Locus 8055

Sequence ID	3R_DroMel_CAF1
Location	21,635,747 – 21,635,963
Length	216
Max. P	0.997400

overview

Window 6

Location	21,635,747 – 21,635,867
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-27.48
Consensus MFE	-27.04
Energy contribution	-27.12
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.51
Structure conservation index	0.98
SVM decision value	1.73
SVM RNA-class probability	0.974309
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21635747 120 + 27905053
CAUUUCGAUUGCGGCUCGGCUGUUGCUAUAUCGUCCUGUUUAUGCCUGAUUAAAGUCAAACAACAAACAUAUUCUGAGCUGCAUUUACCAGACAAUCGUAUAAACAUAUACACAUGUGGU
......((.(((((((((((....))).........(((((.((..((((....))))..))..)))))......)))))))).))((((.(.....(((((....)))))...).)))) ( -25.20)
>DroSec_CAF1 125076 120 + 1
CAUUUCGAUUGCGGCUCGGCUGUUGCCCUAUCGUCCUGUUUAUGCCUGAUUAAAGUCAAACAACAAACAUAUUCUGAGCUGCAUUUACCAGACAAUCGUAUAAACAUAUACACUUGUGGU
......((.(((((((((((....))).........(((((.((..((((....))))..))..)))))......)))))))).))(((..((((..(((((....)))))..))))))) ( -28.30)
>DroSim_CAF1 121684 120 + 1
CAUUUCGAUUGCGGCUCGGCUGUUGCCCUAUCGUCCUGUUUAUGCCUGAUUAAAGUCAAACAACAAACAUAUUCUGAGCUGCAUUUACCAGACAAUCGUAUAAACAUAUACACUUGUGGU
......((.(((((((((((....))).........(((((.((..((((....))))..))..)))))......)))))))).))(((..((((..(((((....)))))..))))))) ( -28.30)
>DroEre_CAF1 117541 117 + 1
CAUUUCGAUUGCGGCUCGGCUGUUGCCCUAU---CCUGUUUAUGCCUGAUUAAAGUCAAACAACAAACAUAUUCUGAGCUGCAUUUACCAGACAAUCGUAUAAACAUAUACACUUGUGGU
......((.(((((((((((....)))....---..(((((.((..((((....))))..))..)))))......)))))))).))(((..((((..(((((....)))))..))))))) ( -28.30)
>DroYak_CAF1 122203 120 + 1
CAUUUCGAUUGCGGCUCGGCUGUUGCCCUAUCGUCCUGUUUAUGCCUGAUUAAAGUCAAACAACAAACAUAUACUGAGCUGCAUUUGCCAGACAAUCGUAUAAACAUAUACACAUGUGGU
.....(((.(((((((((((....))).........(((((.((..((((....))))..))..)))))......)))))))).)))(((.(.....(((((....)))))...).))). ( -27.30)
>consensus
CAUUUCGAUUGCGGCUCGGCUGUUGCCCUAUCGUCCUGUUUAUGCCUGAUUAAAGUCAAACAACAAACAUAUUCUGAGCUGCAUUUACCAGACAAUCGUAUAAACAUAUACACUUGUGGU
......((.(((((((((((....))).........(((((.((..((((....))))..))..)))))......)))))))).))(((..((((..(((((....)))))..))))))) (-27.04 = -27.12 +   0.08)

