Locus 6859

Sequence ID 3R_DroMel_CAF1
Location 18,144,607 – 18,144,737
Length 130
Max. P 0.951322
window11131 window11132 window11133 window11134

overview

Window 1

Location 18,144,607 – 18,144,704
Length 97
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 81.14
Mean single sequence MFE -47.62
Consensus MFE -35.53
Energy contribution -36.82
Covariance contribution 1.28
Combinations/Pair 1.24
Mean z-score -3.14
Structure conservation index 0.75
SVM decision value 1.41
SVM RNA-class probability 0.951322
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18144607 97 + 27905053
CGCCAGCGGCUCCGGUUGGUUGCAGCUGCUGGCGGCACUGCUGCAGCUGCUGCUAGAGGUUGCCUUCAUAGCAGCG---GCAACAGGAGCGAGUUGCACA-----
(((((((((((.(((....))).)))))))))))((((((((.(.((((((((((((((....)))).))))))))---))....).))).)).)))...----- ( -51.90)
>DroSec_CAF1 173230 97 + 1
CGCCAGCGGCUCCGGUUGGUUGCAGCUGCUGGCGGCACUGCUGCAGCUGCUGAUGGAGGUUGCCUUCAUAGCAGCG---GCAACAGGAGCAAGUUGCGCA-----
(((((((((((.(((....))).)))))))))))((.(((.(((.(((((((.((((((...))))))))))))).---))).)))..((.....)))).----- ( -52.90)
>DroEre_CAF1 184802 97 + 1
CGCCAGCGGCUCCGGCUGGUUGCAGCUGCUGGCGGCACUGCUGCAGCUGCUGCUGGAGGUUGCCUUCAUAGCAGCG---GCAACAGGAGCAAGUUGCGCA-----
(((((((((((.(((....))).)))))))))))((.(((.(((.(((((((.((((((...))))))))))))).---))).)))..((.....)))).----- ( -54.00)
>DroYak_CAF1 182408 97 + 1
UGCCAGCGGCUCCGGUUGGUUGCAGCUGCUGGCGGCACUGCUGCAGCUGCUGCUGGAGGUUGCCUUCAUAGCAGCG---GCAACAGGAGCAAGUUGCGCA-----
.((((((.(((((.(((...(((((((((.....)))..))))))((((((((((((((....)))).))))))))---))))).)))))..)))).)).----- ( -51.60)
>DroMoj_CAF1 224173 105 + 1
CGCCAGUGGCUCCAAGUGGUUGAUGCUGCUGGCGGCGCUGCUGCUGCUGCUGUUGACCGUUGCCUUCAUAGCAACGCCUGCAAAGAAACACAACAUCCACAUCCA
((((((..((..(((....)))..))..))))))..((.((....)).))(((((..((((((.......)))))).((....)).....))))).......... ( -34.60)
>DroAna_CAF1 168117 97 + 1
GGCAGCCGCCUCCGGUUGAUUGCAGCUGCUGGCGGCACUGCUGCAACUGCUACUGGAUGUUGCUUUCAUAGCAGCG---GCAACUGGAAAGUGUUAAACG-----
((((((((((..((((((....))))))..))))))..))))((..((((((.((((.......))))))))))..---)).(((....)))........----- ( -40.70)
>consensus
CGCCAGCGGCUCCGGUUGGUUGCAGCUGCUGGCGGCACUGCUGCAGCUGCUGCUGGAGGUUGCCUUCAUAGCAGCG___GCAACAGGAGCAAGUUGCGCA_____
(((((((((((.(((....))).)))))))))))...(((.(((.(((((((.((((((...)))))))))))))....))).)))................... (-35.53 = -36.82 +   1.28)

