Locus 4883

Sequence ID	3L_DroMel_CAF1
Location	13,618,757 – 13,618,979
Length	222
Max. P	0.987161

overview

Window 9

Location	13,618,757 – 13,618,877
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.12
Mean single sequence MFE	-30.68
Consensus MFE	-28.60
Energy contribution	-28.80
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.93
SVM decision value	2.07
SVM RNA-class probability	0.987161
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13618757 120 - 23771897
AUUCGGAUUCAGGUUCAAAUUCAGAUUCCUGACUUGGCAAUAUUUCAAUCAAACUUUUUUUUUGCCACUCUACGGGGCGGCUGUGUAGCCGUCCAAAUGGAUAUUUAUGCUUAUCAUGCU
...((...(((((.((.......))..)))))..((((((.....................)))))).....))((((((((....)))))))).....((((........))))..... ( -29.70)
>DroSec_CAF1 25706 117 - 1
AUUCGGAUUCAGGUUCGAAUUCAGAUUCCUGACUUGGCAAUAUUUCAAUCAAACUUU---UUUGCCACUCUACGGGGCGGCUGUGUAGCCGUCCAAAUGGAUAUUUAUGCUUAUCAUGCU
((((((((....))))))))((((....))))..((((((.................---.)))))).((((..((((((((....))))))))...)))).......((.......)). ( -31.87)
>DroSim_CAF1 34774 117 - 1
AUUCGGAUUCAGGUUCGAAUUCAGAUUCCUGACUUGGCAAUAUUUCAAUCAAACUUU---UUUGCCACUCUACGGGGCGGCUGUGUAGCCGUCCAAAUGGAUAUUUAUGCUUAUCAUGCU
((((((((....))))))))((((....))))..((((((.................---.)))))).((((..((((((((....))))))))...)))).......((.......)). ( -31.87)
>DroEre_CAF1 28483 117 - 1
AUUCGGAUUCAGGCUCAAAUUCAGAUUCCUGACUUGGCAAUAUUUCAAUCAAACUUU---UUUGCCACUCUACGGGGCGGCUGUGUAGCCGUCCAAAUGGAUAUUUAUGCUUAUCAUGCU
.....(((..((((..((((((((....))))..((((((.................---.)))))).((((..((((((((....))))))))...)))).))))..)))))))..... ( -29.57)
>DroYak_CAF1 32805 117 - 1
AUAAGGAUUCAGGUUGAAAUUCAGAUUCCUGACUUGGCAAUAUUUCAAUCAAACUUU---UUUGCCACUCUACGGGGCGGCUGUGUAGCCGUCCAAAUGGAUAUUUAUGCUUAUCAUGCU
(((((.((((((((((.....)))...)))))..((((((.................---.)))))).((((..((((((((....))))))))...)))).....)).)))))...... ( -30.37)
>consensus
AUUCGGAUUCAGGUUCAAAUUCAGAUUCCUGACUUGGCAAUAUUUCAAUCAAACUUU___UUUGCCACUCUACGGGGCGGCUGUGUAGCCGUCCAAAUGGAUAUUUAUGCUUAUCAUGCU
........(((((.((.......))..)))))..((((((.....................)))))).((((..((((((((....))))))))...)))).......((.......)). (-28.60 = -28.80 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	13,618,837 – 13,618,946
Length	109
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	86.26
Mean single sequence MFE	-32.84
Consensus MFE	-24.44
Energy contribution	-25.40
Covariance contribution	0.96
Combinations/Pair	1.04
Mean z-score	-1.78
Structure conservation index	0.74
SVM decision value	0.35
SVM RNA-class probability	0.701616
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13618837 109 - 23771897
AAUCAAUUAAAAUACGUGCCGGGCAUUAGAAGAGUGCGGCGCAUAUACGGC-CGGAGGAUCCGGCUACGGAUUCGGAUUCAGGUUCAAAUUCAGAUUCCUGACUUGGCAA
...............((((((.((.........)).)))))).......((-(((.(((((((....)))))))....(((((.((.......))..))))).))))).. ( -36.50)
>DroSec_CAF1 25783 110 - 1
AAUCAAUUAAAAUACGUGCCGGGCAUUAGAAGAGUGCGGCGCAUGUACGGCCCUGAGGAUCCGGCUACGGAUUCGGAUUCAGGUUCGAAUUCAGAUUCCUGACUUGGCAA
...............((((((.((.........)).)))))).(((.((..((((((((((((....)))))))....)))))..))...((((....))))....))). ( -37.60)
>DroSim_CAF1 34851 110 - 1
AAUCAAUUAAAAUACGUGCCGGGCAUUAGAAGAGUGCGGCGCAUGUACGGCCCUGAGGAUCCGGCUACGGAUUCGGAUUCAGGUUCGAAUUCAGAUUCCUGACUUGGCAA
...............((((((.((.........)).)))))).(((.((..((((((((((((....)))))))....)))))..))...((((....))))....))). ( -37.60)
>DroEre_CAF1 28560 104 - 1
AAUCAAUUAAAAUACGUGCCGGGCAUUAGAAGAGUGCGGCGCAUGGA------UUCGUAUUCGUAUUCGUAUUCGGAUUCAGGCUCAAAUUCAGAUUCCUGACUUGGCAA
...............((((((.((.........)).)))))).((((------((((....((....))....)))))))).((.(((..((((....)))).))))).. ( -29.20)
>DroYak_CAF1 32882 93 - 1
AAUCAAUUAAAAUACGUGCCGGGCAUUAGAAGAGUGCGGCGCAU--------------AUGCG---GCAUAUAAGGAUUCAGGUUGAAAUUCAGAUUCCUGACUUGGCAA
................(((((((..........((((.(((...--------------.))).---))))........((((((((.....)))...)))))))))))). ( -23.30)
>consensus
AAUCAAUUAAAAUACGUGCCGGGCAUUAGAAGAGUGCGGCGCAUGUACGGC_CUGAGGAUCCGGCUACGGAUUCGGAUUCAGGUUCAAAUUCAGAUUCCUGACUUGGCAA
.(((...........((((((.((.........)).))))))..............(((((((....))))))).)))(((((.((.......))..)))))........ (-24.44 = -25.40 +   0.96)

