Locus 3443

Sequence ID	3R_DroMel_CAF1
Location	9,334,137 – 9,334,306
Length	169
Max. P	0.995701

overview

Window 6

Location	9,334,137 – 9,334,243
Length	106
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	76.55
Mean single sequence MFE	-39.34
Consensus MFE	-24.26
Energy contribution	-24.43
Covariance contribution	0.17
Combinations/Pair	1.16
Mean z-score	-1.45
Structure conservation index	0.62
SVM decision value	0.31
SVM RNA-class probability	0.684191
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9334137 106 - 27905053
AU-GAGGGGG-CCGUGGUGGCACGAAGGGGCGU-GGCAGCCGGGUCGGCGUUGAGUUGUUGCCGUGGCCAGCGAUGUCGACGUCGGCCUGUCCAGGUGUGGAAAGUGUG
..-....(.(-((.(((((.((((......)))-).))..((((((((((((((((((((((....).))))))).)))))))))))))).)))))).).......... ( -44.70)
>DroPse_CAF1 102724 104 - 1
AG-GAAGACG-GAGAGGA---GAGAGAGAGAGAGAGUAACGACGUCGGUGCUGAGUUGUAGUCGUGGCCAGCGAUGUCGACGUCGGCCUGUCCAGGUGUGGAAAGUGUG
..-......(-((.(((.---..................((((((((((((((.((..(....)..)))))))...))))))))).))).)))................ ( -31.35)
>DroEre_CAF1 106357 108 - 1
GCCAAAAGGGGCCGAGGUGGCACGAAGGGGCGU-GGCAGCCGGGUCGGCGUUGAGUUGUUGCCGUGGCCAGCGAUGUCGACGUCGGCCUGUCCAGGUGUGGAAAGUGUG
.(((....((((...((((.((((......)))-).)).))(((((((((((((((((((((....).))))))).))))))))))))))))).....)))........ ( -48.20)
>DroYak_CAF1 106631 100 - 1
--------GGGCCGAGGUGGCACGAAGGGGCGU-GGCAGCCGGGUCGGCGUUGAGUUGUUGCCGUGGCCAGCGAUGUCGACGUCGGCCUGUCCAGGUGUGGAAAGUGUG
--------((((...((((.((((......)))-).)).))(((((((((((((((((((((....).))))))).)))))))))))))))))................ ( -44.60)
>DroAna_CAF1 102509 85 - 1
CU-GA----------------------GGGCGG-GGCCGACGGGCCGGUGUUGAGUUGUAGCCGUGGCCAGCGAUGUCGACGUCGGCCUGUCCAGGUGUGGAAAGUGUG
((-(.----------------------.(((..-.)))(((((((((..((((((((((.((....))..))))).)))))..)))))))))))).............. ( -37.50)
>DroPer_CAF1 107482 102 - 1
AG-GAAGGCG-GAGAAGA-----GAGAGAGAGAGAGUAACGACGUCGGUGCUGAGUUGUAGUCGUGGCCAGCGAUGUCGACGUCGGCCUGUCCAGGUGUGGAAAGUGUG
.(-((((((.-.......-----......(......)..((((((((((((((.((..(....)..)))))))...))))))))))))).)))................ ( -29.70)
>consensus
AG_GAAGGGG_CCGAGGU___ACGAAGGGGCGU_GGCAGCCGGGUCGGCGUUGAGUUGUAGCCGUGGCCAGCGAUGUCGACGUCGGCCUGUCCAGGUGUGGAAAGUGUG
........................................(((((((((((((((((((.((....))..))))).))))))))))))))((((....))))....... (-24.26 = -24.43 +   0.17)

