 47.619 0.00 0.00 0.00 2.71
2804 4305 2.228822 GCAATCGTGGGTTCTGACATTT 59.771 45.455 0.00 0.00 0.00 2.32
2805 4306 3.825308 CAATCGTGGGTTCTGACATTTG 58.175 45.455 0.00 0.00 0.00 2.32
2806 4307 1.890876 TCGTGGGTTCTGACATTTGG 58.109 50.000 0.00 0.00 0.00 3.28
2811 4313 3.383185 GTGGGTTCTGACATTTGGTTTGA 59.617 43.478 0.00 0.00 0.00 2.69
3330 4840 4.662961 CTGCAGTGCGTCGACCCA 62.663 66.667 10.58 3.95 0.00 4.51
3455 4970 2.485124 GCAATGAGTAGGCAGAGCAGAT 60.485 50.000 0.00 0.00 0.00 2.90
3587 5215 7.513371 AGTAGTACTACTGTTATCCATCAGC 57.487 40.000 30.33 1.77 44.11 4.26
3649 5277 1.656652 ACGAAGGATGGCGAGAAATG 58.343 50.000 0.00 0.00 0.00 2.32
3650 5278 1.207089 ACGAAGGATGGCGAGAAATGA 59.793 47.619 0.00 0.00 0.00 2.57
3654 5282 1.415659 AGGATGGCGAGAAATGAGGAG 59.584 52.381 0.00 0.00 0.00 3.69
3665 6026 4.273318 AGAAATGAGGAGTTGGTAATGGC 58.727 43.478 0.00 0.00 0.00 4.40
3765 6171 5.050490 AGGAAATGACAGTACATACGATGC 58.950 41.667 0.00 0.00 0.00 3.91
3801 6209 2.880268 CAGATGCACCAGAAGAAACACA 59.120 45.455 0.00 0.00 0.00 3.72
3802 6210 3.058432 CAGATGCACCAGAAGAAACACAG 60.058 47.826 0.00 0.00 0.00 3.66
3803 6211 2.708216 TGCACCAGAAGAAACACAGA 57.292 45.000 0.00 0.00 0.00 3.41
3804 6212 3.213206 TGCACCAGAAGAAACACAGAT 57.787 42.857 0.00 0.00 0.00 2.90
3805 6213 4.350368 TGCACCAGAAGAAACACAGATA 57.650 40.909 0.00 0.00 0.00 1.98
3809 6217 6.096141 TGCACCAGAAGAAACACAGATAAAAA 59.904 34.615 0.00 0.00 0.00 1.94
3836 6246 2.505819 AGATCCATGGTCACTAACACCC 59.494 50.000 12.58 0.00 32.24 4.61
3838 6248 1.628340 TCCATGGTCACTAACACCCAG 59.372 52.381 12.58 0.00 32.24 4.45
3839 6249 1.340017 CCATGGTCACTAACACCCAGG 60.340 57.143 2.57 0.00 32.24 4.45
3844 6254 2.835764 GGTCACTAACACCCAGGACATA 59.164 50.000 0.00 0.00 0.00 2.29
3845 6255 3.454812 GGTCACTAACACCCAGGACATAT 59.545 47.826 0.00 0.00 0.00 1.78
3848 6258 6.183361 GGTCACTAACACCCAGGACATATATT 60.183 42.308 0.00 0.00 0.00 1.28
3878 6307 2.653234 AGAAGCACATCATGATCCCC 57.347 50.000 4.86 0.00 0.00 4.81
3895 6325 2.214216 CCACAGGAGTCGAACCCCA 61.214 63.158 6.32 0.00 0.00 4.96
3915 6345 0.668535 GTCTGCAAGGAAACACCACC 59.331 55.000 0.00 0.00 42.04 4.61
3917 6347 2.335011 GCAAGGAAACACCACCGC 59.665 61.111 0.00 0.00 42.04 5.68
3946 6376 2.833794 CCCAGTTCTCGAAGAAACACA 58.166 47.619 7.49 0.00 35.75 3.72
3961 6391 6.976934 AGAAACACAACATCAAACCCTTAT 57.023 33.333 0.00 0.00 0.00 1.73
3962 6392 7.360113 AGAAACACAACATCAAACCCTTATT 57.640 32.000 0.00 0.00 0.00 1.40
3991 6421 2.869801 CGAACCAGTTGTATGTGTGTGT 59.130 45.455 0.00 0.00 0.00 3.72
3992 6422 3.303066 CGAACCAGTTGTATGTGTGTGTG 60.303 47.826 0.00 0.00 0.00 3.82
4016 6446 5.446073 GCTAGATTACAAACTTCAGAACCGC 60.446 44.000 0.00 0.00 0.00 5.68
4048 6478 3.840763 GTGCGACGAATTCAAAGTTGATC 59.159 43.478 6.22 0.00 37.00 2.92
