Locus 842

Sequence ID 3L_DroMel_CAF1
Location 2,554,419 – 2,554,592
Length 173
Max. P 0.998596
window1295 window1296 window1297

overview

Window 5

Location 2,554,419 – 2,554,530
Length 111
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 76.72
Mean single sequence MFE -22.48
Consensus MFE -10.64
Energy contribution -10.84
Covariance contribution 0.20
Combinations/Pair 1.16
Mean z-score -2.97
Structure conservation index 0.47
SVM decision value 3.15
SVM RNA-class probability 0.998596
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2554419 111 + 23771897
AAAAAUCCCAGAGAAAAAAUGCGAGAAAAAUUCGCAACAGACGCUGACAGAAAAAAUAUGAUUUUGGUCUGCAAGC--UGGCUGAUAACAGAAGAGGGAAAAAAA----CUAAAUAU
.....((((..........((((((.....)))))).(((..(((..((((..(((......)))..))))..)))--...)))...........))))......----........ ( -25.50)
>DroSec_CAF1 16351 109 + 1
AAAAAUCCCAGGGAAAAAAUGCGAGAAAAAUUCGCAACAGACGCUGACAGAAAAAAUAUGAUUUUGGUCUGCAAGC--UGGCUGAUAACAGAAGAGGGGGAAAAA---AA---AUAU
.....((((..........((((((.....)))))).(((..(((..((((..(((......)))..))))..)))--...))).............))))....---..---.... ( -25.30)
>DroEre_CAF1 30308 108 + 1
AAAAAUCGCAAUGAAAAAAUGCGAGAAAAAUUUGCAACAGACGGUGACAGAAAAAAUAUGAUUUUAGUCUGCAAGC--UGGCUGAUAACAGAAGAGG--AAA-----AAAUAAAUAU
.....(((((.(.....).)))))......((((...(((.((((..((((..(((......)))..))))...))--)).)))....)))).....--...-----.......... ( -17.40)
>DroYak_CAF1 14665 115 + 1
AAAAAUCGCAAUGAAAAAAUGCGAGAAAAAUUUGCAACAGACGCUGACAGAAAAAAUAUGAUUUUAGCCUGCAAGC--UGGCUGAUAACAGAAGAGAGCAAAAAAUGAAAUAAAUAU
.....(((((.(.....).)))))......(((((..(((...)))............((...((((((.......--.))))))...)).......)))))............... ( -18.50)
>DroAna_CAF1 15471 95 + 1
AGAAAUCCCAGC-AAAAAGUGCCAGCA-AAUUCGCAGCUGAGGCGGACGGAAUAAAAAACAUUUUCCUCCGCGCUCUCCGGCUGAUAAUAGAACUCG--------------------
........((((-....((.((((((.-........))))..(((((.((((...........))))))))))).))...)))).............-------------------- ( -25.70)
>consensus
AAAAAUCCCAGUGAAAAAAUGCGAGAAAAAUUCGCAACAGACGCUGACAGAAAAAAUAUGAUUUUAGUCUGCAAGC__UGGCUGAUAACAGAAGAGGG_AAAAAA___AAUAAAUAU
...................((((((.....)))))).(((..(((..((((..(((......)))..))))..))).....)))................................. (-10.64 = -10.84 +   0.20) 

