Locus 4391

Sequence ID 2L_DroMel_CAF1
Location 12,635,609 – 12,635,741
Length 132
Max. P 0.883586
window6918 window6919 window6920

overview

Window 8

Location 12,635,609 – 12,635,720
Length 111
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 80.26
Mean single sequence MFE -39.02
Consensus MFE -26.49
Energy contribution -26.55
Covariance contribution 0.06
Combinations/Pair 1.11
Mean z-score -2.09
Structure conservation index 0.68
SVM decision value 0.93
SVM RNA-class probability 0.883586
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12635609 111 - 22407834
CUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAC--------CCGGAGCUCUUGUCCCUGGCCCCAUCCAUCGGCUUUGUGGCCUUUGAAGUCGCUCGUUGCGGUAGCAA
......(((((((((.....((((.(((((((.((((((.(.(--------(.((..(....)..)).))))))).......))...)))))))..)))).....)))))))))..... ( -41.61)
>DroPse_CAF1 18968 89 - 1
CUUUGUGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAG--------UC----------------------UUCUUCGGCUUUUGUGCCUUUGAAGUCGAUUGUUGCGGUAGCAA
..((((((((((((.....(((((..(.(....))..)))))(--------.(----------------------(((...(((......)))...)))).)....))))))))).))) ( -30.90)
>DroSim_CAF1 17035 111 - 1
CUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAC--------CCGGAGCUCUUGUCCCUGGCCCCAUCCAUCGGCUUUGGGGCCUUUGAAGUCGCUCGUUGCGGUAGCAA
......(((((((((.....((((.(((((.(((..((....)--------)))))))))........(((((((.((...))...)))))))...)))).....)))))))))..... ( -44.90)
>DroEre_CAF1 16746 110 - 1
CUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAC--------CCGGACCUCAUGUCCCUGGCCCCAUCCAUCGGCUUUG-GGCCUUUGAAGUCGCUCGUUGCGGUAGCAA
......(((((((((..........((((((.....((....)--------).((((.....)))).)))))).......((((((..-(....)..))))))..)))))))))..... ( -40.30)
>DroYak_CAF1 17275 118 - 1
CUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGACCCGGAGACCCGGAGCUCUUGUCCCUGGCCCCAUCCAUCGGCUUUG-AGCCUUUGAAGUCGCUCGUUGCGGUAGCAA
......(((((((((..........((((((..(.((((((..((((....))))..)))))).)..)))))).......((((((..-(....)..))))))..)))))))))..... ( -45.50)
>DroPer_CAF1 18995 89 - 1
CUUUGUGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAG--------UC----------------------UUCUUCGGCUUUUGUGCCUUUGAAGUCGAUUGUUGCGGUAGCAA
..((((((((((((.....(((((..(.(....))..)))))(--------.(----------------------(((...(((......)))...)))).)....))))))))).))) ( -30.90)
>consensus
CUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAC________CCGGAGCUCUUGUCCCUGGCCCCAUCCAUCGGCUUUGGGGCCUUUGAAGUCGCUCGUUGCGGUAGCAA
......(((((((((.....((((.(((((...(((((..((...........(((.......))).........))..))))).....)))))..)))).....)))))))))..... (-26.49 = -26.55 +   0.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,635,649 – 12,635,741
Length 92
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 86.78
Mean single sequence MFE -40.82
Consensus MFE -30.59
Energy contribution -30.95
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -2.90
Structure conservation index 0.75
SVM decision value 0.33
SVM RNA-class probability 0.690349
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12635649 92 + 22407834
UGGAUGGGGCCAGGGACAAGAGCUCCGG---------GUCUCCCAACAGUAGCCCAAAAGAUUUGCGUUGCGGCUGGGAGCCAAA--GUCCCUGGCCAGAACC
.((....((((((((((....(((((.(---------(((...((((.((((..(....)..)))))))).)))).)))))....--))))))))))....)) ( -43.10)
>DroSec_CAF1 16666 91 + 1
UG-AUGGGGCCAGGGACAAGAGCUCCGG---------GUCUCCCAACAGUAGUCCAAAAGAUUUGCGUUGCGGCUGGGAGCCAAA--GUCCCUGGGCAGAACC
..-....(.((((((((....(((((.(---------(((...((((.((((((.....)).)))))))).)))).)))))....--)))))))).)...... ( -39.10)
