Locus 2905

Sequence ID	X_DroMel_CAF1
Location	7,772,650 – 7,772,780
Length	130
Max. P	0.990342

overview

Window 0

Location	7,772,650 – 7,772,755
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	72.39
Mean single sequence MFE	-48.63
Consensus MFE	-22.38
Energy contribution	-23.02
Covariance contribution	0.64
Combinations/Pair	1.30
Mean z-score	-2.50
Structure conservation index	0.46
SVM decision value	2.21
SVM RNA-class probability	0.990342
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7772650 105 + 22224390
ACAGCUGCAGCUGCAGCUCGUCCGGCGGCUGCUGCAG------------CGG---CAGCAGCUACGGCCGCAAUCGUUGGCGAAUUGGCUGGCGUGUAUUGGACCAGCGAGCUGGUCACC
..((((((....))))))((.(((..(((((((((..------------..)---)))))))).))).))(((((((..((......))..)))...))))((((((....))))))... ( -53.00)
>DroVir_CAF1 197 108 + 1
ACCGG---------UGCGCGUCCAGCGCCACCGGCAACAGCAGCCGCUGCAG---CGGCCGCAACAGCCGCUAUUGGCGGCGAAUUGGCUGGUGUAUAAUGCACCAUCGGUGUGCUAACA
.((((---------(((((.....))).))))))....((((((((((..((---((((.......))))))...))))))..(((((.((((((.....))))))))))).)))).... ( -52.70)
>DroEre_CAF1 5280 99 + 1
ACAGUUG------CGGCUCGUCCGGCGGCUGCUGCAG------------CGG---CAGCAGCUACGGCCGCAAUAGGUGGCGAAUUGGCUGGUGUAUAAUGGACCAGCGAGGUGGUCACC
...((((------((((.(((.....(((((((((..------------..)---))))))))))))))))))).((((((.(.((.((((((.(.....).)))))).)).).)))))) ( -54.10)
>DroWil_CAF1 203 102 + 1
GGGGCAA------CAGUGCGACCAGCUGCCGCUGCAG------------CUGCCACAGCAGCCACAGCUGAAAUUGGCGGCGAAUUGGCUGGUGUAUAAUGCACCACGGGAGUGCUCACU
.((((..------..(((((..(((((((....))))------------)))..(((.((((((..((((.......))))....)))))).)))....))))).((....))))))... ( -42.30)
>DroYak_CAF1 203 99 + 1
ACAGCUG------CUGCUCGUCCGGCGGCUGCUGCAG------------CGG---CAGCAGCUACGGCCGCAAUCGGUGGCGAAUUGGCUGGCGUGUAAUGGACCAGCGAGGUGGUCACC
..(((((------((((.(((.((((....))))..)------------)))---))))))))..((((((..(((....))).((.((((((........).))))).))))))))... ( -45.20)
>DroAna_CAF1 6063 99 + 1
ACGGCCG------CAGCCCGUCCGGCGGCUGCUGCAG------------CUA---CGGCAGCUACAGCCGCUAUCGGCGGCGAAUUGGCCGGAGUAUAAUGCACCAAUGGAGUAGUCACG
.((((((------...((((((.((((((((..((.(------------(..---..)).))..))))))))...))))).)...))))))..((....(((.((...)).)))...)). ( -44.50)
>consensus
ACAGCUG______CAGCUCGUCCGGCGGCUGCUGCAG____________CGG___CAGCAGCUACAGCCGCAAUCGGCGGCGAAUUGGCUGGUGUAUAAUGCACCAGCGAGGUGGUCACC
..................((.(((((((((((((.....................))))))))...(((((.....)))))......))))))).......................... (-22.38 = -23.02 +   0.64)

