Locus 4422

Sequence ID X_DroMel_CAF1
Location 11,657,370 – 11,657,503
Length 133
Max. P 0.832793
window7267 window7268 window7269

overview

Window 7

Location 11,657,370 – 11,657,485
Length 115
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 91.92
Mean single sequence MFE -49.18
Consensus MFE -43.42
Energy contribution -44.67
Covariance contribution 1.25
Combinations/Pair 1.12
Mean z-score -1.34
Structure conservation index 0.88
SVM decision value -0.02
SVM RNA-class probability 0.522542
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11657370 115 - 22224390
CCUCUUCUAGCUGCUACCACAGCUGCUGCCAAUGAUGCAGUGCCUCCA-CACUGGAGGUCAAUGGGCAGCGGCCGGCUGGGGGUGGCAGAUGGCGGAUGGCUGAUGGCAGUGGGUG
(((((.(((.((((((((.((((((((((......(((..(((((((.-....))))).))....))))))).))))))..)))))))).))).)))..((((....))))))... ( -51.30)
>DroSec_CAF1 30567 116 - 1
CCUCUUCCAGCUGCUACCACAGCUGUUGCCAAUGAUGCAGUGCCUCCACCACUGGAGGUCAAUGGGCAGCGGCCGGCUGGGGGUGGCAAAUAGUGGAUGGCUGAUGGCAGUGGGUG
((.((.(((...((((((((.(((((((((..((.......(((((((....)))))))))...)))))))))..(((......))).....)))).))))...))).)).))... ( -47.91)
>DroEre_CAF1 34682 108 - 1
CCUCGUCUAGCUGCUACCACAGCUGCUGCCAAUGAUGCAGUGCCUCCA-CACUGGAGGUCAAUGGGCAGCGGGCGACUGGGGGUGGCAGAUGGCUGAU-------GGCAGUGGGUG
((.(((((.((..(..(((..(((((((((..((.......((((((.-....))))))))...)))))).)))...)))..)..)))))))((((..-------..))))))... ( -46.41)
>DroYak_CAF1 29544 115 - 1
CCUCUUCUAGCUGCUACCACAGCUGCUGCCAAUGAUGCAGUGCCUCCA-CACUGGAGGUCAAUGGGCAGCGGACGGCUGGGGGUGGCAGAUGGCUGAUGGCUAAUGGCAGUGGGUG
((.((.(((.((((((((.((((((((((......(((..(((((((.-....))))).))....))))))).))))))..)))))))).((((.....)))).))).)).))... ( -51.10)
>consensus
CCUCUUCUAGCUGCUACCACAGCUGCUGCCAAUGAUGCAGUGCCUCCA_CACUGGAGGUCAAUGGGCAGCGGCCGGCUGGGGGUGGCAGAUGGCGGAUGGCUGAUGGCAGUGGGUG
((.((.(((.((((((((.((((((((((......(((..((((((((....)))))).))....))))))).))))))..)))))))).((((.....)))).))).)).))... (-43.42 = -44.67 +   1.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,657,409 – 11,657,503
Length 94
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 95.06
Mean single sequence MFE -40.93
Consensus MFE -37.52
Energy contribution -37.34
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.92
SVM decision value 0.62
SVM RNA-class probability 0.802866
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11657409 94 + 22224390
GCCGGCCGCUGCCCAUUGACCUCCAGUG-UGGAGGCACUGCAUCAUUGGCAGCAGCUGUGGUAGCAGCUAGAAGAGGAGCGAUUCCGGCGGCCAG
((((.((((((((((.((.(((((....-.))))))).)).......))))))((((((....))))))......((((...))))))))))... ( -40.81)
>DroSec_CAF1 30606 95 + 1
GCCGGCCGCUGCCCAUUGACCUCCAGUGGUGGAGGCACUGCAUCAUUGGCAACAGCUGUGGUAGCAGCUGGAAGAGGAGCAAUUCCGGCGGUCAG
...((((((((...((((.((((((((((((.((...)).))))))))....(((((((....)))))))...))))..))))..)))))))).. ( -43.80)
>DroEre_CAF1 34714 94 + 1
GUCGCCCGCUGCCCAUUGACCUCCAGUG-UGGAGGCACUGCAUCAUUGGCAGCAGCUGUGGUAGCAGCUAGACGAGGAGCAAUUCCGGCGGUCAG
((((((.((((((((.((.(((((....-.))))))).)).......))))))((((((....))))))......((((...))))))))).).. ( -38.11)
>DroYak_CAF1 29583 94 + 1
GCCGUCCGCUGCCCAUUGACCUCCAGUG-UGGAGGCACUGCAUCAUUGGCAGCAGCUGUGGUAGCAGCUAGAAGAGGAGCGAUUCCGGCGGCCAG
((((((.((((((((.((.(((((....-.))))))).)).......))))))((((((....))))))......((((...))))))))))... ( -41.01)
>consensus
GCCGGCCGCUGCCCAUUGACCUCCAGUG_UGGAGGCACUGCAUCAUUGGCAGCAGCUGUGGUAGCAGCUAGAAGAGGAGCAAUUCCGGCGGCCAG
((((.((((((((((.((.((((((....)))))))).)).......))))))((((((....))))))......((((...))))))))))... (-37.52 = -37.34 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,657,409 – 11,657,503
Length 94
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 95.06
Mean single sequence MFE -37.85
Consensus MFE -34.89
Energy contribution -35.45
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.76
Structure conservation index 0.92
SVM decision value 0.72
SVM RNA-class probability 0.832793
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11657409 94 - 22224390
CUGGCCGCCGGAAUCGCUCCUCUUCUAGCUGCUACCACAGCUGCUGCCAAUGAUGCAGUGCCUCCA-CACUGGAGGUCAAUGGGCAGCGGCCGGC
((((((...(((.....))).......(((((..(((..(((((..........)))))((((((.-....))))))...)))))))))))))). ( -40.30)
>DroSec_CAF1 30606 95 - 1
CUGACCGCCGGAAUUGCUCCUCUUCCAGCUGCUACCACAGCUGUUGCCAAUGAUGCAGUGCCUCCACCACUGGAGGUCAAUGGGCAGCGGCCGGC
......(((((..((((((......((((((......))))))((((.......)))).(((((((....)))))))....))))))...))))) ( -36.10)
>DroEre_CAF1 34714 94 - 1
CUGACCGCCGGAAUUGCUCCUCGUCUAGCUGCUACCACAGCUGCUGCCAAUGAUGCAGUGCCUCCA-CACUGGAGGUCAAUGGGCAGCGGGCGAC
.....(((((((.....))).......(((((..(((..(((((..........)))))((((((.-....))))))...)))))))).)))).. ( -36.60)
>DroYak_CAF1 29583 94 - 1
CUGGCCGCCGGAAUCGCUCCUCUUCUAGCUGCUACCACAGCUGCUGCCAAUGAUGCAGUGCCUCCA-CACUGGAGGUCAAUGGGCAGCGGACGGC
...(((((((((.....))).......(((((..(((..(((((..........)))))((((((.-....))))))...)))))))))).)))) ( -38.40)
>consensus
CUGACCGCCGGAAUCGCUCCUCUUCUAGCUGCUACCACAGCUGCUGCCAAUGAUGCAGUGCCUCCA_CACUGGAGGUCAAUGGGCAGCGGCCGGC
...(((((((((.....))).......(((((..(((..(((((..........)))))(((((((....)))))))...)))))))))).)))) (-34.89 = -35.45 +   0.56)

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 11:24:41 2006