Locus 8741

Sequence ID 3R_DroMel_CAF1
Location 23,329,307 – 23,329,458
Length 151
Max. P 0.998464
window14042 window14043 window14044

overview

Window 2

Location 23,329,307 – 23,329,418
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.72
Mean single sequence MFE -35.08
Consensus MFE -29.30
Energy contribution -29.14
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.72
Structure conservation index 0.84
SVM decision value 1.07
SVM RNA-class probability 0.910105
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23329307 111 - 27905053
AAAUGCUUUUCCACCGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCUCGAAGUGGAGGGCAAAAUGCAUCUGC---------CAACACCAACGCCAUUAUCCUGGGCAUAUGUCUAA
...............((((((((((((((((((......).))))....))).)))))))))).....((((.(((---------(.....................)))).)))).... ( -33.10)
>DroSec_CAF1 126584 113 - 1
AAAUGCUUUUCCACUGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA-AUGCAUCUGCCGCAUCUGCCAA------CGCCAUUAUCCUGGGCAUAUGUCUAA
..((((........(((....(((((((.....)))))))..)))..(((.(((((((..((((.-((((.......)))).))))..------..))))).)).)))))))........ ( -35.90)
>DroSim_CAF1 130931 119 - 1
AAAUGCUUUUGCACUGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA-AUGCAUCUGCCGCAUCUGCCAACGCCAACGCCAUUAUCCUGGGCAUAUGUCUAA
....((...((((.(((((((((((((.(((((......).)))).....)).))))))))))).-.))))...)).((((.((((...((....))((......)))))).)))).... ( -38.90)
>DroEre_CAF1 132941 116 - 1
AAAUGCUUUUCUACCGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA-AUGCAUCUGCCAG---CGCCAACGCCAACGCCGUUAUCCUGGGCAUAUGUCUAA
...............((((((((((((.(((((......).)))).....)).))))))))))..-..((((.((((((---.(..(((((....).))))..))).)))).)))).... ( -34.90)
>DroYak_CAF1 138544 116 - 1
AAAUGCUUUUCUACCGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA-AUGCAUCUGCCAA---CGCCAACGCCAACGCCAUUAUCCUGGGCAUAUGUCUAA
...............((((((((((((.(((((......).)))).....)).))))))))))..-..((((.((((..---.......((....))..........)))).)))).... ( -32.61)
>consensus
AAAUGCUUUUCCACCGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA_AUGCAUCUGCCAC___CGCCAACGCCAACGCCAUUAUCCUGGGCAUAUGUCUAA
..((((.........((((((((((((.(((((......).)))).....)).)))))))))).................................(((......)))))))........ (-29.30 = -29.14 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 23,329,342 – 23,329,458
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.88
Mean single sequence MFE -39.00
Consensus MFE -33.90
Energy contribution -34.26
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -1.52
Structure conservation index 0.87
SVM decision value 0.92
SVM RNA-class probability 0.882196
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23329342 116 + 27905053
----GCAGAUGCAUUUUGCCCUCCACUUCGAGGGGUGCGACACUCGAGCGCAUCGAGUGGAAGGCGGUGGAAAAGCAUUUCAAAUGCAUUCACAAGCAGUAGCGUUUUAAAUUACUCCCA
----((...(((....((((.((((((.(((...((((.........)))).))))))))).))))(((((...((((.....)))).)))))..)))...))................. ( -37.90)
>DroSec_CAF1 126618 119 + 1
UGCGGCAGAUGCAU-UUGCCCUCCACUUCGUGGGGUGCGACACUCGAGCGCAUCGAGUGGAAGGCAGUGGAAAAGCAUUUCAAAUGCAUUCACAAGCAGGAGCGUUUUAAAUUACUCCCA
(((....(((((((-(((((.(((((((.(((.(.(.((.....))).).))).))))))).)))....((((....))))))))))))).....)))((((............)))).. ( -38.60)
>DroSim_CAF1 130971 119 + 1
