Locus 6643

Sequence ID X_DroMel_CAF1
Location 16,574,488 – 16,574,634
Length 146
Max. P 0.999644
window10853 window10854 window10855

overview

Window 3

Location 16,574,488 – 16,574,594
Length 106
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 75.73
Mean single sequence MFE -20.35
Consensus MFE -8.68
Energy contribution -8.72
Covariance contribution 0.04
Combinations/Pair 1.25
Mean z-score -3.22
Structure conservation index 0.43
SVM decision value 3.83
SVM RNA-class probability 0.999644
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16574488 106 + 22224390
AAGAACCAGUAAAAAAAAAAAAUAAAGAACUCACUGAUUCUUUCAGACAUUUGUUUGAACAACGAAGAUAGCAAACAAAUUGCGUCCAUCAAUCAAGAUG-GUCAAA
(((((.((((......................)))).)))))((((((....))))))............((((.....))))(.(((((......))))-).)... ( -20.15)
>DroSim_CAF1 14698 101 + 1
AAGAACCAG-----AAAAAUAAUAAAGAACCAACUGAUUCUUUCAGACAUUUGUUUGAACAACGAAGACAGCAAACAAAUUGCGCCCAUCAAUCAAGAUG-GUCAAA
(((((.(((-----...................))).)))))((((((....))))))........(((.((((.....))))...((((......))))-)))... ( -18.11)
>DroEre_CAF1 14133 82 + 1
AAGAACCA------------------------ACUGAUUCUUUAAAGCAUUUGUUUGAACAACAAAGACAGCAAACAAAUUGCGUCCAUCAAUCAAGAUG-GUUAAA
...(((((------------------------.((((((.......(((((((((((..............)))))))).))).......)))).)).))-)))... ( -17.58)
>DroYak_CAF1 15227 97 + 1
AAGAACCAG-----AA----AAUAAAGAACCCACUGAUUCUUGAAGGCAUUUGUUUGAACAACAAAGACAGCAAACAAAUCGCGUCCAUCAAUCAAGAUG-GCUAAA
(((((.(((-----..----.............))).)))))....(((((((((((..............))))))))).))(.(((((......))))-)).... ( -18.80)
>DroAna_CAF1 23972 94 + 1
AAGAACCAU-----AAGGAGAUUGAAUA-------AAUUCUUCUGGCCAUUUGUUUGCUCAG-GCAGACAGCAAACAAAUGGCUCCCAUCAAUCAAGAUAUGUAAAA
......(((-----(((((((.(.....-------.).))))))(((((((((((((((...-......)))))))))))))))..............))))..... ( -27.10)
>consensus
AAGAACCAG_____AA__A_AAUAAAGAAC__ACUGAUUCUUUAAGACAUUUGUUUGAACAACGAAGACAGCAAACAAAUUGCGUCCAUCAAUCAAGAUG_GUCAAA
.............................................((((((((((((..............)))))))))......((((......)))).)))... ( -8.68 =  -8.72 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,574,488 – 16,574,594
Length 106
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 75.73
Mean single sequence MFE -24.41
Consensus MFE -14.10
Energy contribution -14.42
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -2.96
Structure conservation index 0.58
SVM decision value 3.46
SVM RNA-class probability 0.999247
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16574488 106 - 22224390
UUUGAC-CAUCUUGAUUGAUGGACGCAAUUUGUUUGCUAUCUUCGUUGUUCAAACAAAUGUCUGAAAGAAUCAGUGAGUUCUUUAUUUUUUUUUUUUACUGGUUCUU
.....(-((((......)))))..(((.((((((((....(......)..)))))))))))....(((((((((((((................))))))))))))) ( -25.59)
>DroSim_CAF1 14698 101 - 1
UUUGAC-CAUCUUGAUUGAUGGGCGCAAUUUGUUUGCUGUCUUCGUUGUUCAAACAAAUGUCUGAAAGAAUCAGUUGGUUCUUUAUUAUUUUU-----CUGGUUCUU
..((.(-((((......)))))...))(((((((((....(......)..)))))))))......(((((((((..(((........)))...-----))))))))) ( -22.20)
>DroEre_CAF1 14133 82 - 1
