Locus 5975

Sequence ID 3R_DroMel_CAF1
Location 15,765,365 – 15,765,474
Length 109
Max. P 0.737714
window9755 window9756

overview

Window 5

Location 15,765,365 – 15,765,474
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.50
Mean single sequence MFE -19.82
Consensus MFE -13.68
Energy contribution -13.92
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.88
Structure conservation index 0.69
SVM decision value 0.11
SVM RNA-class probability 0.586432
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15765365 109 + 27905053
ACAUAGUCA-----CACUUAGCAAUCAAACUAGACAA-AAGUUUCUCGAUUAAAAUGAGCAACUU-UUGUGAAA---UUCUCUUAUCUAACAAUUUCCGCUGCUUAGUUGAA-CCGAAAU
......(((-----.(((.((((..........((((-(((((.((((.......)))).)))))-))))((((---((............))))))...)))).)))))).-....... ( -19.90)
>DroSec_CAF1 22542 100 + 1
--------------CACUUAGCAAUCAAACUAGACAA-AAGUUUCUCGAUUAAAAUGAGCAACUU-UUGUGAAA---UUCUCUUAUCUAACAAUUUCCGCUGCUUAGCUGAA-CCGAAAU
--------------...(((((...........((((-(((((.((((.......)))).)))))-))))((((---((............)))))).........))))).-....... ( -17.40)
>DroSim_CAF1 22532 100 + 1
--------------CACUUAGCAAUCAAACUAGACAA-AAGUUUCUCGAUUAAAAUGAGCAACUU-UUGUGAAA---UUCUCUUAUCUAACAAUUUCCGCUGCUUAGUUGAA-CCGAAAU
--------------.(((.((((..........((((-(((((.((((.......)))).)))))-))))((((---((............))))))...)))).)))....-....... ( -17.70)
>DroEre_CAF1 24688 108 + 1
-CAUAGUCA-----CACUUAGCAAUCAAACUAGACAA-AAGUUUCUCGAUUAAAAUGAGCAACUU-UUGCGAAA---UUCUCUUAUCUAACAAUUUCCGCUGCUUAGUUGAA-CCGAAAU
-.....(((-----.(((.((((.........(.(((-(((((.((((.......)))).)))))-))))((((---((............))))))...)))).)))))).-....... ( -18.90)
>DroPer_CAF1 24401 119 + 1
-UAUAGUUUCUGUUCUCUGAGCAAUCAAACUAGACAAAAAGUUUCUCGAUUAAAAUGAGCAACUUUUUGUGAGAAUUUUCUCUUAUCUGACAAUUUCCGCUGCUUAGCCGAAGACCAAAU
-..((((((.(((((...)))))...)))))).((((((((((.((((.......)))).))))))))))((((....))))...........((((.(((....))).))))....... ( -25.20)
>consensus
__AUAGU_______CACUUAGCAAUCAAACUAGACAA_AAGUUUCUCGAUUAAAAUGAGCAACUU_UUGUGAAA___UUCUCUUAUCUAACAAUUUCCGCUGCUUAGUUGAA_CCGAAAU
................((.((((..........((((((((((.((((.......)))).))))))))))(((....)))....................)))).))............. (-13.68 = -13.92 +   0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,765,365 – 15,765,474
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -25.06
Consensus MFE -19.86
Energy contribution -19.82
Covariance contribution -0.04
Combinations/Pair 1.10
Mean z-score -1.68
Structure conservation index 0.79
SVM decision value 0.44
SVM RNA-class probability 0.737714
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15765365 109 - 27905053
AUUUCGG-UUCAACUAAGCAGCGGAAAUUGUUAGAUAAGAGAA---UUUCACAA-AAGUUGCUCAUUUUAAUCGAGAAACUU-UUGUCUAGUUUGAUUGCUAAGUG-----UGACUAUGU
.....((-((..(((.(((((((((((((.((......)).))---))))((((-(((((.(((.........))).)))))-))))......)).))))).))).-----.)))).... ( -25.80)
>DroSec_CAF1 22542 100 - 1
AUUUCGG-UUCAGCUAAGCAGCGGAAAUUGUUAGAUAAGAGAA---UUUCACAA-AAGUUGCUCAUUUUAAUCGAGAAACUU-UUGUCUAGUUUGAUUGCUAAGUG--------------
.......-....(((.(((((((((((((.((......)).))---))))((((-(((((.(((.........))).)))))-))))......)).))))).))).-------------- ( -22.90)
>DroSim_CAF1 22532 100 - 1
AUUUCGG-UUCAACUAAGCAGCGGAAAUUGUUAGAUAAGAGAA---UUUCACAA-AAGUUGCUCAUUUUAAUCGAGAAACUU-UUGUCUAGUUUGAUUGCUAAGUG--------------
.......-....(((.(((((((((((((.((......)).))---))))((((-(((((.(((.........))).)))))-))))......)).))))).))).-------------- ( -22.60)
>DroEre_CAF1 24688 108 - 1
AUUUCGG-UUCAACUAAGCAGCGGAAAUUGUUAGAUAAGAGAA---UUUCGCAA-AAGUUGCUCAUUUUAAUCGAGAAACUU-UUGUCUAGUUUGAUUGCUAAGUG-----UGACUAUG-
.....((-((..(((.(((((((((((((.((......)).))---))))((((-(((((.(((.........))).)))))-))))......)).))))).))).-----.))))...- ( -26.10)
>DroPer_CAF1 24401 119 - 1
AUUUGGUCUUCGGCUAAGCAGCGGAAAUUGUCAGAUAAGAGAAAAUUCUCACAAAAAGUUGCUCAUUUUAAUCGAGAAACUUUUUGUCUAGUUUGAUUGCUCAGAGAACAGAAACUAUA-
.((((.(((((.(((....))).)))...(((((((..((((....))))((((((((((.(((.........))).))))))))))...)))))))........)).)))).......- ( -27.90)
>consensus
AUUUCGG_UUCAACUAAGCAGCGGAAAUUGUUAGAUAAGAGAA___UUUCACAA_AAGUUGCUCAUUUUAAUCGAGAAACUU_UUGUCUAGUUUGAUUGCUAAGUG_______ACUAU__
............(((.(((((((((.............((((....))))((((((((((.(((.........))).))))))))))....)))).))))).)))............... (-19.86 = -19.82 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:32 2006