Locus 403

Sequence ID	X_DroMel_CAF1
Location	1,177,868 – 1,178,057
Length	189
Max. P	0.994146

overview

Window 9

Location	1,177,868 – 1,177,977
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.13
Mean single sequence MFE	-34.64
Consensus MFE	-18.57
Energy contribution	-19.21
Covariance contribution	0.64
Combinations/Pair	1.10
Mean z-score	-2.15
Structure conservation index	0.54
SVM decision value	0.81
SVM RNA-class probability	0.856383
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1177868 109 - 22224390
GAUACAAAUCUCUCUCGAGUGGACACUUAACAUGCGAGGAAGAGAUGGAGAGAGCAAGAGAGAGGGAGGGUGAGAA-----------GGGAGCGACUUGAAUUCUUCCUUGGCGCCCAUG
........((((((((..((.....(((..(((.(........))))..))).))..))))))))..(((((..((-----------(((((...........)))))))..)))))... ( -33.30)
>DroSec_CAF1 13752 109 - 1
GAAACAAAUCUCUCUCGAGUGGGCACUUAACAUGCGAGGAAGAGAUGGAGUGAGCGAGAGAGAGGGAGGGUGAGAA-----------GGGAGCGACUUAAAUUCAUUUUUGGCGCCCAUG
........((((((((..((...(((((......(......).....))))).))..))))))))..(((((...(-----------((((..((.......)).)))))..)))))... ( -30.30)
>DroSim_CAF1 28824 109 - 1
GAAACAAAUCUCUCUCGAGUGGGCACUUAACAUGCGAGGAAGAGAUGGAGUGAGCGAGAGAGAGGGAGGGUGAGAA-----------GGGAGCGACUUAAAUUCCUUUUUGGCGCCCAUG
....((..(((..((((.(((.........))).))))..)))..))..(((.(((...(((((((((..((((..-----------(....)..))))..)))))))))..))).))). ( -35.80)
>DroEre_CAF1 13113 96 - 1
GAUACGAAUCUCUCUCGAGUGGGCACUCAACAUGCGAGGCAGAG-------------GAGAGAGAGAGGGUGCGAA-----------GGGAGCGACUUGAACUCCUUUUUGGCGCCCAUG
........((((((((......((.(((.......)))))....-------------..))))))))(((((((((-----------(((((.........))))))))..))))))... ( -38.90)
>DroYak_CAF1 15950 103 - 1
GAUACAAAUCUCUCUCGAGUGGGCACUCAACAUGCGAGGCAGCG--------------AGACAGCGAGGGAGAGGAGCAGAGGAGGAGAGAGAG---GGAACUCCUUUUUGGCGCCCAUG
........((((((((......((.(((.......))))).((.--------------.....))))))))))((.((.(((((((((......---....))))))))).))..))... ( -34.90)
>consensus
GAUACAAAUCUCUCUCGAGUGGGCACUUAACAUGCGAGGAAGAGAUGGAG_GAGC_AGAGAGAGGGAGGGUGAGAA___________GGGAGCGACUUGAAUUCCUUUUUGGCGCCCAUG
........((((((((((((....))))......(......).................))))))))(((((...............((......))...............)))))... (-18.57 = -19.21 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	1,177,901 – 1,178,017
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.33
Mean single sequence MFE	-44.74
Consensus MFE	-33.18
Energy contribution	-33.26
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-3.38
Structure conservation index	0.74
SVM decision value	2.45
SVM RNA-class probability	0.994146
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1177901 116 + 22224390
----UUCUCACCCUCCCUCUCUCUUGCUCUCUCCAUCUCUUCCUCGCAUGUUAAGUGUCCACUCGAGAGAGAUUUGUAUCUCAAGGACGCACUUAAAGGAGGCGCGAGUGGGAGGGCAGC
----........(((((((((.(((((.(.((((........(......)....((((((.(((....)))..(((.....))))))))).......))))).))))).))))))).)). ( -41.80)
>DroSec_CAF1 13785 116 + 1
----UUCUCACCCUCCCUCUCUCUCGCUCACUCCAUCUCUUCCUCGCAUGUUAAGUGCCCACUCGAGAGAGAUUUGUUUCUCAAGGACGCACUUAAAGGAGGCGCGAGUGGGAGGGCAAC
----......(((((((.....(((((.(.((((........(......)((((((((...((.((((((......)))))).))...)))))))).))))).))))).))))))).... ( -45.50)
>DroSim_CAF1 28857 116 + 1