4073 6503 4.540824 GCATCTTTTGCGTCTTTTTCTCT 58.459 39.130 0.00 0.00 42.54 3.10
4074 6504 4.614702 GCATCTTTTGCGTCTTTTTCTCTC 59.385 41.667 0.00 0.00 42.54 3.20
4079 6509 1.000163 TGCGTCTTTTTCTCTCTCGCT 60.000 47.619 0.00 0.00 42.11 4.93
4114 6545 5.009911 GGCAGTGAATGTGGATTTGCATATA 59.990 40.000 0.00 0.00 28.27 0.86
4117 6548 7.522562 GCAGTGAATGTGGATTTGCATATATGA 60.523 37.037 17.10 0.00 0.00 2.15
4122 6553 7.683437 ATGTGGATTTGCATATATGAGACTG 57.317 36.000 17.10 0.00 0.00 3.51
4132 6563 9.836864 TTGCATATATGAGACTGTGATTTACTT 57.163 29.630 17.10 0.00 0.00 2.24
4140 6571 6.948886 TGAGACTGTGATTTACTTAGAGGACT 59.051 38.462 0.00 0.00 0.00 3.85
4141 6572 7.094162 TGAGACTGTGATTTACTTAGAGGACTG 60.094 40.741 0.00 0.00 0.00 3.51
4223 6655 4.789481 GCAGATTCTCAAGTGCGACAAAAA 60.789 41.667 0.00 0.00 0.00 1.94
4257 6689 7.449247 TGTTCTTATTGAAAATCTTTTGGGGG 58.551 34.615 0.00 0.00 36.30 5.40
4258 6690 6.048732 TCTTATTGAAAATCTTTTGGGGGC 57.951 37.500 0.00 0.00 0.00 5.80
4259 6691 5.545723 TCTTATTGAAAATCTTTTGGGGGCA 59.454 36.000 0.00 0.00 0.00 5.36
4260 6692 4.720775 ATTGAAAATCTTTTGGGGGCAA 57.279 36.364 0.00 0.00 0.00 4.52
4281 6713 5.351740 GCAAGAGGAGTTCTAATGGTTACAC 59.648 44.000 0.00 0.00 34.14 2.90
4304 6736 5.022021 CGGTGATCGCAATACTTCTTTTTC 58.978 41.667 8.82 0.00 0.00 2.29
4311 6744 9.173939 GATCGCAATACTTCTTTTTCCATAATG 57.826 33.333 0.00 0.00 0.00 1.90
4313 6746 6.751425 CGCAATACTTCTTTTTCCATAATGCA 59.249 34.615 0.00 0.00 0.00 3.96
4338 6771 8.302438 CAACAATGGCTAGAAAGAAGAGAAATT 58.698 33.333 0.00 0.00 0.00 1.82
4339 6772 7.824672 ACAATGGCTAGAAAGAAGAGAAATTG 58.175 34.615 0.00 0.00 0.00 2.32
4345 6778 9.178758 GGCTAGAAAGAAGAGAAATTGGATTTA 57.821 33.333 0.00 0.00 31.47 1.40
4387 6820 3.958704 TGTTGTTTTGGTGCAAGATACG 58.041 40.909 0.00 0.00 0.00 3.06
4388 6821 3.243234 TGTTGTTTTGGTGCAAGATACGG 60.243 43.478 0.00 0.00 0.00 4.02
4405 6838 5.817816 AGATACGGAGATGAAAAACCACATC 59.182 40.000 0.00 0.00 41.92 3.06
4439 6872 4.345859 TCTAACCTTTTCGCCTCAGAAA 57.654 40.909 0.00 0.00 38.23 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.038825 TCACGACAAGCCAAAATAAAAGAAGA 59.961 34.615 0.00 0.00 0.00 2.87
1 2 6.205784 TCACGACAAGCCAAAATAAAAGAAG 58.794 36.000 0.00 0.00 0.00 2.85
2 3 6.137794 TCACGACAAGCCAAAATAAAAGAA 57.862 33.333 0.00 0.00 0.00 2.52
3 4 5.278266 CCTCACGACAAGCCAAAATAAAAGA 60.278 40.000 0.00 0.00 0.00 2.52
4 5 4.917415 CCTCACGACAAGCCAAAATAAAAG 59.083 41.667 0.00 0.00 0.00 2.27
5 6 4.580995 TCCTCACGACAAGCCAAAATAAAA 59.419 37.500 0.00 0.00 0.00 1.52
6 7 4.023536 GTCCTCACGACAAGCCAAAATAAA 60.024 41.667 0.00 0.00 41.54 1.40
7 8 3.500680 GTCCTCACGACAAGCCAAAATAA 59.499 43.478 0.00 0.00 41.54 1.40
8 9 3.071479 GTCCTCACGACAAGCCAAAATA 58.929 45.455 0.00 0.00 41.54 1.40
9 10 1.880027 GTCCTCACGACAAGCCAAAAT 59.120 47.619 0.00 0.00 41.54 1.82
