Locus 484

Sequence ID 3L_DroMel_CAF1
Location 1,363,736 – 1,363,882
Length 146
Max. P 0.983464
window716 window717 window718 window719

overview

Window 6

Location 1,363,736 – 1,363,846
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.74
Mean single sequence MFE -31.32
Consensus MFE -27.46
Energy contribution -27.46
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.88
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1363736 110 + 23771897
-----CUC----G-UAACAAGCUUUACGAUAAGCAUACACAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAUG
-----.((----(-(((......))))))..............(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))...... ( -31.70)
>DroSec_CAF1 19052 110 + 1
-----CUC----G-ACACAACCUUUACGAUAAGGAAACACAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAUG
-----...----.-......((((......)))).........(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))...... ( -30.80)
>DroEre_CAF1 20080 110 + 1
-----AUC----C-UAAUAUCAUUUAUGAUAAUCAAACACAACUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAUG
-----...----.-...(((((....)))))............(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))...... ( -29.60)
>DroYak_CAF1 20780 110 + 1
-----CUC----G-AAAUAAUAUUUUUGAUAAACAAACACAACUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAUG
-----.((----(-(((......))))))..............(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))...... ( -30.20)
>DroAna_CAF1 20347 118 + 1
UUUUAAUCCUUUUGCAACACUGUUUGAGAC-GCCAUUUUCAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAACCU-
.............((....(((..(((((.-(((...........((((........))))...((....))))))))))..)))...))(((((.......)))))...((....)).- ( -34.30)
>consensus
_____CUC____G_AAACAACAUUUACGAUAAGCAAACACAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAUG
...........................................(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))...... (-27.46 = -27.46 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,363,736 – 1,363,846
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.74
Mean single sequence MFE -34.06
Consensus MFE -30.32
Energy contribution -30.60
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -1.80
Structure conservation index 0.89
SVM decision value 0.95
SVM RNA-class probability 0.887812
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1363736 110 - 23771897
CAUAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUGUGUAUGCUUAUCGUAAAGCUUGUUA-C----GAG-----
((((..(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))..))))........((((((......)))-)----)).----- ( -36.30)
>DroSec_CAF1 19052 110 - 1
CAUAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUGUGUUUCCUUAUCGUAAAGGUUGUGU-C----GAG-----
((((..(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))..))))...((((......))))......-.----...----- ( -33.70)
>DroEre_CAF1 20080 110 - 1
CAUAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAGUUGUGUUUGAUUAUCAUAAAUGAUAUUA-G----GAU-----
((((.((((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))).))))((((((.((((....))))))))-)----)..----- ( -34.70)
>DroYak_CAF1 20780 110 - 1
CAUAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAGUUGUGUUUGUUUAUCAAAAAUAUUAUUU-C----GAG-----
((((.((((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))).))))((((.....))))..........-.----...----- ( -32.20)
>DroAna_CAF1 20347 118 - 1
-AGGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUGAAAAUGGC-GUCUCAAACAGUGUUGCAAAAGGAUUAAAA
-.((((((((.....)))))((..((((((.....))))))..)))))....(((((........((((...((((((...........-)))))).....)))).....)))))..... ( -33.42)
>consensus
CAUAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUGUGUUUGCUUAUCAUAAAGAUUGUUA_C____GAG_____
((((..(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))..))))..................................... (-30.32 = -30.60 +   0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,363,766 – 1,363,882
Length 116
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 84.21
Mean single sequence MFE -28.95
Consensus MFE -27.45
Energy contribution -27.45
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.25
Structure conservation index 0.95
SVM decision value 0.23
SVM RNA-class probability 0.643612
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1363766 116 + 23771897
AAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAUGGUUUCAGAUCUUUUUUCAACA---UUAUUUUAAAAUGAA
...(((((((.(((((........))))).((((.....((((((.....)))))).......))))))))))).........................((---((.......)))).. ( -27.80)
>DroEre_CAF1 20110 117 + 1
AACUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAUGGAUGCUCA--UUUUUUUAUCGCGUAUAUUUUUAAAUUUA
...(((((((.(((((........))))).((((.....((((((.....)))))).......))))))))))).(((((((((....--......)))).)))))............. ( -30.80)
>DroYak_CAF1 20810 116 + 1
AACUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAUGAAUGCACAAUUUUUUUUAUCG---GUAUUUUAAAAUUUA
...(((((((.(((((........))))).((((.....((((((.....)))))).......))))))))))).....((((((.(.((.......)).)---))))))......... ( -28.40)
>DroAna_CAF1 20386 101 + 1
AAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAACCU-------------UUUUUAUAA----CAUU-UUAAAUUAA
...(((((((.(((((........))))).((((.((..((((((.....))))))..))...))))))))))).....-------------.........----....-......... ( -28.80)
>consensus
AACUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUAUGGAUGCACA__UUUUUUUAUCA____UAUUUUAAAAUUAA
...(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))............................................. (-27.45 = -27.45 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,363,766 – 1,363,882
Length 116
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 84.21
Mean single sequence MFE -29.10
Consensus MFE -28.89
Energy contribution -28.70
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.97
Structure conservation index 0.99
SVM decision value 1.94
SVM RNA-class probability 0.983464
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1363766 116 - 23771897
UUCAUUUUAAAAUAA---UGUUGAAAAAAGAUCUGAAACCAUAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUU
...............---...........................(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))... ( -28.10)
>DroEre_CAF1 20110 117 - 1
UAAAUUUAAAAAUAUACGCGAUAAAAAAA--UGAGCAUCCAUAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAGUU
.................((..........--...))........((((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))).. ( -29.62)
>DroYak_CAF1 20810 116 - 1
UAAAUUUUAAAAUAC---CGAUAAAAAAAAUUGUGCAUUCAUAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAGUU
...............---..........................((((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))).. ( -28.80)
>DroAna_CAF1 20386 101 - 1
UUAAUUUAA-AAUG----UUAUAAAAA-------------AGGUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUU
.........-....----.........-------------.....(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))... ( -29.90)
>consensus
UAAAUUUAAAAAUA____CGAUAAAAAAA__UGUGCAUCCAUAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUU
.............................................(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))... (-28.89 = -28.70 +  -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 09:43:08 2006