Locus 1555

Sequence ID 3L_DroMel_CAF1
Location 4,539,401 – 4,539,507
Length 106
Max. P 0.959508
window2413 window2414

overview

Window 3

Location 4,539,401 – 4,539,507
Length 106
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 88.84
Mean single sequence MFE -38.58
Consensus MFE -29.76
Energy contribution -29.64
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.78
Structure conservation index 0.77
SVM decision value 1.50
SVM RNA-class probability 0.959508
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4539401 106 + 23771897
---GCUGCUGCUUUUACAACAGCUAAGGCUAUACUGCUGCUGCUUUUUGGUCGGUUGGUGCUGUUUUAGCUGCACUGGCAGUGGGUAAAUAUCCAGCGGCGGCCUUUGU
---((((((((((((((..((((((((((..((((...((((((....)).)))).))))..))))))))))(((.....))).))))).....)))))))))...... ( -39.70)
>DroSec_CAF1 116721 100 + 1
---GCUGCUGCUUUUACAACAGCUAAGGCUGUACUGCUGCUGCUUU-UGGUC-----GUGCUGUUUUAGCUGCACUGGCAGUGGGUAAAUAUCCAGCGGCGGCCUUUGU
---((((((((((((((.(((((....))))).(..(((((((...-..)).-----((((.((....)).)))).)))))..)))))).....)))))))))...... ( -40.50)
>DroEre_CAF1 122598 97 + 1
-----UGCUGCUUUUACAACAGCUAAAGCUGAACUGCUGCUGCUUU-G-GUC-----CUGCUGUGUUAGCUGCACUGGCAGUGGGUAAAUAUCCAGCGGCGGCCUUUGU
-----..........((((((((....))))....((((((((...-.-...-----(((((((((.....)))).)))))(((((....)))))))))))))..)))) ( -34.50)
>DroYak_CAF1 120156 103 + 1
GUUGCUGCUGCUUUUACAACAGCUAAAGCUAUACUGCUCCAGCUUU-GGGUC-----UUGCUGGCUUAGCUGCACUGGCAGUGGGUAAAUAUCCAGCGGCGGCCUUUGU
((((((((((..(((((...(((....))).(((((((.(((((..-(((((-----.....))))))))))....))))))).)))))....))))))))))...... ( -39.60)
>consensus
___GCUGCUGCUUUUACAACAGCUAAAGCUAUACUGCUGCUGCUUU_GGGUC_____GUGCUGUUUUAGCUGCACUGGCAGUGGGUAAAUAUCCAGCGGCGGCCUUUGU
...((((((((((((((..((((((((((......)))((.((................)).)).)))))))(((.....))).))))).....)))))))))...... (-29.76 = -29.64 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,539,401 – 4,539,507
Length 106
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 88.84
Mean single sequence MFE -29.15
Consensus MFE -24.67
Energy contribution -24.92
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.85
SVM decision value 0.88
SVM RNA-class probability 0.873692
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4539401 106 - 23771897
ACAAAGGCCGCCGCUGGAUAUUUACCCACUGCCAGUGCAGCUAAAACAGCACCAACCGACCAAAAAGCAGCAGCAGUAUAGCCUUAGCUGUUGUAAAAGCAGCAGC---
...(((((.......((........))(((((...(((.(((.....)))..(....)........)))...)))))...))))).((((((((....))))))))--- ( -27.70)
>DroSec_CAF1 116721 100 - 1
ACAAAGGCCGCCGCUGGAUAUUUACCCACUGCCAGUGCAGCUAAAACAGCAC-----GACCA-AAAGCAGCAGCAGUACAGCCUUAGCUGUUGUAAAAGCAGCAGC---
...(((((.((.(.(((........)))).))..((((.(((.....)))..-----.....-...((....)).)))).))))).((((((((....))))))))--- ( -29.00)
>DroEre_CAF1 122598 97 - 1
ACAAAGGCCGCCGCUGGAUAUUUACCCACUGCCAGUGCAGCUAACACAGCAG-----GAC-C-AAAGCAGCAGCAGUUCAGCUUUAGCUGUUGUAAAAGCAGCA-----
.....((((((.(((((..............))))))).(((.....))).)-----).)-)-((((((((....)))..))))).((((((.....)))))).----- ( -26.84)
>DroYak_CAF1 120156 103 - 1
ACAAAGGCCGCCGCUGGAUAUUUACCCACUGCCAGUGCAGCUAAGCCAGCAA-----GACCC-AAAGCUGGAGCAGUAUAGCUUUAGCUGUUGUAAAAGCAGCAGCAAC
...(((((.((.(((((..............))))))).(((...(((((..-----.....-...))))))))......))))).((((((((....))))))))... ( -33.04)
>consensus
ACAAAGGCCGCCGCUGGAUAUUUACCCACUGCCAGUGCAGCUAAAACAGCAC_____GACCA_AAAGCAGCAGCAGUACAGCCUUAGCUGUUGUAAAAGCAGCAGC___
...(((((.((.(((((..............))))))).(((.....)))................((....))......))))).((((((((....))))))))... (-24.67 = -24.92 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:31 2006