alignment

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secondary structure

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Window 2

Location 18,144,607 – 18,144,704
Length 97
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 81.14
Mean single sequence MFE -42.91
Consensus MFE -29.52
Energy contribution -30.80
Covariance contribution 1.28
Combinations/Pair 1.15
Mean z-score -2.88
Structure conservation index 0.69
SVM decision value 1.24
SVM RNA-class probability 0.935330
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18144607 97 - 27905053
-----UGUGCAACUCGCUCCUGUUGC---CGCUGCUAUGAAGGCAACCUCUAGCAGCAGCUGCAGCAGUGCCGCCAGCAGCUGCAACCAACCGGAGCCGCUGGCG
-----.........((((.((((.((---.(((((((.((.(....).))))))))).)).)))).)))).(((((((.(((.(........).))).))))))) ( -46.30)
>DroSec_CAF1 173230 97 - 1
-----UGCGCAACUUGCUCCUGUUGC---CGCUGCUAUGAAGGCAACCUCCAUCAGCAGCUGCAGCAGUGCCGCCAGCAGCUGCAACCAACCGGAGCCGCUGGCG
-----.((((.....))..(((((((---.(((((((((.(((...))).))).)))))).))))))).))(((((((.(((.(........).))).))))))) ( -47.10)
>DroEre_CAF1 184802 97 - 1
-----UGCGCAACUUGCUCCUGUUGC---CGCUGCUAUGAAGGCAACCUCCAGCAGCAGCUGCAGCAGUGCCGCCAGCAGCUGCAACCAGCCGGAGCCGCUGGCG
-----.((((.....))..(((((((---.((((((.((.(((...))).))..)))))).))))))).))(((((((.(((.(........).))).))))))) ( -46.40)
>DroYak_CAF1 182408 97 - 1
-----UGCGCAACUUGCUCCUGUUGC---CGCUGCUAUGAAGGCAACCUCCAGCAGCAGCUGCAGCAGUGCCGCCAGCAGCUGCAACCAACCGGAGCCGCUGGCA
-----.((((.....))..(((((((---.((((((.((.(((...))).))..)))))).))))))).)).((((((.(((.(........).))).)))))). ( -45.70)
>DroMoj_CAF1 224173 105 - 1
UGGAUGUGGAUGUUGUGUUUCUUUGCAGGCGUUGCUAUGAAGGCAACGGUCAACAGCAGCAGCAGCAGCGCCGCCAGCAGCAUCAACCACUUGGAGCCACUGGCG
....((..((.(........)))..))(((((((((.(((.(....)..)))...((....)))))))))))(((((..((..(((....)))..))..))))). ( -37.50)
>DroAna_CAF1 168117 97 - 1
-----CGUUUAACACUUUCCAGUUGC---CGCUGCUAUGAAAGCAACAUCCAGUAGCAGUUGCAGCAGUGCCGCCAGCAGCUGCAAUCAACCGGAGGCGGCUGCC
-----.......((((.....(((((---.((((((((..............)))))))).)))))))))......((((((((..((....))..)))))))). ( -34.44)
>consensus
_____UGCGCAACUUGCUCCUGUUGC___CGCUGCUAUGAAGGCAACCUCCAGCAGCAGCUGCAGCAGUGCCGCCAGCAGCUGCAACCAACCGGAGCCGCUGGCG
...................(((((((....((((((..((.(....).))....)))))).)))))))....((((((.(((.(........).))).)))))). (-29.52 = -30.80 +   1.28)

