Locus 8990

Sequence ID 3R_DroMel_CAF1
Location 24,102,425 – 24,102,552
Length 127
Max. P 0.998916
window14411 window14412 window14413

overview

Window 1

Location 24,102,425 – 24,102,521
Length 96
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 84.56
Mean single sequence MFE -32.73
Consensus MFE -23.83
Energy contribution -24.78
Covariance contribution 0.95
Combinations/Pair 1.17
Mean z-score -3.32
Structure conservation index 0.73
SVM decision value 0.81
SVM RNA-class probability 0.857538
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24102425 96 + 27905053
UUGGAAACCCAACCCU-UUUGGCCCCUGGUCAUCAUCCGUCGCUCCAUGUGCGGCAUUUUGCAUAAUAAGUG-ACGCACAUGGAGAAACCAUCACUUC
((((....))))....-..(((((...)))))......((..(((((((((((.(((((........)))))-.)))))))))))..))......... ( -32.20)
>DroSec_CAF1 289483 96 + 1
UUGGAACCCCAACCCU-UUUGGCCCAUGGUCGUCAUCCGUCGCUCCAUGUGCGGCAUUUUGCAUAAUAAGUG-CCGCACAUGGAGAAACCAUCACCCC
((((....))))....-...((((...)))).......((..(((((((((((((((((........)))))-))))))))))))..))......... ( -38.60)
>DroSim_CAF1 289621 96 + 1
UUGGAACCCCAACCCU-UUUGGCCCCUGGUCAUCAUCCGUCACUCCAUGUGCGGCAUUUUGCAUAAUAAGUG-CCGCACAUGGAGAAACCAUCACCUA
.(((............-..(((((...)))))..........(((((((((((((((((........)))))-))))))))))))...)))....... ( -38.40)
>DroEre_CAF1 303230 96 + 1
UUGGAGCCCCAACCCU-UUUGGCCCCUGGUCAUCAUCCGUCGCUCCA-GUGCGGCAUUUUGCAUAAUAAGUGGUCGCACAUGGAGAAAACAUCACCUG
((((....))))....-..(((((...)))))......((..(((((-(((((((((((........)))).))))))).)))))...))........ ( -27.20)
>DroYak_CAF1 303362 97 + 1
UUGGAAGCCCAACCCU-UUUGGCCCCUGGUCAUCAUCCGUCGCUCCAUGUGCGGCAUUUUGCAUAAUAAGUGGUCGCACAUGGAGAAAACAUCACCUC
((((....))))....-..(((((...)))))......((..(((((((((((((((((........)))).)))))))))))))...))........ ( -32.10)
>DroPer_CAF1 311341 89 + 1
UUGGAUUCGACUCCCUCUGUCGCCUCUGGUC-------GUGGGUCCAUGUGCGGCAUUUUGCAUAAUAAGUGG-C-CAAGAGGAGGCAGCAAAGCUUC
..(((......)))..(((((.(((((((((-------(((....)))((((((....)))))).......))-)-).))))).)))))......... ( -27.90)
>consensus
UUGGAACCCCAACCCU_UUUGGCCCCUGGUCAUCAUCCGUCGCUCCAUGUGCGGCAUUUUGCAUAAUAAGUG_CCGCACAUGGAGAAACCAUCACCUC
..((...............(((((...)))))..........(((((((((((((((((........))))).)))))))))))).........)).. (-23.83 = -24.78 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 24,102,454 – 24,102,552
Length 98
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 87.72
Mean single sequence MFE -31.14
Consensus MFE -24.36
Energy contribution -24.60
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -4.65
Structure conservation index 0.78
SVM decision value 3.28
SVM RNA-class probability 0.998916
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24102454 98 + 27905053
CAUCAUCCGUCGCUCCAUGUGCGGCAUUUUGCAUAAUAAGUG-ACGCACAUGGAGAAACCAUCACUUCAAAUGAAUGC----AAAACUAAUUGGUAAAAAAAA
.((((...((..(((((((((((.(((((........)))))-.)))))))))))..))......(((....)))...----.........))))........ ( -26.90)
>DroSec_CAF1 289512 97 + 1
CGUCAUCCGUCGCUCCAUGUGCGGCAUUUUGCAUAAUAAGUG-CCGCACAUGGAGAAACCAUCACCCCAAAUGAAUGA----AAAACUAAUUGGUUAA-AAAA
