Locus 2331

Sequence ID	3L_DroMel_CAF1
Location	6,545,735 – 6,545,945
Length	210
Max. P	0.994072

overview

Window 9

Location	6,545,735 – 6,545,838
Length	103
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	87.72
Mean single sequence MFE	-20.25
Consensus MFE	-13.52
Energy contribution	-14.02
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.67
SVM decision value	-0.01
SVM RNA-class probability	0.526484
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6545735 103 - 23771897
GCUGCACCACCACCACAGCAAUCAGGUGAAUCAGCACCACCACCAGCAGCAGCAGAGUCACCACCAUUUGCAGCACGC------CAACUUGCACUCCCACCAUCCACAC
(((((...........(....)..((((......)))).......))))).(((((..........))))).(((...------.....)))................. ( -18.20)
>DroSec_CAF1 8288 100 - 1
GCUACACCACCACCACAGCAGCCAGGUGAAUCAGCACC---ACCAGCAGCAGCAGAGUCACCACCAUUUGCAGCACGC------CAGCUCGCACUCCCACCAUCCACAC
.................(((((..((((.....((...---....)).((.(((((..........))))).)).)))------).))).))................. ( -18.30)
>DroSim_CAF1 8376 100 - 1
GCUGCACCACCACCACAGCAGCCAGGUGAAUCAGCACC---ACCAGCAGCAGCAGAGUCACCACCAUUUGCAGCACGC------CAGCUCGCACUCCCACCAUCCACAC
(((((............)))))..((((.....((...---....)).((.(((((..........)))))(((....------..))).)).....))))........ ( -21.90)
>DroEre_CAF1 8324 103 - 1
GCUGCACCACCACCACGCCAACCAGGUGAAUCCGCACC---AC---CAGCAGCAGAGCCACCACCAUUUGCAGCACUCGAGCUCGAACUCGAACUCCCACCAUCAACAC
((((((..........(.....).((((..((.((...---..---.....)).))..))))......))))))....(((.(((....))).)))............. ( -22.60)
>consensus
GCUGCACCACCACCACAGCAACCAGGUGAAUCAGCACC___ACCAGCAGCAGCAGAGUCACCACCAUUUGCAGCACGC______CAACUCGCACUCCCACCAUCCACAC
((((...((((.............))))...)))).............((.(((((..........))))).))................................... (-13.52 = -14.02 +   0.50)

alignment

secondary structure

dotplot

Window 0

Location	6,545,805 – 6,545,917
Length	112
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	72.38
Mean single sequence MFE	-42.03
Consensus MFE	-23.43
Energy contribution	-23.35
Covariance contribution	-0.08
Combinations/Pair	1.20
Mean z-score	-1.62
Structure conservation index	0.56
SVM decision value	0.63
SVM RNA-class probability	0.805972
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6545805 112 + 23771897
UGAUUCACCUGAUUGCUGU-GGUGGUGGUGCAGC---UGC-UGCGAGUGGCGACCUAAGCCAGUUCCAGCUGCAUCAUGACAGCUGGUGGCCAAGUCGAGAUGGGAAACGGAUUUGU
....(((((.....(((((-....((((((((((---((.-.((...((((.......))))))..)))))))))))).))))).))))).((((((......(....).)))))). ( -41.80)
>DroVir_CAF1 20743 103 + 1
G----------GGUGUUGCGUCUGAUGGUGCAGU---UGCCUGUG-CCUGUGAUCUAUGCCAGCGCCAGCUGCGCCAUGGCAGCUGGUGGCCAAAUCGAGAUGCGAAACGGAUUUGU
.----------.((.(((((((((((((..(((.---...)))..-))..........(((...(((((((((......))))))))))))...))).)))))))).))........ ( -43.30)
>DroGri_CAF1 20196 97 + 1
U----------GCA------GUUGCACUUGCAGU---UGCCUGCG-UUGCCGAUCUAUGCCAGCGCCAGCUGCACCAUGGCAGCUGGUGGCCAAAUCGAGAUGCGAUACGGAUUUGU
.----------(((------..(((....)))..---))).((((-((..((((....(((...(((((((((......))))))))))))...)))).))))))............ ( -38.50)
>DroEre_CAF1 8394 112 + 1
GGAUUCACCUGGUUGGCGU-GGUGGUGGUGCAGC---UGC-UGCGAGUGGCGACCUAAGCCAGUUCCAGCUGCGUCAUGGCAGCUGGUGGCCAAGUCGAGAUGGGAAACGGAUUUGU
((((((..((.(((((((.-.(..((......))---..)-..)((.((((.......)))).))((((((((......))))))))..)))))..).))...(....))))))).. ( -43.20)
>DroAna_CAF1 19923 99 + 1
-----------GCA------GGUGCUGGUGCGACUGGUGG-UGCGGGUGGCGACCUAAGCCAGAACUAGCUGCUUCAUGGCAGCUGGUGGCCAAGUCGAGAUGCGAGACGGAUUUGU
-----------(((------(((.((.((.((((((((((-(..((((....))))..)))...((((((((((....)))))))))).))).)))))....)).))....)))))) ( -40.30)
>DroPer_CAF1 41339 106 + 1
GGAUGCGAGUGGUGGCCGU-GUGGGUGGU---------GC-UGCGUGUGGCGACCUAUGCCAUUGCCAGCUGCUUCAUGGCAGCUGGUGGCCAAAUCGAGAUGCGACACGGAUUUGU
.....(((....(((((((-((((((..(---------((-((....)))))))))))))....((((((((((....)))))))))))))))..)))((((.((...)).)))).. ( -45.10)
>consensus
G__________GUUG__GU_GGUGGUGGUGCAGC___UGC_UGCG_GUGGCGACCUAAGCCAGUGCCAGCUGCAUCAUGGCAGCUGGUGGCCAAAUCGAGAUGCGAAACGGAUUUGU
.........................................((((.....((((....((((...((((((((......))))))))))))...))))...))))............ (-23.43 = -23.35 +  -0.08)