alignment

secondary structure

dotplot

Window 1

Location	7,772,650 – 7,772,755
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	72.39
Mean single sequence MFE	-44.33
Consensus MFE	-20.86
Energy contribution	-21.17
Covariance contribution	0.31
Combinations/Pair	1.29
Mean z-score	-2.02
Structure conservation index	0.47
SVM decision value	1.10
SVM RNA-class probability	0.915689
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7772650 105 - 22224390
GGUGACCAGCUCGCUGGUCCAAUACACGCCAGCCAAUUCGCCAACGAUUGCGGCCGUAGCUGCUG---CCG------------CUGCAGCAGCCGCCGGACGAGCUGCAGCUGCAGCUGU
(....)((((((((((((....(((..(((.((....(((....)))..))))).)))(((((((---(..------------..)))))))).))))).)))))))((((....)))). ( -47.20)
>DroVir_CAF1 197 108 - 1
UGUUAGCACACCGAUGGUGCAUUAUACACCAGCCAAUUCGCCGCCAAUAGCGGCUGUUGCGGCCG---CUGCAGCGGCUGCUGUUGCCGGUGGCGCUGGACGCGCA---------CCGGU
.........((((.(((((.......))))).......(((((.((((((((((((((((((...---)))))))))))))))))).)))))((((.....)))).---------.)))) ( -54.60)
>DroEre_CAF1 5280 99 - 1
GGUGACCACCUCGCUGGUCCAUUAUACACCAGCCAAUUCGCCACCUAUUGCGGCCGUAGCUGCUG---CCG------------CUGCAGCAGCCGCCGGACGAGCCG------CAACUGU
(((((.......((((((.........))))))....))))).....((((((((((.(((((((---(..------------..))))))))......))).))))------))).... ( -42.70)
>DroWil_CAF1 203 102 - 1
AGUGAGCACUCCCGUGGUGCAUUAUACACCAGCCAAUUCGCCGCCAAUUUCAGCUGUGGCUGCUGUGGCAG------------CUGCAGCGGCAGCUGGUCGCACUG------UUGCCCC
((((.(((((.....))))).......((((((......(((((......(((((((.((....)).))))------------)))..))))).))))))..)))).------....... ( -39.50)
>DroYak_CAF1 203 99 - 1
GGUGACCACCUCGCUGGUCCAUUACACGCCAGCCAAUUCGCCACCGAUUGCGGCCGUAGCUGCUG---CCG------------CUGCAGCAGCCGCCGGACGAGCAG------CAGCUGU
(((....)))..(((.((((.......(((.((....(((....)))..))))).(..(((((((---(..------------..))))))))..).)))).)))..------....... ( -39.60)
>DroAna_CAF1 6063 99 - 1
CGUGACUACUCCAUUGGUGCAUUAUACUCCGGCCAAUUCGCCGCCGAUAGCGGCUGUAGCUGCCG---UAG------------CUGCAGCAGCCGCCGGACGGGCUG------CGGCCGU
.(((((((......)))).))).......(((((.....(((((.....)))))((((((((...---)))------------)))))((((((........)))))------)))))). ( -42.40)
>consensus
GGUGACCACCCCGCUGGUCCAUUAUACACCAGCCAAUUCGCCACCGAUUGCGGCCGUAGCUGCUG___CCG____________CUGCAGCAGCCGCCGGACGAGCUG______CAGCUGU
.((((.......((((((.........))))))....)))).........((((.((.(((((......................))))).)).))))...................... (-20.86 = -21.17 +   0.31)

