Locus 2017

Sequence ID 3R_DroMel_CAF1
Location 5,725,041 – 5,725,156
Length 115
Max. P 0.961947
window3304 window3305

overview

Window 4

Location 5,725,041 – 5,725,156
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 82.70
Mean single sequence MFE -37.40
Consensus MFE -26.72
Energy contribution -28.70
Covariance contribution 1.98
Combinations/Pair 1.06
Mean z-score -2.20
Structure conservation index 0.71
SVM decision value 0.81
SVM RNA-class probability 0.857035
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5725041 115 + 27905053
GGAGACGGCGGCAGAUUGAUGAGGCAAAUUGAUUUGCGGCUCUGCAUCUCUCAAUCUAUUGCAAAAUAGAUUGAGUGCACUAUGCCGCCGUGCUGGGUGAGAAUUGAUUGAGCCA
....(((((.((((((..((.......))..))))))(((..((((...(((((((((((....)))))))))))))))....))))))))(((.(((........))).))).. ( -44.50)
>DroYak_CAF1 30207 111 + 1
GGCGACGGCGGCAGAUUGAUGAGGCAAAUUGAUUUGCGGCGCUGCAUCUCUCAAUCUAUUGCAAAA----UUGAGUGCACUCUGCCGCCGUGCUGGGUGAGAAUUGAUUGAGCCA
(((.(((((((((((((((.((((((((....))))).((...))..))))))))))..((((...----.....))))....))))))))))).(((..((.....))..))). ( -41.00)
>DroAna_CAF1 25535 96 + 1
AGAGAUGA-GGGAGAUUGAUGAGGCAAAUUGAUUUGCGGCGCUGCAUCUCUCAAUCUAUUGCGGAA----UUGAGUGCACU--------------GGCGAGAAUUGAUUGGGCCA
........-.............(((.(((..(((..((.((.((((...((((((((.....)).)----))))))))).)--------------).))..)))..)))..))). ( -26.70)
>consensus
GGAGACGGCGGCAGAUUGAUGAGGCAAAUUGAUUUGCGGCGCUGCAUCUCUCAAUCUAUUGCAAAA____UUGAGUGCACU_UGCCGCCGUGCUGGGUGAGAAUUGAUUGAGCCA
....(((((((((((((((.((((((((....))))).((...))..))))))))))..((((............))))....))))))))....(((..((.....))..))). (-26.72 = -28.70 +   1.98)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 5,725,041 – 5,725,156
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 82.70
Mean single sequence MFE -32.00
Consensus MFE -20.56
Energy contribution -22.97
Covariance contribution 2.42
Combinations/Pair 1.00
Mean z-score -3.08
Structure conservation index 0.64
SVM decision value 1.53
SVM RNA-class probability 0.961947
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5725041 115 - 27905053
UGGCUCAAUCAAUUCUCACCCAGCACGGCGGCAUAGUGCACUCAAUCUAUUUUGCAAUAGAUUGAGAGAUGCAGAGCCGCAAAUCAAUUUGCCUCAUCAAUCUGCCGCCGUCUCC
.....................((.(((((((((...(((((((((((((((....)))))))))))...))))(((..(((((....)))))))).......))))))))))).. ( -39.60)
>DroYak_CAF1 30207 111 - 1
UGGCUCAAUCAAUUCUCACCCAGCACGGCGGCAGAGUGCACUCAA----UUUUGCAAUAGAUUGAGAGAUGCAGCGCCGCAAAUCAAUUUGCCUCAUCAAUCUGCCGCCGUCGCC
......................(((((((((((((.....(((((----(((......)))))))).((((.((....(((((....)))))))))))..))))))))))).)). ( -39.80)
>DroAna_CAF1 25535 96 - 1
UGGCCCAAUCAAUUCUCGCC--------------AGUGCACUCAA----UUCCGCAAUAGAUUGAGAGAUGCAGCGCCGCAAAUCAAUUUGCCUCAUCAAUCUCCC-UCAUCUCU
.((((..(((.......((.--------------...)).(((((----((........))))))).)))...).)))(((((....)))))..............-........ ( -16.60)
>consensus
UGGCUCAAUCAAUUCUCACCCAGCACGGCGGCA_AGUGCACUCAA____UUUUGCAAUAGAUUGAGAGAUGCAGCGCCGCAAAUCAAUUUGCCUCAUCAAUCUGCCGCCGUCUCC
........................((((((((....(((..............)))..((((((((((..((...)).(((((....)))))))).))))))))))))))).... (-20.56 = -22.97 +   2.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:19 2006