Locus 906

Sequence ID	X_DroMel_CAF1
Location	2,516,397 – 2,516,717
Length	320
Max. P	0.998236

overview

Window 4

Location	2,516,397 – 2,516,517
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.33
Mean single sequence MFE	-54.08
Consensus MFE	-47.08
Energy contribution	-48.00
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-2.37
Structure conservation index	0.87
SVM decision value	3.04
SVM RNA-class probability	0.998236
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2516397 120 - 22224390
AAUAUAUGUGACCGUCGGUGGCCAGGCUCUUGGCAUCGCGUCGACGUGCCAUGGCCGCCGCCACUGUGAGUUCCGCCUGAUCCGGUGGCAAAAGUCGGUUCUUCGGCUUGGCAUCCACCU
.......(((...((((((((((((((.((((((.....))))).).))).))))))))(((((((.((...........)))))))))..(((((((....))))))))))...))).. ( -51.10)
>DroSec_CAF1 14599 120 - 1
AAUAUAUGUGGCCGUCGGUGGCCAGGCUCUUGGCAUCGCGUCGACGUGCCAUGGCCGCCGCCACUGUGAGUUCCGCCUGAUCCGGUGGCAGAAGUCGGUUCUUCGGCUUGGCAUCCACCU
.......((((..((((((((((((((.((((((.....))))).).))).))))))))(((((((.((...........)))))))))..(((((((....))))))))))..)))).. ( -55.00)
>DroSim_CAF1 14588 120 - 1
AAUAUAUGUGGCCGUCGGUGGCCAGGCUCUUGGCAUCGCGUCGACGUGCCAUGGCCGCCGCCACUGUGAGUUCCGCCUGAUCCGGUGGCAGAAGCCGGUUCUUCGGCUUGGCAUCCACCU
.......((((..((((((((((((((.((((((.....))))).).))).))))))))(((((((.((...........)))))))))..(((((((....))))))))))..)))).. ( -57.70)
>DroEre_CAF1 15384 120 - 1
AAUAUAUGUGACCGUCGGUGGCCAGGCUCUUGGCAUCCCGUCGACGGGCAAUGGCCGCCGCCACUGUCAGUUCCGCCUGAUCCGGUGGCAGAAGUCGAUUUUUCGGCUUGGCAUCCAUCA
.....(((.((..(((((((((((.(((((((((.....))))).))))..))))))))(((((((((((......))))..)))))))..(((((((....)))))))))).))))).. ( -53.10)
>DroYak_CAF1 16623 120 - 1
AAUAGAUGUGGCCAUCGGUGGCCAGGCUCUUGGCAUCCCGGCGACGGGCCAUUGCCGCCGCCACUGUGAGUUCCGCCUGAUCCGGUGGCAGAAGUCGGUUUUUCGGCUUGGCAUCCACCU
....((((....))))(((((...(((...((((...(((....)))))))..)))((((((((((.((...........)))))))))..(((((((....))))))))))..))))). ( -53.50)
>consensus
AAUAUAUGUGGCCGUCGGUGGCCAGGCUCUUGGCAUCGCGUCGACGUGCCAUGGCCGCCGCCACUGUGAGUUCCGCCUGAUCCGGUGGCAGAAGUCGGUUCUUCGGCUUGGCAUCCACCU
.......((((..((((((((((((((.((((((.....))))).).))).))))))))(((((((.((...........)))))))))..(((((((....))))))))))..)))).. (-47.08 = -48.00 +   0.92)

