Locus 7739

Sequence ID 3L_DroMel_CAF1
Location 20,644,142 – 20,644,308
Length 166
Max. P 0.988358
window12602 window12603 window12604

overview

Window 2

Location 20,644,142 – 20,644,239
Length 97
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 90.40
Mean single sequence MFE -19.16
Consensus MFE -17.70
Energy contribution -17.48
Covariance contribution -0.22
Combinations/Pair 1.16
Mean z-score -1.10
Structure conservation index 0.92
SVM decision value 0.07
SVM RNA-class probability 0.566827
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20644142 97 - 23771897
UUAUGCGUUUGUGUGUAGACAAAAUAGAAAAACACAAAAAAACGAGCAAAUUGUUGUUUGUUUAAGGCGCCGCUUUGAAUGGAGAUAAAAAUCUCGG
....((((((((((.................))))))..((((((((((....))))))))))...))))...........(((((....))))).. ( -21.43)
>DroSec_CAF1 17261 95 - 1
ACAUGCGUUUGUGUGUAGACAAAAUAAAAAAACACAA--AAACGGGCAAAUUGUUGUUUGUUUAAGGCGCCGCUUUGAAUGGAGAUAAAAAUCUCGG
.(((.(((((.(((((...............))))).--))))).((((((....))))))(((((((...))))))))))(((((....))))).. ( -20.56)
>DroSim_CAF1 20564 95 - 1
ACAUGCGUUUGUGUGUAGACAAAAUAGAAAAACACAA--AAACGGGCAAAUUGUUGUUUGUUUAAGGCGCCGCUUUGAAUGGAGAUAAAAAUCUCGG
.(((.(((((.(((((...............))))).--))))).((((((....))))))(((((((...))))))))))(((((....))))).. ( -20.56)
>DroEre_CAF1 6112 93 - 1
--AUGCGUUUGUGUGUAGACAAAAUAGAAAAAUACAA-AAAACGGGCAAAUUGUUGUUUGUUUAAGGCGCCGCUUUGAAUGGAGAUA-AAAUCUCGG
--..((((((((((.................))))))-.((((((((((....))))))))))...))))...........(((((.-..))))).. ( -17.53)
>DroYak_CAF1 197256 94 - 1
--AUGCGUUUGAAUGUAGACAAAAUAGAAAAAAUCAA-AAAACGGGCAAAUUGUUGUUUGUUUAAGGCGCCGCUUUGAAUGGAGAUACAAAUCUCGG
--...((((..((.(..(.(......((.....))..-.((((((((((....)))))))))).....))..)))..))))(((((....))))).. ( -16.90)
>DroAna_CAF1 16709 92 - 1
--AUGCGUUAGUGUGUGGACAAAAUAAAA-UAUAAA--AAAACGGGCAAAUUGUUGUUUGUUUAAGGCGCCGCUAUGAAUCGAGAUAAAUAUCUUGA
--..(((((..(((((............)-))))..--.((((((((((....))))))))))..))))).........(((((((....))))))) ( -18.00)
>consensus
__AUGCGUUUGUGUGUAGACAAAAUAGAAAAACACAA_AAAACGGGCAAAUUGUUGUUUGUUUAAGGCGCCGCUUUGAAUGGAGAUAAAAAUCUCGG
....((((((((((.................))))....((((((((((....)))))))))).))))))...........(((((....))))).. (-17.70 = -17.48 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,644,169 – 20,644,268
Length 99
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 90.63
Mean single sequence MFE -23.82
Consensus MFE -20.97
Energy contribution -21.33
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -2.53
Structure conservation index 0.88
SVM decision value 2.12
SVM RNA-class probability 0.988358
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20644169 99 - 23771897
UGGCACGCAAAUGUAUCUUCAAGAUACAUUUAUGCGUUUGUGUGUAGACAAAAUAGAAAAACACAAAAAAACGAGCAAAUUGUUGUUUGUUUAAGGCGC
..(((((((((((((((.....))))))))..)))))((((((.................))))))..((((((((((....))))))))))...)).. ( -27.53)
>DroSec_CAF1 17288 97 - 1
UGGCACGCAAAUGUAUCUUUACGAUACAUACAUGCGUUUGUGUGUAGACAAAAUAAAAAAACACAA--AAACGGGCAAAUUGUUGUUUGUUUAAGGCGC
..(((((((.(((((((.....)))))))...)))))((((((.................))))))--((((((((((....))))))))))...)).. ( -25.13)
>DroSim_CAF1 20591 97 - 1
UGGCACGCAAAUGUAUCUUCAAGAUACAUACAUGCGUUUGUGUGUAGACAAAAUAGAAAAACACAA--AAACGGGCAAAUUGUUGUUUGUUUAAGGCGC
..(((((((.(((((((.....)))))))...)))))((((((.................))))))--((((((((((....))))))))))...)).. ( -25.43)
