Locus 1347

Sequence ID	2L_DroMel_CAF1
Location	3,579,263 – 3,579,400
Length	137
Max. P	0.999758

overview

Window 9

Location	3,579,263 – 3,579,374
Length	111
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	74.15
Mean single sequence MFE	-53.62
Consensus MFE	-32.21
Energy contribution	-32.52
Covariance contribution	0.31
Combinations/Pair	1.30
Mean z-score	-3.16
Structure conservation index	0.60
SVM decision value	4.02
SVM RNA-class probability	0.999758
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3579263 111 + 22407834
CG---CACUCUGCUGCCAGUUCUGCGGCUGUUGCGCAGUCCAGCGCCGCCUGUUGGCUCGCAGCAGCUGCUGCGGCAGCCGCAGCAGCCGCCACUGCAGCACUAACGGUGCCAA
.(---((((.((((((.(((...(((((((((((((......))((((((....)))..(((((....))))))))....))))))))))).))))))))).....)))))... ( -61.90)
>DroPse_CAF1 51511 111 + 1
CG---CACUCGGCGGCCAGCUCUGCGGCUGUUGCACAGUCGAGGGCCGCUUGUUGAUUGGCCGCGGCCGCAGCGGCGGCAGCAGCUGCUGCCACAGCAGCACUCACAGUUCCAA
.(---(.....((((((((.((.((((((.(((......))).)))))).....)))))))))).(((((....))))).)).(((((((...))))))).............. ( -54.50)
>DroSec_CAF1 47013 111 + 1
CG---CACUCUGCUGCGAGUUCUGCGGCUGUUGCGCAGUCCAGCGCUGCCUGUUGGCUCGCAGCAGCUGCUGCGGCAGCCGCAGCAGCCGCCACUGCAGCACUAACGGUGCCAA
.(---((((.((((((.(((...((((((((((((((((.....))))).....((((((((((....))))))..))))))))))))))).))))))))).....)))))... ( -63.00)
>DroWil_CAF1 73896 90 + 1
CGGCACAUUCUGCAGCCAAUUCGGCGG------CACAAUCUAAUGCUGCCUGUUGAUUGGCAGCAACUGCAGCAGCUG------------------CCGCACUCACUGUACCGA
(((((....((((.(((((((.(((((------((........)))))))....))))))).((....)).)))).))------------------)))............... ( -34.20)
>DroPer_CAF1 51618 111 + 1
CG---CACUCGGCGGCCAGCUCUGCGGCUGUUGCACAGUCGAGGGCCGCUUGUUGAUUGGCCGCGGCCGCAGCGGCGGCAGCAGCUGCUGCCACAGCAGCACUCACAGUUCCAA
.(---(.....((((((((.((.((((((.(((......))).)))))).....)))))))))).(((((....))))).)).(((((((...))))))).............. ( -54.50)
>consensus
CG___CACUCUGCGGCCAGUUCUGCGGCUGUUGCACAGUCCAGCGCCGCCUGUUGAUUGGCAGCAGCUGCAGCGGCAGCAGCAGCAGCCGCCACAGCAGCACUCACAGUGCCAA
...........((((((((.((.(((((....((((......)))).))).)).)))))))))).(((((....))))).((.((((......)))).)).............. (-32.21 = -32.52 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	3,579,263 – 3,579,374
Length	111
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	74.15
Mean single sequence MFE	-53.20
Consensus MFE	-35.33
Energy contribution	-37.52
Covariance contribution	2.19
Combinations/Pair	1.30
Mean z-score	-2.42
Structure conservation index	0.66
SVM decision value	2.77
SVM RNA-class probability	0.996905
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3579263 111 - 22407834
UUGGCACCGUUAGUGCUGCAGUGGCGGCUGCUGCGGCUGCCGCAGCAGCUGCUGCGAGCCAACAGGCGGCGCUGGACUGCGCAACAGCCGCAGAACUGGCAGCAGAGUG---CG
...(((((((((((.((((.(..(((((((((((((...)))))))))))))..).........(((.((((......))))....))))))).))))))....).)))---). ( -62.60)
>DroPse_CAF1 51511 111 - 1
UUGGAACUGUGAGUGCUGCUGUGGCAGCAGCUGCUGCCGCCGCUGCGGCCGCGGCCAAUCAACAAGCGGCCCUCGACUGUGCAACAGCCGCAGAGCUGGCCGCCGAGUG---CG
............(..((((.((((((((....)))))))).)).((((((((((((...........)))).....((((((....).))))).)).))))))..))..---). ( -50.60)
>DroSec_CAF1 47013 111 - 1
UUGGCACCGUUAGUGCUGCAGUGGCGGCUGCUGCGGCUGCCGCAGCAGCUGCUGCGAGCCAACAGGCAGCGCUGGACUGCGCAACAGCCGCAGAACUCGCAGCAGAGUG---CG
...(((((.....((((((.(..(((((((((((((...)))))))))))))..)(((......(((.((((......))))....)))......)))))))))).)))---). ( -60.80)
>DroWil_CAF1 73896 90 - 1
UCGGUACAGUGAGUGCGG------------------CAGCUGCUGCAGUUGCUGCCAAUCAACAGGCAGCAUUAGAUUGUG------CCGCCGAAUUGGCUGCAGAAUGUGCCG
.((((((((..(.(((((------------------(....)))))).)..))((((((.....(((.((((......)))------).)))..))))))........)))))) ( -41.40)
>DroPer_CAF1 51618 111 - 1
UUGGAACUGUGAGUGCUGCUGUGGCAGCAGCUGCUGCCGCCGCUGCGGCCGCGGCCAAUCAACAAGCGGCCCUCGACUGUGCAACAGCCGCAGAGCUGGCCGCCGAGUG---CG
............(..((((.((((((((....)))))))).)).((((((((((((...........)))).....((((((....).))))).)).))))))..))..---). ( -50.60)
>consensus
UUGGAACCGUGAGUGCUGCAGUGGCAGCAGCUGCGGCCGCCGCUGCAGCUGCUGCCAAUCAACAGGCGGCCCUCGACUGUGCAACAGCCGCAGAACUGGCAGCAGAGUG___CG
.............((((((.(((((.((....)).))))).)))))).((((((((((......(((.((((......))))....)))......))))))))))......... (-35.33 = -37.52 +   2.19)