UGCGGCAGAUGCAU-UUGCCCUCCACUUCGUGGGGUGCGACACUCGAGCGCAUCGAGUGGAAGGCAGUGCAAAAGCAUUUCAAAUGCAUUCACAAGCAGGAGCGUUUUAAAUUACUCCCA
(((....(((((((-(((((.(((((((.(((.(.(.((.....))).).))).))))))).)))(((((....)))))..))))))))).....)))((((............)))).. ( -41.30)
>DroEre_CAF1 132979 118 + 1
-CUGGCAGAUGCAU-UUGCCCUCCACUUCGUGGGGUGCGACACUCGAGCGCAUCGAGUGGAAGGCGGUAGAAAAGCAUUUCAAAUGCAUUCACGAGCAGGAGCGUUUUAAAUUACUCCCA
-..((((((....)-)))))((((..((((((((.((((.(((((((.....)))))))((((((.........)).))))...))))))))))))..)))).................. ( -38.60)
>DroYak_CAF1 138582 118 + 1
-UUGGCAGAUGCAU-UUGCCCUCCACUUCGUGGGGUGCGACACUCGAGCGCAUCGAGUGGAAGGCGGUAGAAAAGCAUUUCAAAUGCAUUCACGAGCAGGAGCGUUUUAAAUUACUCCCA
-..((((((....)-)))))((((..((((((((.((((.(((((((.....)))))))((((((.........)).))))...))))))))))))..)))).................. ( -38.60)
>consensus
_GCGGCAGAUGCAU_UUGCCCUCCACUUCGUGGGGUGCGACACUCGAGCGCAUCGAGUGGAAGGCGGUGGAAAAGCAUUUCAAAUGCAUUCACAAGCAGGAGCGUUUUAAAUUACUCCCA
....((...(((....((((.(((((((.....((((((.(......)))))))))))))).))))(((((...((((.....)))).)))))..)))...))................. (-33.90 = -34.26 +   0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 23,329,342 – 23,329,458
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.88
Mean single sequence MFE -41.86
Consensus MFE -36.08
Energy contribution -36.48
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.56
Structure conservation index 0.86
SVM decision value 3.11
SVM RNA-class probability 0.998464
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23329342 116 - 27905053
UGGGAGUAAUUUAAAACGCUACUGCUUGUGAAUGCAUUUGAAAUGCUUUUCCACCGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCUCGAAGUGGAGGGCAAAAUGCAUCUGC----
.((.((((...........)))).)).((..((((((((((((....))))....((((((((((((((((((......).))))....))).)))))))))).))))))))..))---- ( -38.50)
>DroSec_CAF1 126618 119 - 1
UGGGAGUAAUUUAAAACGCUCCUGCUUGUGAAUGCAUUUGAAAUGCUUUUCCACUGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA-AUGCAUCUGCCGCA
.((((((..........))))))((..((..((((((((((((....))))....((((((((((((.(((((......).)))).....)).))))))))))))-))))))..)).)). ( -42.80)
>DroSim_CAF1 130971 119 - 1
UGGGAGUAAUUUAAAACGCUCCUGCUUGUGAAUGCAUUUGAAAUGCUUUUGCACUGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA-AUGCAUCUGCCGCA
.((((((..........))))))((..((..((((((((....(((....)))..((((((((((((.(((((......).)))).....)).))))))))))))-))))))..)).)). ( -44.50)
>DroEre_CAF1 132979 118 - 1
UGGGAGUAAUUUAAAACGCUCCUGCUCGUGAAUGCAUUUGAAAUGCUUUUCUACCGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA-AUGCAUCUGCCAG-
.((((((..........)))))).((.((..((((((((((((....))))....((((((((((((.(((((......).)))).....)).))))))))))))-))))))..)).))- ( -41.80)
>DroYak_CAF1 138582 118 - 1
UGGGAGUAAUUUAAAACGCUCCUGCUCGUGAAUGCAUUUGAAAUGCUUUUCUACCGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA-AUGCAUCUGCCAA-
.((((((..........))))))....((..((((((((((((....))))....((((((((((((.(((((......).)))).....)).))))))))))))-))))))..))...- ( -41.70)
>consensus
UGGGAGUAAUUUAAAACGCUCCUGCUUGUGAAUGCAUUUGAAAUGCUUUUCCACCGCCUUCCACUCGAUGCGCUCGAGUGUCGCACCCCACGAAGUGGAGGGCAA_AUGCAUCUGCCAC_
.((((((..........))))))....((..((((((..((((....))))....((((((((((((.(((((......).)))).....)).))))))))))...))))))..)).... (-36.08 = -36.48 +   0.40)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:40 2006