alignment

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secondary structure

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Window 3

Location 18,144,639 – 18,144,737
Length 98
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 81.51
Mean single sequence MFE -34.53
Consensus MFE -26.44
Energy contribution -27.05
Covariance contribution 0.61
Combinations/Pair 1.16
Mean z-score -2.52
Structure conservation index 0.77
SVM decision value 1.13
SVM RNA-class probability 0.919246
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18144639 98 + 27905053
CGGCACUGCUGCAGCUGCUGCUAGAGGUUGCCUUCAUAGCAGCGGCAACAGGAGCGAGUUGCACAGAGUACUCUGUU---CGAAAAAAAAAUUUGAUAAGA----
...(.((.(((..((((((((((((((....)))).))))))))))..))).)).)..(((.(((((....))))).---)))..................---- ( -34.50)
>DroSec_CAF1 173262 96 + 1
CGGCACUGCUGCAGCUGCUGAUGGAGGUUGCCUUCAUAGCAGCGGCAACAGGAGCAAGUUGCGCAGAGCACUCUGUC---GGAAA--AAAAUUAAAUAAGA----
(((((((.((((.(((((((.((((((...))))))))))))).(((((........))))))))))).....))))---)....--..............---- ( -35.40)
>DroSim_CAF1 178181 96 + 1
CGGCACUGCUGCAGCUGCUGCUGGAGGUUGCCUUCAUAGCAGCGGCAACAGGAGCAAGUUGCACAGAGUACUCUGUC---GGAAA--AAAAUUAGGUAAGA----
..((.(((.(((.(((((((.((((((...))))))))))))).))).)))..))...(((.(((((....))))))---))...--..............---- ( -34.20)
>DroEre_CAF1 184834 95 + 1
CGGCACUGCUGCAGCUGCUGCUGGAGGUUGCCUUCAUAGCAGCGGCAACAGGAGCAAGUUGCGCAGUGUACUCUGCG---GGUAG---AAAUAAGUUGGGG----
..(((((((....(((((((.((((((...))))))))))))).(((((........)))))))))))).(((.((.---..((.---...)).)).))).---- ( -40.70)
>DroYak_CAF1 182440 98 + 1
CGGCACUGCUGCAGCUGCUGCUGGAGGUUGCCUUCAUAGCAGCGGCAACAGGAGCAAGUUGCGCAGUGUACUCUGUGUAGUGUAG---AAAGAAGUUAUGA----
..((((((((.(.(((((((.((((((...)))))))))))))(....).).))))...(((((((......)))))))))))..---.............---- ( -38.20)
>DroAna_CAF1 168149 98 + 1
CGGCACUGCUGCAACUGCUACUGGAUGUUGCUUUCAUAGCAGCGGCAACUGGAAAGUGUUAAACGGGAUACUCUGAG---G-AAG---AAAUCAGAAAAUAUAUU
.((((((..(((..((((((.((((.......))))))))))..))).......))))))...........(((((.---.-...---...)))))......... ( -24.20)
>consensus
CGGCACUGCUGCAGCUGCUGCUGGAGGUUGCCUUCAUAGCAGCGGCAACAGGAGCAAGUUGCACAGAGUACUCUGUG___GGAAA___AAAUUAGAUAAGA____
..((.(((.(((.(((((((.((((((...))))))))))))).))).)))..)).......((((......))))............................. (-26.44 = -27.05 +   0.61)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,144,639 – 18,144,737
Length 98
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 81.51
Mean single sequence MFE -30.42
Consensus MFE -22.85
Energy contribution -23.10
Covariance contribution 0.25
Combinations/Pair 1.13
Mean z-score -2.72
Structure conservation index 0.75
SVM decision value 1.19
SVM RNA-class probability 0.928535
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18144639 98 - 27905053
----UCUUAUCAAAUUUUUUUUUCG---AACAGAGUACUCUGUGCAACUCGCUCCUGUUGCCGCUGCUAUGAAGGCAACCUCUAGCAGCAGCUGCAGCAGUGCCG
----....................(---.(((((....))))).)....((((.((((.((.(((((((.((.(....).))))))))).)).)))).))))... ( -32.60)
>DroSec_CAF1 173262 96 - 1
----UCUUAUUUAAUUUU--UUUCC---GACAGAGUGCUCUGCGCAACUUGCUCCUGUUGCCGCUGCUAUGAAGGCAACCUCCAUCAGCAGCUGCAGCAGUGCCG
----..............--....(---(.((((....))))))......((..(((((((.(((((((((.(((...))).))).)))))).))))))).)).. ( -32.20)
>DroSim_CAF1 178181 96 - 1
----UCUUACCUAAUUUU--UUUCC---GACAGAGUACUCUGUGCAACUUGCUCCUGUUGCCGCUGCUAUGAAGGCAACCUCCAGCAGCAGCUGCAGCAGUGCCG
----..............--.....---.(((((....))))).......((..(((((((.((((((.((.(((...))).))..)))))).))))))).)).. ( -31.60)
>DroEre_CAF1 184834 95 - 1
----CCCCAACUUAUUU---CUACC---CGCAGAGUACACUGCGCAACUUGCUCCUGUUGCCGCUGCUAUGAAGGCAACCUCCAGCAGCAGCUGCAGCAGUGCCG
----.............---.....---(((((......)))))......((..(((((((.((((((.((.(((...))).))..)))))).))))))).)).. ( -33.00)
>DroYak_CAF1 182440 98 - 1
----UCAUAACUUCUUU---CUACACUACACAGAGUACACUGCGCAACUUGCUCCUGUUGCCGCUGCUAUGAAGGCAACCUCCAGCAGCAGCUGCAGCAGUGCCG
----.............---.................(((((((((((........))))).((((((.((.(((...))).))..))))))....))))))... ( -29.40)
>DroAna_CAF1 168149 98 - 1
AAUAUAUUUUCUGAUUU---CUU-C---CUCAGAGUAUCCCGUUUAACACUUUCCAGUUGCCGCUGCUAUGAAAGCAACAUCCAGUAGCAGUUGCAGCAGUGCCG
........((((((...---...-.---.))))))............((((.....(((((.((((((((..............)))))))).)))))))))... ( -23.74)
>consensus
____UCUUAUCUAAUUU___CUUCC___CACAGAGUACUCUGCGCAACUUGCUCCUGUUGCCGCUGCUAUGAAGGCAACCUCCAGCAGCAGCUGCAGCAGUGCCG
..............................(((......)))........((..(((((((.((((((.((.(((...))).))..)))))).))))))).)).. (-22.85 = -23.10 +   0.25)

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 12:31:44 2006