Locus 3679

Sequence ID 2L_DroMel_CAF1
Location 10,709,447 – 10,709,592
Length 145
Max. P 0.819870
window5805 window5806 window5807

overview

Window 5

Location 10,709,447 – 10,709,565
Length 118
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 83.14
Mean single sequence MFE -30.12
Consensus MFE -21.69
Energy contribution -22.28
Covariance contribution 0.59
Combinations/Pair 1.23
Mean z-score -2.61
Structure conservation index 0.72
SVM decision value 0.68
SVM RNA-class probability 0.819870
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10709447 118 + 22407834
UGCUGAAUGAGUCAAAAGAAUGGCCAAGAGAAAUGAGCCAUCUGGCCGAGAUAAAUGCCA-AGUGUGAAUUGAAACUCAAAGUCGCUCAUGUGAAUGAGUUUCUAAUUAAGCCAGGCAA
....................((((((.((...........)))))))).......((((.-.((...((((((((((((...((((....)))).)))))))).))))..))..)))). ( -32.40)
>DroSec_CAF1 40385 104 + 1
--------------AAAGAAUGGCCAAGAGAAAUGAGCCAUCUGGCCGAGAUAAAUGCCA-AGUGUGAAUUGAAACUCAAAGUCGCUCGUGUGAAUGAGUUUCUAAUUAAGCCAGGCAA
--------------......((((((.((...........)))))))).......((((.-.((...((((((((((((...((((....)))).)))))))).))))..))..)))). ( -32.40)
>DroSim_CAF1 41360 104 + 1
--------------AAAGAAUGGCCAAGAGAAAUGAGCCAUCUGGCCGAGAUAAAUGCCA-AGUGUGAAUUGAAACUCAAAGUCGCUCGUGUGAAUGAGUUUCUAAUUAAGCCAGGCAA
--------------......((((((.((...........)))))))).......((((.-.((...((((((((((((...((((....)))).)))))))).))))..))..)))). ( -32.40)
>DroEre_CAF1 41595 115 + 1
---UAAAUGAGUCAAAAGAAUGGCCAAGAGAAAUGAGCCAUCUGGCCGAGAUUAAUGCCA-ACUGUGAAUUGAAACUCAAAGUCUCUCAUGUGAAUGAGUUUCUAAUUAAGCCAGGCAA
---.................((((((.((...........)))))))).......((((.-.((...((((((((((((...((.(....).)).)))))))).)))).))...)))). ( -26.90)
>DroYak_CAF1 39745 115 + 1
---UAAAUGACUCAAAAGAAUGGCCAAGAGAAAUGAGCCAUCUGGCCGAGAUUAUUGCCA-AGUGUGAAUGGAAACUCAAAGUCGCUCAUGUGAAUGAGUUUCUAAUUAAGCCUGGCAA
---..((((((((...(((.((((((.......)).)))))))....))).)))))((((-.((.(((.((((((((((...((((....)))).)))))))))).))).)).)))).. ( -38.60)
>DroAna_CAF1 40594 112 + 1
-------UGAGACAAAAAAGCGGCCAAGUAAAAUAAGUCAACUGCCAGAGAUAAAGGCCAGAGCUUCAAUUGUAUCUCAAAGUCGUUCAUGUGGUUGGAAUCGUAAUUAAGACAGUCAA
-------...(((........((((..........((....))............)))).((..((((((..(((..(......)...)))..)))))).))............))).. ( -18.05)
>consensus
_______UGAGUCAAAAGAAUGGCCAAGAGAAAUGAGCCAUCUGGCCGAGAUAAAUGCCA_AGUGUGAAUUGAAACUCAAAGUCGCUCAUGUGAAUGAGUUUCUAAUUAAGCCAGGCAA
....................((((((.((...........)))))))).......((((...((...((((((((((((...((((....)))).)))))))).))))..))..)))). (-21.69 = -22.28 +   0.59)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,709,447 – 10,709,565
Length 118
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 83.14
Mean single sequence MFE -25.95
Consensus MFE -17.53
Energy contribution -17.90
Covariance contribution 0.37
Combinations/Pair 1.20
Mean z-score -2.02
Structure conservation index 0.68
SVM decision value 0.16
SVM RNA-class probability 0.614509
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10709447 118 - 22407834
UUGCCUGGCUUAAUUAGAAACUCAUUCACAUGAGCGACUUUGAGUUUCAAUUCACACU-UGGCAUUUAUCUCGGCCAGAUGGCUCAUUUCUCUUGGCCAUUCUUUUGACUCAUUCAGCA
.(((((((((......((((((((.((.(....).))...))))))))...(((....-)))..........))))))(((((.((.......)))))))................))) ( -26.60)
>DroSec_CAF1 40385 104 - 1
UUGCCUGGCUUAAUUAGAAACUCAUUCACACGAGCGACUUUGAGUUUCAAUUCACACU-UGGCAUUUAUCUCGGCCAGAUGGCUCAUUUCUCUUGGCCAUUCUUU--------------
.((((.((...((((.((((((((.((.(....).))...))))))))))))....))-.))))........((((((..((......))..)))))).......-------------- ( -26.20)
>DroSim_CAF1 41360 104 - 1
UUGCCUGGCUUAAUUAGAAACUCAUUCACACGAGCGACUUUGAGUUUCAAUUCACACU-UGGCAUUUAUCUCGGCCAGAUGGCUCAUUUCUCUUGGCCAUUCUUU--------------