UUUAAC-CAUCUUGAUUGAUGGACGCAAUUUGUUUGCUGUCUUUGUUGUUCAAACAAAUGCUUUAAAGAAUCAGU------------------------UGGUUCUU
.....(-((((......)))))..(((.((((((((....(......)..)))))))))))....(((((((...------------------------.))))))) ( -20.90)
>DroYak_CAF1 15227 97 - 1
UUUAGC-CAUCUUGAUUGAUGGACGCGAUUUGUUUGCUGUCUUUGUUGUUCAAACAAAUGCCUUCAAGAAUCAGUGGGUUCUUUAUU----UU-----CUGGUUCUU
....((-((((......))))).)((.(((((((((....(......)..)))))))))))....(((((((((..(((.....)))----..-----))))))))) ( -25.40)
>DroAna_CAF1 23972 94 - 1
UUUUACAUAUCUUGAUUGAUGGGAGCCAUUUGUUUGCUGUCUGC-CUGAGCAAACAAAUGGCCAGAAGAAUU-------UAUUCAAUCUCCUU-----AUGGUUCUU
.....((((....((((((...(.((((((((((((((......-...))))))))))))))).........-------...))))))....)-----)))...... ( -27.96)
>consensus
UUUAAC_CAUCUUGAUUGAUGGACGCAAUUUGUUUGCUGUCUUCGUUGUUCAAACAAAUGCCUGAAAGAAUCAGU__GUUCUUUAUU_U__UU_____CUGGUUCUU
.......((((......))))...((.(((((((((....(......)..)))))))))))....(((((((((........................))))))))) (-14.10 = -14.42 +   0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,574,519 – 16,574,634
Length 115
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 77.88
Mean single sequence MFE -25.38
Consensus MFE -8.68
Energy contribution -8.72
Covariance contribution 0.04
Combinations/Pair 1.25
Mean z-score -2.85
Structure conservation index 0.34
SVM decision value 2.45
SVM RNA-class probability 0.994074
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16574519 115 + 22224390
CACUGAUUCUUUCAGACAUUUGUUUGAACAACGAAGAUAGCAAACAAAUUGCGUCCAUCAAUCAAGAUG-GUCAAAGCUAUAGUUUCAAGUAUAUGCACACAUGUUCAAACAUUCU
..((((.....)))).....((((((((((.........((((.....))))(.(((((......))))-).)...((((((.(....).)))).)).....)))))))))).... ( -28.50)
>DroSim_CAF1 14724 115 + 1
AACUGAUUCUUUCAGACAUUUGUUUGAACAACGAAGACAGCAAACAAAUUGCGCCCAUCAAUCAAGAUG-GUCAAAGCUAUAAUUUCAAGUAUAUGCACAACCGGUCAAACAUUCC
..((((.....)))).....(((((((....((..(((.((((.....))))...((((......))))-)))...((((((........)))).)).....)).))))))).... ( -23.90)
>DroEre_CAF1 14141 114 + 1
-ACUGAUUCUUUAAAGCAUUUGUUUGAACAACAAAGACAGCAAACAAAUUGCGUCCAUCAAUCAAGAUG-GUUAAAGCUAUAAUUUCAAAUAAAUGCGCACAUGGUCAAAUAUGCG
-..............(((((((((((((...........((((.....))))..(((((......))))-).............)))))))))))))(((.((......)).))). ( -27.10)
>DroYak_CAF1 15249 115 + 1
CACUGAUUCUUGAAGGCAUUUGUUUGAACAACAAAGACAGCAAACAAAUCGCGUCCAUCAAUCAAGAUG-GCUAAAGCUAAAAUUUCAAAUAUAUGCGCAAAUGGUCAAGUGUGCG
((((((((.(((...((((.((((((((...........((.........))(.(((((......))))-))............)))))))).)))).)))..)))).)))).... ( -24.10)
>DroAna_CAF1 23995 108 + 1
----AAUUCUUCUGGCCAUUUGUUUGCUCAG-GCAGACAGCAAACAAAUGGCUCCCAUCAAUCAAGAUAUGUAAAAACUAUACUUUAAUCCAUGUUUGCUUAUACUAAAAAAA---
----.........(((((((((((((((...-......)))))))))))))))...........(((((((((((........))))...)))))))................--- ( -23.30)
>consensus
_ACUGAUUCUUUAAGACAUUUGUUUGAACAACGAAGACAGCAAACAAAUUGCGUCCAUCAAUCAAGAUG_GUCAAAGCUAUAAUUUCAAAUAUAUGCGCAAAUGGUCAAACAUGCG
..............((((((((((((..............)))))))))......((((......)))).)))........................................... ( -8.68 =  -8.72 +   0.04)

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 12:19:05 2006