alignment

secondary structure

dotplot

Window 2

Location	7,772,687 – 7,772,780
Length	93
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	68.13
Mean single sequence MFE	-42.93
Consensus MFE	-18.02
Energy contribution	-18.52
Covariance contribution	0.50
Combinations/Pair	1.47
Mean z-score	-2.30
Structure conservation index	0.42
SVM decision value	1.90
SVM RNA-class probability	0.981784
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7772687 93 + 22224390
---------CGG---CAGCAGCUACGGCCGCAAUCGUUGGCGAAUUGGCUGGCGUGUAUUGGACCAGCGAGCUGGUCACCGCAGCCGA------CGGAACAUACUUGUUG---C
---------(((---(.((.((....)).))...(((..((......))..)))(((....((((((....))))))...))))))).------.(.((((....)))).---) ( -36.50)
>DroVir_CAF1 228 102 + 1
CAGCCGCUGCAG---CGGCCGCAACAGCCGCUAUUGGCGGCGAAUUGGCUGGUGUAUAAUGCACCAUCGGUGUGCUAACACCAGCCGG---------UGCAUAUUCCUUAAAGG
..((((((..((---((((.......))))))...))))))(.((((((((((((.((..(((((...)))))..)))))))))))))---------).).............. ( -49.10)
>DroEre_CAF1 5311 93 + 1
---------CGG---CAGCAGCUACGGCCGCAAUAGGUGGCGAAUUGGCUGGUGUAUAAUGGACCAGCGAGGUGGUCACCGCAGCCGG------UGCUGCAUACUUGUUG---C
---------(((---(((((((..((((.((....((((((.(.((.((((((.(.....).)))))).)).).)))))))).)))).------.))))).....)))))---. ( -42.30)
>DroWil_CAF1 234 98 + 1
---------CUGCCACAGCAGCCACAGCUGAAAUUGGCGGCGAAUUGGCUGGUGUAUAAUGCACCACGGGAGUGCUCACUGUUGCCGGUUGCUGUGGGGAAUAUUUG-------
---------...(((((((((((...(((......)))(((((..((((.(((((.....)))))((....)))).))...))))))))))))))))..........------- ( -43.20)
>DroYak_CAF1 234 99 + 1
---------CGG---CAGCAGCUACGGCCGCAAUCGGUGGCGAAUUGGCUGGCGUGUAAUGGACCAGCGAGGUGGUCACCGCAGCCGGUGGCGGUGGUGCAUACUUGUUG---C
---------..(---(((((((.((.(((((.((((((.((......((((((........).)))))..(((....))))).)))))).))))).)))).....)))))---) ( -43.60)
>DroMoj_CAF1 7188 102 + 1
CGGCCGCCGCAG---CAGCGGCCACAGCGGCUAUUGGUGGUGAAUUGGCCGGCGUAUAGUGCACCAUCGGUGUGGUGACACCAGCGGG---------UGCAUACUCCUUGAAUG
.(((((((((..---..)))))..((.((.(....).)).))....))))((.((...(((((((....(.(((....))))....))---------))))))).))....... ( -42.90)
>consensus
_________CGG___CAGCAGCUACAGCCGCAAUUGGUGGCGAAUUGGCUGGCGUAUAAUGCACCAGCGAGGUGGUCACCGCAGCCGG______UGGUGCAUACUUGUUG___C
...................(((((..(((((.....)))))....)))))(((........((((((....))))))......)))............................ (-18.02 = -18.52 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	7,772,687 – 7,772,780
Length	93
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	68.13
Mean single sequence MFE	-36.93
Consensus MFE	-13.74
Energy contribution	-14.68
Covariance contribution	0.95
Combinations/Pair	1.24
Mean z-score	-2.14
Structure conservation index	0.37
SVM decision value	1.23
SVM RNA-class probability	0.934226
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7772687 93 - 22224390
G---CAACAAGUAUGUUCCG------UCGGCUGCGGUGACCAGCUCGCUGGUCCAAUACACGCCAGCCAAUUCGCCAACGAUUGCGGCCGUAGCUGCUG---CCG---------
(---((.((..((((..(((------(.(((((((((((((((....))))))....)).)).)))))...(((....)))..)))).))))..)).))---)..--------- ( -32.70)
>DroVir_CAF1 228 102 - 1
CCUUUAAGGAAUAUGCA---------CCGGCUGGUGUUAGCACACCGAUGGUGCAUUAUACACCAGCCAAUUCGCCGCCAAUAGCGGCUGUUGCGGCCG---CUGCAGCGGCUG
.......((........---------))(((((((((..((((.......)))).....))))))))).....(((((...(((((((((...))))))---)))..))))).. ( -47.30)
>DroEre_CAF1 5311 93 - 1
G---CAACAAGUAUGCAGCA------CCGGCUGCGGUGACCACCUCGCUGGUCCAUUAUACACCAGCCAAUUCGCCACCUAUUGCGGCCGUAGCUGCUG---CCG---------
.---......(((.(((((.------.(((((((((((........((((((.........))))))........))))....)))))))..)))))))---)..--------- ( -36.89)
>DroWil_CAF1 234 98 - 1
-------CAAAUAUUCCCCACAGCAACCGGCAACAGUGAGCACUCCCGUGGUGCAUUAUACACCAGCCAAUUCGCCGCCAAUUUCAGCUGUGGCUGCUGUGGCAG---------
-------..........((((((((...(((...(((....)))....(((((.......)))))))).....(((((...........)))))))))))))...--------- ( -31.30)
>DroYak_CAF1 234 99 - 1
G---CAACAAGUAUGCACCACCGCCACCGGCUGCGGUGACCACCUCGCUGGUCCAUUACACGCCAGCCAAUUCGCCACCGAUUGCGGCCGUAGCUGCUG---CCG---------
(---((.......))).....((.((.((((((((((.........((((((.........)))))).....(((........))))))))))))).))---.))--------- ( -32.20)
>DroMoj_CAF1 7188 102 - 1
CAUUCAAGGAGUAUGCA---------CCCGCUGGUGUCACCACACCGAUGGUGCACUAUACGCCGGCCAAUUCACCACCAAUAGCCGCUGUGGCCGCUG---CUGCGGCGGCCG
.......((.(((((((---------((...((((((....))))))..))))))...))).))((........)).......(((((((..((....)---)..))))))).. ( -41.20)
>consensus
G___CAACAAGUAUGCACCA______CCGGCUGCGGUGACCACCCCGCUGGUCCAUUAUACACCAGCCAAUUCGCCACCAAUUGCGGCCGUAGCUGCUG___CCG_________
............................(((((..(((((((......)))))......))..)))))...............(((((....)))))................. (-13.74 = -14.68 +   0.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:21 2006