----UUCUCACCCUCCCUCUCUCUCGCUCACUCCAUCUCUUCCUCGCAUGUUAAGUGCCCACUCGAGAGAGAUUUGUUUCUCAAGGACGCACUUAAAGGAGGCGCGAGUGGGAGGGCAGC
----........(((((((((.(((((.(.((((........(......)((((((((...((.((((((......)))))).))...)))))))).))))).))))).))))))).)). ( -45.90)
>DroEre_CAF1 13146 103 + 1
----UUCGCACCCUCUCUCUCUC-------------CUCUGCCUCGCAUGUUGAGUGCCCACUCGAGAGAGAUUCGUAUCUCAAGGACGCACUUAAAGGAGGCGCGAGUGGGAGGGCAGC
----...((.(((((((.(((..-------------...((((((.(...((((((((...((.((((..........)))).))...)))))))).))))))).))).)))))))..)) ( -40.80)
>DroYak_CAF1 15987 106 + 1
CUGCUCCUCUCCCUCGCUGUCU--------------CGCUGCCUCGCAUGUUGAGUGCCCACUCGAGAGAGAUUUGUAUCUCAAGGACGCACUUAAAGGAGGCGCGAGUGGGAGGGCAGC
((((.((((((.(((((.((((--------------(((......))...((((((((((.(((....)))..(((.....)))))..))))))))..)))))))))).)))))))))). ( -49.70)
>consensus
____UUCUCACCCUCCCUCUCUCU_GCUC_CUCCAUCUCUUCCUCGCAUGUUAAGUGCCCACUCGAGAGAGAUUUGUAUCUCAAGGACGCACUUAAAGGAGGCGCGAGUGGGAGGGCAGC
..........(((((((.(((....................((((.(...((((((((((.(((....)))..(((.....)))))..)))))))).)))))...))).))))))).... (-33.18 = -33.26 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	1,177,901 – 1,178,017
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.33
Mean single sequence MFE	-45.68
Consensus MFE	-35.66
Energy contribution	-37.06
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-2.95
Structure conservation index	0.78
SVM decision value	2.42
SVM RNA-class probability	0.993693
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1177901 116 - 22224390
GCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAUACAAAUCUCUCUCGAGUGGACACUUAACAUGCGAGGAAGAGAUGGAGAGAGCAAGAGAGAGGGAGGGUGAGAA----
.((((((((((.(((((((((......)).)))).((((........((((((((((.(((.........))).))))..))))))........)))).))).)))))))).))..---- ( -43.89)
>DroSec_CAF1 13785 116 - 1
GUUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAAACAAAUCUCUCUCGAGUGGGCACUUAACAUGCGAGGAAGAGAUGGAGUGAGCGAGAGAGAGGGAGGGUGAGAA----
.(..(((((((.(((.(((((((.((((((((.(.(((((((..........))))))).).))))))))....(......)....))))...)))...))).)))))))..)...---- ( -49.50)
>DroSim_CAF1 28857 116 - 1
GCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAAACAAAUCUCUCUCGAGUGGGCACUUAACAUGCGAGGAAGAGAUGGAGUGAGCGAGAGAGAGGGAGGGUGAGAA----
.((((((((((.(((.(((((((.((((((((.(.(((((((..........))))))).).))))))))....(......)....))))...)))...))).)))))))).))..---- ( -48.20)
>DroEre_CAF1 13146 103 - 1
GCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAUACGAAUCUCUCUCGAGUGGGCACUCAACAUGCGAGGCAGAG-------------GAGAGAGAGAGGGUGCGAA----
((.((((((.(.(((.(((((((.((.(((((.(.(((((((..........))))))).).))))).))...).))))).)..-------------..))).).))))))))...---- ( -40.00)
>DroYak_CAF1 15987 106 - 1
GCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAUACAAAUCUCUCUCGAGUGGGCACUCAACAUGCGAGGCAGCG--------------AGACAGCGAGGGAGAGGAGCAG
.((((((((((.(((((((((((.((.(((((.(.(((((((..........))))))).).))))).))...).))))).(..--------------...).))))))).)))).)))) ( -46.80)
>consensus
GCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAUACAAAUCUCUCUCGAGUGGGCACUUAACAUGCGAGGAAGAGAUGGAG_GAGC_AGAGAGAGGGAGGGUGAGAA____
...((((((((.(((...(((((.((((((((.(.(((((((..........))))))).).))))))))...).))))....................))).))))))))......... (-35.66 = -37.06 +   1.40)