alignment

secondary structure

dotplot

Window 5

Location	2,516,437 – 2,516,557
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.50
Mean single sequence MFE	-47.50
Consensus MFE	-41.68
Energy contribution	-42.04
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.70
Structure conservation index	0.88
SVM decision value	1.48
SVM RNA-class probability	0.957548
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2516437 120 + 22224390
UCAGGCGGAACUCACAGUGGCGGCGGCCAUGGCACGUCGACGCGAUGCCAAGAGCCUGGCCACCGACGGUCACAUAUAUUUCCCACUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUC
....(((((.(((..((((((((.(((((((((((((....))).)))))......))))).)))..(....).........)))))(((.......))))))..))))).......... ( -42.60)
>DroSec_CAF1 14639 120 + 1
UCAGGCGGAACUCACAGUGGCGGCGGCCAUGGCACGUCGACGCGAUGCCAAGAGCCUGGCCACCGACGGCCACAUAUAUUUCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUC
....(((((.......(((((((.(((((((((((((....))).)))))......))))).))....))))).......((((((((........))))).)))))))).......... ( -48.00)
>DroSim_CAF1 14628 120 + 1
UCAGGCGGAACUCACAGUGGCGGCGGCCAUGGCACGUCGACGCGAUGCCAAGAGCCUGGCCACCGACGGCCACAUAUAUUUCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUC
....(((((.......(((((((.(((((((((((((....))).)))))......))))).))....))))).......((((((((........))))).)))))))).......... ( -48.00)
>DroEre_CAF1 15424 120 + 1
UCAGGCGGAACUGACAGUGGCGGCGGCCAUUGCCCGUCGACGGGAUGCCAAGAGCCUGGCCACCGACGGUCACAUAUAUUUCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUC
....(((((..((((..(((.((((((..(((((((....))))....)))..)))..))).)))...))))........((((((((........))))).)))))))).......... ( -45.30)
>DroYak_CAF1 16663 120 + 1
UCAGGCGGAACUCACAGUGGCGGCGGCAAUGGCCCGUCGCCGGGAUGCCAAGAGCCUGGCCACCGAUGGCCACAUCUAUUUCCCGCUGCUGAAGAUCAGCGAGGAUCCGCACAUUGAUGC
....(((((.(((..((((((((((((....).))))))))((((.....(((...((((((....))))))..)))...)))))))((((.....)))))))..))))).......... ( -53.60)
>consensus
UCAGGCGGAACUCACAGUGGCGGCGGCCAUGGCACGUCGACGCGAUGCCAAGAGCCUGGCCACCGACGGCCACAUAUAUUUCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUC
....(((((.......(((((((.(((((.(((.((((.....))))......)))))))).))....))))).......((((((((........))))).)))))))).......... (-41.68 = -42.04 +   0.36)

