Locus 1540

Sequence ID	3L_DroMel_CAF1
Location	4,454,992 – 4,455,254
Length	262
Max. P	0.999606

overview

Window 2

Location	4,454,992 – 4,455,097
Length	105
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	90.50
Mean single sequence MFE	-35.88
Consensus MFE	-31.41
Energy contribution	-30.73
Covariance contribution	-0.69
Combinations/Pair	1.12
Mean z-score	-2.53
Structure conservation index	0.88
SVM decision value	1.98
SVM RNA-class probability	0.984678
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4454992 105 + 23771897
GCUGGUCAAAGACCUCAAAGACCUGCGCAAAACCAAUAUGAUCCCAACCUUCAGCUAGGUGGCCCUUUUGACCCCUCCGUGGGUGCUCAAUUGGGCGCAGGUCAG
...((((...)))).....(((((((((...............(((.(((......)))))).((..((((((((.....))).).))))..))))))))))).. ( -40.10)
>DroSec_CAF1 32238 102 + 1
GCUGGUCAA---GCUCAAAGACCUGUGCAAAACCAAUAUGAUCCCAAUCUUCAGCUAGGUGGCCCUUUUGAUCCUUCUUUAGGUGCUCAAUUGGGCGCAGGUCAG
(((.....)---)).....(((((((.....(((....(((.........)))....))).((((..((((.(((.....)))...))))..))))))))))).. ( -33.10)
>DroSim_CAF1 32176 102 + 1
GCUGGUCAA---GCUCAAAGACCUGUGCAAAACCAAUAUGAUCCCAAUCUUCAGCUCGGUGGCCCAUUUGAUCCUUCUUUAGGUGCUCAAUUGGGCGCAGGUCAG
(((.....)---)).....(((((((.....(((....(((.........)))....))).(((((.((((.(((.....)))...)))).)))))))))))).. ( -34.10)
>DroYak_CAF1 33883 102 + 1
GGAGGUCAA---GCUCAAAGACCUGCGCAAAACCAAUAUGAUCCCAACCUACAGCUAGGUCGUCCUUUUGAUCCCUCCUUGGGUGCUCAAUUGGGCGCAGGUCAG
.(((.....---.)))...(((((((((..................(((((....)))))...((..((((.(((.....)))...))))..))))))))))).. ( -36.20)
>consensus
GCUGGUCAA___GCUCAAAGACCUGCGCAAAACCAAUAUGAUCCCAACCUUCAGCUAGGUGGCCCUUUUGAUCCCUCCUUAGGUGCUCAAUUGGGCGCAGGUCAG
...................(((((((.....(((....(((.........)))....))).((((..((((.(((.....)))...))))..))))))))))).. (-31.41 = -30.73 +  -0.69)

alignment

secondary structure

dotplot

Window 3

Location	4,454,992 – 4,455,097
Length	105
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	90.50
Mean single sequence MFE	-34.55
Consensus MFE	-31.95
Energy contribution	-31.33
Covariance contribution	-0.63
Combinations/Pair	1.11
Mean z-score	-1.47
Structure conservation index	0.92
SVM decision value	0.45
SVM RNA-class probability	0.741827
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4454992 105 - 23771897
CUGACCUGCGCCCAAUUGAGCACCCACGGAGGGGUCAAAAGGGCCACCUAGCUGAAGGUUGGGAUCAUAUUGGUUUUGCGCAGGUCUUUGAGGUCUUUGACCAGC
..(((((((((((((((((...((((((((((((((.....)))).)))..))).....)))).))).)))))....))))))))).....((((...))))... ( -42.10)
>DroSec_CAF1 32238 102 - 1
CUGACCUGCGCCCAAUUGAGCACCUAAAGAAGGAUCAAAAGGGCCACCUAGCUGAAGAUUGGGAUCAUAUUGGUUUUGCACAGGUCUUUGAGC---UUGACCAGC
..((((((.((((((((.(((.(((.....)))......(((....))).)))...))))))((((.....))))..)).)))))).....((---(.....))) ( -28.60)
>DroSim_CAF1 32176 102 - 1
CUGACCUGCGCCCAAUUGAGCACCUAAAGAAGGAUCAAAUGGGCCACCGAGCUGAAGAUUGGGAUCAUAUUGGUUUUGCACAGGUCUUUGAGC---UUGACCAGC
(((...((.(((((.((((...(((.....))).)))).))))))).(((((((((((((..((((.....))))..).....)))))).)))---)))..))). ( -30.90)
>DroYak_CAF1 33883 102 - 1
CUGACCUGCGCCCAAUUGAGCACCCAAGGAGGGAUCAAAAGGACGACCUAGCUGUAGGUUGGGAUCAUAUUGGUUUUGCGCAGGUCUUUGAGC---UUGACCUCC
..(((((((((((((((((.(.(((.....)))..........(((((((....))))))).).))).)))))....)))))))))...(((.---.....))). ( -36.60)
>consensus
CUGACCUGCGCCCAAUUGAGCACCCAAAGAAGGAUCAAAAGGGCCACCUAGCUGAAGAUUGGGAUCAUAUUGGUUUUGCACAGGUCUUUGAGC___UUGACCAGC
..(((((((((((((((.(((.(((.....)))......(((....))).)))...))))))((((.....))))..)))))))))................... (-31.95 = -31.33 +  -0.63)