alignment

secondary structure

dotplot

Window 7

Location	9,334,213 – 9,334,306
Length	93
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	89.19
Mean single sequence MFE	-26.60
Consensus MFE	-21.80
Energy contribution	-22.08
Covariance contribution	0.28
Combinations/Pair	1.10
Mean z-score	-2.55
Structure conservation index	0.82
SVM decision value	2.42
SVM RNA-class probability	0.993736
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9334213 93 + 27905053
CGCCCCUUCGUGCCACCACGG-CCCCCUC-AUUCCAUUCGGCCAUGGUCCUUACCCUCAGCUACUUCCGGCUAACACACACAUAUAGAGGGGCAG
.(((((((..((..((((.((-((.....-.........)))).))))..........((((......))))..........))..))))))).. ( -28.94)
>DroSec_CAF1 106503 94 + 1
CGCCCCUUCGUGCCACCACGGGCCCCCCU-AUUCCAUUCGGCCAUGGUCCUUACCCUCAGCUACUUCCGGCUAACACAUACACAUACAGGGGCAG
.((((((..(((..((((..((((.....-.........)))).))))..........((((......))))..........)))..)))))).. ( -26.54)
>DroSim_CAF1 115782 94 + 1
CGCCCCUUCGUGCCACCACGGGCCCCCCU-AUUCCAUUCGGCCAUGGUCCUUACCCUCAGCUACUUCCGGCUAACACAUACACAUACAGGGGCAG
.((((((..(((..((((..((((.....-.........)))).))))..........((((......))))..........)))..)))))).. ( -26.54)
>DroEre_CAF1 106433 95 + 1
CGCCCCUUCGUGCCACCUCGGCCCCUUUUGGCCCCUUUCGGCCAUGGUCCUUACCCUCAGCUACUUCCGGCUAACACAUACACAUACAGCGGCAG
.(((.((..(((.......((((.....(((((......))))).)))).........((((......))))..........)))..)).))).. ( -22.30)
>DroYak_CAF1 106707 85 + 1
CGCCCCUUCGUGCCACCUCGGCCC----------CUUUCGGCCAUGGUCCUUACCCUCAGCUACUUCCGGCUAACACAUACACACACAGGGGCAG
.((((((..(((..(((..((((.----------.....))))..)))..........((((......))))..........)))..)))))).. ( -28.70)
>consensus
CGCCCCUUCGUGCCACCACGGCCCCCCCU_AUUCCAUUCGGCCAUGGUCCUUACCCUCAGCUACUUCCGGCUAACACAUACACAUACAGGGGCAG
.((((((..(((..((((.((.((...............)))).))))..........((((......))))..........)))..)))))).. (-21.80 = -22.08 +   0.28)

alignment

secondary structure

dotplot

Window 8

Location	9,334,213 – 9,334,306
Length	93
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	89.19
Mean single sequence MFE	-36.14
Consensus MFE	-31.28
Energy contribution	-32.08
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.31
Structure conservation index	0.87
SVM decision value	2.61
SVM RNA-class probability	0.995701
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9334213 93 - 27905053
CUGCCCCUCUAUAUGUGUGUGUUAGCCGGAAGUAGCUGAGGGUAAGGACCAUGGCCGAAUGGAAU-GAGGGGG-CCGUGGUGGCACGAAGGGGCG
..((((((.....(((((.(.((((((....)..))))).)......(((((((((.........-.....))-))))))).))))).)))))). ( -37.14)
>DroSec_CAF1 106503 94 - 1
CUGCCCCUGUAUGUGUAUGUGUUAGCCGGAAGUAGCUGAGGGUAAGGACCAUGGCCGAAUGGAAU-AGGGGGGCCCGUGGUGGCACGAAGGGGCG
..((((((...(((((...(.((((((....)..))))).)......(((((((((.........-.....)).))))))).))))).)))))). ( -35.74)
>DroSim_CAF1 115782 94 - 1
CUGCCCCUGUAUGUGUAUGUGUUAGCCGGAAGUAGCUGAGGGUAAGGACCAUGGCCGAAUGGAAU-AGGGGGGCCCGUGGUGGCACGAAGGGGCG
..((((((...(((((...(.((((((....)..))))).)......(((((((((.........-.....)).))))))).))))).)))))). ( -35.74)
>DroEre_CAF1 106433 95 - 1
CUGCCGCUGUAUGUGUAUGUGUUAGCCGGAAGUAGCUGAGGGUAAGGACCAUGGCCGAAAGGGGCCAAAAGGGGCCGAGGUGGCACGAAGGGGCG
..(((.((...(((((...(.((((((....)..))))).)......(((....((....))((((......))))..))).))))).)).))). ( -34.40)
>DroYak_CAF1 106707 85 - 1
CUGCCCCUGUGUGUGUAUGUGUUAGCCGGAAGUAGCUGAGGGUAAGGACCAUGGCCGAAAG----------GGGCCGAGGUGGCACGAAGGGGCG
..((((((.(((((.....(.((((((....)..))))).)......(((.(((((.....----------.))))).))).))))).)))))). ( -37.70)
>consensus
CUGCCCCUGUAUGUGUAUGUGUUAGCCGGAAGUAGCUGAGGGUAAGGACCAUGGCCGAAUGGAAU_AAGGGGGCCCGUGGUGGCACGAAGGGGCG
..((((((...(((((...(.((((((....)..))))).)......(((((((((...............)).))))))).))))).)))))). (-31.28 = -32.08 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:10 2006