Locus 2581

Sequence ID 3R_DroMel_CAF1
Location 6,973,631 – 6,973,750
Length 119
Max. P 0.992092
window4208 window4209 window4210 window4211

overview

Window 8

Location 6,973,631 – 6,973,723
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.38
Mean single sequence MFE -27.87
Consensus MFE -14.65
Energy contribution -14.98
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.58
Structure conservation index 0.53
SVM decision value 2.31
SVM RNA-class probability 0.992092
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6973631 92 + 27905053
U--UCCGGACUUUU------------------GAG---ACAGUGCCAAAU-U--UCUUGGCAGUC--GCAUUAACGACAAAUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCGUCAU
.--.((((...(((------------------(..---...(((((((.(-(--.((((((((((--(......))))......))))))).)).)))))))....))))))))...... ( -26.80)
>DroVir_CAF1 10906 116 + 1
CCAGCCAACCUAUUUGUCUACCCUCUCCCUGGGUGGUUGGUCUGCCAAAAUUUCCUUUGGCAUC----CAUAAACGACAACUGUUGCCAAGGCAAGUGGCAUAAAGCAAAUCGGCAUUGG
(((((((......((((((((((.......)))))..(((..(((((((......))))))).)----)).....)))))...((((....)))).)))).....((......))..))) ( -35.40)
>DroPse_CAF1 41309 94 + 1
C--UCCAGACUUUUC----------------AGAG---CCUGUGCCAAAU-U--CCUUGGCACUC--GCAUUAACGACAACUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCAUCGU
.--............----------------.(((---((((((((((.(-(--.((((((((((--(......))).....).))))))).)).)))))))).........))).)).. ( -24.60)
>DroEre_CAF1 12970 92 + 1
U--UGCGGAGUUUU------------------GAG---ACAGUGCCAAAU-U--UCUUGGCAGUC--GCAUUAACGACAAAUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCGUCAU
.--.((.(((((..------------------..)---)).(((((((.(-(--.((((((((((--(......))))......))))))).)).)))))))........)).))..... ( -28.80)
>DroAna_CAF1 10195 91 + 1
U--UUUGCAC---U------------------GAG---GCAGUGCCAAAU-A--UUUUGGCACCCGGGCAUUAAGGACAAAUGUUGCCAAGUAAAUUGGCAUAAAGCAAAUAGGCGUCGU
.--..(((.(---(------------------(.(---(...((((((..-.--..)))))))))))))).....(((......((((((.....))))))....((......))))).. ( -27.00)
>DroPer_CAF1 42121 94 + 1
C--UCCAGACUUUUC----------------AGAG---CCUGUGCCAAAU-U--CCUUGGCACUC--GCAUUAACGACAACUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCAUCGU
.--............----------------.(((---((((((((((.(-(--.((((((((((--(......))).....).))))))).)).)))))))).........))).)).. ( -24.60)
>consensus
C__UCCAGACUUUU__________________GAG___ACAGUGCCAAAU_U__CCUUGGCACUC__GCAUUAACGACAAAUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCAUCGU
..........................................((((((........)))))).....((......(((....)))(((((.....))))).............))..... (-14.65 = -14.98 +   0.33)

