Locus 7419

Sequence ID 3R_DroMel_CAF1
Location 19,745,903 – 19,746,033
Length 130
Max. P 0.996010
window11993 window11994 window11995

overview

Window 3

Location 19,745,903 – 19,745,993
Length 90
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 81.79
Mean single sequence MFE -32.67
Consensus MFE -20.65
Energy contribution -20.43
Covariance contribution -0.22
Combinations/Pair 1.32
Mean z-score -2.41
Structure conservation index 0.63
SVM decision value 0.63
SVM RNA-class probability 0.805336
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19745903 90 - 27905053
CAAUAAAGUCAGCGGCAACAACGGGAGUAACGGCAGCAACUGUUGCUGCUGCAA---CUGC---UGCUACUGGGGCAACGCAUUGCAUGUCGAC------AA
.......(((.(((((((...(((.(((..((((((((.....))))))))..)---)).)---))....((.(....).)))))).))).)))------.. ( -32.10)
>DroSec_CAF1 13130 90 - 1
CAAUAAAGUCAGUGGCAACAACGGGAGUAACGGCGGCAACUGUUGCUGCUGCAA---CGGC---UGCUACUGGGGCAACGCAUUGCAUGUCGAC------AA
.......(((.(..(((.((((((..((.......))..)))))).)))..)..---.(((---(((...((.(....).))..))).))))))------.. ( -31.40)
>DroSim_CAF1 15268 90 - 1
CAAUAAAGUCAGCGGCAACAACGGGAGUAACGGCGGCAACUGUUGCUGCUGCAA---CGGC---UGCUACUGGGGCAACGCAUUGCAUGUCGAC------AA
.......(((.((((((.((((((..((.......))..)))))).))))))..---.(((---(((...((.(....).))..))).))))))------.. ( -33.90)
>DroEre_CAF1 26202 90 - 1
CAAUAAAGUCAGCGGCAACAACGGGAGCAACGGCAGCAACUGUUGCUGCUGCAA---CUGC---UGCUACUGGGGCAACGCAUUGCAUGUCGAC------AA
.......((((((((((....(((.((((((((......)))))))).)))...---.)))---))))..((.(....).)).........)))------.. ( -33.60)
>DroYak_CAF1 26378 99 - 1
CAAUAAAGUCAGCGGCAACAACGGGAGUAACGGCAGCAACUGUUGCUGCUGCAA---CUGCUACUGCUACUGGGGCAACGCAUUGCAUGUCCACAACAACAA
.........(((..(((.....((.(((..((((((((.....))))))))..)---)).))..)))..)))(((((..((...)).))))).......... ( -30.20)
>DroAna_CAF1 26488 81 - 1
CAGUUAAAUCGACGG---------------CGGCGGCAACUGUUGCUGCUGCUGUCUCCGUCACUGUUGCUAGUGCGGCGCAUUGCCUGCCGAC------AA
..........(((((---------------((((((((.....)))))))))))))...(((...(((((....)))))(((.....))).)))------.. ( -34.80)
>consensus
CAAUAAAGUCAGCGGCAACAACGGGAGUAACGGCAGCAACUGUUGCUGCUGCAA___CUGC___UGCUACUGGGGCAACGCAUUGCAUGUCGAC______AA
............(((((..............(((((((.....)))))))((((.....((...((((.....))))..)).)))).))))).......... (-20.65 = -20.43 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 19,745,935 – 19,746,033
Length 98
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 68.36
Mean single sequence MFE -28.62
Consensus MFE -12.48
Energy contribution -14.93
Covariance contribution 2.45
Combinations/Pair 1.17
Mean z-score -1.61
Structure conservation index 0.44
SVM decision value 0.12
SVM RNA-class probability 0.594432
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19745935 98 + 27905053
-GCAG---UUGCAGCAGCAACAGUUGCUGCCGUUACUCCCGUUGUUGCCGCUGACUUUAUUGGCAACUUUAUUUGCGCCUGGCGCUGUUUGGUUUGUUGCUG
-.(((---(.((((((((...(((.((....)).)))...)))))))).))))........((((((.(((...((((...))))....)))...)))))). ( -31.00)
>DroVir_CAF1 26525 74 + 1
-ACA------------------GUUGCUGCU---------GCGGCUGCUGCUGACUUUAAAGGCAACUUUAUUUGUGCAGCACGCUGUUUGGUUUGCUGUUG
-(((------------------((.(((...---------(((((((((((......(((((....))))).....)))))).)))))..)))..))))).. ( -30.30)
>DroSec_CAF1 13162 98 + 1
-GCCG---UUGCAGCAGCAACAGUUGCCGCCGUUACUCCCGUUGUUGCCACUGACUUUAUUGGCAACUUUAUUUGCGCCUGGCGCUGUUUGGUUUGUUGCUG
