Locus 1469

Sequence ID 3R_DroMel_CAF1
Location 4,238,982 – 4,239,105
Length 123
Max. P 0.943482
window2443 window2444 window2445

overview

Window 3

Location 4,238,982 – 4,239,076
Length 94
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 79.60
Mean single sequence MFE -26.13
Consensus MFE -19.20
Energy contribution -20.09
Covariance contribution 0.89
Combinations/Pair 1.05
Mean z-score -1.76
Structure conservation index 0.73
SVM decision value 0.91
SVM RNA-class probability 0.878802
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4238982 94 + 27905053
-AUAUGU--AUGUAUGUACCUAUAAAAUGGGUGCAUGGAAACAUUCGCUCACGCAAUGAUUUAUUACGCGUGAUUGGCGUGAUUGCCACUUUGCUGC
-..((((--.(.(((((((((((...))))))))))).).))))..((((((((.............)))))).(((((....)))))....))... ( -29.92)
>DroSec_CAF1 40910 90 + 1
-AUAUGUGUAUAUAU------AUAAAAUGGGUGCAUGGAAACAUUCGCUCACGCAAUGAUUUAUUACGCGUGAUUGGCGUGAUUGCCACUUUGCUGC
-.((((((....)))------)))...((((((.(((....))).)))))).((((......(((((((.......))))))).......))))... ( -24.62)
>DroSim_CAF1 41984 96 + 1
-AUAUGUGUAUGUAUGUACCUAUAAAAUGGGUGCAUGGAAACAUUCGCUCACGCAAUGAUUUAUUACGCGUGAUUGGCGUGAUUGCCACUUUGCUGC
-....((((.(.(((((((((((...))))))))))).).))))..((((((((.............)))))).(((((....)))))....))... ( -30.22)
>DroYak_CAF1 42074 95 + 1
UAUAUAC--UUGUAUAUCCCUAUAAAAUGGGCGCAUGGAAACAUUCGCUCACGCAAUGAUUUAUUACGCGUGAUUGGCGUGAUUGCCACUUUGCUGC
.(((((.--...)))))..........((((((.(((....))).)))))).((((......(((((((.......))))))).......))))... ( -25.92)
>DroAna_CAF1 43283 94 + 1
-GUUGGGGUGCGUGUGUAGGUUU--UGGGGGUGCUGGGCAACAUUCGCUCACGCAAUGAUUUAUUACGCGUGAUUGGCGUGAUUGCCACUUUGCUGC
-((..((..((((((((((((((--((((((((...(....)...))))).).))).)))))).)))))))...(((((....)))))))..))... ( -27.80)
>DroPer_CAF1 46388 76 + 1
CC-------------CUCCCU--------CGCACAUGCGGACAUUCACUCACGCAAUGAUUUAUUACGCGUGAUUGGCGUGAUUGCCACUUUGCUGC
..-------------......--------.(((...(.((.((.((((((((((.............)))))).....)))).)))).)..)))... ( -18.32)
>consensus
_AUAUGU__AUGUAUGUACCUAUAAAAUGGGUGCAUGGAAACAUUCGCUCACGCAAUGAUUUAUUACGCGUGAUUGGCGUGAUUGCCACUUUGCUGC
............................(((((.(((....))).)))))..((((......(((((((.......))))))).......))))... (-19.20 = -20.09 +   0.89)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,238,982 – 4,239,076
Length 94
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 79.60
Mean single sequence MFE -21.68
Consensus MFE -16.99
Energy contribution -17.05
Covariance contribution 0.06
Combinations/Pair 1.11
Mean z-score -1.75
Structure conservation index 0.78
SVM decision value 0.97
SVM RNA-class probability 0.891893
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4238982 94 - 27905053
GCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGCGAAUGUUUCCAUGCACCCAUUUUAUAGGUACAUACAU--ACAUAU-
...((....((((......)))).(((((((...........)))))))))..((((....(((.(((.........))).)))....--))))..- ( -22.10)
>DroSec_CAF1 40910 90 - 1
GCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGCGAAUGUUUCCAUGCACCCAUUUUAU------AUAUAUACACAUAU-
(((((....((((......)))).(((((((...........)))))))))((.....))..)))...........------..............- ( -18.40)
>DroSim_CAF1 41984 96 - 1
GCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGCGAAUGUUUCCAUGCACCCAUUUUAUAGGUACAUACAUACACAUAU-
...((....((((......)))).(((((((...........)))))))))(.((((....(((.(((.........))).))))))).)......- ( -20.90)
>DroYak_CAF1 42074 95 - 1
GCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGCGAAUGUUUCCAUGCGCCCAUUUUAUAGGGAUAUACAA--GUAUAUA
(((((....((((......)))).(((((((...........)))))))))((.....))..))).(((........)))(((((...--.))))). ( -23.50)
>DroAna_CAF1 43283 94 - 1
GCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGCGAAUGUUGCCCAGCACCCCCA--AAACCUACACACGCACCCCAAC-
((((((...((((......)))).(((((((...........))))))).....))))))............--......................- ( -21.90)
>DroPer_CAF1 46388 76 - 1
GCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGUGAAUGUCCGCAUGUGCG--------AGGGAG-------------GG
...(((..((((((.((((.....(((((((...........))))))))))).)).))))...))).--------......-------------.. ( -23.30)
>consensus
GCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGCGAAUGUUUCCAUGCACCCAUUUUAUAGGUACAUACAU__ACAUAU_
((.((....((((......)))).(((((((...........)))))))))..(((....)))))................................ (-16.99 = -17.05 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,239,000 – 4,239,105
Length 105
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 75.35
Mean single sequence MFE -27.38
Consensus MFE -18.99
Energy contribution -19.10
Covariance contribution 0.11
Combinations/Pair 1.30
Mean z-score -1.65
Structure conservation index 0.69
SVM decision value 1.34
SVM RNA-class probability 0.943482
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4239000 105 - 27905053
GCGACACCGUCG-----GGGCAGCCUGAAAUAAAGCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGCGAAUGUUUCCAUG----CACCCAUUUUAU
..(((...)))(-----(((((....((((((..((.......((((......)))).(((((((...........)))))))))...))))))..))----).)))....... ( -31.70)
>DroPse_CAF1 46018 96 - 1
-GGACACGGAGA-----GGGGAAGCUAAAAUAAGGCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGUGAAUGUCCGCAUG----UGCG--------
-(((((......-----......(((.......))).((....((((......)))).(((((((...........)))))))))...)))))((...----.)).-------- ( -25.70)
>DroGri_CAF1 53140 100 - 1
GGUACAACAGCG-------GGAAGAUGAAAUAAAGCAACAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGUCCAUGCACACAUAUAUUU-------UUAC
.........(((-------(((.....................((((......)))).(((((((...........))))))).))).)))............-------.... ( -21.00)
>DroMoj_CAF1 53903 96 - 1
GUUACAGCAACG-------GGAAGAUGAAAUAAAGCAUCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGUGUAUGCGUGCAUA----C-------UUAU
......(((.((-------.(..((((........))))....((((......)))).(((((((...........))))))).....).)))))...----.-------.... ( -22.40)
>DroAna_CAF1 43303 108 - 1
GCGACACCGCCGCCGGGGAGGAAGUUGAAAUAAAGCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGCGAAUGUUGCCCAG----CACCCCCA--AA
(((....)))....((((..(..((((........))))...(.((((((..(((...(((((((...........))))))))))...)))))))..----)..)))).--.. ( -34.90)
>DroPer_CAF1 46396 96 - 1
-GGACACGGAGA-----GGGGAAGCUGAAAUAAGGCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGUGAAUGUCCGCAUG----UGCG--------
-(((((....((-----..((..((((........))))...(((.....))).))..)).((((((((.....))))))))......)))))((...----.)).-------- ( -28.60)
>consensus
GGGACACCGACG_____GGGGAAGCUGAAAUAAAGCAGCAAAGUGGCAAUCACGCCAAUCACGCGUAAUAAAUCAUUGCGUGAGUGAAUGUCCGCAUG____C_C_______A_
.(((((.................((((........))))....((((......)))).(((((((...........))))))).....)))))..................... (-18.99 = -19.10 +   0.11)

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 10:11:23 2006