>DroSim_CAF1 17075 92 + 1
UGGAUGGGGCCAGGGACAAGAGCUCCGG---------GUCUCCCAACAGUAGCCCAAAAGAUUUGCGUUGCGGCUGGGAGCCAAA--GUCCCUGGCCAGAACC
.((....((((((((((....(((((.(---------(((...((((.((((..(....)..)))))))).)))).)))))....--))))))))))....)) ( -43.10)
>DroEre_CAF1 16785 92 + 1
UGGAUGGGGCCAGGGACAUGAGGUCCGG---------GUCUCCCAACAGUAGCCCAAAAGAUUUGCGUUGCGGCUGGGAGCCAAA--GUCCCUGGCCAGAACC
.((....((((((((((.((.....))(---------(.((((((.(.(((((.(((.....))).))))).).))))))))...--))))))))))....)) ( -42.80)
>DroYak_CAF1 17314 100 + 1
UGGAUGGGGCCAGGGACAAGAGCUCCGGG-UCUCCGGGUCUCCCAACAGUAGCCCAAAAGAUUUGCGUUGCGGCUGGGAGCCAAA--GUCCCUGGCCAGAGCC
.((....((((((((((....(((((.((-((...(((...)))....(((((.(((.....))).))))))))).)))))....--))))))))))....)) ( -50.10)
>DroAna_CAF1 11479 103 + 1
UGGCUGUGACCAGGGACAGUAGCACCAGCAGCCACAUACAUCCCAACAGUAGCCCAAAAGAUUUGCGUUGCGGCCCAAAGCCAAAGAGUCCCAGGCCAGAAAC
(((((..((((.((((..((.((.......)).)).....))))....(((((.(((.....))).)))))(((.....)))...).)))...)))))..... ( -26.70)
>consensus
UGGAUGGGGCCAGGGACAAGAGCUCCGG_________GUCUCCCAACAGUAGCCCAAAAGAUUUGCGUUGCGGCUGGGAGCCAAA__GUCCCUGGCCAGAACC
.......((((((((((...............................(((((.(((.....))).)))))(((.....))).....))))))))))...... (-30.59 = -30.95 +   0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,635,649 – 12,635,741
Length 92
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 86.78
Mean single sequence MFE -41.72
Consensus MFE -32.56
Energy contribution -33.20
Covariance contribution 0.64
Combinations/Pair 1.15
Mean z-score -3.15
Structure conservation index 0.78
SVM decision value 0.88
SVM RNA-class probability 0.873813
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12635649 92 - 22407834
GGUUCUGGCCAGGGAC--UUUGGCUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAC---------CCGGAGCUCUUGUCCCUGGCCCCAUCCA
((....((((((((((--...((((((.((((.(((..........)))))))......((....)---------).))))))...))))))))))....)). ( -46.00)
>DroSec_CAF1 16666 91 - 1
GGUUCUGCCCAGGGAC--UUUGGCUCCCAGCCGCAACGCAAAUCUUUUGGACUACUGUUGGGAGAC---------CCGGAGCUCUUGUCCCUGGCCCCAU-CA
(((...(((.((((((--...((((((..((......))...(((((..(.(....))..))))).---------..))))))...)))))))))...))-). ( -33.40)
>DroSim_CAF1 17075 92 - 1
GGUUCUGGCCAGGGAC--UUUGGCUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAC---------CCGGAGCUCUUGUCCCUGGCCCCAUCCA
((....((((((((((--...((((((.((((.(((..........)))))))......((....)---------).))))))...))))))))))....)). ( -46.00)
>DroEre_CAF1 16785 92 - 1
GGUUCUGGCCAGGGAC--UUUGGCUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAC---------CCGGACCUCAUGUCCCUGGCCCCAUCCA
((....((((((((((--(((((((((((((.(...(.(((.....))).)...).))))))))..---------)))))......))))))))))....)). ( -40.90)
>DroYak_CAF1 17314 100 - 1
GGCUCUGGCCAGGGAC--UUUGGCUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGACCCGGAGA-CCCGGAGCUCUUGUCCCUGGCCCCAUCCA
((....((((((((((--...((((((..((......)).........(((((.(((..((....))))))).-)))))))))...))))))))))....)). ( -49.10)
>DroAna_CAF1 11479 103 - 1
GUUUCUGGCCUGGGACUCUUUGGCUUUGGGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAUGUAUGUGGCUGCUGGUGCUACUGUCCCUGGUCACAGCCA
(((..(((((.(((((....((((.(..(((((((..(((..(((..(((....)))..))).))).))))))..)..).))))..))))).))))).))).. ( -34.90)
>consensus
GGUUCUGGCCAGGGAC__UUUGGCUCCCAGCCGCAACGCAAAUCUUUUGGGCUACUGUUGGGAGAC_________CCGGAGCUCUUGUCCCUGGCCCCAUCCA
((....((((((((((.....((((((..((......))...(((((..(.(....))..)))))............))))))...))))))))))....)). (-32.56 = -33.20 +   0.64)

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 11:16:45 2006