Locus 1936

Sequence ID 3R_DroMel_CAF1
Location 5,466,879 – 5,466,993
Length 114
Max. P 0.998743
window3183 window3184

overview

Window 3

Location 5,466,879 – 5,466,970
Length 91
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 83.22
Mean single sequence MFE -26.04
Consensus MFE -19.08
Energy contribution -19.32
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.73
SVM decision value 1.41
SVM RNA-class probability 0.951354
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5466879 91 - 27905053
UCCCAUUUGAUUAGGCCGUAAAA--AAAUCAGCACAAAAGGCCAAUCAUUUGGGAAUCUGCAGCUCAGGGGUGG-----AGCAAAGAAAAUUACCAGG
(((((..(((((.((((......--..............)))))))))..))))).(((...((((.......)-----)))..)))........... ( -27.15)
>DroSec_CAF1 6971 97 - 1
UCCCAUUUGAUUAGGCCGUAAAAA-AAAUCAGCACAAAAGGCCAAUAAUUUGGGAAUCUGCAGCGCAGGGGAGGUGGGUGGCAAAGAAAAUUACCAGG
(((((....(((.((((.......-..............)))))))....))))).(((((...)))))...(((((.............)))))... ( -21.72)
>DroEre_CAF1 6213 88 - 1
UCCCAUUUGAUUAGGCCGUAAAA--AAAUCAGCACAAAAGGCCAAUCAUUUGGGAAUCUGU--------GGCCCGGGGGAGCAAAGAAAAUUACAAGG
(((((..(((((.((((......--..............)))))))))..))))).(((.(--------(.((....))..)).)))........... ( -25.85)
>DroYak_CAF1 5664 98 - 1
UCCCAUUUGAUUGGGCCGUAAAAAGAAAUCAGCACAAAAGGCCAAUCAUUUGGGAAUCUGGCGACCAGGCGCCCAGGGGAGCAAACGAAAUUACAAGG
(((((..(((((((.((......................)))))))))..)))))..((((...))))((.((....)).))................ ( -29.45)
>consensus
UCCCAUUUGAUUAGGCCGUAAAA__AAAUCAGCACAAAAGGCCAAUCAUUUGGGAAUCUGCAGC_CAGGGGCCC_GGGGAGCAAAGAAAAUUACAAGG
(((((..(((((.((((......................)))))))))..)))))........................................... (-19.08 = -19.32 +   0.25)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 4

Location 5,466,900 – 5,466,993
Length 93
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 64.70
Mean single sequence MFE -31.27
Consensus MFE -14.46
Energy contribution -16.78
Covariance contribution 2.32
Combinations/Pair 1.11
Mean z-score -3.04
Structure conservation index 0.46
SVM decision value 3.21
SVM RNA-class probability 0.998743
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5466900 93 - 27905053
C-----------------UGGCCGCUUUAAAGGCCGUAAAUCCCAUUUGAUU-AGGCCGUAAAA---AAAUCAGCACAAAAGGCCAAUCAUUUGGGAAUCUGC------AGCUCAGGGGU
.-----------------.((((........))))(((..(((((..(((((-.((((......---..............)))))))))..)))))...)))------.(((....))) ( -30.85)
>DroSec_CAF1 6997 109 - 1
CCUCUGGCUG--CCUGACUGGCCGCUUUAAAGGCCGUAAAUCCCAUUUGAUU-AGGCCGUAAAAA--AAAUCAGCACAAAAGGCCAAUAAUUUGGGAAUCUGC------AGCGCAGGGGA
((((((((((--(..((..((((........)))).....(((((....(((-.((((.......--..............)))))))....))))).)).))------))).)))))). ( -42.80)
>DroEre_CAF1 6239 81 - 1
C---------------------CGCUUUAAAGGCCGUAAAUCCCAUUUGAUU-AGGCCGUAAAA---AAAUCAGCACAAAAGGCCAAUCAUUUGGGAAUCUGU--------------GGC
.---------------------..........((((((..(((((..(((((-.((((......---..............)))))))))..)))))...)))--------------))) ( -24.35)
>DroYak_CAF1 5690 111 - 1
CCUCUGGUUGUGUCUUAC-GGCCGCUUUAAAGGCCGUAAAUCCCAUUUGAUU-GGGCCGUAAAAAG-AAAUCAGCACAAAAGGCCAAUCAUUUGGGAAUCUGG------CGACCAGGCGC
..(((((((((...((((-((((........)))))))).(((((..(((((-((.((........-..............)))))))))..))))).....)------))))))))... ( -47.05)
>DroAna_CAF1 10104 92 - 1
A---------------------UGCUCUCGUCGGCAUAAAUCAGAUUUUAGUAAUGCCAUAAAACGGAAAUU-----UCAAGGUCAACCAAUUCGUAAAGUAAAUCCCCAGGACAAU--A
.---------------------.......((((((((................))))).....(((((....-----))..((....))....)))...............)))...--. ( -11.29)
>consensus
C__________________GGCCGCUUUAAAGGCCGUAAAUCCCAUUUGAUU_AGGCCGUAAAA___AAAUCAGCACAAAAGGCCAAUCAUUUGGGAAUCUGC______AGC_CAGGGGA
...................((((........)))).....(((((..(((((..((((.......................)))))))))..)))))....................... (-14.46 = -16.78 +   2.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:18 2006