10 11 1.134220 AGTCCTCACGACAAGCCAAAA 60.134 47.619 0.00 0.00 44.66 2.44
11 12 0.468226 AGTCCTCACGACAAGCCAAA 59.532 50.000 0.00 0.00 44.66 3.28
13 14 0.468226 AAAGTCCTCACGACAAGCCA 59.532 50.000 0.00 0.00 44.66 4.75
14 15 0.868406 CAAAGTCCTCACGACAAGCC 59.132 55.000 0.00 0.00 44.66 4.35
15 16 1.583054 ACAAAGTCCTCACGACAAGC 58.417 50.000 0.00 0.00 44.66 4.01
18 19 1.948104 CCAACAAAGTCCTCACGACA 58.052 50.000 0.00 0.00 44.66 4.35
19 20 0.586802 GCCAACAAAGTCCTCACGAC 59.413 55.000 0.00 0.00 42.32 4.34
20 21 0.468226 AGCCAACAAAGTCCTCACGA 59.532 50.000 0.00 0.00 0.00 4.35
21 22 0.588252 CAGCCAACAAAGTCCTCACG 59.412 55.000 0.00 0.00 0.00 4.35
22 23 1.334869 CACAGCCAACAAAGTCCTCAC 59.665 52.381 0.00 0.00 0.00 3.51
24 25 1.334869 CACACAGCCAACAAAGTCCTC 59.665 52.381 0.00 0.00 0.00 3.71
25 26 1.392589 CACACAGCCAACAAAGTCCT 58.607 50.000 0.00 0.00 0.00 3.85
26 27 0.249031 GCACACAGCCAACAAAGTCC 60.249 55.000 0.00 0.00 37.23 3.85
27 28 0.455410 TGCACACAGCCAACAAAGTC 59.545 50.000 0.00 0.00 44.83 3.01
28 29 1.067516 GATGCACACAGCCAACAAAGT 59.932 47.619 0.00 0.00 44.83 2.66
29 30 1.338973 AGATGCACACAGCCAACAAAG 59.661 47.619 0.00 0.00 44.83 2.77
30 31 1.401761 AGATGCACACAGCCAACAAA 58.598 45.000 0.00 0.00 44.83 2.83
33 34 2.154462 ACTAAGATGCACACAGCCAAC 58.846 47.619 0.00 0.00 44.83 3.77
36 37 4.542662 CATAACTAAGATGCACACAGCC 57.457 45.455 0.00 0.00 44.83 4.85
45 46 4.302455 CCGGTCTCTGCATAACTAAGATG 58.698 47.826 0.00 0.00 0.00 2.90
46 47 3.322254 CCCGGTCTCTGCATAACTAAGAT 59.678 47.826 0.00 0.00 0.00 2.40
47 48 2.693591 CCCGGTCTCTGCATAACTAAGA 59.306 50.000 0.00 0.00 0.00 2.10
49 50 2.167693 CACCCGGTCTCTGCATAACTAA 59.832 50.000 0.00 0.00 0.00 2.24
50 51 1.754803 CACCCGGTCTCTGCATAACTA 59.245 52.381 0.00 0.00 0.00 2.24
51 52 0.537188 CACCCGGTCTCTGCATAACT 59.463 55.000 0.00 0.00 0.00 2.24
52 53 0.249398 ACACCCGGTCTCTGCATAAC 59.751 55.000 0.00 0.00 0.00 1.89
54 55 1.855295 TTACACCCGGTCTCTGCATA 58.145 50.000 0.00 0.00 0.00 3.14
55 56 1.134401 CATTACACCCGGTCTCTGCAT 60.134 52.381 0.00 0.00 0.00 3.96
56 57 0.249120 CATTACACCCGGTCTCTGCA 59.751 55.000 0.00 0.00 0.00 4.41
57 58 0.535335 TCATTACACCCGGTCTCTGC 59.465 55.000 0.00 0.00 0.00 4.26
58 59 3.543680 AATCATTACACCCGGTCTCTG 57.456 47.619 0.00 0.00 0.00 3.35
59 60 5.425630 GTTTAATCATTACACCCGGTCTCT 58.574 41.667 0.00 0.00 0.00 3.10
60 61 4.573607 GGTTTAATCATTACACCCGGTCTC 59.426 45.833 0.00 0.00 31.28 3.36
61 62 4.226620 AGGTTTAATCATTACACCCGGTCT 59.773 41.667 8.86 0.00 36.79 3.85
62 63 4.520179 AGGTTTAATCATTACACCCGGTC 58.480 43.478 8.86 0.00 36.79 4.79
63 64 4.579647 AGGTTTAATCATTACACCCGGT 57.420 40.909 8.86 0.00 36.79 5.28
64 65 5.907866 AAAGGTTTAATCATTACACCCGG 57.092 39.130 8.86 0.00 36.79 5.73
