Locus 8527

Sequence ID 3L_DroMel_CAF1
Location 22,312,707 – 22,312,907
Length 200
Max. P 0.930187
window13966 window13967 window13968

overview

Window 6

Location 22,312,707 – 22,312,827
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.30
Mean single sequence MFE -28.56
Consensus MFE -24.52
Energy contribution -24.16
Covariance contribution -0.36
Combinations/Pair 1.13
Mean z-score -1.65
Structure conservation index 0.86
SVM decision value 1.20
SVM RNA-class probability 0.930187
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22312707 120 - 23771897
AUUGGCUGCCUAAUGAAUUAUGCAUGGGCAGUCCAAAAAGCACGGCACGCCUCCUUUACAGCCAAAUAAAUCAAAAUAUAAUGCAUAUUAAGUGCGAACAACGAAUCGUAUUGAACGAGG
.(((((((((((.((.......))))))))).))))...(((((((..............)))...........(((((.....)))))..))))..........((((.....)))).. ( -27.64)
>DroSec_CAF1 71422 119 - 1
AUUGGCUGCCUAAUGUAAUAUGCAUGGGCAGCCCAAAAAG-ACGACACGCCUCCUUUACAGCCAAAUAAAUCAAAAUACAAUGCAUAUUAAGUGCGAACAACGAAUCGUAUCGAACGAGG
...(((((((((.(((.....)))))))))))).......-........((((............................(((((.....))))).....(((......)))...)))) ( -27.90)
>DroSim_CAF1 53135 119 - 1
AUUGGCUGCCUAAUGAAAUAUGCAUGGGCAGCCCAAAAAG-ACGGCACGCCUCCUUUACAGCCAAAUAAAUCAAAAUACAAUGCAUAUUAAGUGCGAACAACGAAUCGUAUCGAACGAGG
...(((((((((.((.......)))))))))))...((((-..((....))..))))....((..................(((((.....))))).........((((.....)))))) ( -26.80)
>DroEre_CAF1 69781 119 - 1
AUUGGCUGCCUAAUGAAAUAUGCAUGGGCAGCCCAAGAAG-GCGGCACGCCUCCUUUACAGCUAGAUAAAUCAAAAUACAAUGCAUAUUAAGUGCGAGCGACGAAUCGUAUCGAACGAGG
...(((((((((.((.......)))))))))))...((((-(.((....)).)))))...(((.((....)).........(((((.....))))))))......((((.....)))).. ( -33.20)
>DroYak_CAF1 49898 119 - 1
AUUGGCUGCCUAAUGAAAUAUGCAAAGGCAGUCCAAAAAG-GCGGCACGCCUCCUUUACAGCUAGAUAAAUCAAAAUACAAUGCAUAUUAAGUGCGAACAACGAAUCGUAUCGAACGAGG
.((((((((((..............)))))).))))((((-(.((....)).)))))........................(((((.....))))).........((((.....)))).. ( -27.24)
>consensus
AUUGGCUGCCUAAUGAAAUAUGCAUGGGCAGCCCAAAAAG_ACGGCACGCCUCCUUUACAGCCAAAUAAAUCAAAAUACAAUGCAUAUUAAGUGCGAACAACGAAUCGUAUCGAACGAGG
...(((((((((.((.......)))))))))))................((((............................(((((.....))))).....(((......)))...)))) (-24.52 = -24.16 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 22,312,747 – 22,312,867
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.63
Mean single sequence MFE -33.63
Consensus MFE -28.22
Energy contribution -28.22
Covariance contribution 0.00
Combinations/Pair 1.15
Mean z-score -1.63
Structure conservation index 0.84
SVM decision value 0.97
SVM RNA-class probability 0.891203
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22312747 120 - 23771897
UUGGCAGACUGUUCAAGACGCAGGGCCGGGGGAGGAAUUCAUUGGCUGCCUAAUGAAUUAUGCAUGGGCAGUCCAAAAAGCACGGCACGCCUCCUUUACAGCCAAAUAAAUCAAAAUAUA
(((((...((((.......))))....((((((((......(((((((((((.((.......))))))))).))))...((...))...))))))))...)))))............... ( -36.30)
>DroSec_CAF1 71462 119 - 1
CUGGCAGACUGUUCAAGACGCAGGGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGUAAUAUGCAUGGGCAGCCCAAAAAG-ACGACACGCCUCCUUUACAGCCAAAUAAAUCAAAAUACA
.((((...((((.......))))......((((((...((...(((((((((.(((.....))))))))))))(.....)-..))....)))))).....))))................ ( -35.40)
>DroSim_CAF1 53175 119 - 1
CUGGCAGACUGUUCAAGACGCAGGGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGAAAUAUGCAUGGGCAGCCCAAAAAG-ACGGCACGCCUCCUUUACAGCCAAAUAAAUCAAAAUACA