alignment

secondary structure

dotplot

Window 4

Location	4,455,057 – 4,455,177
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.67
Mean single sequence MFE	-47.54
Consensus MFE	-33.34
Energy contribution	-36.70
Covariance contribution	3.36
Combinations/Pair	1.17
Mean z-score	-3.09
Structure conservation index	0.70
SVM decision value	3.78
SVM RNA-class probability	0.999606
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4455057 120 + 23771897
UUUUGACCCCUCCGUGGGUGCUCAAUUGGGCGCAGGUCAGGGUGUUUCUAACCAAAGACCAAGUGGACAGGGAGCAUUUGAUCCUUCUACAGGUGCUCAAUUGGGCGCAGGUGAGGGUGU
.....(((((.((....((((((((((((((((.((((..(((.......)))...))))..(((((..((((........)))))))))..)))))))))))))))).)).).)))).. ( -56.10)
>DroPse_CAF1 39689 92 + 1
-------------------GCACAAUUUGG---AGGUCAGCUGCCCGCUGCCCAACAGCCGAAUCAACUCGGA------AAUCCCGCUCUGGGCGCUCAGCUGGGAGUUGGACAGGCUCC
-------------------((.....(((.---.((.((((.....)))).))..)))((((......)))).------..(((.(((((.(((.....))).))))).)))...))... ( -31.80)
>DroSec_CAF1 32300 120 + 1
UUUUGAUCCUUCUUUAGGUGCUCAAUUGGGCGCAGGUCAGGGUGCUUCUAACCAAAGACCAAGUGGACAGGGAGCAUUUGAUCCUUCUACGGGUGCUCAAUUGGGCGCAGGUCAGGGUAU
((((((((((.....))((((((((((((((((.((((..(((.......)))...))))..(((((..((((........)))))))))..)))))))))))))))).))))))))... ( -50.80)
>DroSim_CAF1 32238 120 + 1
AUUUGAUCCUUCUUUAGGUGCUCAAUUGGGCGCAGGUCAGGGUGUUUCCAACCAAAGACCAAGUGGACAGGGAGCAUUUGAUCCUUCUGCGGGUGCUCAAUUGGGCGCAGGUCAGGGUAU
.(((((((((.....))((((((((((((((((.((((..(((.......)))...))))..(..((..((((........))))))..)..)))))))))))))))).))))))).... ( -49.90)
>DroYak_CAF1 33945 120 + 1
UUUUGAUCCCUCCUUGGGUGCUCAAUUGGGCGCAGGUCAGGGUGUUUCUAACCAAAGACCAAGUGGACAGGGAGCAUUUGAUCCUGCUACAGGUGCUCAAUUAGGCGCUGGUCAGGGUGU
.......((((...(.(((((..((((((((((.((((..(((.......)))...))))..((((.(((((..(....).)))))))))..))))))))))..))))).)..))))... ( -49.10)
>consensus
UUUUGAUCCCUCCUUAGGUGCUCAAUUGGGCGCAGGUCAGGGUGUUUCUAACCAAAGACCAAGUGGACAGGGAGCAUUUGAUCCUUCUACGGGUGCUCAAUUGGGCGCAGGUCAGGGUAU
.......((((......((((((((((((((((.((((..(((.......)))...))))..(((((..((((........)))))))))..)))))))))))))))).....))))... (-33.34 = -36.70 +   3.36)