65 66 8.517056 ACTTAAAAGGTTTAATCATTACACCCG 58.483 33.333 8.86 0.00 36.79 5.28
76 77 9.577110 GGCGCTTTATTACTTAAAAGGTTTAAT 57.423 29.630 7.64 0.00 34.07 1.40
77 78 8.028354 GGGCGCTTTATTACTTAAAAGGTTTAA 58.972 33.333 7.64 0.00 34.07 1.52
78 79 7.394077 AGGGCGCTTTATTACTTAAAAGGTTTA 59.606 33.333 7.64 0.00 34.07 2.01
79 80 6.209986 AGGGCGCTTTATTACTTAAAAGGTTT 59.790 34.615 7.64 0.00 34.07 3.27
80 81 5.713389 AGGGCGCTTTATTACTTAAAAGGTT 59.287 36.000 7.64 0.00 34.07 3.50
81 82 5.258841 AGGGCGCTTTATTACTTAAAAGGT 58.741 37.500 7.64 0.00 34.07 3.50
82 83 5.830000 AGGGCGCTTTATTACTTAAAAGG 57.170 39.130 7.64 0.00 34.07 3.11
83 84 7.274904 GGAAAAGGGCGCTTTATTACTTAAAAG 59.725 37.037 26.79 0.00 36.09 2.27
84 85 7.092079 GGAAAAGGGCGCTTTATTACTTAAAA 58.908 34.615 26.79 0.00 29.52 1.52
85 86 6.623331 CGGAAAAGGGCGCTTTATTACTTAAA 60.623 38.462 26.79 0.00 0.00 1.52
86 87 5.163733 CGGAAAAGGGCGCTTTATTACTTAA 60.164 40.000 26.79 0.00 0.00 1.85
87 88 4.333372 CGGAAAAGGGCGCTTTATTACTTA 59.667 41.667 26.79 0.00 0.00 2.24
88 89 3.128068 CGGAAAAGGGCGCTTTATTACTT 59.872 43.478 26.79 11.90 0.00 2.24
89 90 2.681344 CGGAAAAGGGCGCTTTATTACT 59.319 45.455 26.79 12.61 0.00 2.24
90 91 2.793585 GCGGAAAAGGGCGCTTTATTAC 60.794 50.000 26.79 13.64 0.00 1.89
91 92 1.402613 GCGGAAAAGGGCGCTTTATTA 59.597 47.619 26.79 0.00 0.00 0.98
92 93 0.172578 GCGGAAAAGGGCGCTTTATT 59.827 50.000 26.79 14.05 0.00 1.40
93 94 0.963355 TGCGGAAAAGGGCGCTTTAT 60.963 50.000 26.79 17.25 0.00 1.40
94 95 1.173444 TTGCGGAAAAGGGCGCTTTA 61.173 50.000 26.79 10.09 0.00 1.85
95 96 2.022240 TTTGCGGAAAAGGGCGCTTT 62.022 50.000 21.93 21.93 0.00 3.51
96 97 2.022240 TTTTGCGGAAAAGGGCGCTT 62.022 50.000 11.06 10.73 0.00 4.68
97 98 1.815817 ATTTTGCGGAAAAGGGCGCT 61.816 50.000 19.64 0.00 34.53 5.92
98 99 0.109039 TATTTTGCGGAAAAGGGCGC 60.109 50.000 19.64 0.00 34.53 6.53
99 100 2.577449 ATATTTTGCGGAAAAGGGCG 57.423 45.000 19.64 0.00 34.53 6.13
100 101 5.006153 AGTTATATTTTGCGGAAAAGGGC 57.994 39.130 19.64 8.45 34.53 5.19
101 102 6.451064 AGAGTTATATTTTGCGGAAAAGGG 57.549 37.500 19.64 0.00 34.53 3.95
102 103 8.757164 AAAAGAGTTATATTTTGCGGAAAAGG 57.243 30.769 19.64 0.00 34.53 3.11
107 108 9.661563 TCTCTAAAAAGAGTTATATTTTGCGGA 57.338 29.630 2.56 0.00 37.23 5.54
155 156 9.947669 ACACTCTAAAATACGTCTGTATACATC 57.052 33.333 5.91 2.34 40.42 3.06
162 163 8.737175 TGAATCTACACTCTAAAATACGTCTGT 58.263 33.333 0.00 0.00 0.00 3.41
163 164 9.737427 ATGAATCTACACTCTAAAATACGTCTG 57.263 33.333 0.00 0.00 0.00 3.51
175 176 9.606631 GGAGTAAAATGAATGAATCTACACTCT 57.393 33.333 0.00 0.00 0.00 3.24
176 177 8.543774 CGGAGTAAAATGAATGAATCTACACTC 58.456 37.037 0.00 0.00 0.00 3.51
177 178 8.041323 ACGGAGTAAAATGAATGAATCTACACT 58.959 33.333 0.00 0.00 41.94 3.55
178 179 8.197988 ACGGAGTAAAATGAATGAATCTACAC 57.802 34.615 0.00 0.00 41.94 2.90
