Locus 2720

Sequence ID X_DroMel_CAF1
Location 7,300,345 – 7,300,471
Length 126
Max. P 0.790917
window4453 window4454 window4455

overview

Window 3

Location 7,300,345 – 7,300,447
Length 102
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 83.17
Mean single sequence MFE -23.97
Consensus MFE -15.96
Energy contribution -16.07
Covariance contribution 0.11
Combinations/Pair 1.15
Mean z-score -2.82
Structure conservation index 0.67
SVM decision value 0.59
SVM RNA-class probability 0.790917
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7300345 102 + 22224390
UGUGUUUUUUUU--AACCGUGUAUUUUC--GC----UGCAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU--------
...........(--(((.(((......)--))----.(((.((((((.(((.......((((((((((((.......))))))))))))..))).))))))))).)))).-------- ( -21.80)
>DroSec_CAF1 50255 102 + 1
UGUGUUUUUUUU--AACCGUGUAUUUUC--GC----UGCAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU--------
...........(--(((.(((......)--))----.(((.((((((.(((.......((((((((((((.......))))))))))))..))).))))))))).)))).-------- ( -21.80)
>DroSim_CAF1 49233 102 + 1
UGUGUUUUUUUU--AACCGUGUAUUUUC--GC----UGCAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU--------
...........(--(((.(((......)--))----.(((.((((((.(((.......((((((((((((.......))))))))))))..))).))))))))).)))).-------- ( -21.80)
>DroEre_CAF1 60543 102 + 1
UGUGUUUUUUUU--AACCGUGUAUUUUC--GC----UGCAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU--------
...........(--(((.(((......)--))----.(((.((((((.(((.......((((((((((((.......))))))))))))..))).))))))))).)))).-------- ( -21.80)
>DroYak_CAF1 76915 110 + 1
UGUGUUUUUUUU--AAAUGUGUAUUUUC--GC----UGCAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUAUGUUGCUGUUUGUGCUA
............--....(((......)--))----.((((.((.(((((((((((..((((((((((((.......))))))))))))......)))).))))))).))..)))).. ( -24.70)
>DroPer_CAF1 110547 94 + 1
------UUUUUCGCUUUGGUGUACGGGCGGGCGGCAUACGCUGCCGCUGUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUAGCCAU------------------
------..........((((.(((((((((((((((.....))))))).)))))))).((((((((((((.......))))))))))))......)))).------------------ ( -31.90)
>consensus
UGUGUUUUUUUU__AACCGUGUAUUUUC__GC____UGCAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU________
..................(((((.............)))))((((((.(((.......((((((((((((.......))))))))))))..))).))))))................. (-15.96 = -16.07 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,300,345 – 7,300,447
Length 102
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 83.17
Mean single sequence MFE -12.82
Consensus MFE -8.31
Energy contribution -7.62
Covariance contribution -0.69
Combinations/Pair 1.28
Mean z-score -2.40
Structure conservation index 0.65
SVM decision value 0.27
SVM RNA-class probability 0.661689
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7300345 102 - 22224390
--------ACAACAACACACUGCCAUAACAAUUAAUUAACAAAUAAAAUGUCAAUUAAUUUUACAAACAUUGCAGCGAUGCA----GC--GAAAAUACACGGUU--AAAAAAAACACA
--------.............(((.....((((((((.(((.......))).)))))))).......(.(((((....))))----).--).........))).--............ ( -11.20)
>DroSec_CAF1 50255 102 - 1
--------ACAACAACACACUGCCAUAACAAUUAAUUAACAAAUAAAAUGUCAAUUAAUUUUACAAACAUUGCAGCGAUGCA----GC--GAAAAUACACGGUU--AAAAAAAACACA
--------.............(((.....((((((((.(((.......))).)))))))).......(.(((((....))))----).--).........))).--............ ( -11.20)
>DroSim_CAF1 49233 102 - 1
--------ACAACAACACACUGCCAUAACAAUUAAUUAACAAAUAAAAUGUCAAUUAAUUUUACAAACAUUGCAGCGAUGCA----GC--GAAAAUACACGGUU--AAAAAAAACACA
