Locus 6213

Sequence ID 2R_DroMel_CAF1
Location 19,545,662 – 19,545,791
Length 129
Max. P 0.747744
window9950 window9951

overview

Window 0

Location 19,545,662 – 19,545,770
Length 108
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 83.52
Mean single sequence MFE -39.17
Consensus MFE -28.42
Energy contribution -28.90
Covariance contribution 0.48
Combinations/Pair 1.30
Mean z-score -1.76
Structure conservation index 0.73
SVM decision value 0.09
SVM RNA-class probability 0.577940
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19545662 108 + 20766785
--UGGAUCGCGGGAAAGGAAGCGGCUCCAACCGAUCGCAGAAGAAGGUUCCGCUGGGCGGAGAACUCUUUGCGCUCGGC---AAGAGCGUACGCGAUGACUCCAAGUCGAAGA
--...((((((.....(....).((((...((((.((((((.((...((((((...))))))...)))))))).)))).---..))))...))))))(((.....)))..... ( -40.30)
>DroSec_CAF1 2 108 + 1
--UGGAUCGCGGGAAAGGAAGCGGCUCCAACCGAUCGCAGAAGAAGGUUCCGCUGGGCGGAGAACUCUUUGCGCUCGGC---AAGAGCGUACGCGAUGAUUCCAAGUCGAAGA
--(((((((((.....(....).((((...((((.((((((.((...((((((...))))))...)))))))).)))).---..))))...)))))....))))......... ( -39.70)
>DroEre_CAF1 3 108 + 1
--UGGAUCGCGGGAAAGGAAGCGGGUCGAACCGGUCGCAAAAGAAGGUUCCGCUGGGCGGAGAACUCUUUGCGCUCGGC---AAGAGCGUUCGCGAUGACUCCAAGUCAAAGA
--...((((((((........(.(((.(((((..((......)).))))).))).)((((((....))))))((((...---..)))).))))))))(((.....)))..... ( -38.40)
>DroWil_CAF1 12300 113 + 1
UAUGGAGCGCUCCAAAAGUAGCGGCUCAAAUAGGGGCCAAAAGAAAGUGCCGCUUGGUGGCGAACUCUUUGCACUGGGCACAAAAAGUGUUCGCGAUGAUUCAAAAUCCAAAA
..((((((........(((.(((((((......))))).(((((...((((((...))))))...))))))))))((((((.....))))))))((....))....))))... ( -36.10)
>DroYak_CAF1 2 108 + 1
--UGGAUCGCGGGAAAGGAAGCGGAUCCAACCGAUCGCAGAAGAAGGUUCCGCUGGGCGGAGAACUCUUCGCGCUCGGC---AAGAGCGUACGCGAUGACUCCAAAUCAAAGA
--((((((.(((....(((......)))..)))(((((.(((((...((((((...))))))...)))))((((((...---..))))))..))))))).))))......... ( -41.60)
>DroAna_CAF1 3 111 + 1
--UGGAUCGCGGUAAAGGCGGCGGAUCCAAUAGAUCCCAGAAAAAAGUGCCUCUGGGCGGCGAACUCUUUGCCCUCGGCACCAAAAGCGUCCGCGAUGACUCCAAGUCCAAGA
--((((((((((...(.((.(.(((((.....))))))........(((((...((((((.(....).))))))..))))).....)).)))))))....))))......... ( -38.90)
>consensus
__UGGAUCGCGGGAAAGGAAGCGGCUCCAACCGAUCGCAGAAGAAGGUUCCGCUGGGCGGAGAACUCUUUGCGCUCGGC___AAGAGCGUACGCGAUGACUCCAAGUCAAAGA
..((((((((..........)).))))))....(((((.(((((...((((((...))))))...)))))((((((........))))))..)))))(((.....)))..... (-28.42 = -28.90 +   0.48)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,545,693 – 19,545,791
Length 98
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 82.12
Mean single sequence MFE -33.62
Consensus MFE -24.04
Energy contribution -23.43
Covariance contribution -0.61
Combinations/Pair 1.39
Mean z-score -1.91
Structure conservation index 0.72
SVM decision value 0.47
SVM RNA-class probability 0.747744
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19545693 98 + 20766785
AUCGCAGAAGAAGGUUCCGCUGGGCGGAGAACUCUUUGCGCUCGGC---AAGAGCGUACGCGAUGACUCCAAGUCGAAGAUCCUGCCCAUUAAGGGC------AUGU
(((((.(((((...((((((...))))))...)))))((((((...---..))))))..)))))(((.....)))........(((((.....))))------)... ( -38.60)
>DroSec_CAF1 33 98 + 1
AUCGCAGAAGAAGGUUCCGCUGGGCGGAGAACUCUUUGCGCUCGGC---AAGAGCGUACGCGAUGAUUCCAAGUCGAAGAUCCUGCCCAUUAAGGGC------AUGU
(((((.(((((...((((((...))))))...)))))((((((...---..))))))..)))))(((.....)))........(((((.....))))------)... ( -36.70)
>DroEre_CAF1 34 98 + 1
GUCGCAAAAGAAGGUUCCGCUGGGCGGAGAACUCUUUGCGCUCGGC---AAGAGCGUUCGCGAUGACUCCAAGUCAAAGAUCCUGCCCAUUAAGGGC------AUAU
(((((....(((.((((.((((((((.(((....))).))))))))---..)))).))))))))(((.....)))........(((((.....))))------)... ( -38.40)
>DroWil_CAF1 12333 107 + 1
GGGCCAAAAGAAAGUGCCGCUUGGUGGCGAACUCUUUGCACUGGGCACAAAAAGUGUUCGCGAUGAUUCAAAAUCCAAAAUUUUGCCCAUUAAGACAACAAUAACGG
((((.((((......(((((...)))))(((.((.((((...((((((.....)))))))))).)))))...........))))))))................... ( -26.80)
>DroYak_CAF1 33 98 + 1
AUCGCAGAAGAAGGUUCCGCUGGGCGGAGAACUCUUCGCGCUCGGC---AAGAGCGUACGCGAUGACUCCAAAUCAAAGAUCCUGCCCAUUAAGGGC------AUGU
(((((.(((((...((((((...))))))...)))))((((((...---..))))))..)))))...................(((((.....))))------)... ( -38.80)
>DroAna_CAF1 34 101 + 1
AUCCCAGAAAAAAGUGCCUCUGGGCGGCGAACUCUUUGCCCUCGGCACCAAAAGCGUCCGCGAUGACUCCAAGUCCAAGAUACUGCCCAUAAAGUCC------AUAU
....(((......(((((...((((((.(....).))))))..))))).....((....))...(((.....))).......)))............------.... ( -22.40)
>consensus
AUCGCAGAAGAAGGUUCCGCUGGGCGGAGAACUCUUUGCGCUCGGC___AAGAGCGUACGCGAUGACUCCAAGUCAAAGAUCCUGCCCAUUAAGGGC______AUGU
(((((.(((((...((((((...))))))...)))))((((((........))))))..)))))(((.....)))......(((........)))............ (-24.04 = -23.43 +  -0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:43 2006