Locus 2597

Sequence ID 3L_DroMel_CAF1
Location 7,206,799 – 7,207,022
Length 223
Max. P 0.864540
window4060 window4061 window4062 window4063

overview

Window 0

Location 7,206,799 – 7,206,913
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.43
Mean single sequence MFE -38.93
Consensus MFE -28.20
Energy contribution -27.43
Covariance contribution -0.77
Combinations/Pair 1.16
Mean z-score -2.59
Structure conservation index 0.72
SVM decision value 0.84
SVM RNA-class probability 0.864540
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7206799 114 + 23771897
CCCGAGAAUUCACUCCUUUGGCCACCCGCUGCCUAAUUGCGGCCAAGAAAAAUAAAGUUUCUGGCUGUGCCAAAUUGGGCAAAAGGAGCUGGC-GAACGGGCCAAGUGAAAAUGG-----
........(((((((((((.(((((((..((((((((((((((((.((((.......)))))))))))....)))))))))...)).).))))-.)).)))...)))))).....----- ( -40.70)
>DroEre_CAF1 20345 118 + 1
CC--AGAAUCUACUACUCCGUGCACCCGCUGCCUAAUUGUGGCCAAGAAAAAUAAAGUUCCUGGCUGUGCCAAAUUGGGCAAAAGGAGCAGGCAGAACGGGCCAAGUAAGAAUGGGCAAA
((--(...((((((.((((..((....))((((((((((..((((.(((........))).))))..)....)))))))))...))))..(((.......))).))).))).)))..... ( -35.90)
>DroYak_CAF1 17659 117 + 1
CC--AGAAACUACUCCUUCGUGCACCCGCUGCCUAAUUGCGGCCAAGAAAAAUAAGUUCUCUGGCUGUGCCAAAUUGGGCAAAAGGAGCGGGC-GAAUGGGCCAAGUAAAAAUGGACAAA
((--(.....((((..(((((.(.((((((.(((....(((((((((((.......)))).)))))))(((......)))...))))))))).-).)))))...))))....)))..... ( -40.20)
>consensus
CC__AGAAUCUACUCCUUCGUGCACCCGCUGCCUAAUUGCGGCCAAGAAAAAUAAAGUUUCUGGCUGUGCCAAAUUGGGCAAAAGGAGCAGGC_GAACGGGCCAAGUAAAAAUGG_CAAA
..........((((......(((.((...((((((((((((((((.(((........))).)))))))....)))))))))...)).)))(((.......))).))))............ (-28.20 = -27.43 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 7,206,799 – 7,206,913
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.43
Mean single sequence MFE -37.53
Consensus MFE -29.66
Energy contribution -29.00
Covariance contribution -0.66
Combinations/Pair 1.15
Mean z-score -1.82
Structure conservation index 0.79
SVM decision value 0.16
SVM RNA-class probability 0.613316
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7206799 114 - 23771897
-----CCAUUUUCACUUGGCCCGUUC-GCCAGCUCCUUUUGCCCAAUUUGGCACAGCCAGAAACUUUAUUUUUCUUGGCCGCAAUUAGGCAGCGGGUGGCCAAAGGAGUGAAUUCUCGGG
-----(((........)))((((...-....((((((((.((((..((((((...)))))).................((((.........))))).))).)))))))).......)))) ( -36.44)
>DroEre_CAF1 20345 118 - 1
UUUGCCCAUUCUUACUUGGCCCGUUCUGCCUGCUCCUUUUGCCCAAUUUGGCACAGCCAGGAACUUUAUUUUUCUUGGCCACAAUUAGGCAGCGGGUGCACGGAGUAGUAGAUUCU--GG
.....(((.(((.(((..((((((.(.((((((((((..((((......))))..((((((((........)))))))).......))).)))))))).)))).))))))))...)--)) ( -40.00)
>DroYak_CAF1 17659 117 - 1
UUUGUCCAUUUUUACUUGGCCCAUUC-GCCCGCUCCUUUUGCCCAAUUUGGCACAGCCAGAGAACUUAUUUUUCUUGGCCGCAAUUAGGCAGCGGGUGCACGAAGGAGUAGUUUCU--GG
.....(((...((((((........(-((((((((((.((((((.....))....(((((((((.....))))).)))).))))..))).)))))))).......))))))....)--)) ( -36.16)
>consensus
UUUG_CCAUUUUUACUUGGCCCGUUC_GCCAGCUCCUUUUGCCCAAUUUGGCACAGCCAGAAACUUUAUUUUUCUUGGCCGCAAUUAGGCAGCGGGUGCACGAAGGAGUAGAUUCU__GG
...........(((((((((.......))).((.(((.(((((.((((((((.((...(((((.......))))))))))).)))).))))).))).))......))))))......... (-29.66 = -29.00 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 7,206,879 – 7,206,982