>DroEre_CAF1 6138 94 - 1
UGGCACGCAAAUGUAUCUUCGAGAUAC----AUGCGUUUGUGUGUAGACAAAAUAGAAAAAUACAA-AAAACGGGCAAAUUGUUGUUUGUUUAAGGCGC
..((((((((((((((...........----)))))))))))))).....................-.((((((((((....))))))))))....... ( -23.20)
>DroYak_CAF1 197283 94 - 1
UGGCACGCAAAUGUAUCUUCAAGAUAC----AUGCGUUUGAAUGUAGACAAAAUAGAAAAAAUCAA-AAAACGGGCAAAUUGUUGUUUGUUUAAGGCGC
..(((((((..((((((.....)))))----)))))).............................-.((((((((((....))))))))))...)).. ( -20.70)
>DroAna_CAF1 16736 92 - 1
UGGCACGCAAAUGUAUCUUCAAGAUAC----AUGCGUUAGUGUGUGGACAAAAUAAAA-UAUAAA--AAAACGGGCAAAUUGUUGUUUGUUUAAGGCGC
(.((((((..(((((((.....)))))----))......)))))).)...........-......--.((((((((((....))))))))))....... ( -20.90)
>consensus
UGGCACGCAAAUGUAUCUUCAAGAUAC____AUGCGUUUGUGUGUAGACAAAAUAGAAAAACACAA_AAAACGGGCAAAUUGUUGUUUGUUUAAGGCGC
..((((((((((((((...............)))))))))))))).......................((((((((((....))))))))))....... (-20.97 = -21.33 +   0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,644,205 – 20,644,308
Length 103
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 78.05
Mean single sequence MFE -22.87
Consensus MFE -10.17
Energy contribution -10.33
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.44
SVM decision value 0.79
SVM RNA-class probability 0.850782
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20644205 103 - 23771897
UAGCCGCACAAUUGAUAUGUUAAGUGGUAAAUUACGCCAUUGGCACGCAAAUGUAUCUUCAA-----------GAUACAUUUAUGCGUUUGUGUGUAGACAAAAUAGAAAAACA-
....(((((((.......(((((.((((.......)))))))))(((((((((((((.....-----------))))))))..))))))))))))...................- ( -27.40)
>DroPse_CAF1 23451 88 - 1
UAGCCGCACAAUUGAUAUGUUAAGUGGUAAAUUACUCCAUUGGCACGCAAAUGUAUCUUGAA----------CAAUACAAAUA----------------C-AAAUACAAAUACAA
..(((..(((.......)))..(((((.........)))))))).......(((((.(((..----------.....))))))----------------)-)............. (  -9.90)
>DroSec_CAF1 17322 103 - 1
UAGCCGCACAAUUGAUAUGUUAAGUGGUAAAUUACGCCAUUGGCACGCAAAUGUAUCUUUAC-----------GAUACAUACAUGCGUUUGUGUGUAGACAAAAUAAAAAAACA-
....(((((((.......(((((.((((.......)))))))))(((((.(((((((.....-----------)))))))...))))))))))))...................- ( -25.90)
>DroWil_CAF1 11539 109 - 1
UAGCCGCACAAUUGAUAUGUUAAGUGGUAAAUUACGCCAUUGGCACGCAAAUGUGUCUUGAUAUAAAUUGAAAAAAAUAUAUAUACAUAGGUAUAUAAA--AAUGAGGAAA----
...((.(((((((..(((((((((((((.......))))))((((((....)))))).)))))))))))).........(((((((....)))))))..--..)).))...---- ( -23.20)
>DroYak_CAF1 197318 99 - 1
UAGCCGCACAAUUGAUAUGUUAAGUGGUAAAUUACGCCAUUGGCACGCAAAUGUAUCUUCAA-----------GAUAC----AUGCGUUUGAAUGUAGACAAAAUAGAAAAAAU-
..(((((..(((......)))..)))))...(((((((...)))(((((..((((((.....-----------)))))----))))))......))))................- ( -22.10)
>DroAna_CAF1 16770 98 - 1
UAGCCGCACAAUUGAUAUGUUAAGUGGUAAAUUACGCCAUUGGCACGCAAAUGUAUCUUCAA-----------GAUAC----AUGCGUUAGUGUGUGGACAAAAUAAAA-UAUA-
..((((((((.(((((.((((((.((((.......)))))))))).(((..((((((.....-----------)))))----)))))))))))))))).).........-....- ( -28.70)
>consensus
UAGCCGCACAAUUGAUAUGUUAAGUGGUAAAUUACGCCAUUGGCACGCAAAUGUAUCUUCAA___________GAUACAUAUAUGCGUUUGUGUGUAGACAAAAUAGAAAAACA_
.......(((.(((...((((((.((((.......))))))))))..))).)))............................................................. (-10.17 = -10.33 +   0.17)

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 12:55:38 2006