Locus 2971

Sequence ID	3R_DroMel_CAF1
Location	7,930,988 – 7,931,182
Length	194
Max. P	0.824860

overview

Window 0

Location	7,930,988 – 7,931,082
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	88.30
Mean single sequence MFE	-20.28
Consensus MFE	-14.16
Energy contribution	-15.08
Covariance contribution	0.92
Combinations/Pair	1.08
Mean z-score	-1.78
Structure conservation index	0.70
SVM decision value	-0.01
SVM RNA-class probability	0.528807
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7930988 94 - 27905053
CUGUUUUCCAGGGCUAAGAUAUCAGUGGUUUGAUAAAAUAGAAUUUGCAUUUUUAAAUUAUUUCAUUUCACGUGCUUGUCAGAGCCUUGAUUUA
........(((((((..((((.((((((..((((((..(((((.......)))))..)))..)))..)))).))..))))..)))))))..... ( -21.70)
>DroSec_CAF1 62562 94 - 1
CUGUUUUCCAGGGCUAAGAUAUCAGUGGUUUGAUAAAAUAGAAUUUGCAUUUUUAAAUUAUUUCAUUUCACGUGCUUGUCAGAGCCUUGAUUUA
........(((((((..((((.((((((..((((((..(((((.......)))))..)))..)))..)))).))..))))..)))))))..... ( -21.70)
>DroSim_CAF1 64654 79 - 1
CUGUUUUCCGGG--UAAAAUA--AGUGGUUG----AAAAAAAAAUUGCCUU-UUAAAUUU--UUCUUUCCCG-GCUUGUCA-AGCCUUG--UUA
.........(((--(...(((--(((.(..(----(((.(((((((.....-...)))))--)).)))).).-))))))..-.))))..--... ( -15.00)
>DroEre_CAF1 63463 94 - 1
CUGUUUUCCAGGGCUAAGAUAUCAGUGGGUUGAUAAAAUAGAAUUUGCAUUUUUAAAUUAUUUCAUUUCACGUGCUUGUCAGAGCCUUGAUUUA
........(((((((..((((.(((((((..(((((..(((((.......)))))..)))))....))))).))..))))..)))))))..... ( -21.50)
>DroYak_CAF1 64842 94 - 1
CUGUUUUCCAGGGCUAAGAUAUCAGUGGGUUGAUAAAAUAGAAUUUGCAUUUUUAAAUUAUUUCAUUUCACGUGCUUGUCAGAGCCUUGAUUUA
........(((((((..((((.(((((((..(((((..(((((.......)))))..)))))....))))).))..))))..)))))))..... ( -21.50)
>consensus
CUGUUUUCCAGGGCUAAGAUAUCAGUGGUUUGAUAAAAUAGAAUUUGCAUUUUUAAAUUAUUUCAUUUCACGUGCUUGUCAGAGCCUUGAUUUA
........(((((((..((((...((((..(((........((((((......))))))...)))..)))).....))))..)))))))..... (-14.16 = -15.08 +   0.92)

