Locus 5748

Sequence ID 2L_DroMel_CAF1
Location 16,372,258 – 16,372,407
Length 149
Max. P 0.973107
window9104 window9105

overview

Window 4

Location 16,372,258 – 16,372,373
Length 115
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 79.14
Mean single sequence MFE -37.10
Consensus MFE -24.21
Energy contribution -24.65
Covariance contribution 0.44
Combinations/Pair 1.10
Mean z-score -2.35
Structure conservation index 0.65
SVM decision value 1.70
SVM RNA-class probability 0.973107
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16372258 115 - 22407834
UCUACAUGCCGCGUGGCUCUAAUGGGCCAACUUGUAAGCCUCCACUGCUGCCCCGAGGGCAGUACUUCCCGCGA-CAAUCGCGC-CCCAAUACUCUGGGAAUCCCCAAACCUGAAAU
.........((((((((((....))))))..((((..((......((((((((...))))))))......)).)-))).)))).-((((......)))).................. ( -34.40)
>DroSim_CAF1 47531 115 - 1
UCUACAAGGCGCGUGGCUCUAAUGGGCCAACUUGUAAGCCUCCACUGCUGCCCCGAGGGCAGUACUUCCCGCGA-CAAUCCCGC-CCCAAUACUCUGGGAAUCCCCAAACCUGAAAU
.......((.(((((((((....))))))..((((..((......((((((((...))))))))......)).)-)))...)))-.)).......((((....)))).......... ( -36.00)
>DroEre_CAF1 47781 87 - 1
UCCACCAGGCGCGUGGCCCUAAUGGGCCAACUUGUAAGCCUGCACUGCUGCC-CGAGGGCAGUA----------------------------CUCUCGGAAUCCACG-ACAUGGAAU
(((..((((((((((((((....))))))...)))..)))))...(((((((-....)))))))----------------------------.....))).((((..-...)))).. ( -37.90)
>DroYak_CAF1 47946 116 - 1
UCUACAAGGCGCGUGGCUCUAAUGGGCCAACUUGUAAGCCUCCAAUGCUGCCCCGAGGGCAGUACUUCCCGCGUCCAAUACCGCGCCCAGUACUCUCCGAAUUCCCA-ACGUGGAAU
..(((..((((((((((((....))))))..(((...((......((((((((...))))))))......))...)))...))))))..)))........(((((..-....))))) ( -40.10)
>consensus
UCUACAAGGCGCGUGGCUCUAAUGGGCCAACUUGUAAGCCUCCACUGCUGCCCCGAGGGCAGUACUUCCCGCGA_CAAUCCCGC_CCCAAUACUCUCGGAAUCCCCA_ACCUGAAAU
((((((((.....((((((....)))))).)))))..........(((((((.....))))))).................................)))................. (-24.21 = -24.65 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,372,297 – 16,372,407
Length 110
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 77.13
Mean single sequence MFE -31.41
Consensus MFE -18.74
Energy contribution -20.10
Covariance contribution 1.36
Combinations/Pair 1.05
Mean z-score -1.52
Structure conservation index 0.60
SVM decision value 0.23
SVM RNA-class probability 0.644200
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16372297 110 - 22407834
CCUUGGCCCCUCCCAAAAUCCACAAA------AGAGCGACUCUACAUGCCGCGUGGCUCUAAUGGGCCAACUUGUAAGCCUCCACUGCUGCCCCGAGGGCAGUACU-UCCCGCGA-CA
..(((((((.................------(((((.((.(........).)).)))))...))))))).......((......((((((((...))))))))..-....))..-.. ( -32.35)
>DroPse_CAF1 41511 91 - 1
-------------CACCGCCCACAAA------AGA--CACUCU--CAGACACG-GCCUCUAAUGGGCCAACUUGUAAGCCUCCAAUGCUGCCCCGAGGGCAGUACUCUCCCGCGU---
-------------...(((.......------.((--..((..--(((....(-((((.....)))))...)))..))..))...((((((((...)))))))).......))).--- ( -24.50)
>DroSim_CAF1 47570 110 - 1
CCUUGGCCCCUCCCAAAAUCCACAAA------AGAGCGACUCUACAAGGCGCGUGGCUCUAAUGGGCCAACUUGUAAGCCUCCACUGCUGCCCCGAGGGCAGUACU-UCCCGCGA-CA
..((((......))))..........------...(((....((((((.....((((((....)))))).)))))).........((((((((...))))))))..-...)))..-.. ( -33.90)
>DroEre_CAF1 47805 97 - 1
CAUUGGCCCCACCCAAAGUCCACAAA------AGAGCGACUCCACCAGGCGCGUGGCCCUAAUGGGCCAACUUGUAAGCCUGCACUGCUGCC-CGAGGGCAGUA--------------
..((((......))))(((((.....------...).))))....((((((((((((((....))))))...)))..)))))...(((((((-....)))))))-------------- ( -35.30)
>DroYak_CAF1 47985 117 - 1
CCUUGGCCCCUCCCAAAGUCCACAAGCGACACAGAGCGACUCUACAAGGCGCGUGGCUCUAAUGGGCCAACUUGUAAGCCUCCAAUGCUGCCCCGAGGGCAGUACU-UCCCGCGUCCA
..(((((((........((((....).)))..(((((.((.(........).)).)))))...))))))).......((......((((((((...))))))))..-....))..... ( -37.90)
>DroPer_CAF1 42893 91 - 1
-------------CACCGCCCACAAA------AGA--CACUCU--CAGACACG-GCCUCUAAUGGGCCAACUUGUAAGCCUCCAAUGCUGCCCCGAGGGCAGUACUCUCCCGCGU---
-------------...(((.......------.((--..((..--(((....(-((((.....)))))...)))..))..))...((((((((...)))))))).......))).--- ( -24.50)
>consensus
CCUUGGCCCCUCCCAAAGUCCACAAA______AGAGCGACUCUACAAGGCGCGUGGCUCUAAUGGGCCAACUUGUAAGCCUCCAAUGCUGCCCCGAGGGCAGUACU_UCCCGCGU___
.....................((((..........(((.((.....)).)))..(((((....)))))...))))..........(((((((.....))))))).............. (-18.74 = -20.10 +   1.36)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:44 2006