Locus 318

Sequence ID 2L_DroMel_CAF1
Location 905,967 – 906,091
Length 124
Max. P 0.903228
window508 window509 window510

overview

Window 8

Location 905,967 – 906,064
Length 97
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 81.10
Mean single sequence MFE -18.93
Consensus MFE -8.27
Energy contribution -8.55
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -3.14
Structure conservation index 0.44
SVM decision value 0.61
SVM RNA-class probability 0.799664
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 905967 97 + 22407834
CGCAUGC---AUGUAAAUAAAUA----CAAAUACAUGUGAGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAGUCU
.((.(((---(((((........----....)))))))).)).....(((((......)))))((((.(((((((((........))))))))).))))..... ( -23.00)
>DroVir_CAF1 47304 98 + 1
AACAUGC---ACACACAGAAACACACCCGAAUAAAUAUAAGCAUAAAUAAUAAAAGCAUAUUAGUGUACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAG---
....(((---.(.........(......)...........((((...((((((((((..(((((........)))))..))))))))))..))))).))).--- ( -14.70)
>DroGri_CAF1 36442 86 + 1
AACAUGC---ACACA------------CGAAUAAAUAUAAACAUAAAUAAUAAACGCAUAUUAGUGCACAGUUUAAUUCGUUUUUAUUUAAAAGCAAACAG---
....(((---....(------------(((((...(((........))).(((((((((....))))...)))))))))))((((....))))))).....--- (  -8.70)
>DroSim_CAF1 32903 97 + 1
CGCUUGC---AUGUAAAUAAAUA----CAAAUACAUGUGAGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAAGCGCGCAGUCU
.(((..(---(((((........----....))))))..))).....(((((......)))))((((.(.(((((((........))))))).).))))..... ( -23.60)
>DroYak_CAF1 36273 97 + 1
CGCAUGC---AUGUAAAUAAAUA----CAAAUACAUGUGCGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAAGCGCGCAGUCU
.((..((---(((((........----....)))))))((((.....((((((((((..(((((........)))))..))))))))))....))))))..... ( -23.70)
>DroAna_CAF1 33944 96 + 1
AACAUGCAACAUGCAAAUAAAUA----CAGAUA----UAAGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAGCAU
...((((...((((..(((....----....))----)..))))...................((((.(((((((((........))))))))).)))).)))) ( -19.90)
>consensus
AACAUGC___AUGCAAAUAAAUA____CAAAUACAUGUAAGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAAGCGCGCAGUCU
........................................((.....((((((((((..(((((........)))))..))))))))))....))......... ( -8.27 =  -8.55 +   0.28) 

alignment

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secondary structure

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Window 9

Location 905,992 – 906,091
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 80.60
Mean single sequence MFE -21.08
Consensus MFE -13.52
Energy contribution -13.30
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -2.45
Structure conservation index 0.64
SVM decision value 1.03
SVM RNA-class probability 0.903228
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 905992 99 + 22407834
ACAUGUGAGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAGUCUGUCGAAAGCGGCAAGGUUUUCCCGGGA
...((((.((((...((((((((((..(((((........)))))..))))))))))..)))).)))).((((..((((((......)))))).)))). ( -25.00)
>DroVir_CAF1 47333 79 + 1
AAAUAUAAGCAUAAAUAAUAAAAGCAUAUUAGUGUACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAG---GUAAAAAGCG-----------------
........((.....(((((......)))))(((..(((((((((........)))))))))..)))..---.......)).----------------- ( -14.80)
>DroSec_CAF1 35172 98 + 1
ACAUGUGAGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAGUCUGUCGAAA-UGGCAAGGUUUUCCCGGGG
...((((.((((...((((((((((..(((((........)))))..))))))))))..)))).)))).((((..((((-(......)))))..)))). ( -21.90)
>DroEre_CAF1 42239 98 + 1
ACAUGUGAGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAGUCUGUCGAAAGCGGGAAGGUUUUC-CCGGA
...((((.((((...((((((((((..(((((........)))))..))))))))))..)))).))))......(....)((((((....)))-))).. ( -26.00)
>DroMoj_CAF1 46268 89 + 1
ACAUAUAAACAUAAAUAAUAAAAGCAUAUUAGUGUACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAG---GUAUGAAACAGAAAG-------CGAGA
........................(((((..(((..(((((((((........)))))))))..)))..---)))))..........-------..... ( -17.20)
>DroAna_CAF1 33972 87 + 1
A----UAAGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAGCAUGUCAAGAGCAUG-AGGU-------GGA
.----...((((...((((((((((..(((((........)))))..))))))))))..)))).(((..(((((.....)))))-..))-------).. ( -21.60)
>consensus
ACAUGUAAGCAUAAAUAAUAAAAACAUAUUAGUGCACAUUUUAAUUCGUUUUUAUUAAAAUGCGCGCAGUCUGUCGAAAGCGGCAAGGU_____CGGGA
...............(((((......)))))((((.(((((((((........))))))))).))))................................ (-13.52 = -13.30 +  -0.22) 