197 198 6.971726 TTCAATATGGACTACATACGGAGT 57.028 37.500 0.00 0.00 44.41 3.85
198 199 7.926555 AGTTTTCAATATGGACTACATACGGAG 59.073 37.037 0.00 0.00 44.41 4.63
199 200 7.788026 AGTTTTCAATATGGACTACATACGGA 58.212 34.615 0.00 0.00 44.41 4.69
200 201 7.926555 AGAGTTTTCAATATGGACTACATACGG 59.073 37.037 0.00 0.00 44.41 4.02
201 202 8.873215 AGAGTTTTCAATATGGACTACATACG 57.127 34.615 0.00 0.00 44.41 3.06
207 208 9.886132 GGTCTTTAGAGTTTTCAATATGGACTA 57.114 33.333 0.00 0.00 0.00 2.59
208 209 8.606830 AGGTCTTTAGAGTTTTCAATATGGACT 58.393 33.333 0.00 0.00 0.00 3.85
209 210 8.794335 AGGTCTTTAGAGTTTTCAATATGGAC 57.206 34.615 0.00 0.00 0.00 4.02
217 218 9.198475 CCTAGGTATAGGTCTTTAGAGTTTTCA 57.802 37.037 0.00 0.00 43.33 2.69
233 234 2.109657 ACTCCCCCGTTCCTAGGTATAG 59.890 54.545 9.08 0.00 0.00 1.31
234 235 2.146998 ACTCCCCCGTTCCTAGGTATA 58.853 52.381 9.08 0.00 0.00 1.47
235 236 0.939698 ACTCCCCCGTTCCTAGGTAT 59.060 55.000 9.08 0.00 0.00 2.73
236 237 1.496429 CTACTCCCCCGTTCCTAGGTA 59.504 57.143 9.08 0.00 0.00 3.08
237 238 0.261109 CTACTCCCCCGTTCCTAGGT 59.739 60.000 9.08 0.00 0.00 3.08
238 239 0.554792 TCTACTCCCCCGTTCCTAGG 59.445 60.000 0.82 0.82 0.00 3.02
239 240 2.679429 ATCTACTCCCCCGTTCCTAG 57.321 55.000 0.00 0.00 0.00 3.02
240 241 3.205056 TGTAATCTACTCCCCCGTTCCTA 59.795 47.826 0.00 0.00 0.00 2.94
241 242 2.023695 TGTAATCTACTCCCCCGTTCCT 60.024 50.000 0.00 0.00 0.00 3.36
242 243 2.102084 GTGTAATCTACTCCCCCGTTCC 59.898 54.545 0.00 0.00 0.00 3.62
243 244 3.029570 AGTGTAATCTACTCCCCCGTTC 58.970 50.000 0.00 0.00 0.00 3.95
244 245 3.111741 AGTGTAATCTACTCCCCCGTT 57.888 47.619 0.00 0.00 0.00 4.44
245 246 2.842645 AGTGTAATCTACTCCCCCGT 57.157 50.000 0.00 0.00 0.00 5.28
246 247 3.793559 CAAAGTGTAATCTACTCCCCCG 58.206 50.000 0.00 0.00 0.00 5.73
247 248 3.054655 TGCAAAGTGTAATCTACTCCCCC 60.055 47.826 0.00 0.00 0.00 5.40
248 249 4.216411 TGCAAAGTGTAATCTACTCCCC 57.784 45.455 0.00 0.00 0.00 4.81
249 250 4.576463 CCATGCAAAGTGTAATCTACTCCC 59.424 45.833 0.00 0.00 0.00 4.30
250 251 4.576463 CCCATGCAAAGTGTAATCTACTCC 59.424 45.833 0.00 0.00 0.00 3.85
251 252 4.576463 CCCCATGCAAAGTGTAATCTACTC 59.424 45.833 0.00 0.00 0.00 2.59
252 253 4.018415 ACCCCATGCAAAGTGTAATCTACT 60.018 41.667 0.00 0.00 0.00 2.57
253 254 4.096382 CACCCCATGCAAAGTGTAATCTAC 59.904 45.833 0.00 0.00 0.00 2.59
283 284 7.500227 CCATCATCATCATCATCATCATCATCA 59.500 37.037 0.00 0.00 0.00 3.07
284 285 7.040823 CCCATCATCATCATCATCATCATCATC 60.041 40.741 0.00 0.00 0.00 2.92
285 286 6.774656 CCCATCATCATCATCATCATCATCAT 59.225 38.462 0.00 0.00 0.00 2.45
286 287 6.122277 CCCATCATCATCATCATCATCATCA 58.878 40.000 0.00 0.00 0.00 3.07
287 288 6.038714 CACCCATCATCATCATCATCATCATC 59.961 42.308 0.00 0.00 0.00 2.92
288 289 5.888161 CACCCATCATCATCATCATCATCAT 59.112 40.000 0.00 0.00 0.00 2.45