-....---...(((((((((((((.((((.(((..........(((((((.((....)).))))))).......))).).))))))))......)))))))) ( -30.13)
>DroYak_CAF1 26418 99 + 1
AGCAG---UUGCAGCAGCAACAGUUGCUGCCGUUACUCCCGUUGUUGCCGCUGACUUUAUUGGCAACUUUAUUUGCGCCUGGCGCUGUUUGGUUUGUUGCUG
(((((---..((((((((....))))))))........(((..(((((((.((....)).))))))).......((((...))))....)))....))))). ( -31.50)
>DroMoj_CAF1 26812 74 + 1
-ACA------------------GUUGCCGAU---------GUGUUUGCUGCUGGUUUCACAGGCAACUUUAUUUGUGCUGUACGCUGCUUAGCUUGUUGCUG
-..(------------------((((((..(---------(((...((.....))..)))))))))))........((..((.(((....))).))..)).. ( -18.10)
>DroAna_CAF1 26522 87 + 1
GACGGAGACAGCAGCAGCAACAGUUGCCGCCG---------------CCGUCGAUUUAACUGGCAACUUUAUUUGCGCCUGGCGCUGUUUGGCUUGCUGCUG
........((((((((((((.((((((((...---------------.............))))))))....))))(((..((...))..))).)))))))) ( -30.69)
>consensus
_ACAG___UUGCAGCAGCAACAGUUGCCGCCG________GUUGUUGCCGCUGACUUUAUUGGCAACUUUAUUUGCGCCUGGCGCUGUUUGGUUUGUUGCUG
...........(((((((((..((((((.................................)))))).......(((.....)))........))))))))) (-12.48 = -14.93 +   2.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 19,745,935 – 19,746,033
Length 98
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 68.36
Mean single sequence MFE -27.36
Consensus MFE -10.63
Energy contribution -13.58
Covariance contribution 2.94
Combinations/Pair 1.17
Mean z-score -2.76
Structure conservation index 0.39
SVM decision value 2.64
SVM RNA-class probability 0.996010
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19745935 98 - 27905053
CAGCAACAAACCAAACAGCGCCAGGCGCAAAUAAAGUUGCCAAUAAAGUCAGCGGCAACAACGGGAGUAACGGCAGCAACUGUUGCUGCUGCAA---CUGC-
..((......((.....((((...)))).......((((((............))))))...)).(((..((((((((.....))))))))..)---))))- ( -31.50)
>DroVir_CAF1 26525 74 - 1
CAACAGCAAACCAAACAGCGUGCUGCACAAAUAAAGUUGCCUUUAAAGUCAGCAGCAGCCGC---------AGCAGCAAC------------------UGU-
..............((((..((((((.........((((.((....)).)))).((....))---------.)))))).)------------------)))- ( -18.90)
>DroSec_CAF1 13162 98 - 1
CAGCAACAAACCAAACAGCGCCAGGCGCAAAUAAAGUUGCCAAUAAAGUCAGUGGCAACAACGGGAGUAACGGCGGCAACUGUUGCUGCUGCAA---CGGC-
((((......((.....((((...)))).......(((((((..........)))))))...)).((((((((......))))))))))))...---....- ( -31.20)
>DroYak_CAF1 26418 99 - 1
CAGCAACAAACCAAACAGCGCCAGGCGCAAAUAAAGUUGCCAAUAAAGUCAGCGGCAACAACGGGAGUAACGGCAGCAACUGUUGCUGCUGCAA---CUGCU
.(((......((.....((((...)))).......((((((............))))))...)).(((..((((((((.....))))))))..)---))))) ( -33.20)
>DroMoj_CAF1 26812 74 - 1
CAGCAACAAGCUAAGCAGCGUACAGCACAAAUAAAGUUGCCUGUGAAACCAGCAGCAAACAC---------AUCGGCAAC------------------UGU-
..((.....(((....))).....))........(((((((((((..............)))---------)..))))))------------------)..- ( -15.94)
>DroAna_CAF1 26522 87 - 1
CAGCAGCAAGCCAAACAGCGCCAGGCGCAAAUAAAGUUGCCAGUUAAAUCGACGG---------------CGGCGGCAACUGUUGCUGCUGCUGUCUCCGUC
((((((((((((.....((((...)))).......((((((.(((.....)))))---------------))))))).....)))))))))........... ( -33.40)
>consensus
CAGCAACAAACCAAACAGCGCCAGGCGCAAAUAAAGUUGCCAAUAAAGUCAGCGGCAACAAC________CGGCAGCAACUGUUGCUGCUGCAA___CUGC_
((((((((.........((((...)))).......((((((..............................))))))...)))))))).............. (-10.63 = -13.58 +   2.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:32 2006