Locus 1959

Sequence ID 2L_DroMel_CAF1
Location 5,296,875 – 5,296,975
Length 100
Max. P 0.996441
window3171 window3172

overview

Window 1

Location 5,296,875 – 5,296,975
Length 100
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 80.00
Mean single sequence MFE -30.97
Consensus MFE -22.67
Energy contribution -23.90
Covariance contribution 1.23
Combinations/Pair 1.15
Mean z-score -2.93
Structure conservation index 0.73
SVM decision value 2.70
SVM RNA-class probability 0.996441
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5296875 100 + 22407834
UGUAAAGCUUAGAUGCAAAUCUGCAUCUA----------UGCACAUAUAGCAGUGCAAUUUUUACGCCUGUACCGCUGAAGUUUUCACCCAUCUGCCGCUGCAGAAAUGU
......((.((((((((....))))))))----------.))((((.((((.(((((...........))))).)))).............(((((....))))).)))) ( -28.90)
>DroEre_CAF1 69539 110 + 1
UAUAGAGCUUAGAUGCAGAACUGCAUCUGAUCUUUAAACUGCCCAUCUUGUGGUGCAAUUUUUCCGUCUGUACCGCCGGAGUUUUCACCCAUCUGCCGCUGCAGAAAUGU
..(((((.(((((((((....))))))))).))))).........(((.((((((((...........)))))))).)))...........(((((....)))))..... ( -34.60)
>DroYak_CAF1 76909 100 + 1
UCUGCAUCUUAGAUGCAGAAAUGCAUCCA----------UGUCCAUCUUAUGGUGCAAUUUUUCUGUCUGUACCGCUGGAGUUUUCACCCAUCUGCCGCUGCAGAAAUGU
((((((((...))))))))..((((.(((----------((.......))))))))).........(((((((.(((((.((....)))))...)).).))))))..... ( -29.40)
>consensus
UAUAAAGCUUAGAUGCAGAACUGCAUCUA__________UGCCCAUCUUGUGGUGCAAUUUUUCCGUCUGUACCGCUGGAGUUUUCACCCAUCUGCCGCUGCAGAAAUGU
...(((((((.((((((....))))))......................((((((((...........))))))))..)))))))......(((((....)))))..... (-22.67 = -23.90 +   1.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,296,875 – 5,296,975
Length 100
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 80.00
Mean single sequence MFE -30.70
Consensus MFE -21.43
Energy contribution -21.43
Covariance contribution 0.01
Combinations/Pair 1.11
Mean z-score -2.23
Structure conservation index 0.70
SVM decision value 1.39
SVM RNA-class probability 0.949326
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5296875 100 - 22407834
ACAUUUCUGCAGCGGCAGAUGGGUGAAAACUUCAGCGGUACAGGCGUAAAAAUUGCACUGCUAUAUGUGCA----------UAGAUGCAGAUUUGCAUCUAAGCUUUACA
.....(((((....)))))(((((....)).)))...(((.((((........(((((........)))))----------(((((((......))))))).))))))). ( -29.70)
>DroEre_CAF1 69539 110 - 1
ACAUUUCUGCAGCGGCAGAUGGGUGAAAACUCCGGCGGUACAGACGGAAAAAUUGCACCACAAGAUGGGCAGUUUAAAGAUCAGAUGCAGUUCUGCAUCUAAGCUCUAUA
.....(((((....))))).((((((....((((.(......).)))).(((((((.(((.....)))))))))).....))(((((((....)))))))..)))).... ( -32.80)
>DroYak_CAF1 76909 100 - 1
ACAUUUCUGCAGCGGCAGAUGGGUGAAAACUCCAGCGGUACAGACAGAAAAAUUGCACCAUAAGAUGGACA----------UGGAUGCAUUUCUGCAUCUAAGAUGCAGA
...((((((.....((...(((((....)).)))...)).....))))))...((((((((.........)----------))).))))..((((((((...)))))))) ( -29.60)
>consensus
ACAUUUCUGCAGCGGCAGAUGGGUGAAAACUCCAGCGGUACAGACGGAAAAAUUGCACCACAAGAUGGGCA__________UAGAUGCAGUUCUGCAUCUAAGCUCUACA
.(((((((((....)))))(((((....)).)))(((((............))))).......))))..............((((((((....))))))))......... (-21.43 = -21.43 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:01 2006