alignment

secondary structure

dotplot

Window 6

Location	2,516,437 – 2,516,557
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-52.42
Consensus MFE	-46.62
Energy contribution	-47.46
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.93
Structure conservation index	0.89
SVM decision value	2.26
SVM RNA-class probability	0.991347
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2516437 120 - 22224390
GAAUCAAUGUGCGGAUCCUCGCUGAUCUUGAGCAGUGGGAAAUAUAUGUGACCGUCGGUGGCCAGGCUCUUGGCAUCGCGUCGACGUGCCAUGGCCGCCGCCACUGUGAGUUCCGCCUGA
..........((((((((.(((((........))))))))..((((.(((...(.((((((((((((.((((((.....))))).).))).)))))))))))))))))...))))).... ( -48.50)
>DroSec_CAF1 14639 120 - 1
GAAUCAAUGUGCGGAUCCUCGCUGAUCUUGAGCAGCGGGAAAUAUAUGUGGCCGUCGGUGGCCAGGCUCUUGGCAUCGCGUCGACGUGCCAUGGCCGCCGCCACUGUGAGUUCCGCCUGA
..........((((((((.(((((........))))))))..((((.(((((....(((((((((((.((((((.....))))).).))).)))))))))))))))))...))))).... ( -54.70)
>DroSim_CAF1 14628 120 - 1
GAAUCAAUGUGCGGAUCCUCGCUGAUCUUGAGCAGCGGGAAAUAUAUGUGGCCGUCGGUGGCCAGGCUCUUGGCAUCGCGUCGACGUGCCAUGGCCGCCGCCACUGUGAGUUCCGCCUGA
..........((((((((.(((((........))))))))..((((.(((((....(((((((((((.((((((.....))))).).))).)))))))))))))))))...))))).... ( -54.70)
>DroEre_CAF1 15424 120 - 1
GAAUCAAUGUGCGGAUCCUCGCUGAUCUUGAGCAGCGGGAAAUAUAUGUGACCGUCGGUGGCCAGGCUCUUGGCAUCCCGUCGACGGGCAAUGGCCGCCGCCACUGUCAGUUCCGCCUGA
..........((((((((.(((((........))))))))........((((.(((((((((((.(((((((((.....))))).))))..)))))))))..)).))))..))))).... ( -52.30)
>DroYak_CAF1 16663 120 - 1
GCAUCAAUGUGCGGAUCCUCGCUGAUCUUCAGCAGCGGGAAAUAGAUGUGGCCAUCGGUGGCCAGGCUCUUGGCAUCCCGGCGACGGGCCAUUGCCGCCGCCACUGUGAGUUCCGCCUGA
..........(((((..(((((((.....)))).((((......((((....))))((((((..(((...((((...(((....)))))))..))))))))).))))))).))))).... ( -51.90)
>consensus
GAAUCAAUGUGCGGAUCCUCGCUGAUCUUGAGCAGCGGGAAAUAUAUGUGGCCGUCGGUGGCCAGGCUCUUGGCAUCGCGUCGACGUGCCAUGGCCGCCGCCACUGUGAGUUCCGCCUGA
..........((((((((.(((((........)))))))).......((((....((((((((((((.((((((.....))))).).))).))))))))))))).......))))).... (-46.62 = -47.46 +   0.84)

alignment

secondary structure

dotplot

Window 7

Location	2,516,477 – 2,516,597
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-39.47
Consensus MFE	-36.42
Energy contribution	-36.38
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.25
Structure conservation index	0.92
SVM decision value	0.27
SVM RNA-class probability	0.662365
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2516477 120 + 22224390
CGCGAUGCCAAGAGCCUGGCCACCGACGGUCACAUAUAUUUCCCACUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUG
.(((((.....((((.(((((......)))))...............))))..(((((((..(((((........)))))...))))))).)))))..((.((.((....)).))))... ( -37.29)
>DroSec_CAF1 14679 120 + 1
CGCGAUGCCAAGAGCCUGGCCACCGACGGCCACAUAUAUUUCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUG
.(((((.....((((.(((((......)))))...............))))..(((((((..(((((........)))))...))))))).)))))..((.((.((....)).))))... ( -39.99)
>DroSim_CAF1 14668 120 + 1
CGCGAUGCCAAGAGCCUGGCCACCGACGGCCACAUAUAUUUCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUG
.(((((.....((((.(((((......)))))...............))))..(((((((..(((((........)))))...))))))).)))))..((.((.((....)).))))... ( -39.99)
>DroEre_CAF1 15464 120 + 1
CGGGAUGCCAAGAGCCUGGCCACCGACGGUCACAUAUAUUUCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUG
..((.((((..((((((((((......)))))..........((..(((....(((((((..(((((........)))))...)))))))....))).))..)).)))..)).))))... ( -38.20)
>DroYak_CAF1 16703 120 + 1
CGGGAUGCCAAGAGCCUGGCCACCGAUGGCCACAUCUAUUUCCCGCUGCUGAAGAUCAGCGAGGAUCCGCACAUUGAUGCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUG
..(((.(((((((...((((((....))))))..))).....((..(((.((.(((((((..(.(((........))).)...)))))))..))))).)).)))).)))........... ( -41.90)
>consensus
CGCGAUGCCAAGAGCCUGGCCACCGACGGCCACAUAUAUUUCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUG
...(.((((..((((((((((......)))))..........((..(((....(((((((..(((((........)))))...)))))))....))).))..)).)))..)).)).)... (-36.42 = -36.38 +  -0.04)