--------.............(((.....((((((((.(((.......))).)))))))).......(.(((((....))))----).--).........))).--............ ( -11.20)
>DroEre_CAF1 60543 102 - 1
--------ACAACAACACACUGCCAUAACAAUUAAUUAACAAAUAAAAUGUCAAUUAAUUUUACAAACAUUGCAGCGAUGCA----GC--GAAAAUACACGGUU--AAAAAAAACACA
--------.............(((.....((((((((.(((.......))).)))))))).......(.(((((....))))----).--).........))).--............ ( -11.20)
>DroYak_CAF1 76915 110 - 1
UAGCACAAACAGCAACAUACUGCCAUAACAAUUAAUUAACAAAUAAAAUGUCAAUUAAUUUUACAAACAUUGCAGCGAUGCA----GC--GAAAAUACACAUUU--AAAAAAAACACA
..((.......(((......)))......((((((((.(((.......))).))))))))..........((((....))))----))--..............--............ ( -11.40)
>DroPer_CAF1 110547 94 - 1
------------------AUGGCUAUAACAAUUAAUUAACAAAUAAAAUGUCAAUUAAUUUUACAAACACAGCGGCAGCGUAUGCCGCCCGCCCGUACACCAAAGCGAAAAA------
------------------..(((......((((((((.(((.......))).))))))))...........((((((.....))))))..)))(((........))).....------ ( -20.70)
>consensus
________ACAACAACACACUGCCAUAACAAUUAAUUAACAAAUAAAAUGUCAAUUAAUUUUACAAACAUUGCAGCGAUGCA____GC__GAAAAUACACGGUU__AAAAAAAACACA
..................((((.......((((((((.(((.......))).))))))))...........(((....)))..................))))............... ( -8.31 =  -7.62 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,300,375 – 7,300,471
Length 96
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 86.98
Mean single sequence MFE -18.42
Consensus MFE -16.45
Energy contribution -16.07
Covariance contribution -0.39
Combinations/Pair 1.17
Mean z-score -1.54
Structure conservation index 0.89
SVM decision value 0.42
SVM RNA-class probability 0.730717
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7300375 96 + 22224390
CAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU---------UGUUCUUGUUAUUGUUUGGUUGAC
((.((((((.(((.......((((((((((((.......))))))))))))..))).)))))))).......---------........................ ( -18.00)
>DroSec_CAF1 50285 90 + 1
CAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU---------U------GUUAUUGUUUGGUUGGC
((.((((((.(((.......((((((((((((.......))))))))))))..))).)))))))).......---------.------................. ( -18.00)
>DroSim_CAF1 49263 90 + 1
CAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU---------U------GUUAUUGUUUGGUUGGC
((.((((((.(((.......((((((((((((.......))))))))))))..))).)))))))).......---------.------................. ( -18.00)
>DroEre_CAF1 60573 96 + 1
CAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU---------UGUUCUUGUUAUUGUUUGGUUGGC
((.((((((.(((.......((((((((((((.......))))))))))))..))).)))))))).......---------........................ ( -18.00)
>DroYak_CAF1 76945 105 + 1
CAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUAUGUUGCUGUUUGUGCUAUUGUUGUUGUUAUUGUUUGGUUGGC
.((((..((((((.......((((((((((((.......))))))))))))((...((((((.....))))))...))............)))))).)))).... ( -20.40)
>DroAna_CAF1 53558 82 + 1
---CGCUGCAGUGUUUGUGAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCCGUGUGUUGUUGC--------------------CCGGUUGGUUGGC
---.(((.........((((((((((((((((.......)))))))))))).))))(((((.((......))--------------------.)))))....))) ( -18.10)
>consensus
CAUCGCUGCAAUGUUUGUAAAAUUAAUUGACAUUUUAUUUGUUAAUUAAUUGUUAUGGCAGUGUGUUGUUGU_________U______GUUAUUGUUUGGUUGGC
....((.((((..(((((..((((((((((((.......))))))))))))......)))).)..)))).))................................. (-16.45 = -16.07 +  -0.39)

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 10:41:46 2006