alignment

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secondary structure

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Window 0

Location 905,992 – 906,091
Length 99
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 80.60
Mean single sequence MFE -17.23
Consensus MFE -13.42
Energy contribution -13.62
Covariance contribution 0.19
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.78
SVM decision value 0.84
SVM RNA-class probability 0.862693
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 905992 99 - 22407834
UCCCGGGAAAACCUUGCCGCUUUCGACAGACUGCGCGCAUUUUAAUAAAAACGAAUUAAAAUGUGCACUAAUAUGUUUUUAUUAUUUAUGCUCACAUGU
....((.((....)).))((..((....))..))((((((((((((........))))))))))))....((((((...(((.....)))...)))))) ( -20.50)
>DroVir_CAF1 47333 79 - 1
-----------------CGCUUUUUAC---CUGCGCGCAUUUUAAUAAAAACGAAUUAAAAUGUACACUAAUAUGCUUUUAUUAUUUAUGCUUAUAUUU
-----------------(((.......---..))).((((..((((((((.((.((((..........)))).)).))))))))...))))........ ( -10.80)
>DroSec_CAF1 35172 98 - 1
CCCCGGGAAAACCUUGCCA-UUUCGACAGACUGCGCGCAUUUUAAUAAAAACGAAUUAAAAUGUGCACUAAUAUGUUUUUAUUAUUUAUGCUCACAUGU
....((.((....)).)).-.....(((....((((((((((((((........))))))))))))..(((((......))))).....)).....))) ( -18.90)
>DroEre_CAF1 42239 98 - 1
UCCGG-GAAAACCUUCCCGCUUUCGACAGACUGCGCGCAUUUUAAUAAAAACGAAUUAAAAUGUGCACUAAUAUGUUUUUAUUAUUUAUGCUCACAUGU
...((-(((....)))))((..((....))..))((((((((((((........))))))))))))....((((((...(((.....)))...)))))) ( -25.20)
>DroMoj_CAF1 46268 89 - 1
UCUCG-------CUUUCUGUUUCAUAC---CUGCGCGCAUUUUAAUAAAAACGAAUUAAAAUGUACACUAAUAUGCUUUUAUUAUUUAUGUUUAUAUGU
.....-------..........((((.---..(((..(((((((((........)))))))))..)..(((((......))))).....))...)))). ( -10.60)
>DroAna_CAF1 33972 87 - 1
UCC-------ACCU-CAUGCUCUUGACAUGCUGCGCGCAUUUUAAUAAAAACGAAUUAAAAUGUGCACUAAUAUGUUUUUAUUAUUUAUGCUUA----U
...-------....-(((((....).))))..((((((((((((((........))))))))))))..(((((......))))).....))...----. ( -17.40)
>consensus
UCCCG_____ACCUUCCCGCUUUCGACAGACUGCGCGCAUUUUAAUAAAAACGAAUUAAAAUGUGCACUAAUAUGUUUUUAUUAUUUAUGCUCACAUGU
................................((((((((((((((........))))))))))))..(((((......))))).....))........ (-13.42 = -13.62 +   0.19) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:56 2006