alignment

secondary structure

dotplot

Window 8

Location	2,516,517 – 2,516,637
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-41.82
Consensus MFE	-38.64
Energy contribution	-39.24
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.79
Structure conservation index	0.92
SVM decision value	1.90
SVM RNA-class probability	0.982016
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2516517 120 + 22224390
UCCCACUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAAUUCGGCAGUCCAAAGUUGCGAGAGA
........(((..(((((((..(((((........)))))...)))))))..((((((((.((.((....)).))))........(((((((..........))))))).))))))))). ( -40.40)
>DroSec_CAF1 14719 120 + 1
UCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAGUUGCGGGAGA
((((((.(((...(((((((..(((((........)))))...)))))))........((((.(((....((((.(((.........)))....))))))).))))..))).)))))).. ( -42.60)
>DroSim_CAF1 14708 120 + 1
UCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAGUUGCGGGAGA
((((((.(((...(((((((..(((((........)))))...)))))))........((((.(((....((((.(((.........)))....))))))).))))..))).)))))).. ( -42.60)
>DroEre_CAF1 15504 120 + 1
UCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAAUUGCGGGAGA
(((((((((....(((((((..(((((........)))))...)))))))....))).((((.(((....((((.(((.........)))....))))))).))))......)))))).. ( -42.10)
>DroYak_CAF1 16743 120 + 1
UCCCGCUGCUGAAGAUCAGCGAGGAUCCGCACAUUGAUGCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAGUUGCGGGAGA
((((((.(((...(((((((..(.(((........))).)...)))))))........((((.(((....((((.(((.........)))....))))))).))))..))).)))))).. ( -41.40)
>consensus
UCCCGCUGCUCAAGAUCAGCGAGGAUCCGCACAUUGAUUCGAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAGUUGCGGGAGA
(((((((((....(((((((..(((((........)))))...)))))))....))).((((.(((((((((((.....))....)))))).(....)))).))))......)))))).. (-38.64 = -39.24 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	2,516,557 – 2,516,677
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.58
Mean single sequence MFE	-40.02
Consensus MFE	-37.92
Energy contribution	-38.12
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.24
Structure conservation index	0.95
SVM decision value	0.37
SVM RNA-class probability	0.709147
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2516557 120 + 22224390
GAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAAUUCGGCAGUCCAAAGUUGCGAGAGAAGUUCGCCCGCAAGCAGAAGCAGCUGCUCGCCAAGCAGCA
...((((.((..((((((((.((.((....)).))))........(((((((..........))))))).))))))..)).........((.(((((......))))).))....)))). ( -37.30)
>DroSec_CAF1 14759 120 + 1
GAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAGUUGCGGGAGAAGUUCGCCCGCAAGCAGAAGCAGCUGCUCGCCAAGCAGCA
...((((.......(((.((.((.((....)).)))).)))....(((((.(((((..(((.........(((((((.(.....).)))))))((....)).))))))))))))))))). ( -41.90)
>DroSim_CAF1 14748 120 + 1
GAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAGUUGCGGGAGAAGUUCGCCCGCAAGCAGAAGCAGCUGCUCGCCAAGCAGCA
...((((.......(((.((.((.((....)).)))).)))....(((((.(((((..(((.........(((((((.(.....).)))))))((....)).))))))))))))))))). ( -41.90)