alignment

secondary structure

dotplot

Window 1

Location	6,545,805 – 6,545,917
Length	112
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	72.38
Mean single sequence MFE	-35.73
Consensus MFE	-26.24
Energy contribution	-25.97
Covariance contribution	-0.28
Combinations/Pair	1.16
Mean z-score	-2.69
Structure conservation index	0.73
SVM decision value	2.45
SVM RNA-class probability	0.994072
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6545805 112 - 23771897
ACAAAUCCGUUUCCCAUCUCGACUUGGCCACCAGCUGUCAUGAUGCAGCUGGAACUGGCUUAGGUCGCCACUCGCA-GCA---GCUGCACCACCACC-ACAGCAAUCAGGUGAAUCA
........(.(((((....(((((((((((((((((((......))))))))...)))).))))))).........-...---((((..........-.)))).....)).))).). ( -35.20)
>DroVir_CAF1 20743 103 - 1
ACAAAUCCGUUUCGCAUCUCGAUUUGGCCACCAGCUGCCAUGGCGCAGCUGGCGCUGGCAUAGAUCACAGG-CACAGGCA---ACUGCACCAUCAGACGCAACACC----------C
.............((.(((.((((((((((((((((((......))))))))...)))).))))))...((-..(((...---.)))..))...))).))......----------. ( -37.60)
>DroGri_CAF1 20196 97 - 1
ACAAAUCCGUAUCGCAUCUCGAUUUGGCCACCAGCUGCCAUGGUGCAGCUGGCGCUGGCAUAGAUCGGCAA-CGCAGGCA---ACUGCAAGUGCAAC------UGC----------A
.............(((...(((((((((((((((((((......))))))))...)))).)))))))(((.-.((((...---.))))...)))...------)))----------. ( -42.80)
>DroEre_CAF1 8394 112 - 1
ACAAAUCCGUUUCCCAUCUCGACUUGGCCACCAGCUGCCAUGACGCAGCUGGAACUGGCUUAGGUCGCCACUCGCA-GCA---GCUGCACCACCACC-ACGCCAACCAGGUGAAUCC
...................(((((((((((((((((((......))))))))...)))).)))))))......(((-(..---.)))).........-.((((.....))))..... ( -37.20)
>DroAna_CAF1 19923 99 - 1
ACAAAUCCGUCUCGCAUCUCGACUUGGCCACCAGCUGCCAUGAAGCAGCUAGUUCUGGCUUAGGUCGCCACCCGCA-CCACCAGUCGCACCAGCACC------UGC-----------
.............((....((((((((((((.((((((......)))))).))...))).)))))))......)).-....(((..((....))..)------)).----------- ( -27.40)
>DroPer_CAF1 41339 106 - 1
ACAAAUCCGUGUCGCAUCUCGAUUUGGCCACCAGCUGCCAUGAAGCAGCUGGCAAUGGCAUAGGUCGCCACACGCA-GC---------ACCACCCAC-ACGGCCACCACUCGCAUCC
......((((((........((((((((((((((((((......))))))))...)))).))))))((........-))---------.......))-))))............... ( -34.20)
>consensus
ACAAAUCCGUUUCGCAUCUCGACUUGGCCACCAGCUGCCAUGAAGCAGCUGGCACUGGCAUAGGUCGCCAC_CGCA_GCA___GCUGCACCACCACC_AC__CAAC__________C
...................(((((((((((((((((((......))))))))...)))).))))))).................................................. (-26.24 = -25.97 +  -0.28)