289 290 5.222048 ACACCCATCATCATCATCATCATCA 60.222 40.000 0.00 0.00 0.00 3.07
290 291 5.123979 CACACCCATCATCATCATCATCATC 59.876 44.000 0.00 0.00 0.00 2.92
291 292 5.010282 CACACCCATCATCATCATCATCAT 58.990 41.667 0.00 0.00 0.00 2.45
292 293 4.394729 CACACCCATCATCATCATCATCA 58.605 43.478 0.00 0.00 0.00 3.07
310 311 9.363763 CATGATAGTATCAGTCATTATCCACAC 57.636 37.037 17.52 0.00 43.53 3.82
329 330 4.486090 GGGTGTACGTAGATGCATGATAG 58.514 47.826 2.46 0.00 0.00 2.08
330 331 3.257375 GGGGTGTACGTAGATGCATGATA 59.743 47.826 2.46 0.00 0.00 2.15
331 332 2.037251 GGGGTGTACGTAGATGCATGAT 59.963 50.000 2.46 0.00 0.00 2.45
354 355 6.092748 ACATACATTTTCGTTTTGATGAGGC 58.907 36.000 0.00 0.00 0.00 4.70
355 356 8.233868 TGTACATACATTTTCGTTTTGATGAGG 58.766 33.333 0.00 0.00 0.00 3.86
356 357 9.773328 ATGTACATACATTTTCGTTTTGATGAG 57.227 29.630 6.56 0.00 43.99 2.90
377 378 8.135529 TCATACAACTCTACTGCATGTATGTAC 58.864 37.037 23.56 0.00 46.99 2.90
471 476 2.893895 CACATCGCATCGCAGCCT 60.894 61.111 0.00 0.00 0.00 4.58
627 636 0.890996 CAGGAGTCCAGGTGTTTGGC 60.891 60.000 12.86 0.00 38.16 4.52
632 641 1.229336 CCTCCAGGAGTCCAGGTGT 60.229 63.158 19.43 0.00 37.39 4.16
633 642 2.664081 GCCTCCAGGAGTCCAGGTG 61.664 68.421 19.43 16.68 37.39 4.00
634 643 2.284995 GCCTCCAGGAGTCCAGGT 60.285 66.667 19.43 0.00 37.39 4.00
635 644 2.040278 AGCCTCCAGGAGTCCAGG 59.960 66.667 14.49 14.49 37.39 4.45
636 645 2.365586 CCAGCCTCCAGGAGTCCAG 61.366 68.421 15.86 2.60 37.39 3.86
637 646 2.284921 CCAGCCTCCAGGAGTCCA 60.285 66.667 15.86 0.00 37.39 4.02
638 647 2.039624 TCCAGCCTCCAGGAGTCC 59.960 66.667 15.86 0.00 37.39 3.85
639 648 3.627690 CTCCAGCCTCCAGGAGTC 58.372 66.667 15.86 1.79 45.08 3.36
671 680 4.803426 GCCTCGGCCACAGAGACG 62.803 72.222 2.24 0.00 37.93 4.18
734 754 4.803426 GCGAGCACGGGTCTCTGG 62.803 72.222 5.52 0.00 40.15 3.86
755 776 2.959707 AGTTCTGTTGGTCTCGACTCTT 59.040 45.455 0.00 0.00 0.00 2.85
853 880 0.104672 TGGTGAAGGAGAGGGGTTGA 60.105 55.000 0.00 0.00 0.00 3.18
880 914 3.724914 GAGGGTGTAGCTGGCGAGC 62.725 68.421 13.51 13.51 46.64 5.03
882 916 3.075005 GGAGGGTGTAGCTGGCGA 61.075 66.667 0.00 0.00 0.00 5.54
884 918 3.009115 TGGGAGGGTGTAGCTGGC 61.009 66.667 0.00 0.00 0.00 4.85
885 919 1.918293 TGTGGGAGGGTGTAGCTGG 60.918 63.158 0.00 0.00 0.00 4.85
887 921 0.905337 GAGTGTGGGAGGGTGTAGCT 60.905 60.000 0.00 0.00 0.00 3.32
888 922 1.597461 GAGTGTGGGAGGGTGTAGC 59.403 63.158 0.00 0.00 0.00 3.58
889 923 1.890894 CGAGTGTGGGAGGGTGTAG 59.109 63.158 0.00 0.00 0.00 2.74
890 924 2.280552 GCGAGTGTGGGAGGGTGTA 61.281 63.158 0.00 0.00 0.00 2.90
891 925 3.626924 GCGAGTGTGGGAGGGTGT 61.627 66.667 0.00 0.00 0.00 4.16
892 926 3.596066 CTGCGAGTGTGGGAGGGTG 62.596 68.421 0.00 0.00 0.00 4.61