>DroEre_CAF1 15544 120 + 1
GAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAAUUGCGGGAGAAGUUCGCCCGCAAGCAGAAGCAACUGCUAGCCAAGCAGCA
...((((.....((....)).((((.....((((.(((.........))).((....))...)))).....((((((.(.....).))))))(((((......))))).))))..)))). ( -39.40)
>DroYak_CAF1 16783 120 + 1
GAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAGUUGCGGGAGAAGUUCGCCCGCAAGCAGAAGCAACUGCUUGCCAAGCAGCA
...(((((....(((...(((.....)))......(((.........))).)))..)))))........((((((((.(.....).)))((((((((......))))))))...))))). ( -39.60)
>consensus
GAAGCUGAUCAAUCGCAAGGAUGGCCUCCAGGACACCAUGUAUUAUUUGGACGAGUUCGGCAGUCCCAAGUUGCGGGAGAAGUUCGCCCGCAAGCAGAAGCAGCUGCUCGCCAAGCAGCA
...((((.....((....)).((((.....((((.(((.........))).((....))...))))....(((((((.(.....).)))))))((((......))))..))))..)))). (-37.92 = -38.12 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	2,516,597 – 2,516,717
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.08
Mean single sequence MFE	-31.84
Consensus MFE	-27.36
Energy contribution	-27.12
Covariance contribution	-0.24
Combinations/Pair	1.11
Mean z-score	-1.32
Structure conservation index	0.86
SVM decision value	0.20
SVM RNA-class probability	0.630498
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2516597 120 - 22224390
CUGCUCCUCGCUCCUCCUUUCACGUUUCAUCAACUGCUUCUGCUGCUUGGCGAGCAGCUGCUUCUGCUUGCGGGCGAACUUCUCUCGCAACUUUGGACUGCCGAAUUCGUCCAAAUAAUA
.......((((((.................((((.((....)).).)))((((((((......))))))))))))))..............(((((((..........)))))))..... ( -30.40)
>DroSec_CAF1 14799 120 - 1
CUGCUCCUCGCUCCUCCUCUCCCGUUUCAUCAUCUGCUUCUGCUGCUUGGCGAGCAGCUGCUUCUGCUUGCGGGCGAACUUCUCCCGCAACUUGGGACUGCCGAACUCGUCCAAAUAAUA
..(((.((((((...........(......)....((....)).....)))))).))).((....))(((((((.(.....).)))))))....((((..........))))........ ( -29.80)
>DroSim_CAF1 14788 120 - 1
CUGCUCCUCGCUCCUCCGCUCCCGUUUCAUCAUCUGCUUCUGCUGCUUGGCGAGCAGCUGCUUCUGCUUGCGGGCGAACUUCUCCCGCAACUUGGGACUGCCGAACUCGUCCAAAUAAUA
..((.....))...((.(((((((...........((....(((((((...))))))).))......(((((((.(.....).)))))))..)))))..)).))................ ( -31.90)
>DroEre_CAF1 15584 120 - 1
CUGCUCCUCGCUCCUUCUCUCCCGUUUCAUCAACUGCUUCUGCUGCUUGGCUAGCAGUUGCUUCUGCUUGCGGGCGAACUUCUCCCGCAAUUUGGGACUGCCGAACUCGUCCAAAUAAUA
..((.....))........((((((.....((((((((...(((....))).)))))))).....))(((((((.(.....).)))))))...))))....................... ( -33.70)
>DroYak_CAF1 16823 120 - 1
CUGCUCCUCGCUCCUUCGCUCCCGCUUCAUCAUCUGCUUCUGCUGCUUGGCAAGCAGUUGCUUCUGCUUGCGGGCGAACUUCUCCCGCAACUUGGGACUGCCGAACUCGUCCAAAUAAUA
..((.....))...(((((((((((.....((.(((((..((((....))))))))).)).....))(((((((.(.....).)))))))...))))..).))))............... ( -33.40)
>consensus
CUGCUCCUCGCUCCUCCUCUCCCGUUUCAUCAUCUGCUUCUGCUGCUUGGCGAGCAGCUGCUUCUGCUUGCGGGCGAACUUCUCCCGCAACUUGGGACUGCCGAACUCGUCCAAAUAAUA
..((.....))............((.....((.((((((..(((....))))))))).)).....))(((((((.(.....).)))))))....((((..........))))........ (-27.36 = -27.12 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:55 2006