alignment

secondary structure

dotplot

Window 2

Location	6,545,838 – 6,545,945
Length	107
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	83.06
Mean single sequence MFE	-45.34
Consensus MFE	-31.80
Energy contribution	-31.30
Covariance contribution	-0.50
Combinations/Pair	1.15
Mean z-score	-2.17
Structure conservation index	0.70
SVM decision value	0.37
SVM RNA-class probability	0.709552
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6545838 107 - 23771897
---UUGAGA------GCCGCUGGCUGGAGACACACGCACAAAUCCGUUUCCCAUCUCGACUUGGCCACCAGCUGUCAUGAUGCAGCUGGAACUGGCUUAGGUCGCCACUCGCA-GCA
---......------((.((((((.((((((..............))))))......((((((((((((((((((......))))))))...)))).))))))))))...)).-)). ( -41.44)
>DroVir_CAF1 20767 107 - 1
---CUGCGC------GCCGCCGGCUGGCGACACACGCACAAAUCCGUUUCGCAUCUCGAUUUGGCCACCAGCUGCCAUGGCGCAGCUGGCGCUGGCAUAGAUCACAGG-CACAGGCA
---......------(((...(.(((((((...(((........))).)))).....((((((((((((((((((......))))))))...)))).)))))).))).-)...))). ( -42.60)
>DroGri_CAF1 20214 107 - 1
---CUGCGA------GCCGCUGGCUGGCGGCACACGCACAAAUCCGUAUCGCAUCUCGAUUUGGCCACCAGCUGCCAUGGUGCAGCUGGCGCUGGCAUAGAUCGGCAA-CGCAGGCA
---(((((.------((((((....))))))....((((......)).........(((((((((((((((((((......))))))))...)))).)))))))))..-)))))... ( -48.70)
>DroMoj_CAF1 7493 107 - 1
---CUGCGC------GCCGCUGGCUGGCGACACACGCACAAAUCCGUCUCGCAUCUCGAUUUGGCCACCAGCUGCCAUGGCGCAGCUGGCGCUGGCAUAGAUCACAGG-CAGAGGCA
---......------(((.(((.(((((((...(((........))).)))).....((((((((((((((((((......))))))))...)))).)))))).))).-))).))). ( -47.80)
>DroAna_CAF1 19943 107 - 1
---UUGAGA------GCCGCCGGCUGGCGACACACCCACAAAUCCGUCUCGCAUCUCGACUUGGCCACCAGCUGCCAUGAAGCAGCUAGUUCUGGCUUAGGUCGCCACCCGCA-CCA
---......------...((.((.(((((((.................(((.....)))((.((((((.((((((......)))))).))...)))).))))))))))).)).-... ( -36.50)
>DroPer_CAF1 41367 115 - 1
GGACUGCGGGCUGCUGCCGCUGGCUGGCGGCACACGCACAAAUCCGUGUCGCAUCUCGAUUUGGCCACCAGCUGCCAUGAAGCAGCUGGCAAUGGCAUAGGUCGCCACACGCA-GC-
...((((((((....)))(.((((..(((((((............))))))).....((((((((((((((((((......))))))))...)))).))))))))))).))))-).- ( -55.00)
>consensus
___CUGCGA______GCCGCUGGCUGGCGACACACGCACAAAUCCGUCUCGCAUCUCGAUUUGGCCACCAGCUGCCAUGAAGCAGCUGGCGCUGGCAUAGAUCGCCAC_CGCA_GCA
...............(((...)))..((((.((............)).)))).....((((((((((((((((((......))))))))...)))).)))))).............. (-31.80 = -31.30 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:46 2006