893 927 3.314331 CTGCGAGTGTGGGAGGGT 61.314 66.667 0.00 0.00 0.00 4.34
913 953 1.853963 TTCGAGGAGGAGGAAGAAGG 58.146 55.000 0.00 0.00 0.00 3.46
967 1007 5.126067 CCGAATTGGTCACCAGAATATTCT 58.874 41.667 12.37 12.37 38.25 2.40
982 1022 0.744414 ATGTCTGTCGGCCGAATTGG 60.744 55.000 32.93 19.32 42.50 3.16
1039 1085 1.064611 CAGGACGAGGAGGAGGAGTAA 60.065 57.143 0.00 0.00 0.00 2.24
1545 1609 1.973812 GAGCTTGGTGGAGTTGGCC 60.974 63.158 0.00 0.00 0.00 5.36
1751 3224 3.129502 CGAGCTGGTACGTCCCGA 61.130 66.667 0.00 0.00 34.77 5.14
1956 3429 0.251386 TGAGGTTGACGAGGCTCTCT 60.251 55.000 13.50 0.00 0.00 3.10
1967 3440 2.110213 GCGTGGTGGTGAGGTTGA 59.890 61.111 0.00 0.00 0.00 3.18
2391 3876 3.881019 TTCCGCCTCTGACGTCCCT 62.881 63.158 14.12 0.00 0.00 4.20
2753 4238 6.175712 GAGTTCAGCTCAAAGGATTAACAG 57.824 41.667 0.00 0.00 43.58 3.16
2774 4275 1.081892 CCCACGATTGCAGAGTTGAG 58.918 55.000 0.00 0.00 0.00 3.02
2803 4304 6.922957 GCTACAGTCAAATGAAATCAAACCAA 59.077 34.615 0.00 0.00 0.00 3.67
2804 4305 6.265196 AGCTACAGTCAAATGAAATCAAACCA 59.735 34.615 0.00 0.00 0.00 3.67
2805 4306 6.681777 AGCTACAGTCAAATGAAATCAAACC 58.318 36.000 0.00 0.00 0.00 3.27
2806 4307 6.521133 CGAGCTACAGTCAAATGAAATCAAAC 59.479 38.462 0.00 0.00 0.00 2.93
2811 4313 3.062639 CGCGAGCTACAGTCAAATGAAAT 59.937 43.478 0.00 0.00 0.00 2.17
2896 4406 2.423898 CGTCGTGGAGGTAGGCCAT 61.424 63.158 5.01 0.00 37.81 4.40
3165 4675 2.358247 ATGCCGTTGGTCGTGTCC 60.358 61.111 0.00 0.00 37.94 4.02
3455 4970 1.071699 CTCCTGGTTTTCTCCGGTTGA 59.928 52.381 0.00 0.00 32.33 3.18
3567 5082 5.184340 ACGCTGATGGATAACAGTAGTAC 57.816 43.478 0.00 0.00 36.62 2.73
3587 5215 4.614555 TGCCTGCTATACAAATCAAACG 57.385 40.909 0.00 0.00 0.00 3.60
3649 5277 0.919710 AGGGCCATTACCAACTCCTC 59.080 55.000 6.18 0.00 0.00 3.71
3650 5278 0.919710 GAGGGCCATTACCAACTCCT 59.080 55.000 6.18 0.00 0.00 3.69
3654 5282 2.802719 TCAAAGAGGGCCATTACCAAC 58.197 47.619 6.18 0.00 0.00 3.77
3665 6026 6.015940 ACAAGAGCTGTAAAAATCAAAGAGGG 60.016 38.462 0.00 0.00 36.10 4.30
3752 6158 5.759963 GCTAGTGTAAGCATCGTATGTACT 58.240 41.667 0.00 0.00 42.30 2.73
3780 6188 2.880268 TGTGTTTCTTCTGGTGCATCTG 59.120 45.455 0.00 0.00 0.00 2.90
3809 6217 6.431234 GTGTTAGTGACCATGGATCTCTTTTT 59.569 38.462 21.47 0.00 0.00 1.94
3814 6222 3.432326 GGGTGTTAGTGACCATGGATCTC 60.432 52.174 21.47 12.75 34.89 2.75
3820 6230 1.628340 TCCTGGGTGTTAGTGACCATG 59.372 52.381 0.00 0.00 34.89 3.66
3823 6233 1.053424 TGTCCTGGGTGTTAGTGACC 58.947 55.000 0.00 0.00 0.00 4.02
3871 6281 0.252057 TTCGACTCCTGTGGGGATCA 60.252 55.000 0.00 0.00 44.15 2.92
3878 6307 1.293498 CTGGGGTTCGACTCCTGTG 59.707 63.158 5.66 0.00 40.26 3.66
3895 6325 1.680338 GTGGTGTTTCCTTGCAGACT 58.320 50.000 0.00 0.00 37.07 3.24
3915 6345 1.810030 GAACTGGGCTAAGGACGCG 60.810 63.158 3.53 3.53 0.00 6.01