alignment

secondary structure

dotplot

Window 5

Location	4,455,137 – 4,455,254
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.46
Mean single sequence MFE	-43.59
Consensus MFE	-21.08
Energy contribution	-22.20
Covariance contribution	1.12
Combinations/Pair	1.24
Mean z-score	-1.80
Structure conservation index	0.48
SVM decision value	0.11
SVM RNA-class probability	0.588223
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4455137 117 + 23771897
AUCCUUCUACAGGUGCUCAAUUGGGCGCAGGUGAGGGUGUUUCUAACCAAAGACCAAGUGGACAGGGAGCAUUUGAUCCUUCUACGGGUGCUCAAUUGGGUGCAGGUCAGGGC---UUUA
.((((...((..(..(((((((((((((.(((...(((.......)))....)))..(((((..((((........)))))))))..)))))))))))))..)..)).)))).---.... ( -44.80)
>DroPse_CAF1 39741 111 + 1
AUCCCGCUCUGGGCGCUCAGCUGGGAGUUGGACAGGCUCCUCUUGGACAGAGGCCGAAUCAGC------CAAAUCCUCCUCCGUUCGGUGCUCAGCUUGGUGCUGGACAGGCGCCUC---
..........(((((((......((((..(((..(((((((((.....))))).......)))------)...)))..))))((((((..((......))..)))))).))))))).--- ( -44.11)
>DroSec_CAF1 32380 117 + 1
AUCCUUCUACGGGUGCUCAAUUGGGCGCAGGUCAGGGUAU---UAACCAGAGACCAAGUGCACAGGGAGCAUUUGAUCCUUCGACAGGUGCCCAACUAGGAGCUGGACAGGGUAUUUCUA
(((((((((.....((((..((((((((..(((..(((..---..)))((.((.(((((((.......))))))).))))..)))..))))))))....)))))))).)))))....... ( -42.50)
>DroSim_CAF1 32318 117 + 1
AUCCUUCUGCGGGUGCUCAAUUGGGCGCAGGUCAGGGUAU---UAACCAGAGACCAAGUGCACAGGGAGCAUUUGAUCCUUCGACAGGUGCCCAACUUGGAGCUGGACAGGGUAUUUCUA
....((((((.(((..((((((((((((..(((..(((..---..)))((.((.(((((((.......))))))).))))..)))..)))))))).)))).))).).)))))........ ( -41.90)
>DroEre_CAF1 35173 118 + 1
--CCCUCCUUGGGUGCUCAAUUGGGAGCAGCUCAGGGUGUUCCUAACCAAAGACCAAGUGGACAGGGAGCAUUUGAUCCUUCUACAGGUGCUCAACUUGGCGCUGGGCAGAGUGUUCCUA
--..(..(((((...((...(((((((((.(....).)))))))))....)).)))))..)...((((((((((..(((..(..(((((.....)))))..)..)))..)))))))))). ( -43.20)
>DroYak_CAF1 34025 120 + 1
AUCCUGCUACAGGUGCUCAAUUAGGCGCUGGUCAGGGUGUUUCUAACCAGAGACCAAGUGGACAGGGAGCAUUUGAUCCUUCUACAGGUGCCCAACUUGGAACUGGACAGGGUGUUCCUA
...(((((((.((((((......))))))((((..(((.......)))...))))..)))).)))(((((((((..(((.....(((((.....))))).....)))..))))))))).. ( -45.00)
>consensus
AUCCUUCUACGGGUGCUCAAUUGGGCGCAGGUCAGGGUGUU_CUAACCAGAGACCAAGUGGACAGGGAGCAUUUGAUCCUUCGACAGGUGCCCAACUUGGAGCUGGACAGGGUAUUCCUA
..(((.....))).((((((((((((((.((((..(((.......)))...))))........(((((........)))))......)))))))).)))).))................. (-21.08 = -22.20 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:12 2006