Locus 2618

Sequence ID	2L_DroMel_CAF1
Location	7,263,103 – 7,263,252
Length	149
Max. P	0.969525

overview

Window 1

Location	7,263,103 – 7,263,202
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	92.76
Mean single sequence MFE	-20.90
Consensus MFE	-20.90
Energy contribution	-20.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	1.00
SVM decision value	1.64
SVM RNA-class probability	0.969525
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7263103 99 - 22407834
UGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCAGCAGCAUCAGCAACAUCAGCUUCCGCUGCACUCAGAAAAAAACUCCAACUUAAAC
.(((((((((((.........)))))))))))((....))....(((((...(((.......)))...))))).......................... ( -20.90)
>DroSec_CAF1 56363 99 - 1
UGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCAGCAGCAUCAGCAACAUCAGCUUCCGCUGCACUCAGAAAAAAACUCCAAUUUAAAC
.(((((((((((.........)))))))))))((....))....(((((...(((.......)))...))))).......................... ( -20.90)
>DroSim_CAF1 62929 99 - 1
UGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCAGCAGCAUCAGCAACAUCAGCUUCCGCUGCACUCAAAAAAAAACUCCAAUUUAAAC
.(((((((((((.........)))))))))))((....))....(((((...(((.......)))...))))).......................... ( -20.90)
>DroYak_CAF1 56836 92 - 1
UGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCAGCAGCAUCAGCAACAUCAGCUUCCGCUGCACUCAGAUCAAA---UUCACUU----
.(((((((((((.........)))))))))))((....))....(((((...(((.......)))...)))))............---.......---- ( -20.90)
>consensus
UGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCAGCAGCAUCAGCAACAUCAGCUUCCGCUGCACUCAGAAAAAAACUCCAACUUAAAC
.(((((((((((.........)))))))))))((....))....(((((...(((.......)))...))))).......................... (-20.90 = -20.90 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	7,263,139 – 7,263,231
Length	92
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	90.20
Mean single sequence MFE	-28.16
Consensus MFE	-24.92
Energy contribution	-25.12
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.88
SVM decision value	0.89
SVM RNA-class probability	0.875325
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7263139 92 - 22407834
---------GCCCCAAUGUGAGGGUUGCAAGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCA------GCAGCAUCAGCAACAUCAG
---------.........(((..(((((..(((...((((((((((((((.........))))))))))))))..))).((.------...))....))))).))). ( -28.20)
>DroSec_CAF1 56399 92 - 1
---------GCCCCAAUGUGAGGGUUGCAGGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCA------GCAGCAUCAGCAACAUCAG
---------.........(((..(((((..(((...((((((((((((((.........))))))))))))))..))).((.------...))....))))).))). ( -28.00)
>DroSim_CAF1 62965 92 - 1
---------GCCCCAAUGUGAGGGUUGCAAGCCAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCA------GCAGCAUCAGCAACAUCAG
---------.........(((..(((((..((....((((((((((((((.........))))))))))))))...)).((.------...))....))))).))). ( -25.40)
>DroYak_CAF1 56865 92 - 1
---------GCCCCAAUGUGAGGGUUGCAAGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCA------GCAGCAUCAGCAACAUCAG
---------.........(((..(((((..(((...((((((((((((((.........))))))))))))))..))).((.------...))....))))).))). ( -28.20)
>DroPer_CAF1 77480 104 - 1
GCACGGCCCGGCCCUAUGUGAGGGUUGCAAGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCAUUAGGAGUAGCAGCAGCAACAU---
((((..(((((((((.....)))))))...(((...((((((((((((((.........))))))))))))))..))).......)).)).))...........--- ( -31.00)
>consensus
_________GCCCCAAUGUGAGGGUUGCAAGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGCAGCA______GCAGCAUCAGCAACAUCAG
...........(((.....).))(((((..(((...((((((((((((((.........))))))))))))))..))).((..........))....)))))..... (-24.92 = -25.12 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	7,263,162 – 7,263,252
Length	90
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	83.02
Mean single sequence MFE	-29.93
Consensus MFE	-19.45
Energy contribution	-19.20
Covariance contribution	-0.25
Combinations/Pair	1.13
Mean z-score	-1.77
Structure conservation index	0.65
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7263162 90 - 22407834
-UAUAUGUAGGG--CUGUGCUUGU-------------------------GCCCCAAUGUGAGGGUUGCAAGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGC
-..........(--((((((((((-------------------------..(((.......)))..)))))).....(((((((((((((.........)))))))))))))))).)) ( -28.60)
>DroSec_CAF1 56422 90 - 1
-UAUAUGUAAGG--CUGUGUUUCU-------------------------GCCCCAAUGUGAGGGUUGCAGGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGC
-..........(--(.((((.(((-------------------------(((((.......)))..)))))......(((((((((((((.........))))))))))))))))))) ( -24.70)
>DroSim_CAF1 62988 90 - 1
-UAUAUGUAAGG--CUGUGUUUGU-------------------------GCCCCAAUGUGAGGGUUGCAAGCCAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGC
-.........((--((.(((....-------------------------(((((.....).)))).)))))))...((((((((((((((.........))))))))))))))..... ( -26.80)
>DroEre_CAF1 57160 90 - 1
-UAUAUGUAGGG--CUGUGUUUGU-------------------------GCCCCAAUGUGAGGGUUGCAAGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGC
-..........(--((((((((((-------------------------..(((.......)))..)))))).....(((((((((((((.........)))))))))))))))).)) ( -26.20)
>DroAna_CAF1 57233 93 - 1
CUCUCUGUGGGUGUGUGUGUGUGU-------------------------GCCCUAAUGUGAGGGUUGCAAGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACAC
..........((((((((((.(((-------------------------(((((......)))).)))).)).......(((((((((((.........))))))))))))))))))) ( -29.00)
>DroPer_CAF1 77506 115 - 1
-UGUGGGUUGGU--GCGUGAGUGUGGCCCGGCACGGCACGGCACGGCCCGGCCCUAUGUGAGGGUUGCAAGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGC
-(((((((((.(--(((((.((((......))))..))).)))))))))((((((.....))))))))).(((...((((((((((((((.........))))))))))))))..))) ( -44.30)
>consensus
_UAUAUGUAGGG__CUGUGUUUGU_________________________GCCCCAAUGUGAGGGUUGCAAGCGAAAUGUGUCGUAAAGAUUUUUAUUGCAUUUUUAUGGCGCACACGC
...............((((..............................(((((.......)))..))........((((((((((((((.........)))))))))))))))))). (-19.45 = -19.20 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:04 2006