.((((.((...((((.((((((((.((.(....).))...))))))))))))....))-.))))........((((((..((......))..)))))).......-------------- ( -26.20)
>DroEre_CAF1 41595 115 - 1
UUGCCUGGCUUAAUUAGAAACUCAUUCACAUGAGAGACUUUGAGUUUCAAUUCACAGU-UGGCAUUAAUCUCGGCCAGAUGGCUCAUUUCUCUUGGCCAUUCUUUUGACUCAUUUA---
.((((.((((.((((.((((((((.((........))...))))))))))))...)))-)))))........((((((..((......))..))))))..................--- ( -26.80)
>DroYak_CAF1 39745 115 - 1
UUGCCAGGCUUAAUUAGAAACUCAUUCACAUGAGCGACUUUGAGUUUCCAUUCACACU-UGGCAAUAAUCUCGGCCAGAUGGCUCAUUUCUCUUGGCCAUUCUUUUGAGUCAUUUA---
((((((((........((((((((.((.(....).))...))))))))........))-))))))....(((((...((((((.((.......))))))))...))))).......--- ( -31.59)
>DroAna_CAF1 40594 112 - 1
UUGACUGUCUUAAUUACGAUUCCAACCACAUGAACGACUUUGAGAUACAAUUGAAGCUCUGGCCUUUAUCUCUGGCAGUUGACUUAUUUUACUUGGCCGCUUUUUUGUCUCA-------
..(((((((((((...((.(((.........)))))...)))))))).....(((((...((((.........(((....).))..........)))))))))...)))...------- ( -18.31)
>consensus
UUGCCUGGCUUAAUUAGAAACUCAUUCACAUGAGCGACUUUGAGUUUCAAUUCACACU_UGGCAUUUAUCUCGGCCAGAUGGCUCAUUUCUCUUGGCCAUUCUUUUGACUCA_______
....((((((......((((((((.((........))...))))))))............((........))))))))(((((.((.......)))))))................... (-17.53 = -17.90 +   0.37)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,709,486 – 10,709,592
Length 106
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 81.23
Mean single sequence MFE -29.32
Consensus MFE -16.78
Energy contribution -16.73
Covariance contribution -0.05
Combinations/Pair 1.32
Mean z-score -2.33
Structure conservation index 0.57
SVM decision value 0.46
SVM RNA-class probability 0.745688
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10709486 106 + 22407834
AUCUGGCCGAGAUAAAUGCCA-AGUGUGAAUUGAAACUCAAAGUCGCUCAUGUGAAUGAGUUUCUAAUUAAGCCAGGCAAACUGGAAGCCUCAUGCCAGUCUGAAU-----A
..(((((.(((.....((((.-.((...((((((((((((...((((....)))).)))))))).))))..))..))))....(....))))..))))).......-----. ( -31.90)
>DroSec_CAF1 40410 106 + 1
AUCUGGCCGAGAUAAAUGCCA-AGUGUGAAUUGAAACUCAAAGUCGCUCGUGUGAAUGAGUUUCUAAUUAAGCCAGGCAAACUGGAAGCCUCACGCCAGUCAGAAU-----A
.((((((.(.(........).-.((((((...((((((((...((((....)))).))))))))........((((.....)))).....))))))).))))))..-----. ( -32.30)
>DroSim_CAF1 41385 106 + 1
AUCUGGCCGAGAUAAAUGCCA-AGUGUGAAUUGAAACUCAAAGUCGCUCGUGUGAAUGAGUUUCUAAUUAAGCCAGGCAAACUGGAAGCCUCACGCCAGUCUGAAU-----A
..(((((.(((.....((((.-.((...((((((((((((...((((....)))).)))))))).))))..))..))))....(....))))..))))).......-----. ( -31.90)
>DroEre_CAF1 41631 106 + 1
AUCUGGCCGAGAUUAAUGCCA-ACUGUGAAUUGAAACUCAAAGUCUCUCAUGUGAAUGAGUUUCUAAUUAAGCCAGGCAAACUGGAAGCCUCACGCAAGUCAGAAC-----A
.((((...(((..........-.((...((((((((((((...((.(....).)).)))))))).)))).))((((.....))))....)))((....))))))..-----. ( -26.00)
>DroYak_CAF1 39781 106 + 1
AUCUGGCCGAGAUUAUUGCCA-AGUGUGAAUGGAAACUCAAAGUCGCUCAUGUGAAUGAGUUUCUAAUUAAGCCUGGCAAACUGAAAGACUGAAUCAAGUCAGAAU-----A
.((((((...((((.((((((-.((.(((.((((((((((...((((....)))).)))))))))).))).)).)))))).(.....)....))))..))))))..-----. ( -35.50)
>DroAna_CAF1 40626 94 + 1
AACUGCCAGAGAUAAAGGCCAGAGCUUCAAUUGUAUCUCAAAGUCGUUCAUGUGGUUGGAAUCGUAAUUAAGACAGUCAA------------------GUCUCAAUUGUCGA
..(.((((((((((.((((....))))......))))))...(.....)...)))).)...((((((((.((((......------------------)))).))))).))) ( -18.30)
>consensus
AUCUGGCCGAGAUAAAUGCCA_AGUGUGAAUUGAAACUCAAAGUCGCUCAUGUGAAUGAGUUUCUAAUUAAGCCAGGCAAACUGGAAGCCUCACGCCAGUCAGAAU_____A
.((((((........((((....)))).....((((((((...((((....)))).)))))))).......))))))................................... (-16.78 = -16.73 +  -0.05)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:32 2006