Locus 7821

Sequence ID 3L_DroMel_CAF1
Location 20,922,598 – 20,922,716
Length 118
Max. P 0.790394
window12732 window12733

overview

Window 2

Location 20,922,598 – 20,922,694
Length 96
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 82.03
Mean single sequence MFE -26.38
Consensus MFE -19.29
Energy contribution -19.68
Covariance contribution 0.39
Combinations/Pair 1.10
Mean z-score -1.98
Structure conservation index 0.73
SVM decision value 0.58
SVM RNA-class probability 0.790394
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20922598 96 + 23771897
----------ACG-UCGGACAUGGCCGAAAGCCGCUGGC-GCGCAUUGUCCACUCUCUGUGGGCCU-UUUUGCUUUAUUAUAGCAGCGCUUAUACAGAUUAGAAUAAAU
----------..(-((((....((.(....))).)))))-((((...((((((.....))))))..-...((((.......)))))))).................... ( -29.60)
>DroVir_CAF1 207867 97 + 1
-------AGAACU-GCAAGCCUGGCCAAGAGCCGCUGGC-CAGCAUUGUCCACU--CAGUGGGCAC-UUUUGCUUUAUUAUAGCCAUGCUUAUACAGAUUAGAAUAAAU
-------....((-(.((((.((((...(.(((...)))-)((((.(((((((.--..))))))).-...))))........)))).))))...)))............ ( -26.80)
>DroGri_CAF1 189436 87 + 1
------------------ACUUGGCCAAAAGCCGCUGGC-CAGCAUUGUCCACU--CUGUGUGCAC-UUUUGCUUUAUUAUAGCAAUGCUUAUACAGAUUAGAAUAAAU
------------------..(((((((........))))-)))..........(--(((((((((.-..(((((.......))))))))..)))))))........... ( -22.60)
>DroWil_CAF1 230107 97 + 1
----------GCUUUUGGACAUGACCAAAAGCCGCUGGCCAAGCAUUGUCCACU--CCGUGGGCCUCUUUUGCUUUAUUAUAGCAACGCUUAUACAGAUUAGAAUAAAU
----------((((((((......))))))))..(((...((((...((((((.--..)))))).....(((((.......))))).))))...)))............ ( -28.10)
>DroMoj_CAF1 199172 104 + 1
AACAAGUAGAACU-GAAAAGCUGGUCAAAAGCCGCUGGC-CAGCAUUGUCCACU--CAGUGGGCAC-UUUUGCUUUAUUAUAGCAAUGCUUAUACAGAUUAGAAUAAAU
...(((((.....-.....((((((((........))))-))))..(((((((.--..))))))).-..(((((.......)))))))))).................. ( -28.30)
>DroPer_CAF1 187754 94 + 1
----------GCC-UCGGACAUGGCCAAAAGCCGCUGGC-GAGCAUUGUCCACU--CCGUGGGCUC-UUUUGCUUUAUUAUAGCAACGCUUAUACAGAUUAGAAUAAAU
----------...-(((((((.(((.....)))(((...-.)))..))))).((--..((((((..-..(((((.......))))).))))))..))....))...... ( -22.90)
>consensus
__________ACU_UCGGACAUGGCCAAAAGCCGCUGGC_CAGCAUUGUCCACU__CAGUGGGCAC_UUUUGCUUUAUUAUAGCAACGCUUAUACAGAUUAGAAUAAAU
......................(((.....))).(((....(((...((((((.....)))))).....(((((.......))))).)))....)))............ (-19.29 = -19.68 +   0.39)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,922,626 – 20,922,716
Length 90
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 77.49
Mean single sequence MFE -19.22
Consensus MFE -13.21
Energy contribution -13.49
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -1.31
Structure conservation index 0.69
SVM decision value 0.47
SVM RNA-class probability 0.750720
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20922626 90 + 23771897
GCGCAUUGUCCACUC-----------UCUGUGGGCCU-UUUUGCUUUAUUAUAGCAGCGCUUAUACAGAUUAGAAUAAAUCAACUUGUCC-CCCGCGC-AAC----GA
((((...((((((..-----------...))))))..-..(((((.......)))))..........((((......)))).........-...))))-...----.. ( -21.40)
>DroVir_CAF1 207898 81 + 1
CAGCAUUGUCCACU-------------CAGUGGGCAC-UUUUGCUUUAUUAUAGCCAUGCUUAUACAGAUUAGAAUAAAUCAACUUGCGCCCUG-C------------
.((((((((((((.-------------..))))))).-....(((.......))).)))))......((((......)))).............-.------------ ( -14.70)
>DroGri_CAF1 189457 81 + 1
CAGCAUUGUCCACU-------------CUGUGUGCAC-UUUUGCUUUAUUAUAGCAAUGCUUAUACAGAUUAGAAUAAAUCAACUUGCCCCCAC-C------------
..(((........(-------------(((((((((.-..(((((.......))))))))..)))))))...((.....))....)))......-.------------ ( -14.00)
>DroWil_CAF1 230137 92 + 1
AAGCAUUGUCCACU-------------CCGUGGGCCUCUUUUGCUUUAUUAUAGCAACGCUUAUACAGAUUAGAAUAAAUCAACUUGGGCCCCAAA---AACGGUCGC
((((...((((((.-------------..)))))).....(((((.......))))).)))).....((((......))))......((((.....---...)))).. ( -20.00)
>DroMoj_CAF1 199210 81 + 1
CAGCAUUGUCCACU-------------CAGUGGGCAC-UUUUGCUUUAUUAUAGCAAUGCUUAUACAGAUUAGAAUAAAUCAACUGGCCCCCUC-U------------
.((((.(((((((.-------------..))))))).-..(((((.......)))))))))......((((......)))).............-.------------ ( -16.60)
>DroAna_CAF1 175801 103 + 1
GAGCAUUGUCCACCCAAUGGACCCAGUCUGUGGGCGC-UUUUGCUUUAUUAUAGCAGCGCUUAUACAGAUUAGAAUAAAUCAACUUGUCCCCCCGCUAGGAG----GA
(..((..(((((.....)))))..(((((((((((((-(...(((.......)))))))))..))))))))..............))..)((((....)).)----). ( -28.60)
>consensus
CAGCAUUGUCCACU_____________CUGUGGGCAC_UUUUGCUUUAUUAUAGCAACGCUUAUACAGAUUAGAAUAAAUCAACUUGCCCCCCC_C____________
.(((...((((((................)))))).....(((((.......))))).)))......((((......))))........................... (-13.21 = -13.49 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:52 2006