Length 103
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.29
Mean single sequence MFE -28.14
Consensus MFE -18.72
Energy contribution -19.17
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.81
Structure conservation index 0.67
SVM decision value -0.02
SVM RNA-class probability 0.521825
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7206879 103 + 23771897
AAAAGGAGCUGGC-GAACGGGCCAAGUGAAAAUGG-------------GGAAAAACAUGUGCAAUGUCAUAGGACUGAGCAUGAGAUACGGCAAUGUCGGCAU---GAAACAAGCUUUUG
...((((((((((-......)))..((....(((.-------------.......(((((.....(((....)))...))))).....((((...)))).)))---...)).))))))). ( -23.40)
>DroEre_CAF1 20423 120 + 1
AAAAGGAGCAGGCAGAACGGGCCAAGUAAGAAUGGGCAAAGACGGCUGGGAAAAACAUGUGCAAUGUCGUAUGACAGAGCAUGAGAUACGGCAAUGUUGCAAUGUUGAAACAAGCUUUUG
...((((((.(((......(.(((........))).).......))).(....(((((.(((((((((((((..((.....))..))))))))...))))))))))....)..)))))). ( -30.62)
>DroYak_CAF1 17737 119 + 1
AAAAGGAGCGGGC-GAAUGGGCCAAGUAAAAAUGGACAAAGACGGCUGGGAAAAACGUGUGCAAUGUCGUAUGGCAGAGCAUGAGAUACGGCAAUGUUGCAAUGUUGAAACAAGCUUUUG
...((((((((.(-(..(..((((........))).)..)..)).)).(....(((((.(((((((((((((..((.....))..))))))))...))))))))))....)..)))))). ( -30.40)
>consensus
AAAAGGAGCAGGC_GAACGGGCCAAGUAAAAAUGG_CAAAGACGGCUGGGAAAAACAUGUGCAAUGUCGUAUGACAGAGCAUGAGAUACGGCAAUGUUGCAAUGUUGAAACAAGCUUUUG
...((((((.(((.......)))..............................(((((.(((..((((.((((......)))).))))..))))))))...............)))))). (-18.72 = -19.17 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 7,206,913 – 7,207,022
Length 109
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.33
Mean single sequence MFE -29.81
Consensus MFE -21.37
Energy contribution -23.93
Covariance contribution 2.56
Combinations/Pair 1.06
Mean z-score -2.29
Structure conservation index 0.72
SVM decision value 0.11
SVM RNA-class probability 0.587268
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7206913 109 + 23771897
--------GGAAAAACAUGUGCAAUGUCAUAGGACUGAGCAUGAGAUACGGCAAUGUCGGCAU---GAAACAAGCUUUUGCCAAAAAUAUUGCAAACAAGUGCACAUAUGCAACCAUAAA
--------((......(((((((..(((....)))...(((........(((((....(((.(---(...)).))).)))))........))).......)))))))......))..... ( -22.99)
>DroEre_CAF1 20463 120 + 1
GACGGCUGGGAAAAACAUGUGCAAUGUCGUAUGACAGAGCAUGAGAUACGGCAAUGUUGCAAUGUUGAAACAAGCUUUUGCCAAAAAUAUUGCAAGCAACUGCACAUAUGCAACCAUAAA
......(((.......(((((((.((((((((..((.....))..)))))))).((((((((((((.......((....))....)))))))).))))..)))))))......))).... ( -32.32)
>DroYak_CAF1 17776 120 + 1
GACGGCUGGGAAAAACGUGUGCAAUGUCGUAUGGCAGAGCAUGAGAUACGGCAAUGUUGCAAUGUUGAAACAAGCUUUUGCCAAAAAUAUUGCAAGCAAGUGCACAUAUGCAACCAUAAA
......(((.......(((((((.((((((((..((.....))..)))))))).((((((((((((.......((....))....)))))))).))))..)))))))......))).... ( -34.12)
>consensus
GACGGCUGGGAAAAACAUGUGCAAUGUCGUAUGACAGAGCAUGAGAUACGGCAAUGUUGCAAUGUUGAAACAAGCUUUUGCCAAAAAUAUUGCAAGCAAGUGCACAUAUGCAACCAUAAA
........((......(((((((.((((((((..((.....))..)))))))).((((((((((((.......((....))....)))))))).))))..)))))))......))..... (-21.37 = -23.93 +   2.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:03 2006