Locus 5145

Sequence ID 3R_DroMel_CAF1
Location 13,533,035 – 13,533,173
Length 138
Max. P 0.961804
window8395 window8396 window8397

overview

Window 5

Location 13,533,035 – 13,533,133
Length 98
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -24.07
Consensus MFE -22.15
Energy contribution -22.14
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.92
SVM decision value 0.15
SVM RNA-class probability 0.608463
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13533035 98 - 27905053
UAUGUUAUGAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCUAUUUGCACAUUCAUUGGAUGUUUGGCCGUGGGACCACCCAG----UAGUCCCCCAU
..((((((......)))))).......((((.((((((....(((................))))))))).))))(((((.((...)----).))))).... ( -24.49)
>DroSec_CAF1 7769 102 - 1
UAUGUUAUUAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCUAUUUGCACAUUCAUUGGAUGUUUGGCCGUGGGACCACCCAGUAAGUAGUCCCCUAU
..(((((((....))))))).......((((.((((((....(((................))))))))).))))(((((.((.......)).))))).... ( -24.89)
>DroEre_CAF1 7664 98 - 1
UAUGUUAUGAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCCAUUUGCACAUUCAUUGGAUGUUUGACCGUGGGACCACCCAG----UAGUCCCCCAU
..((((((......))))))((.....(((((.((.....)).)))))..))(((((.....)))))......(.(((((.((...)----).))))).).. ( -22.40)
>DroYak_CAF1 8458 98 - 1
UAUGUUAUGAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCUAUUUGCACGUUCAUUGGAUGUUUGGCCGUGGGACCACCCAG----UAGUCCCCCAU
..((((((......)))))).......((((.((((((....(((................))))))))).))))(((((.((...)----).))))).... ( -24.49)
>consensus
UAUGUUAUGAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCUAUUUGCACAUUCAUUGGAUGUUUGGCCGUGGGACCACCCAG____UAGUCCCCCAU
..((((((......)))))).......((((.((((((....(((....((......))..))))))))).))))(((((.............))))).... (-22.15 = -22.14 +  -0.00)

alignment

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secondary structure

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Window 6

Location 13,533,056 – 13,533,173
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -31.00
Consensus MFE -26.98
Energy contribution -29.23
Covariance contribution 2.25
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.87
SVM decision value 1.53
SVM RNA-class probability 0.961804
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13533056 117 + 27905053
CCACGGCCAAACAUCCAAUGAAUGUGCAAAUAGGAAAUGUGCUUGCCCAUAUAAAGCUGUUAUUGUAUCAUAACAUACUAUGGGUGAAUGCAUUACCGCACAUUCGAUUGGAACGUA
.............((((((((((((((.....((.(((((..(..((((((......((((((......))))))...))))))..)..))))).)))))))))).))))))..... ( -38.60)
>DroSec_CAF1 7794 117 + 1
CCACGGCCAAACAUCCAAUGAAUGUGCAAAUAGGAAAUGUGCUUGCCCAUAUAAAGCUGUUAUUGUAUAAUAACAUAAUAUGUGUGAAUGCAUUACCGCACAUUCGAUUGGAGCUUA
.............((((((((((((((.....((.(((((..(..(.(((((.....(((((((....)))))))..))))).)..)..))))).)))))))))).))))))..... ( -33.60)
>DroEre_CAF1 7685 115 + 1
CCACGGUCAAACAUCCAAUGAAUGUGCAAAUGGGAAAUGUGCUUGCCCAUAUAAAGCUGUUAUUGUAUCAUAACAUACUAUGGCUGAUUGCAUUACCGC--AUUCGAUUGGAGCUUA
.............(((((((((((((..((((.((.(((((......)))))..((((((...(((......)))....))))))..)).))))..)))--)))).))))))..... ( -26.30)
>DroYak_CAF1 8479 115 + 1
CCACGGCCAAACAUCCAAUGAACGUGCAAAUAGGAAAUGUGCUUGCCCAUAUAAAGCUGUUAUUGUAUCAUAACAUACUACGGCUGAAUGCAUUACCGC--AUUCGAUUGGAGCUUA
.((((..((.........))..))))..................(((((.....((((((...(((......)))....))))))((((((......))--))))...))).))... ( -25.50)
>consensus
CCACGGCCAAACAUCCAAUGAAUGUGCAAAUAGGAAAUGUGCUUGCCCAUAUAAAGCUGUUAUUGUAUCAUAACAUACUAUGGCUGAAUGCAUUACCGC__AUUCGAUUGGAGCUUA
.............((((((((((((((.....((.(((((..(((((((((......((((((......))))))...)))))))))..))))).)))))))))).))))))..... (-26.98 = -29.23 +   2.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,533,056 – 13,533,173
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 94.00
Mean single sequence MFE -31.02
Consensus MFE -26.44
Energy contribution -27.88
Covariance contribution 1.44
Combinations/Pair 1.08
Mean z-score -1.96
Structure conservation index 0.85
SVM decision value 0.72
SVM RNA-class probability 0.832626
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13533056 117 - 27905053
UACGUUCCAAUCGAAUGUGCGGUAAUGCAUUCACCCAUAGUAUGUUAUGAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCUAUUUGCACAUUCAUUGGAUGUUUGGCCGUGG
.((((.(((((.((((((((((.((((..((..((((((...((((((......))))))......))))))..))..)))).)).....))))))))))))))))).......... ( -34.80)
>DroSec_CAF1 7794 117 - 1
UAAGCUCCAAUCGAAUGUGCGGUAAUGCAUUCACACAUAUUAUGUUAUUAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCUAUUUGCACAUUCAUUGGAUGUUUGGCCGUGG
(((((((((((.((((((((((.((((........(((((..(((((((....))))))).....)))))........)))).)).....)))))))))))))).)))))....... ( -31.79)
>DroEre_CAF1 7685 115 - 1
UAAGCUCCAAUCGAAU--GCGGUAAUGCAAUCAGCCAUAGUAUGUUAUGAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCCAUUUGCACAUUCAUUGGAUGUUUGACCGUGG
(((((((((((.((((--(......(((((......((((..((((((......))))))...))))(((((.((.....)).))))))))))))))))))))).)))))....... ( -27.60)
>DroYak_CAF1 8479 115 - 1
UAAGCUCCAAUCGAAU--GCGGUAAUGCAUUCAGCCGUAGUAUGUUAUGAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCUAUUUGCACGUUCAUUGGAUGUUUGGCCGUGG
.((((.......((((--(((....)))))))..........((((((......))))))))))..(((((.((((((....(((................))))))))).))))). ( -29.89)
>consensus
UAAGCUCCAAUCGAAU__GCGGUAAUGCAUUCACCCAUAGUAUGUUAUGAUACAAUAACAGCUUUAUAUGGGCAAGCACAUUUCCUAUUUGCACAUUCAUUGGAUGUUUGGCCGUGG
(((((((((((.((((((((((.((((......((((((...((((((......))))))......))))))......)))).)).....)))))))))))))).)))))....... (-26.44 = -27.88 +   1.44)

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 11:47:29 2006