3917 6347 0.179134 CGAGAACTGGGCTAAGGACG 60.179 60.000 0.00 0.00 0.00 4.79
3946 6376 7.014808 TCGAAGGAAAAATAAGGGTTTGATGTT 59.985 33.333 0.00 0.00 0.00 2.71
3961 6391 5.591067 ACATACAACTGGTTCGAAGGAAAAA 59.409 36.000 0.00 0.00 33.05 1.94
3962 6392 5.008217 CACATACAACTGGTTCGAAGGAAAA 59.992 40.000 0.00 0.00 33.05 2.29
3991 6421 5.637810 CGGTTCTGAAGTTTGTAATCTAGCA 59.362 40.000 0.00 0.00 0.00 3.49
3992 6422 5.446073 GCGGTTCTGAAGTTTGTAATCTAGC 60.446 44.000 0.00 0.00 0.00 3.42
4016 6446 1.629013 TTCGTCGCACTCTTATGCAG 58.371 50.000 0.00 0.00 46.47 4.41
4079 6509 0.391228 TTCACTGCCTTGTACGCTCA 59.609 50.000 0.00 0.00 0.00 4.26
4114 6545 7.617723 AGTCCTCTAAGTAAATCACAGTCTCAT 59.382 37.037 0.00 0.00 0.00 2.90
4117 6548 6.948886 TCAGTCCTCTAAGTAAATCACAGTCT 59.051 38.462 0.00 0.00 0.00 3.24
4122 6553 9.490379 TTCTTTTCAGTCCTCTAAGTAAATCAC 57.510 33.333 0.00 0.00 0.00 3.06
4157 6588 9.988350 CGCAGCTTTTCTATTTCTTTTTAGATA 57.012 29.630 0.00 0.00 0.00 1.98
4167 6599 3.440522 ACCCTTCGCAGCTTTTCTATTTC 59.559 43.478 0.00 0.00 0.00 2.17
4170 6602 2.789409 ACCCTTCGCAGCTTTTCTAT 57.211 45.000 0.00 0.00 0.00 1.98
4179 6611 2.691409 TTCATAGGAACCCTTCGCAG 57.309 50.000 0.00 0.00 34.61 5.18
4182 6614 2.874701 CTGCATTCATAGGAACCCTTCG 59.125 50.000 0.00 0.00 35.46 3.79
4235 6667 5.545723 TGCCCCCAAAAGATTTTCAATAAGA 59.454 36.000 0.00 0.00 0.00 2.10
4236 6668 5.803552 TGCCCCCAAAAGATTTTCAATAAG 58.196 37.500 0.00 0.00 0.00 1.73
4244 6676 2.158173 TCCTCTTGCCCCCAAAAGATTT 60.158 45.455 0.00 0.00 32.20 2.17
4257 6689 5.351740 GTGTAACCATTAGAACTCCTCTTGC 59.648 44.000 0.00 0.00 35.41 4.01
4258 6690 5.577164 CGTGTAACCATTAGAACTCCTCTTG 59.423 44.000 0.00 0.00 35.41 3.02
4259 6691 5.337330 CCGTGTAACCATTAGAACTCCTCTT 60.337 44.000 0.00 0.00 35.41 2.85
4260 6692 4.159879 CCGTGTAACCATTAGAACTCCTCT 59.840 45.833 0.00 0.00 38.28 3.69
4281 6713 4.600012 AAAAGAAGTATTGCGATCACCG 57.400 40.909 0.00 0.00 42.21 4.94
4304 6736 5.518848 TTCTAGCCATTGTTGCATTATGG 57.481 39.130 14.63 14.63 41.40 2.74
4311 6744 4.697352 TCTCTTCTTTCTAGCCATTGTTGC 59.303 41.667 0.00 0.00 0.00 4.17
4313 6746 8.302438 CAATTTCTCTTCTTTCTAGCCATTGTT 58.698 33.333 0.00 0.00 0.00 2.83
4347 6780 6.108015 ACAACATTGTCATCAAGCACTTTTT 58.892 32.000 0.00 0.00 36.50 1.94
4348 6781 5.663456 ACAACATTGTCATCAAGCACTTTT 58.337 33.333 0.00 0.00 36.50 2.27
4352 6785 5.276963 CCAAAACAACATTGTCATCAAGCAC 60.277 40.000 0.00 0.00 41.31 4.40
4368 6801 3.215151 TCCGTATCTTGCACCAAAACAA 58.785 40.909 0.00 0.00 0.00 2.83
4387 6820 5.902613 TCATGATGTGGTTTTTCATCTCC 57.097 39.130 0.00 0.00 40.46 3.71
4388 6821 6.917533 ACTTCATGATGTGGTTTTTCATCTC 58.082 36.000 13.08 0.00 40.46 2.75
4405 6838 8.850452 GCGAAAAGGTTAGAAAAATACTTCATG 58.150 33.333 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.