..((((..((..(((((((((((((((((........)))))-))))))))))))..))..(((.......)))))))----..((((....))))..-.... ( -34.40)
>DroSim_CAF1 289650 97 + 1
CAUCAUCCGUCACUCCAUGUGCGGCAUUUUGCAUAAUAAGUG-CCGCACAUGGAGAAACCAUCACCUAAAAUGAAUGA----AAAACUAAUUGGCUAA-AAAA
........(((((((((((((((((((((........)))))-))))))))))))....(((((.......)).))).----.........))))...-.... ( -34.40)
>DroEre_CAF1 303259 98 + 1
CAUCAUCCGUCGCUCCA-GUGCGGCAUUUUGCAUAAUAAGUGGUCGCACAUGGAGAAAACAUCACCUGAAAUCAAUGC----AAAGCGAAUGGGCUUACAAAA
.....((((((((((((-(((((((((((........)))).))))))).)))).......((....)).........----...))).)))))......... ( -25.30)
>DroYak_CAF1 303391 102 + 1
CAUCAUCCGUCGCUCCAUGUGCGGCAUUUUGCAUAAUAAGUGGUCGCACAUGGAGAAAACAUCACCUCAAAUCAAGGCCUUCAAAG-GAAUUGGUUUACAAAA
........((..(((((((((((((((((........)))).)))))))))))))...))........(((((((..(((....))-)..)))))))...... ( -34.70)
>consensus
CAUCAUCCGUCGCUCCAUGUGCGGCAUUUUGCAUAAUAAGUG_CCGCACAUGGAGAAACCAUCACCUCAAAUGAAUGC____AAAACUAAUUGGUUAA_AAAA
............(((((((((((((((((........))))).))))))))))))................................................ (-24.36 = -24.60 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 24,102,454 – 24,102,552
Length 98
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 87.72
Mean single sequence MFE -29.54
Consensus MFE -20.34
Energy contribution -20.98
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -2.49
Structure conservation index 0.69
SVM decision value 0.70
SVM RNA-class probability 0.827840
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24102454 98 - 27905053
UUUUUUUUACCAAUUAGUUUU----GCAUUCAUUUGAAGUGAUGGUUUCUCCAUGUGCGU-CACUUAUUAUGCAAAAUGCCGCACAUGGAGCGACGGAUGAUG
.........((........(.----.(.(((....))))..)..(((.(((((((((((.-((.((........)).)).))))))))))).)))))...... ( -27.40)
>DroSec_CAF1 289512 97 - 1
UUUU-UUAACCAAUUAGUUUU----UCAUUCAUUUGGGGUGAUGGUUUCUCCAUGUGCGG-CACUUAUUAUGCAAAAUGCCGCACAUGGAGCGACGGAUGACG
....-....((..........----((((((.....))))))..(((.((((((((((((-((.((........)).)))))))))))))).)))))...... ( -36.50)
>DroSim_CAF1 289650 97 - 1
UUUU-UUAGCCAAUUAGUUUU----UCAUUCAUUUUAGGUGAUGGUUUCUCCAUGUGCGG-CACUUAUUAUGCAAAAUGCCGCACAUGGAGUGACGGAUGAUG
....-................----(((((((((......))).(((.((((((((((((-((.((........)).)))))))))))))).))))))))).. ( -34.60)
>DroEre_CAF1 303259 98 - 1
UUUUGUAAGCCCAUUCGCUUU----GCAUUGAUUUCAGGUGAUGUUUUCUCCAUGUGCGACCACUUAUUAUGCAAAAUGCCGCAC-UGGAGCGACGGAUGAUG
...........(((((...(.----.(.(((....))))..).(((..(((((.(((((............((.....)))))))-))))).))))))))... ( -21.50)
>DroYak_CAF1 303391 102 - 1
UUUUGUAAACCAAUUC-CUUUGAAGGCCUUGAUUUGAGGUGAUGUUUUCUCCAUGUGCGACCACUUAUUAUGCAAAAUGCCGCACAUGGAGCGACGGAUGAUG
..............((-(.......(((((.....)))))...(((..(((((((((((............((.....))))))))))))).))))))..... ( -27.70)
>consensus
UUUU_UUAACCAAUUAGUUUU____GCAUUCAUUUGAGGUGAUGGUUUCUCCAUGUGCGA_CACUUAUUAUGCAAAAUGCCGCACAUGGAGCGACGGAUGAUG
.........((...............((((.......))))...(((.(((((((((((.....................))))))))))).)))))...... (-20.34 = -20.98 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:24:22 2006