Locus 3530

Sequence ID 3L_DroMel_CAF1
Location 10,353,082 – 10,353,176
Length 94
Max. P 0.944860
window5508 window5509

overview

Window 8

Location 10,353,082 – 10,353,176
Length 94
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 90.49
Mean single sequence MFE -15.14
Consensus MFE -13.58
Energy contribution -13.58
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.32
Structure conservation index 0.90
SVM decision value 0.42
SVM RNA-class probability 0.729387
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10353082 94 + 23771897
AUAAAAUGCAUUAAA---AUAUCGGGGAAAAAAUGAAAAUAAAAGGAGAUGUGGAAAACAAAAGGCGGCCAUGUUGCGGCCAACCGCAGAGUUAUUA
((((..(((......---...(((.........)))........((...(((.....)))...(((.((......)).)))..)))))...)))).. ( -14.90)
>DroSec_CAF1 226930 90 + 1
AUAAAAUGCAUUAAA---AUAUCGGGGAAAAA----AAAGAAAAGGAGAUGUGGAAAACAAAAGGCGGCCAUGUUGCGGCCAACCGCAGAGUUAUUA
((((..(((......---...((.........----...))...((...(((.....)))...(((.((......)).)))..)))))...)))).. ( -14.50)
>DroSim_CAF1 236980 90 + 1
AUAAAAUGCAUUAAA---AUAUCGGGGAAAAA----AAAGAAAAGGAGAUGUGGAAAACAAAAGGCGGCCAUGUUGCGGCCAACCGCAGAGUUAUUA
((((..(((......---...((.........----...))...((...(((.....)))...(((.((......)).)))..)))))...)))).. ( -14.50)
>DroEre_CAF1 241138 89 + 1
AUAAAGUGCAAU---AAAAUAUCG-UGGAAAA----AAUAAAAAGGAGAUGUGGAAAACAAAAGGCGGCCAUGUUGCGGCCAACCGCAGAGUUAUUA
.........(((---((....(((-(((....----.............(((.....)))...(((.((......)).)))..)))).)).))))). ( -16.90)
>DroYak_CAF1 238630 85 + 1
AUAAAAUGCAUU--------AUCGGUGAAAAA----AAAUAAAAGGAGAUGUGGAAAACAAAAGGCGGCCAUGUUGCGGCCAACCGCAGAGUUAUUA
((((..(((.((--------((...(....).----..))))..((...(((.....)))...(((.((......)).)))..)))))...)))).. ( -14.90)
>consensus
AUAAAAUGCAUUAAA___AUAUCGGGGAAAAA____AAAGAAAAGGAGAUGUGGAAAACAAAAGGCGGCCAUGUUGCGGCCAACCGCAGAGUUAUUA
((((..(((........................................(((.....)))...(((.((......)).)))....)))...)))).. (-13.58 = -13.58 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 10,353,082 – 10,353,176
Length 94
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 90.49
Mean single sequence MFE -12.68
Consensus MFE -12.68
Energy contribution -12.68
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 1.00
SVM decision value 1.35
SVM RNA-class probability 0.944860
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10353082 94 - 23771897
UAAUAACUCUGCGGUUGGCCGCAACAUGGCCGCCUUUUGUUUUCCACAUCUCCUUUUAUUUUCAUUUUUUCCCCGAUAU---UUUAAUGCAUUUUAU
.........((((((.(((((.....))))))))...(((.....)))...............................---......)))...... ( -12.70)
>DroSec_CAF1 226930 90 - 1
UAAUAACUCUGCGGUUGGCCGCAACAUGGCCGCCUUUUGUUUUCCACAUCUCCUUUUCUUU----UUUUUCCCCGAUAU---UUUAAUGCAUUUUAU
.........((((((.(((((.....))))))))...(((.....))).............----..............---......)))...... ( -12.70)
>DroSim_CAF1 236980 90 - 1
UAAUAACUCUGCGGUUGGCCGCAACAUGGCCGCCUUUUGUUUUCCACAUCUCCUUUUCUUU----UUUUUCCCCGAUAU---UUUAAUGCAUUUUAU
.........((((((.(((((.....))))))))...(((.....))).............----..............---......)))...... ( -12.70)
>DroEre_CAF1 241138 89 - 1
UAAUAACUCUGCGGUUGGCCGCAACAUGGCCGCCUUUUGUUUUCCACAUCUCCUUUUUAUU----UUUUCCA-CGAUAUUUU---AUUGCACUUUAU
.........((((((.(((((.....))))))))...(((.....))).............----.......-.........---...)))...... ( -12.60)
>DroYak_CAF1 238630 85 - 1
UAAUAACUCUGCGGUUGGCCGCAACAUGGCCGCCUUUUGUUUUCCACAUCUCCUUUUAUUU----UUUUUCACCGAU--------AAUGCAUUUUAU
.........((((((.(((((.....))))))))...(((.....))).............----............--------...)))...... ( -12.70)
>consensus
UAAUAACUCUGCGGUUGGCCGCAACAUGGCCGCCUUUUGUUUUCCACAUCUCCUUUUAUUU____UUUUUCCCCGAUAU___UUUAAUGCAUUUUAU
.........((((((.(((((.....))))))))...(((.....)))........................................)))...... (-12.68 = -12.68 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:19 2006