Locus 1618

Sequence ID	3R_DroMel_CAF1
Location	4,687,554 – 4,687,712
Length	158
Max. P	0.969755

overview

Window 3

Location	4,687,554 – 4,687,674
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.83
Mean single sequence MFE	-33.20
Consensus MFE	-28.02
Energy contribution	-28.02
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.84
SVM decision value	-0.03
SVM RNA-class probability	0.520041
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4687554 120 - 27905053
CGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGUUGGCAACUCUGAAAAAUAUGACUAACAUAAAGACGGGCUUUACA
.(((((((.((((.......))))......((((((.....)))))).((((........))))..))))))).((.(((...(((......((((.....)))).)))...)))..)). ( -33.40)
>DroSec_CAF1 36972 120 - 1
CGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGUUGGCAACUACGAAAAAUAUGACUAACAUAAAGACAGGCUUUACA
.(((((((.((((.......))))......((((((.....)))))).((((........))))..))))))).(((((((.............)).))))).(((((.....))))).. ( -33.12)
>DroEre_CAF1 40059 120 - 1
CGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCCGCUGGUAGCACAGAAAAAAAGGACAGGCAUAAAGACAGGCUUUACG
.(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))..(((......)))................(((((.....))))).. ( -31.40)
>DroYak_CAF1 39085 120 - 1
CGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGCUGGCAACUCCGAAAAAUAGGACUGGCAUAGAGACAGGCUUUACA
.(((((((.((((.......))))......((((((.....)))))).((((........))))..))))))).((..(....(((........))))..)).(((((.....))))).. ( -37.60)
>DroAna_CAF1 37949 105 - 1
CGACCGUGACAGGACUUGAACCUGCAAUCCUCGGAUCAGAAGUCCGAUGCCUUAUCCAUUAGGCCACACGGUC---UUGCAACUAAAACAAUAAGGA------------GCUUGUUUAUA
.(((((((...((((((....(((..(((....))))))))))))...((((........))))..)))))))---.........((((((......------------..))))))... ( -30.50)
>consensus
CGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGCUGGCAACUCAGAAAAAUAGGACUAACAUAAAGACAGGCUUUACA
.(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))............................................... (-28.02 = -28.02 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	4,687,594 – 4,687,712
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	79.07
Mean single sequence MFE	-32.72
Consensus MFE	-29.34
Energy contribution	-29.74
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.15
Structure conservation index	0.90
SVM decision value	0.23
SVM RNA-class probability	0.644799
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4687594 118 + 27905053
GCCAACUGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGUAAAAUUAACUUUUUUCUUUUGUAUCCAGAAUUUUUUU
.......(((((((..((((........)))).((((((....).))))).....(((((.......))))))))))))..................(((((....)))))....... ( -31.90)
>DroSec_CAF1 37012 102 + 1
GCCAACUGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAGACAAUAACUUUUUUU----------------AUUUU
.....(((((((((..((((........)))).((((((....).))))).....(((((.......)))))))))))).))...............----------------..... ( -31.70)
>DroEre_CAF1 40099 116 + 1
ACCAGCGGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAAAAGUAAUCUUUUUUU-UUUA-AUCUUAUAUUCAAUC
.......(((((((..((((........)))).((((((....).))))).....(((((.......))))))))))))((((((....))))))..-....-............... ( -33.30)
>DroYak_CAF1 39125 117 + 1
GCCAGCUGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAAAAAUAAUCUUUUUUU-UUUGUAGCUUAAAUUCAAUC
...(((((((((((..((((........)))).((((((....).))))).....(((((.......))))))))))))((((((......))))))-.....))))........... ( -35.20)
>DroAna_CAF1 37977 103 + 1
GCAA---GACCGUGUGGCCUAAUGGAUAAGGCAUCGGACUUCUGAUCCGAGGAUUGCAGGUUCAAGUCCUGUCACGGUCGGAAAAGGGGUUUCUUUU----U-GGUUAAGA-------
....---(((((((..((((........)))).((((((....).))))).....(((((.......)))))))))))).(((((((....))))))----)-........------- ( -31.50)
>consensus
GCCAACUGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAAAAAUAAACUUUUUUU_UUUG_AGCUAAAAUUCAAUC
.......(((((((..((((........))))...(((((.((((((.(.......).)))))))))))...)))))))....................................... (-29.34 = -29.74 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	4,687,594 – 4,687,712
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	79.07
Mean single sequence MFE	-29.74
Consensus MFE	-28.02
Energy contribution	-28.02
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.94
SVM decision value	1.65
SVM RNA-class probability	0.969755
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4687594 118 - 27905053
AAAAAAAUUCUGGAUACAAAAGAAAAAAGUUAAUUUUACGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGUUGGC
.......((((.........))))....(((((((....(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))))))))) ( -30.60)
>DroSec_CAF1 37012 102 - 1
AAAAU----------------AAAAAAAGUUAUUGUCUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGUUGGC
.....----------------..................(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))....... ( -28.60)
>DroEre_CAF1 40099 116 - 1
GAUUGAAUAUAAGAU-UAAA-AAAAAAAGAUUACUUUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCCGCUGGU
...............-....-...........(((....(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))....))) ( -28.30)
>DroYak_CAF1 39125 117 - 1
GAUUGAAUUUAAGCUACAAA-AAAAAAAGAUUAUUUUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGCUGGC
...........((((.....-.......((.......))(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))))))... ( -32.10)
>DroAna_CAF1 37977 103 - 1
-------UCUUAACC-A----AAAAGAAACCCCUUUUCCGACCGUGACAGGACUUGAACCUGCAAUCCUCGGAUCAGAAGUCCGAUGCCUUAUCCAUUAGGCCACACGGUC---UUGC
-------........-.----(((((......)))))..(((((((...((((((....(((..(((....))))))))))))...((((........))))..)))))))---.... ( -29.10)
>consensus
AAAAGAAUUUAAGAU_CAAA_AAAAAAAGAUAAUUUUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCAGCUGGC
.......................................(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))....... (-28.02 = -28.02 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:58 2006