.((((...((((.......))))(((.((((((....)))...(((((((((.((.......))))))))))).......-.)))...))).........))))................ ( -33.60)
>DroEre_CAF1 69821 119 - 1
UUGGCAGACAAUUCAAGACGCAGGGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGAAAUAUGCAUGGGCAGCCCAAGAAG-GCGGCACGCCUCCUUUACAGCUAGAUAAAUCAAAAUACA
(((((.................(((..((....))..)))...(((((((((.((.......)))))))))))...((((-(.((....)).)))))...)))))............... ( -32.50)
>DroYak_CAF1 49938 119 - 1
UUGGCAGACUAUUCAAGACACAGUGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGAAAUAUGCAAAGGCAGUCCAAAAAG-GCGGCACGCCUCCUUUACAGCUAGAUAAAUCAAAAUACA
..(((.((....))........(((((((.(((....))).((((((((((..............)))))).))))...)-).))))))))............................. ( -30.34)
>consensus
UUGGCAGACUGUUCAAGACGCAGGGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGAAAUAUGCAUGGGCAGCCCAAAAAG_ACGGCACGCCUCCUUUACAGCCAAAUAAAUCAAAAUACA
.((((...((((.......))))......((((((........(((((((((.((.......))))))))))).........((...)))))))).....))))................ (-28.22 = -28.22 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,312,787 – 22,312,907
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.92
Mean single sequence MFE -37.79
Consensus MFE -30.32
Energy contribution -30.80
Covariance contribution 0.48
Combinations/Pair 1.13
Mean z-score -1.53
Structure conservation index 0.80
SVM decision value 0.34
SVM RNA-class probability 0.698047
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22312787 120 - 23771897
GACCCAAGACUUGUACCACUUUAUCGAAUCGAUAAGCCCCUUGGCAGACUGUUCAAGACGCAGGGCCGGGGGAGGAAUUCAUUGGCUGCCUAAUGAAUUAUGCAUGGGCAGUCCAAAAAG
...............((..(((((((...))))))).((((((((...((((.......)))).)))))))).))......(((((((((((.((.......))))))))).)))).... ( -39.70)
>DroSec_CAF1 71501 120 - 1
GGCCCCAGACUUGUACUACUUUAUCGAAUCGAUAAGCCCCCUGGCAGACUGUUCAAGACGCAGGGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGUAAUAUGCAUGGGCAGCCCAAAAAG
(((((..(.((((.((....((((((...))))))(((....))).....)).)))).)...)))))((....))........(((((((((.(((.....))))))))))))....... ( -42.70)
>DroSim_CAF1 53214 120 - 1
GGCCCCAGACUUGUACUACUUUAUCGAAUCGAUAAGCCCCCUGGCAGACUGUUCAAGACGCAGGGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGAAAUAUGCAUGGGCAGCCCAAAAAG
(((((..(.((((.((....((((((...))))))(((....))).....)).)))).)...)))))((....))........(((((((((.((.......)))))))))))....... ( -40.70)
>DroEre_CAF1 69860 119 - 1
GCCCG-AGACUUGUACUACCAUAUCGAUUCGAUAAGCCCCUUGGCAGACAAUUCAAGACGCAGGGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGAAAUAUGCAUGGGCAGCCCAAGAAG
((((.-.(.((((........(((((...))))).(((....)))........)))).)...)))).((....))..(((...(((((((((.((.......)))))))))))...))). ( -37.20)
>DroYak_CAF1 49977 120 - 1
GGCCGAAGACUUGUACUACUAUAUCGAAUCGAUAAGCCCCUUGGCAGACUAUUCAAGACACAGUGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGAAAUAUGCAAAGGCAGUCCAAAAAG
((((.....((((........(((((...))))).(((....)))........)))).....).)))((....))......((((((((((..............)))))).)))).... ( -28.64)
>consensus
GGCCCAAGACUUGUACUACUUUAUCGAAUCGAUAAGCCCCUUGGCAGACUGUUCAAGACGCAGGGCCCCGGGAGGAAUUCAUUGGCUGCCUAAUGAAAUAUGCAUGGGCAGCCCAAAAAG
..((...............(((((((...))))))).(((..(((...((((.......)))).)))..))).))........(((((((((.((.......)))))))))))....... (-30.32 = -30.80 +   0.48)

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 13:18:05 2006