alignment

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secondary structure

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Window 9

Location 6,973,631 – 6,973,723
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.38
Mean single sequence MFE -29.40
Consensus MFE -15.53
Energy contribution -15.33
Covariance contribution -0.19
Combinations/Pair 1.20
Mean z-score -2.47
Structure conservation index 0.53
SVM decision value 2.13
SVM RNA-class probability 0.988575
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6973631 92 - 27905053
AUGACGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAUUUGUCGUUAAUGC--GACUGCCAAGA--A-AUUUGGCACUGU---CUC------------------AAAAGUCCGGA--A
......(((.((((...((((((((.((.(((((((......(((((....))--)))))))))).--)-).)))))).)).---..)------------------)))....))).--. ( -28.00)
>DroVir_CAF1 10906 116 - 1
CCAAUGCCGAUUUGCUUUAUGCCACUUGCCUUGGCAACAGUUGUCGUUUAUG----GAUGCCAAAGGAAAUUUUGGCAGACCAACCACCCAGGGAGAGGGUAGACAAAUAGGUUGGCUGG
(((..(((((((((.....(((((.......)))))....(((((.....((----(.((((((((....))))))))..)))...((((.......)))).))))).)))))))))))) ( -39.60)
>DroPse_CAF1 41309 94 - 1
ACGAUGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAGUUGUCGUUAAUGC--GAGUGCCAAGG--A-AUUUGGCACAGG---CUCU----------------GAAAAGUCUGGA--G
...................((((((....(((((((.......((((....))--)).))))))).--.-..))))))((((---((..----------------....))))))..--. ( -28.60)
>DroEre_CAF1 12970 92 - 1
AUGACGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAUUUGUCGUUAAUGC--GACUGCCAAGA--A-AUUUGGCACUGU---CUC------------------AAAACUCCGCA--A
.....((.((((((...((((((((.((.(((((((......(((((....))--)))))))))).--)-).)))))).)).---..)------------------)))..)).)).--. ( -28.60)
>DroAna_CAF1 10195 91 - 1
ACGACGCCUAUUUGCUUUAUGCCAAUUUACUUGGCAACAUUUGUCCUUAAUGCCCGGGUGCCAAAA--U-AUUUGGCACUGC---CUC------------------A---GUGCAAA--A
.....((......))....((((((.....))))))...((((..((....((...((((((((..--.-..))))))))))---...------------------)---)..))))--. ( -23.00)
>DroPer_CAF1 42121 94 - 1
ACGAUGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAGUUGUCGUUAAUGC--GAGUGCCAAGG--A-AUUUGGCACAGG---CUCU----------------GAAAAGUCUGGA--G
...................((((((....(((((((.......((((....))--)).))))))).--.-..))))))((((---((..----------------....))))))..--. ( -28.60)
>consensus
ACGACGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAGUUGUCGUUAAUGC__GAGUGCCAAGA__A_AUUUGGCACAGC___CUC__________________AAAAGUCCGGA__A
(((((((......))....((((((.....))))))......)))))...........(((((((......))))))).......................................... (-15.53 = -15.33 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,973,648 – 6,973,750
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.63
Mean single sequence MFE -26.52
Consensus MFE -14.93
Energy contribution -15.40
Covariance contribution 0.47
Combinations/Pair 1.13
Mean z-score -2.11
Structure conservation index 0.56
SVM decision value 1.82
SVM RNA-class probability 0.978489
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6973648 102 + 27905053
AGUGCCAAAU-U--UCUUGGCAGUC--GCAUUAACGACAAAUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCGUCAUCAUCGUUAUUAGC---AUUCCC-CCCUUCCG---------
.(((((((.(-(--.((((((((((--(......))))......))))))).)).)))))))..........((((.......))))......---......-........--------- ( -25.00)
>DroVir_CAF1 10946 115 + 1
UCUGCCAAAAUUUCCUUUGGCAUC----CAUAAACGACAACUGUUGCCAAGGCAAGUGGCAUAAAGCAAAUCGGCAUUGGCAUCAUCGUCAGCAUCAGUGUCU-GCCUCAGACCGAGACU
..(((((((......)))))))..----.......(((...((.((((((.((.....((.....))......)).)))))).))..)))((..((.(.((((-(...))))))))..)) ( -30.10)
>DroPse_CAF1 41328 88 + 1
UGUGCCAAAU-U--CCUUGGCACUC--GCAUUAACGACAACUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCAUCGUCAUCGUUGUUGGC---------------------------
