Locus 8988

Sequence ID 3R_DroMel_CAF1
Location 24,099,804 – 24,099,911
Length 107
Max. P 0.701913
window14408 window14409

overview

Window 8

Location 24,099,804 – 24,099,911
Length 107
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 88.71
Mean single sequence MFE -32.48
Consensus MFE -27.04
Energy contribution -26.85
Covariance contribution -0.19
Combinations/Pair 1.17
Mean z-score -1.66
Structure conservation index 0.83
SVM decision value -0.03
SVM RNA-class probability 0.519377
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24099804 107 + 27905053
--U-AUAUCCAAAGGGGGUUGGUAAAACCAGCA---GCGCAUUUUCAACGCAAAUCAAGCGCUGAAAAGUGCACAGCCAAAGUUCCAGAUGAAAA--GCGAAU-GGCGGCGGGGUU---
--.-..((((.......(((((.....))))).---((((.((((((.(((.......))).))))))))))...(((...((((....(....)--..))))-...))).)))).--- ( -30.60)
>DroSec_CAF1 287106 107 + 1
--U-AUAUCCAAAUGGGGUUGGGAAAACCAGCA---GCGCAUUUUCAACGCAAAUCAAGCGCUGAAAAGUGCACAGCCAAAGUUCCAGAUGAGAA--GCGAAU-GGCGGCGGGGCU---
--.-...(((....)))(((((.....))))).---((((.((((((.(((.......))).))))))))))..((((...((((((..((....--.))..)-)).)))..))))--- ( -33.80)
>DroSim_CAF1 287039 107 + 1
--U-AUAUCCAAAGGGGGUUGGGAAAACCAGCA---GCGCAUUUUCAACGCAAAUCAAGCGCUGAAAAGUGCACAGCCAAAGUUCCAGAUGAGAA--GCGAAU-GGCGGCGGGGCU---
--.-...(((....)))(((((.....))))).---((((.((((((.(((.......))).))))))))))..((((...((((((..((....--.))..)-)).)))..))))--- ( -33.40)
>DroEre_CAF1 300672 107 + 1
--U-AUAUCCAAAGGGGGUUGGGAAAACCAGCA---GCGCAUUUUCAACGCAAAUCAAGCGCUGAAAAGUGCACAGCCAAAGUUCCAGAUGAAAA--GCGAAU-GGCGGCGGGGUU---
--.-..((((.......(((((.....))))).---((((.((((((.(((.......))).))))))))))...(((...((((....(....)--..))))-...))).)))).--- ( -31.10)
>DroYak_CAF1 300627 109 + 1
--U-AUAUCUAAAGGGGGUUGGGAAAACCAGCA---GCGCAUUUUCAACGCAAAUCAAGCGCUGAAAAGUGCACAGCCAAAGUUCCAGAUGAAAAUGGCGAAU-GGCGGCGGGGUU---
--.-.........(.(.(((((.....))))).---.).)..(..(..(((...((..(((((....)))))...((((...(((.....)))..))))))..-.)))..)..)..--- ( -31.00)
>DroAna_CAF1 296293 113 + 1
GUUGCUGUCUG-AUGAGGAUGAG-AAGCCAGCAGACGCGCAUUUUCAACGCAAAUCAAGCGCUGAAAAGUGCACACCCAAACUUCCAGAUGAA----GCCAGUCGGUUGGGGGGCUGAG
...(((.(((.-((....)).))-))))((((....((((.((((((.(((.......))).))))))))))...(((...((((.....)))----)((((....))))))))))).. ( -35.00)
>consensus
__U_AUAUCCAAAGGGGGUUGGGAAAACCAGCA___GCGCAUUUUCAACGCAAAUCAAGCGCUGAAAAGUGCACAGCCAAAGUUCCAGAUGAAAA__GCGAAU_GGCGGCGGGGCU___
......((((.......(((((.....)))))....((((.((((((.(((.......))).))))))))))...(((....(((.....)))....((......))))).)))).... (-27.04 = -26.85 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 24,099,804 – 24,099,911
Length 107
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 88.71
Mean single sequence MFE -33.68
Consensus MFE -26.16
Energy contribution -26.52
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -2.76
Structure conservation index 0.78
SVM decision value 0.35
SVM RNA-class probability 0.701913
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24099804 107 - 27905053
---AACCCCGCCGCC-AUUCGC--UUUUCAUCUGGAACUUUGGCUGUGCACUUUUCAGCGCUUGAUUUGCGUUGAAAAUGCGC---UGCUGGUUUUACCAACCCCCUUUGGAUAU-A--
---...((.((.(((-(....(--(........)).....)))).(((((.((((((((((.......)))))))))))))))---.)).)).....((((......))))....-.-- ( -32.00)
>DroSec_CAF1 287106 107 - 1
---AGCCCCGCCGCC-AUUCGC--UUCUCAUCUGGAACUUUGGCUGUGCACUUUUCAGCGCUUGAUUUGCGUUGAAAAUGCGC---UGCUGGUUUUCCCAACCCCAUUUGGAUAU-A--
---....((...((.-....))--.........((((..(..((.(((((.((((((((((.......)))))))))))))))---.))..)..))))...........))....-.-- ( -33.40)
>DroSim_CAF1 287039 107 - 1
---AGCCCCGCCGCC-AUUCGC--UUCUCAUCUGGAACUUUGGCUGUGCACUUUUCAGCGCUUGAUUUGCGUUGAAAAUGCGC---UGCUGGUUUUCCCAACCCCCUUUGGAUAU-A--
---....((...((.-....))--.........((((..(..((.(((((.((((((((((.......)))))))))))))))---.))..)..))))...........))....-.-- ( -33.40)
>DroEre_CAF1 300672 107 - 1
---AACCCCGCCGCC-AUUCGC--UUUUCAUCUGGAACUUUGGCUGUGCACUUUUCAGCGCUUGAUUUGCGUUGAAAAUGCGC---UGCUGGUUUUCCCAACCCCCUUUGGAUAU-A--
---....((...((.-....))--.........((((..(..((.(((((.((((((((((.......)))))))))))))))---.))..)..))))...........))....-.-- ( -33.40)
>DroYak_CAF1 300627 109 - 1
---AACCCCGCCGCC-AUUCGCCAUUUUCAUCUGGAACUUUGGCUGUGCACUUUUCAGCGCUUGAUUUGCGUUGAAAAUGCGC---UGCUGGUUUUCCCAACCCCCUUUAGAUAU-A--
---...((.((.(((-(....(((........))).....)))).(((((.((((((((((.......)))))))))))))))---.)).)).......................-.-- ( -32.10)
>DroAna_CAF1 296293 113 - 1
CUCAGCCCCCCAACCGACUGGC----UUCAUCUGGAAGUUUGGGUGUGCACUUUUCAGCGCUUGAUUUGCGUUGAAAAUGCGCGUCUGCUGGCUU-CUCAUCCUCAU-CAGACAGCAAC
....((..(((((.(..(..(.----.....)..)..).))))).(((((.((((((((((.......)))))))))))))))(((((.(((...-.......))).-))))).))... ( -37.80)
>consensus
___AACCCCGCCGCC_AUUCGC__UUUUCAUCUGGAACUUUGGCUGUGCACUUUUCAGCGCUUGAUUUGCGUUGAAAAUGCGC___UGCUGGUUUUCCCAACCCCCUUUGGAUAU_A__
.................................((((..(..((.(((((.((((((((((.......)))))))))))))))....))..)..))))..................... (-26.16 = -26.52 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:24:18 2006