alignment

secondary structure

dotplot

Window 7

Location	21,635,747 – 21,635,867
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.17
Mean single sequence MFE	-33.02
Consensus MFE	-31.36
Energy contribution	-32.16
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.95
SVM decision value	2.85
SVM RNA-class probability	0.997400
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21635747 120 - 27905053
ACCACAUGUGUAUAUGUUUAUACGAUUGUCUGGUAAAUGCAGCUCAGAAUAUGUUUGUUGUUUGACUUUAAUCAGGCAUAAACAGGACGAUAUAGCAACAGCCGAGCCGCAAUCGAAAUG
((((.((.((((((....))))))...)).))))...(((.((((......(((((((.((((((......)))))))))))))..........((....)).)))).)))......... ( -28.80)
>DroSec_CAF1 125076 120 - 1
ACCACAAGUGUAUAUGUUUAUACGAUUGUCUGGUAAAUGCAGCUCAGAAUAUGUUUGUUGUUUGACUUUAAUCAGGCAUAAACAGGACGAUAGGGCAACAGCCGAGCCGCAAUCGAAAUG
(((((((.((((((....)))))).))))..)))...(((.((((......(((((((.((((((......))))))))))))).........(((....))))))).)))......... ( -34.20)
>DroSim_CAF1 121684 120 - 1
ACCACAAGUGUAUAUGUUUAUACGAUUGUCUGGUAAAUGCAGCUCAGAAUAUGUUUGUUGUUUGACUUUAAUCAGGCAUAAACAGGACGAUAGGGCAACAGCCGAGCCGCAAUCGAAAUG
(((((((.((((((....)))))).))))..)))...(((.((((......(((((((.((((((......))))))))))))).........(((....))))))).)))......... ( -34.20)
>DroEre_CAF1 117541 117 - 1
ACCACAAGUGUAUAUGUUUAUACGAUUGUCUGGUAAAUGCAGCUCAGAAUAUGUUUGUUGUUUGACUUUAAUCAGGCAUAAACAGG---AUAGGGCAACAGCCGAGCCGCAAUCGAAAUG
(((((((.((((((....)))))).))))..)))...(((.((((......(((((((.((((((......)))))))))))))..---....(((....))))))).)))......... ( -34.20)
>DroYak_CAF1 122203 120 - 1
ACCACAUGUGUAUAUGUUUAUACGAUUGUCUGGCAAAUGCAGCUCAGUAUAUGUUUGUUGUUUGACUUUAAUCAGGCAUAAACAGGACGAUAGGGCAACAGCCGAGCCGCAAUCGAAAUG
.......(((((......)))))((((((...((....)).((((.((...(((((((.((((((......)))))))))))))..)).....(((....))))))).))))))...... ( -33.70)
>consensus
ACCACAAGUGUAUAUGUUUAUACGAUUGUCUGGUAAAUGCAGCUCAGAAUAUGUUUGUUGUUUGACUUUAAUCAGGCAUAAACAGGACGAUAGGGCAACAGCCGAGCCGCAAUCGAAAUG
(((((((.((((((....)))))).))))..)))...(((.((((......(((((((.((((((......))))))))))))).........(((....))))))).)))......... (-31.36 = -32.16 +   0.80)

alignment

secondary structure

dotplot

Window 8

Location	21,635,867 – 21,635,963
Length	96
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	73.46
Mean single sequence MFE	-16.67
Consensus MFE	-2.28
Energy contribution	-5.08
Covariance contribution	2.80
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.14
SVM decision value	0.38
SVM RNA-class probability	0.713345
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21635867 96 + 27905053
CAUCAGAAUAGAAUU-----UAUUAGUUGGGAGAUCU---------ACAAAUCUGCCAAUUAUUUUAAGCAAAUUGUUUUUACUCUCCUU-UAACGCAAACAACUUUUAUU
......(((((((((-----((.(((((((.((((..---------....)))).)))))))...))))....((((((...........-......)))))).))))))) ( -13.33)
>DroSec_CAF1 125196 100 + 1
CAUAAGAAUAGAAUUCCU--UAUUAGUUGGCAGAUCU---------ACACAUCUGCCAAGUAUUUCAAGCAAAUUGUUUUUACUCCCCUUUUUAAACAAACAACUUUUGUU
..(((((((((.....((--(..((.(((((((((..---------....))))))))).))....)))....)))))))))............((((((.....)))))) ( -19.20)
>DroSim_CAF1 121804 100 + 1
CAUAAGAAUAGAAUUCCU--UAUUAGUUGGCAGAUCU---------ACAUAUAUGCCAAUUAUUUCAAGCAAAUUGUUUUUACUCCCCUUUUUAAACAAACAACUUUUGUU
..(((((((((.....((--(..(((((((((.....---------.......)))))))))....)))....)))))))))............((((((.....)))))) ( -14.90)
>DroEre_CAF1 117658 109 + 1
CAUAAGAAUAGAAUUGCUCGAAAUAGUCUCGAGAAUUAAUUCAAACACAAGUCUGCCAAUUAUUUCUGGCAAAUUGUU-UUACUUAG-UUCUGAAAUACACAACUUUUGUU
....(((((.(((((((((((.......)))))...))))))....((((...(((((........)))))..)))).-.......)-))))................... ( -19.90)
>DroYak_CAF1 122323 104 + 1
CAUAAGAAUAGAAUUGUC--UAUUAGGCCCGAGAAUUAAUUCAAAGACAAAUCUGACAAUUAGUUCAAGGAAAUUGUUAUUACUAAG-UUUGAAAAUAAACU----AUGUA
......((((((....))--))))....((..(((((((((...(((....)))...)))))))))..))..........(((..((-((((....))))))----..))) ( -16.00)
>consensus
CAUAAGAAUAGAAUUCCU__UAUUAGUUGGGAGAUCU_________ACAAAUCUGCCAAUUAUUUCAAGCAAAUUGUUUUUACUCACCUUUUAAAACAAACAACUUUUGUU
..(((((((((............(((((((.((((...............)))).)))))))...........)))))))))............................. ( -2.28 =  -5.08 +   2.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:29 2006