alignment

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secondary structure

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dotplot

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Window 6

Location 2,554,419 – 2,554,530
Length 111
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 76.72
Mean single sequence MFE -21.09
Consensus MFE -10.02
Energy contribution -9.46
Covariance contribution -0.56
Combinations/Pair 1.27
Mean z-score -2.46
Structure conservation index 0.48
SVM decision value 1.95
SVM RNA-class probability 0.983761
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2554419 111 - 23771897
AUAUUUAG----UUUUUUUCCCUCUUCUGUUAUCAGCCA--GCUUGCAGACCAAAAUCAUAUUUUUUCUGUCAGCGUCUGUUGCGAAUUUUUCUCGCAUUUUUUCUCUGGGAUUUUU
........----......((((...........(((...--(((.(((((..((((......))))))))).)))..))).(((((.......)))))..........))))..... ( -22.30)
>DroSec_CAF1 16351 109 - 1
AUAU---UU---UUUUUCCCCCUCUUCUGUUAUCAGCCA--GCUUGCAGACCAAAAUCAUAUUUUUUCUGUCAGCGUCUGUUGCGAAUUUUUCUCGCAUUUUUUCCCUGGGAUUUUU
....---..---....((((.............(((...--(((.(((((..((((......))))))))).)))..))).(((((.......)))))..........))))..... ( -21.90)
>DroEre_CAF1 30308 108 - 1
AUAUUUAUUU-----UUU--CCUCUUCUGUUAUCAGCCA--GCUUGCAGACUAAAAUCAUAUUUUUUCUGUCACCGUCUGUUGCAAAUUUUUCUCGCAUUUUUUCAUUGCGAUUUUU
..........-----...--......(((....)))...--((..((((((........................)))))).)).........(((((.........)))))..... ( -14.36)
>DroYak_CAF1 14665 115 - 1
AUAUUUAUUUCAUUUUUUGCUCUCUUCUGUUAUCAGCCA--GCUUGCAGGCUAAAAUCAUAUUUUUUCUGUCAGCGUCUGUUGCAAAUUUUUCUCGCAUUUUUUCAUUGCGAUUUUU
...............(((((......(((....)))...--(((.(((((..(((......)))..))))).))).......)))))......(((((.........)))))..... ( -19.00)
>DroAna_CAF1 15471 95 - 1
--------------------CGAGUUCUAUUAUCAGCCGGAGAGCGCGGAGGAAAAUGUUUUUUAUUCCGUCCGCCUCAGCUGCGAAUU-UGCUGGCACUUUUU-GCUGGGAUUUCU
--------------------(((((((......((((....(((.(((((((((...........)))).)))))))).)))).)))))-))(..(((.....)-))..)....... ( -27.90)
>consensus
AUAUUUAUU___UUUUUU_CCCUCUUCUGUUAUCAGCCA__GCUUGCAGACCAAAAUCAUAUUUUUUCUGUCAGCGUCUGUUGCGAAUUUUUCUCGCAUUUUUUCACUGGGAUUUUU
.................................((((....(((.(((((..(((......)))..))))).)))....)))).................................. (-10.02 =  -9.46 +  -0.56) 

alignment

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secondary structure

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dotplot

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Window 7

Location 2,554,495 – 2,554,592
Length 97
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 89.32
Mean single sequence MFE -22.52
Consensus MFE -19.26
Energy contribution -19.70
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.81
Structure conservation index 0.86
SVM decision value 0.82
SVM RNA-class probability 0.859650
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2554495 97 + 23771897
UGGCUGAUAACAGAAGAGGGAAAAAAA----CUAAAUAUUUAAAAGCAAGUCGGAAACUGACGUUGCAUAAGAGGCAAAAAUGCUGUCAAGUGCCUCCCCU
...(((....)))...((((.......----..............((((((((....).))).))))....((((((....((....))..)))))))))) ( -24.00)
>DroSec_CAF1 16427 95 + 1
UGGCUGAUAACAGAAGAGGGGGAAAAA---AA---AUAUUUAAACGCAUGUCGGAAACUGGCGUUGCAUAAGAGGCAAAAAUGCUGUCAAGUGCCUCCCCU
...(((....)))....((((((....---..---.......(((((.....(....)..)))))((((..((((((....)))).))..)))).)))))) ( -24.80)
>DroEre_CAF1 30384 94 + 1
UGGCUGAUAACAGAAGAGG--AAA-----AAAUAAAUAUUUAAAAGCAAGUCGGAAACUGACGUUGCAUAAGAGGCAAAAAUGCUGUCAAGUGCCUCCCCU
...(((....)))...(((--...-----................((((((((....).))).))))....((((((....((....))..)))))).))) ( -20.70)
>DroYak_CAF1 14741 101 + 1
UGGCUGAUAACAGAAGAGAGCAAAAAAUGAAAUAAAUAUUUAAACGCAGGUCGGAAACUGACGUUGCAUAAGAGGCUAAAAUGCUGUCAAGUGCCUCCCCU
.(((.....((((.....(((........((((....))))....((((((((....).))).)))).......)))......)))).....)))...... ( -20.60)
>consensus
UGGCUGAUAACAGAAGAGGG_AAAAAA___AAUAAAUAUUUAAAAGCAAGUCGGAAACUGACGUUGCAUAAGAGGCAAAAAUGCUGUCAAGUGCCUCCCCU
...(((....)))...((((.........................((((((((....).))).))))....(((((......(((....)))))))))))) (-19.26 = -19.70 +   0.44) 

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 09:52:33 2006