.(((((((..-.--..)))))))..--.......(((((((...((((((.....))))))...........(((...)))...)))))))..--------------------------- ( -26.80)
>DroEre_CAF1 12987 103 + 1
AGUGCCAAAU-U--UCUUGGCAGUC--GCAUUAACGACAAAUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCGUCAUCAUCGUUAUUAUC---AUUCCCUCUCUUCCG---------
.(((((((.(-(--.((((((((((--(......))))......))))))).)).)))))))..........((((.......))))......---...............--------- ( -25.00)
>DroAna_CAF1 10209 102 + 1
AGUGCCAAAU-A--UUUUGGCACCCGGGCAUUAAGGACAAAUGUUGCCAAGUAAAUUGGCAUAAAGCAAAUAGGCGUCGUCAUUGUUA---UC---GUUCCACCGCUUUUG---------
.(((((((..-.--..))))))).(((........(((((....((((((.....))))))....((......)).......))))).---..---......)))......--------- ( -25.43)
>DroPer_CAF1 42140 88 + 1
UGUGCCAAAU-U--CCUUGGCACUC--GCAUUAACGACAACUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCAUCGUCAUCGUUGUUGGC---------------------------
.(((((((..-.--..)))))))..--.......(((((((...((((((.....))))))...........(((...)))...)))))))..--------------------------- ( -26.80)
>consensus
AGUGCCAAAU_U__CCUUGGCACUC__GCAUUAACGACAAAUGUUGCCAAGUAAAUUGGCAUAAAACAAAUCGGCAUCGUCAUCGUUAUUAGC___AUUCCC___CUUC_G_________
..((((((........)))))).........((((((....(((((((((.....))))))....)))....((.....)).))))))................................ (-14.93 = -15.40 +   0.47)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,973,648 – 6,973,750
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.63
Mean single sequence MFE -28.43
Consensus MFE -18.83
Energy contribution -18.38
Covariance contribution -0.44
Combinations/Pair 1.22
Mean z-score -1.64
Structure conservation index 0.66
SVM decision value 1.43
SVM RNA-class probability 0.953313
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6973648 102 - 27905053
---------CGGAAGGG-GGGAAU---GCUAAUAACGAUGAUGACGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAUUUGUCGUUAAUGC--GACUGCCAAGA--A-AUUUGGCACU
---------(....)((-.(..((---.(..........)))..).))...........((((((.((.(((((((......(((((....))--)))))))))).--)-).)))))).. ( -28.10)
>DroVir_CAF1 10946 115 - 1
AGUCUCGGUCUGAGGC-AGACACUGAUGCUGACGAUGAUGCCAAUGCCGAUUUGCUUUAUGCCACUUGCCUUGGCAACAGUUGUCGUUUAUG----GAUGCCAAAGGAAAUUUUGGCAGA
.(((...(((((...)-))))...)))...((((((..((((((.((......((.....)).....)).))))))...)))))).......----..((((((((....)))))))).. ( -35.00)
>DroPse_CAF1 41328 88 - 1
---------------------------GCCAACAACGAUGACGAUGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAGUUGUCGUUAAUGC--GAGUGCCAAGG--A-AUUUGGCACA
---------------------------((....(((((..((..((((((.(((........))).....))))))...))..)))))...))--..((((((((.--.-.)))))))). ( -27.90)
>DroEre_CAF1 12987 103 - 1
---------CGGAAGAGAGGGAAU---GAUAAUAACGAUGAUGACGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAUUUGUCGUUAAUGC--GACUGCCAAGA--A-AUUUGGCACU
---------.((((.(((.((.((---.((.......)).))....))..))).)))).((((((.((.(((((((......(((((....))--)))))))))).--)-).)))))).. ( -27.10)
>DroAna_CAF1 10209 102 - 1
---------CAAAAGCGGUGGAAC---GA---UAACAAUGACGACGCCUAUUUGCUUUAUGCCAAUUUACUUGGCAACAUUUGUCCUUAAUGCCCGGGUGCCAAAA--U-AUUUGGCACU
---------..(((((((.((..(---(.---.........))...))...))))))).((((((.....))))))....................((((((((..--.-..)))))))) ( -24.60)
>DroPer_CAF1 42140 88 - 1
---------------------------GCCAACAACGAUGACGAUGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAGUUGUCGUUAAUGC--GAGUGCCAAGG--A-AUUUGGCACA
---------------------------((....(((((..((..((((((.(((........))).....))))))...))..)))))...))--..((((((((.--.-.)))))))). ( -27.90)
>consensus
_________C_GAAG___GGGAAU___GCUAACAACGAUGACGACGCCGAUUUGUUUUAUGCCAAUUUACUUGGCAACAGUUGUCGUUAAUGC__GAGUGCCAAGA__A_AUUUGGCACA
....................................((((((((.((......))....((((((.....))))))....))))))))..........(((((((......))))))).. (-18.83 = -18.38 +  -0.44)

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 10:39:50 2006