alignment

secondary structure

dotplot

Window 1

Location	7,931,042 – 7,931,153
Length	111
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	84.83
Mean single sequence MFE	-30.03
Consensus MFE	-20.72
Energy contribution	-22.21
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.69
SVM decision value	0.69
SVM RNA-class probability	0.824860
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7931042 111 + 27905053
UAUUUUAUCAAACCACUGAUAUCUUAGCCCUGGAAAACAGUACCAAGUCCCAGUCCUUUUAUCUCGGCCCACCUUUGUUGGCCAUUGAACUGGCUGGCAUUGGUGGUUGGU
...........((((((((.((...((..((((...((........)).))))..))...)).)))).(((((..(((..((((......))))..)))..))))).)))) ( -34.30)
>DroSec_CAF1 62616 111 + 1
UAUUUUAUCAAACCACUGAUAUCUUAGCCCUGGAAAACAGUACCAACUCCCAGUCCUUUCAUCUCGGCCCACCUUUGUUGGCCAUUGAACUGGCUGCCAUUGGUGGUUGGU
......(((((.((((..((......(..(((.....)))..).......(((((..((((....((((.((....)).))))..))))..)))))..))..))))))))) ( -29.90)
>DroSim_CAF1 64701 100 + 1
UUUUU----CAACCACU--UAUUUUA--CCCGGAAAACAGUACC-ACUCCCAG-CCUUUCAUUUGGGCCCACCUUUGUUGGCCAU-GGACUGGCUCCCAUUGGUGGUGGGU
.....----........--......(--((((............-.......(-(((.......))))(((((..((..(((((.-....)))))..))..)))))))))) ( -29.30)
>DroEre_CAF1 63517 108 + 1
UAUUUUAUCAACCCACUGAUAUCUUAGCCCUGGAAAACAGUACCAAAUCCCAGUCCGUGCAACUCGGGCCCCCAUUGUUGGCCAUUGAACUGGCUGCCAUUGGUGGUU---
.....(((((......))))).....((((((.....))((((.............)))).....))))(((((.((..(((((......)))))..)).))).))..--- ( -26.62)
>consensus
UAUUUUAUCAAACCACUGAUAUCUUAGCCCUGGAAAACAGUACCAACUCCCAGUCCUUUCAUCUCGGCCCACCUUUGUUGGCCAUUGAACUGGCUGCCAUUGGUGGUUGGU
...............((((......((..((((................))))..))......)))).(((((..((..(((((......)))))..))..)))))..... (-20.72 = -22.21 +   1.50)

alignment

secondary structure

dotplot

Window 2

Location	7,931,082 – 7,931,182
Length	100
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	85.67
Mean single sequence MFE	-30.30
Consensus MFE	-19.64
Energy contribution	-19.95
Covariance contribution	0.31
Combinations/Pair	1.05
Mean z-score	-1.82
Structure conservation index	0.65
SVM decision value	0.17
SVM RNA-class probability	0.619063
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7931082 100 + 27905053
UACCAAGUCCCAGUCCUUUUAUCUCGGCCCACCUUUGUUGGCCAUUGAACUGGCUGGCAUUGGUGGUUGGU----UCACCGCAAAUGAGUUCGUUUUCCUCUCA
.((((((.((.((.........)).)))(((((..(((..((((......))))..)))..))))))))))----..........((((...........)))) ( -29.00)
>DroSec_CAF1 62656 104 + 1
UACCAACUCCCAGUCCUUUCAUCUCGGCCCACCUUUGUUGGCCAUUGAACUGGCUGCCAUUGGUGGUUGGUUGGUUCACCGCAAAUGAGUUCGUUUUCCUCUCA
.(((((((((.((.........)).)).(((((..((..(((((......)))))..))..)))))..)))))))..........((((...........)))) ( -28.20)
>DroSim_CAF1 64733 98 + 1
UACC-ACUCCCAG-CCUUUCAUUUGGGCCCACCUUUGUUGGCCAU-GGACUGGCUCCCAUUGGUGGUGGGUG--GUCACCGCAAAUGAGUUCGUU-UCCUCUCA
.(((-((((...(-(((.......))))(((((..((..(((((.-....)))))..))..))))).)))))--))....(.(((((....))))-).)..... ( -34.40)
>DroEre_CAF1 63557 100 + 1
UACCAAAUCCCAGUCCGUGCAACUCGGGCCCCCAUUGUUGGCCAUUGAACUGGCUGCCAUUGGUGGUU----GGUUCGCCGCAAAUGAGUUCAUUUUCCUCUCA
................(((.(((((((....)).((((.(((....((((..((..((...))..)).----.)))))))))))..)))))))).......... ( -29.60)
>consensus
UACCAACUCCCAGUCCUUUCAUCUCGGCCCACCUUUGUUGGCCAUUGAACUGGCUGCCAUUGGUGGUUGGU___UUCACCGCAAAUGAGUUCGUUUUCCUCUCA
.........................((.(((((..((..(((((......)))))..))..)))))................(((((....))))).))..... (-19.64 = -19.95 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:06 2006