Locus 7090

Sequence ID 3L_DroMel_CAF1
Location 19,147,145 – 19,147,254
Length 109
Max. P 0.955602
window11501 window11502

overview

Window 1

Location 19,147,145 – 19,147,254
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.71
Mean single sequence MFE -34.60
Consensus MFE -18.25
Energy contribution -19.78
Covariance contribution 1.53
Combinations/Pair 1.14
Mean z-score -4.12
Structure conservation index 0.53
SVM decision value 1.23
SVM RNA-class probability 0.934090
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19147145 109 + 23771897
CUCACGCGCACUGC-----GAUGAGAAAUGUAUUGAUAUGUAAUUCAAUAGAAAAACUAAUAAACUGCUACUGCA------AUGGCAAUGGCAAUUGCAAUUGCGAGUGCGAAUGGGAGU
((((..((((((((-----(((......(.((((((........)))))).).............(((((.(((.------...))).)))))......))))).))))))..))))... ( -32.80)
>DroSec_CAF1 10028 109 + 1
CUCACUCGCACUGC-----AAUGAGAAAUGCAUUGAUAUGUAAUUCAAUAGAAAAACUAAUAAACUGCUACUGCA------AUGGCAAUGGCAAUUGCAAUUGCGAGUGCGAAUGGGAGU
((((.(((((((((-----(((..(((.(((((....))))).)))...................(((((.(((.------...))).)))))......))))).))))))).))))... ( -35.40)
>DroAna_CAF1 2971 103 + 1
CACACUCGCAAGGCAUUCGAAUGAGAAAUGCAUUGAUAUGUAAUUCAAUAGCAAAACUAAUAGACUGCCAAUGCU-----------AUUGGAAAUUGCAGUUGCGAGUGCGAA------U
(.(((((((((((((.((.....((...((((((((........))))).)))...))....)).))))..(((.-----------..(....)..))).))))))))).)..------. ( -32.00)
>DroSim_CAF1 9686 109 + 1
CUCACUCGCACUGC-----AAUGAGAAAUGCAUUGAUAUGUAAUUCAAUAGAAAAACUAAUAAACUGCUACUGCA------AUGGCAAUGGCAAUUGCAAUUGCGAGUGCGAAUGGGAGU
((((.(((((((((-----(((..(((.(((((....))))).)))...................(((((.(((.------...))).)))))......))))).))))))).))))... ( -35.40)
>DroEre_CAF1 10436 103 + 1
CUCACUCGCACUGC-----GCUGAGAAAUGCAUUGAUAUGUAAUUCAAUGGGAAAACUAAUAAACUGCAA------------CUGCAAUGGCAAUGGCAAUUGCCACUGCGAAAGCGAGU
...((((((..(((-----.....(((.(((((....))))).)))..(((.....))).......))).------------.((((.(((((((....))))))).))))...)))))) ( -32.80)
>DroYak_CAF1 10544 115 + 1
CUCACUCGCACUUC-----GAUGAGAAGUGCAUUGAUAUGUAAUUUAAUAGGAAAACUAAUAAACUGCAACUGCAAAUGCAACUGCAAUGGCAAUGGCAAUUGCCAGUGCGAAAGCGAGU
...(((((((((((-----.....)))))((((((...((((.((((.(((.....))).)))).))))...((((.(((...(((....)))...))).))))))))))....)))))) ( -39.20)
>consensus
CUCACUCGCACUGC_____AAUGAGAAAUGCAUUGAUAUGUAAUUCAAUAGAAAAACUAAUAAACUGCUACUGCA______AUGGCAAUGGCAAUUGCAAUUGCGAGUGCGAAUGGGAGU
(((..((((((.............(((.(((((....))))).)))...................(((((.(((..........))).))))).((((....))))))))))....))). (-18.25 = -19.78 +   1.53)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 19,147,145 – 19,147,254
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.71
Mean single sequence MFE -34.32
Consensus MFE -18.55
Energy contribution -20.55
Covariance contribution 2.00
Combinations/Pair 1.11
Mean z-score -4.44
Structure conservation index 0.54
SVM decision value 1.46
SVM RNA-class probability 0.955602
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19147145 109 - 23771897
ACUCCCAUUCGCACUCGCAAUUGCAAUUGCCAUUGCCAU------UGCAGUAGCAGUUUAUUAGUUUUUCUAUUGAAUUACAUAUCAAUACAUUUCUCAUC-----GCAGUGCGCGUGAG
.....(((.(((((((((.((((((((.((....)).))------)))))).))((((((.(((.....))).))))))......................-----).)))))).))).. ( -29.20)
>DroSec_CAF1 10028 109 - 1
ACUCCCAUUCGCACUCGCAAUUGCAAUUGCCAUUGCCAU------UGCAGUAGCAGUUUAUUAGUUUUUCUAUUGAAUUACAUAUCAAUGCAUUUCUCAUU-----GCAGUGCGAGUGAG
.....((((((((((.((((((((((((((.(((((...------.))))).)))))......((..(((....)))..)).......))))......)))-----)))))))))))).. ( -36.10)
>DroAna_CAF1 2971 103 - 1
A------UUCGCACUCGCAACUGCAAUUUCCAAU-----------AGCAUUGGCAGUCUAUUAGUUUUGCUAUUGAAUUACAUAUCAAUGCAUUUCUCAUUCGAAUGCCUUGCGAGUGUG
.------..(((((((((((.(((..........-----------.)))..((((.((.((.((...(((.(((((........))))))))...)).))..)).))))))))))))))) ( -31.10)
>DroSim_CAF1 9686 109 - 1
ACUCCCAUUCGCACUCGCAAUUGCAAUUGCCAUUGCCAU------UGCAGUAGCAGUUUAUUAGUUUUUCUAUUGAAUUACAUAUCAAUGCAUUUCUCAUU-----GCAGUGCGAGUGAG
.....((((((((((.((((((((((((((.(((((...------.))))).)))))......((..(((....)))..)).......))))......)))-----)))))))))))).. ( -36.10)
>DroEre_CAF1 10436 103 - 1
ACUCGCUUUCGCAGUGGCAAUUGCCAUUGCCAUUGCAG------------UUGCAGUUUAUUAGUUUUCCCAUUGAAUUACAUAUCAAUGCAUUUCUCAGC-----GCAGUGCGAGUGAG
.(((((((..((((((((....))))))))((((((.(------------(((.((..............((((((........)))))).....))))))-----)))))).))))))) ( -33.81)
>DroYak_CAF1 10544 115 - 1
ACUCGCUUUCGCACUGGCAAUUGCCAUUGCCAUUGCAGUUGCAUUUGCAGUUGCAGUUUAUUAGUUUUCCUAUUAAAUUACAUAUCAAUGCACUUCUCAUC-----GAAGUGCGAGUGAG
.(((((((..((((((.(((.(((.(((((....))))).))).)))))).)))((((((.(((.....))).))))))..........(((((((.....-----)))))))))))))) ( -39.60)
>consensus
ACUCCCAUUCGCACUCGCAAUUGCAAUUGCCAUUGCCAU______UGCAGUAGCAGUUUAUUAGUUUUUCUAUUGAAUUACAUAUCAAUGCAUUUCUCAUC_____GCAGUGCGAGUGAG
...........((((((((.((((.(((((.(((((..........))))).))))).............((((((........))))))................)))))))))))).. (-18.55 = -20.55 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:34 2006