alignment

secondary structure

dotplot

Window 1

Location	13,618,877 – 13,618,979
Length	102
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	78.40
Mean single sequence MFE	-32.85
Consensus MFE	-23.10
Energy contribution	-22.72
Covariance contribution	-0.39
Combinations/Pair	1.14
Mean z-score	-1.30
Structure conservation index	0.70
SVM decision value	0.42
SVM RNA-class probability	0.730166
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13618877 102 + 23771897
CCGUAGCCGGAUCCUCCG-GCCGUAUAUGCGCCGCAC---UCUUCUAAUGCCCGGCACGUAUUUUAAUUGAUUCGUGCCGCACAAGGAGCCGCAGGAGUGGCAU-CA----
.....(((((.....)))-)).........(((((.(---((((((..(((..((((((.(((......))).)))))))))..))))).....)).)))))..-..---- ( -37.00)
>DroPse_CAF1 8628 100 + 1
--CGAGCCGCCUGGCCACGACCA---------CACACUCUUCUUCUAAUGCUUGGCACGUAUUUUAAUUGAUUCGUGCCACACAGGGAGCGGCACCAGCAGCAGGCAGUAC
--...(((((((((((..((...---------.....))..(((((..((..(((((((.(((......))).)))))))..))))))).)))..)))..)).)))..... ( -28.20)
>DroSec_CAF1 25823 103 + 1
CCGUAGCCGGAUCCUCAGGGCCGUACAUGCGCCGCAC---UCUUCUAAUGCCCGGCACGUAUUUUAAUUGAUUCGUGCCGCACAAGGAGCCGCAGGAGUGGCAU-CA----
.....((((..((((...(((.((....)))))((..---.(((((..(((..((((((.(((......))).)))))))))..)))))..)))))).))))..-..---- ( -35.60)
>DroSim_CAF1 34891 103 + 1
CCGUAGCCGGAUCCUCAGGGCCGUACAUGCGCCGCAC---UCUUCUAAUGCCCGGCACGUAUUUUAAUUGAUUCGUGCCGCACAAGGAGCCGCAGGAGUGGCAU-CA----
.....((((..((((...(((.((....)))))((..---.(((((..(((..((((((.(((......))).)))))))))..)))))..)))))).))))..-..---- ( -35.60)
>DroEre_CAF1 28600 97 + 1
ACGAAUACGAAUACGAA------UCCAUGCGCCGCAC---UCUUCUAAUGCCCGGCACGUAUUUUAAUUGAUUCGUGCCGCACAAGGAGCCGCAGGAGUGGCAU-CA----
..............((.------(((.((.((.(((.---........)))..((((((.(((......))).)))))))).)).)))(((((....))))).)-).---- ( -28.80)
>DroYak_CAF1 32922 86 + 1
AUGC---CGCAU--------------AUGCGCCGCAC---UCUUCUAAUGCCCGGCACGUAUUUUAAUUGAUUCGUGCCGCACAAGGAGCCGCAGGAGUGGCAU-CA----
((((---(((..--------------.((((.....(---((((....((..(((((((.(((......))).)))))))..))))))).))))...)))))))-..---- ( -31.90)
>consensus
CCGUAGCCGGAUCCUCAG_GCCGUACAUGCGCCGCAC___UCUUCUAAUGCCCGGCACGUAUUUUAAUUGAUUCGUGCCGCACAAGGAGCCGCAGGAGUGGCAU_CA____
..........................................((((..((..(((((((.(((......))).)))))))..))))))(((((....)))))......... (-23.10 = -22.72 +  -0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:06 2006