alignment

secondary structure

dotplot

Window 2

Location	1,177,937 – 1,178,057
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-36.98
Consensus MFE	-35.16
Energy contribution	-35.60
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.35
Structure conservation index	0.95
SVM decision value	1.06
SVM RNA-class probability	0.908663
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1177937 120 - 22224390
UCAUAAGCGUGACUCACGGCCAUGACCCCGUCCAAAUGUGGCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAUACAAAUCUCUCUCGAGUGGACACUUAACAUGCGAGGA
......(((((.....((((((((((...))).....))))))).....((((((((((((......)).))))....(((((....)))))....))))))........)))))..... ( -35.80)
>DroSec_CAF1 13821 120 - 1
UCAUAUGCGUGACUCACGGCCAUGACUCCGUCCAAAUGUGGUUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAAACAAAUCUCUCUCGAGUGGGCACUUAACAUGCGAGGA
......((((((...((((........))))......((((........))))))))))((((.((((((((.(.(((((((..........))))))).).))))))))...).))).. ( -36.70)
>DroSim_CAF1 28893 120 - 1
UCAUAAGCGUGACUCACGGCCAUGACCCCGUCCAAAUGUGGCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAAACAAAUCUCUCUCGAGUGGGCACUUAACAUGCGAGGA
......(((((.....((((((((((...))).....)))))))....(((((((((((((......)).))))....((((......))))....))))))).......)))))..... ( -37.10)
>DroEre_CAF1 13169 120 - 1
UCAUAAGCGUGACUCACGGCCAUGACCCCGUGCAAAUGUGGCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAUACGAAUCUCUCUCGAGUGGGCACUCAACAUGCGAGGC
......(((((.....(((((((..............)))))))....(((((((((((((......)).))))....(((((....)))))....))))))).......)))))..... ( -37.64)
>DroYak_CAF1 16013 120 - 1
UCAUAAGCGUGACUCACGGCCAUGACCCCGUGCAAAUGUGGCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAUACAAAUCUCUCUCGAGUGGGCACUCAACAUGCGAGGC
......(((((.....(((((((..............)))))))....(((((((((((((......)).))))....(((((....)))))....))))))).......)))))..... ( -37.64)
>consensus
UCAUAAGCGUGACUCACGGCCAUGACCCCGUCCAAAUGUGGCUGCCCUCCCACUCGCGCCUCCUUUAAGUGCGUCCUUGAGAUACAAAUCUCUCUCGAGUGGGCACUUAACAUGCGAGGA
......(((((.....(((((((..............)))))))....(((((((((((((......)).))))....(((((....)))))....))))))).......)))))..... (-35.16 = -35.60 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:47 2006