Locus 2828

Sequence ID X_DroMel_CAF1
Location 7,556,046 – 7,556,159
Length 113
Max. P 0.718444
window4640 window4641

overview

Window 0

Location 7,556,046 – 7,556,159
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 62.40
Mean single sequence MFE -23.66
Consensus MFE -12.18
Energy contribution -13.90
Covariance contribution 1.72
Combinations/Pair 1.21
Mean z-score -1.52
Structure conservation index 0.51
SVM decision value 0.39
SVM RNA-class probability 0.718444
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7556046 113 + 22224390
AUUAAAAGGAACAAAUGAAAAUUGAU--AAAGA-AAUAUUUUGAACGGCGCGCCAAUUAAGUGCUACCCAUGCGGGC-AAUUUAA-CAUGGCUAGCAUUGACCGUCGAUAAA-UUUUUA-
...............(((((((((((--(....-..)))).....(((((.(.((.....((((((.(((((.....-.......-))))).)))))))).))))))...))-))))))- ( -19.90)
>DroSec_CAF1 48548 117 + 1
AUUAAAAGGAACAAAUGAAAAUUGAUUAAAAAA-AAUAUUUUGAACGGGGCGCCAAUUCUGUGCUACCCAUGAAGAC-AAUAUAAGUAUGGGUAGCAUUGGCCGUCGAUAAUCUUUUUA-
..((((((((...............((((((..-....)))))).(((.(.((((.....((((((((((((.....-........))))))))))))))))).)))....))))))))- ( -31.92)
>DroEre_CAF1 59924 117 + 1
AUUAAAACAAACAAAUGAAAUUUGAUAAAAAAA-AACAUUUUGAAAAUCGCGCCAAUUAAGUGCGACCCAUGCCUCCGAAUGUACGUAUGGGCAGCAUUGGCUAACGAUUAA-CUUUUA-
...........(((((...))))).........-...........(((((.((((.....((((..(((((((............)))))))..))))))))...)))))..-......- ( -23.60)
>DroYak_CAF1 50034 100 + 1
AUUAAAACCAACAAAUGCAAAUUGAUAAAAAUG-GACAUUUUGAAAUGCGCGCCAAUUCAGUGCGACCCAUGACUGCUAAUAUACAUAUGGGCAGCAUUGG-------------------
................((..(((....(((((.-...)))))..)))..)).......((((((..((((((..((........))))))))..)))))).------------------- ( -19.00)
>DroAna_CAF1 51463 93 + 1
UUUAA--------AUUCAAAUUUA---AACGCGGAAGAACCGGAAGAUGGCGCCCAAACAGUGCUGCCCAUGUCUG----------UCU-GGCAACACUGCC----AGUUGG-CCGUUAC
(((((--------((....)))))---)).((((..((..((((....(((((.(.....).)).)))....))))----------.((-((((....))))----))))..-))))... ( -23.90)
>consensus
AUUAAAACGAACAAAUGAAAAUUGAU_AAAAAA_AACAUUUUGAAAAGCGCGCCAAUUCAGUGCUACCCAUGACUGC_AAUAUAA_UAUGGGCAGCAUUGGC___CGAUAAA_CUUUUA_
..........................................................((((((((((((((..............)))))))))))))).................... (-12.18 = -13.90 +   1.72)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,556,046 – 7,556,159
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 62.40
Mean single sequence MFE -24.40
Consensus MFE -12.67
Energy contribution -13.43
Covariance contribution 0.76
Combinations/Pair 1.33
Mean z-score -1.43
Structure conservation index 0.52
SVM decision value 0.19
SVM RNA-class probability 0.623987
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7556046 113 - 22224390
-UAAAAA-UUUAUCGACGGUCAAUGCUAGCCAUG-UUAAAUU-GCCCGCAUGGGUAGCACUUAAUUGGCGCGCCGUUCAAAAUAUU-UCUUU--AUCAAUUUUCAUUUGUUCCUUUUAAU
-......-.....((.((((((((((((.(((((-(......-....)))))).))))).....))))).)).))...........-.....--.......................... ( -21.20)
>DroSec_CAF1 48548 117 - 1
-UAAAAAGAUUAUCGACGGCCAAUGCUACCCAUACUUAUAUU-GUCUUCAUGGGUAGCACAGAAUUGGCGCCCCGUUCAAAAUAUU-UUUUUUAAUCAAUUUUCAUUUGUUCCUUUUAAU
-((((((((.(((.(((((((((((((((((((((.......-))....)))))))))).....)))))....))))....))).)-))))))).......................... ( -25.20)
>DroEre_CAF1 59924 117 - 1
-UAAAAG-UUAAUCGUUAGCCAAUGCUGCCCAUACGUACAUUCGGAGGCAUGGGUCGCACUUAAUUGGCGCGAUUUUCAAAAUGUU-UUUUUUUAUCAAAUUUCAUUUGUUUGUUUUAAU
-((((((-..((((((..((((((((.((((((.(.(........).).)))))).))).....)))))))))))..)........-.........(((((.......)))))))))).. ( -25.00)
>DroYak_CAF1 50034 100 - 1
-------------------CCAAUGCUGCCCAUAUGUAUAUUAGCAGUCAUGGGUCGCACUGAAUUGGCGCGCAUUUCAAAAUGUC-CAUUUUUAUCAAUUUGCAUUUGUUGGUUUUAAU
-------------------(((((((.((((((.(((......)))...)))))).))..((((.((.....)).))))((((((.-.(((......)))..)))))))))))....... ( -21.40)
>DroAna_CAF1 51463 93 - 1
GUAACGG-CCAACU----GGCAGUGUUGCC-AGA----------CAGACAUGGGCAGCACUGUUUGGGCGCCAUCUUCCGGUUCUUCCGCGUU---UAAAUUUGAAU--------UUAAA
..(((((-((....----((((((((((((-...----------........))))))))))))..))).........(((.....)))))))---...........--------..... ( -29.20)
>consensus
_UAAAAA_UUAAUCG___GCCAAUGCUGCCCAUA_GUAUAUU_GCAGGCAUGGGUAGCACUGAAUUGGCGCGCCGUUCAAAAUAUU_UUUUUU_AUCAAUUUUCAUUUGUUCCUUUUAAU
..................(((((((((((((((................)))))))))).....)))))................................................... (-12.67 = -13.43 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:31 2006