Locus 3863

Sequence ID X_DroMel_CAF1
Location 10,294,498 – 10,294,596
Length 98
Max. P 0.712605
window6354 window6355

overview

Window 4

Location 10,294,498 – 10,294,596
Length 98
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.22
Mean single sequence MFE -23.16
Consensus MFE -13.81
Energy contribution -13.75
Covariance contribution -0.06
Combinations/Pair 1.12
Mean z-score -2.10
Structure conservation index 0.60
SVM decision value 0.38
SVM RNA-class probability 0.712605
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10294498 98 + 22224390
UCCUUCCAUUUUUGGCAUUGAGCCGGCUUAAGUAUGCCAUACCUGCUUGAUUUUCAUUUUCAUUUUGAU------------------UUUGAUGCCGGCA----CAUUCCAUUUUGGUGC
.....(((....(((...((.(((((((((((((.(.....).)))))))...(((...((.....)).------------------..))).)))))).----))..)))...)))... ( -25.40)
>DroSec_CAF1 34979 101 + 1
UCCUUCCAUUUUCGG-AUUGAGCCGGCUUAAGUAUGCCAUACCUGCUUGAUUUUCAUUUUCAUUUUGAU------------------UUUGAUGCCGGCAUUUCCAUUCCAUUUUGGUGC
((..(((......))-)..))(((((((((((((.(.....).)))))))...(((...((.....)).------------------..))).))))))....(((........)))... ( -24.20)
>DroEre_CAF1 21677 109 + 1
UCCUUCCAUUUUCGC-AUUGAGCCGGCUUAAGUGUGCCAUACCUGCUUGAUUCUCAUUUUGAUUUUCAUUUUGAUUUU------GAUUUUGAUGCCAGCA----CAUUCCAUUUUGCUGC
.............((-((..((..(((........)))...............(((...((.....))...)))....------...))..))))(((((----.(......).))))). ( -17.60)
>DroYak_CAF1 22548 115 + 1
UCCUUCCAUUUUCGC-AUUGAGCCGGCUUAAGUAUGGCAUACCUGCUUGAUUUUGAUUUUCAUUUUGAUUUUGAUUUUCAUUUGGGUUCCGAUGCCAGCA----CAUUCCAUUUUGGUGC
.............((-((..((..((........((((((....(((..(...(((...(((.........)))...))).)..)))....))))))...----....))..))..)))) ( -25.46)
>consensus
UCCUUCCAUUUUCGC_AUUGAGCCGGCUUAAGUAUGCCAUACCUGCUUGAUUUUCAUUUUCAUUUUGAU__________________UUUGAUGCCAGCA____CAUUCCAUUUUGGUGC
.....................(((((((((((((.(.....).))))))).........((.....)).........................))))))..................... (-13.81 = -13.75 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 10,294,498 – 10,294,596
Length 98
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.22
Mean single sequence MFE -20.98
Consensus MFE -13.77
Energy contribution -13.40
Covariance contribution -0.37
Combinations/Pair 1.15
Mean z-score -1.69
Structure conservation index 0.66
SVM decision value 0.13
SVM RNA-class probability 0.598641
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10294498 98 - 22224390
GCACCAAAAUGGAAUG----UGCCGGCAUCAAA------------------AUCAAAAUGAAAAUGAAAAUCAAGCAGGUAUGGCAUACUUAAGCCGGCUCAAUGCCAAAAAUGGAAGGA
...(((...(((..((----.((((((.(((..------------------.((.....))...))).........((((((...))))))..)))))).))...)))....)))..... ( -23.80)
>DroSec_CAF1 34979 101 - 1
GCACCAAAAUGGAAUGGAAAUGCCGGCAUCAAA------------------AUCAAAAUGAAAAUGAAAAUCAAGCAGGUAUGGCAUACUUAAGCCGGCUCAAU-CCGAAAAUGGAAGGA
...(((...((((.(((....((((((.(((..------------------.((.....))...))).........((((((...))))))..))))))))).)-)))....)))..... ( -22.80)
>DroEre_CAF1 21677 109 - 1
GCAGCAAAAUGGAAUG----UGCUGGCAUCAAAAUC------AAAAUCAAAAUGAAAAUCAAAAUGAGAAUCAAGCAGGUAUGGCACACUUAAGCCGGCUCAAU-GCGAAAAUGGAAGGA
((((((........))----)((((((.........------..........(((...((.....))...))).((.......))........))))))....)-))............. ( -17.30)
>DroYak_CAF1 22548 115 - 1
GCACCAAAAUGGAAUG----UGCUGGCAUCGGAACCCAAAUGAAAAUCAAAAUCAAAAUGAAAAUCAAAAUCAAGCAGGUAUGCCAUACUUAAGCCGGCUCAAU-GCGAAAAUGGAAGGA
(((((.....))..((----.((((((.............(((...(((.........)))...))).......(((....))).........)))))).)).)-))............. ( -20.00)
>consensus
GCACCAAAAUGGAAUG____UGCCGGCAUCAAA__________________AUCAAAAUGAAAAUGAAAAUCAAGCAGGUAUGGCAUACUUAAGCCGGCUCAAU_CCGAAAAUGGAAGGA
.....................((((((.........................((.....))...............(((((.....)))))..))))))..................... (-13.77 = -13.40 +  -0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:33 2006