alignment

secondary structure

dotplot

Window 1

Location	3,579,300 – 3,579,400
Length	100
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	67.22
Mean single sequence MFE	-43.08
Consensus MFE	-22.91
Energy contribution	-23.62
Covariance contribution	0.71
Combinations/Pair	1.38
Mean z-score	-1.52
Structure conservation index	0.53
SVM decision value	0.15
SVM RNA-class probability	0.606427
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3579300 100 + 22407834
CAGCGCCGCCUGUUGGCUCGCAGCAGCUGCUGCGGCAGCCGCAGCAGCCGCCACUGCAGCACUAACGGUGCCAAUGGAGGGCAGAGGCACGCACUUGGAU-----------
..(((..((((....(((((((((.((((((((((...)))))))))).))...))).((((.....)))).......))))..)))).)))........----------- ( -46.80)
>DroPse_CAF1 51548 111 + 1
GAGGGCCGCUUGUUGAUUGGCCGCGGCCGCAGCGGCGGCAGCAGCUGCUGCCACAGCAGCACUCACAGUUCCAAUCGAAGGCAGUGGCAGGCACUUGGUGGCACAUGAAGU
(...((((((..((((((((..((.(((((....))))).)).(((((((...)))))))..........))))))))....))))))...)((((.(((...))).)))) ( -47.60)
>DroSec_CAF1 47050 100 + 1
CAGCGCUGCCUGUUGGCUCGCAGCAGCUGCUGCGGCAGCCGCAGCAGCCGCCACUGCAGCACUAACGGUGCCAAUGGAGGGCAGAGGCAGGCACUUGGAU-----------
(((.(.((((((((.(((((((((.((((((((((...)))))))))).))...))).((((.....)))).......))))...))))))))))))...----------- ( -50.10)
>DroWil_CAF1 73930 82 + 1
UAAUGCUGCCUGUUGAUUGGCAGCAACUGCAGCAGCUG------------------CCGCACUCACUGUACCGAUUGAGGGUAAUUUUGUUCGAUUUGUU-----------
...(((((((........)))))))..(((.((....)------------------).)))........((.(((((((.(......).))))))).)).----------- ( -23.30)
>DroPer_CAF1 51655 111 + 1
GAGGGCCGCUUGUUGAUUGGCCGCGGCCGCAGCGGCGGCAGCAGCUGCUGCCACAGCAGCACUCACAGUUCCAAUCGAAGGCAGUGGCAGGCACUUGGUGGCACAUGAAGU
(...((((((..((((((((..((.(((((....))))).)).(((((((...)))))))..........))))))))....))))))...)((((.(((...))).)))) ( -47.60)
>consensus
CAGCGCCGCCUGUUGAUUGGCAGCAGCUGCAGCGGCAGCAGCAGCAGCCGCCACAGCAGCACUCACAGUGCCAAUCGAGGGCAGUGGCAGGCACUUGGUU___________
....(((((((.((((((((..((.(((((....))))).)).((((......)))).............))))))))))))...)))....................... (-22.91 = -23.62 +   0.71)

alignment

secondary structure

dotplot

Window 2

Location	3,579,300 – 3,579,400
Length	100
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	67.22
Mean single sequence MFE	-44.32
Consensus MFE	-25.49
Energy contribution	-26.72
Covariance contribution	1.23
Combinations/Pair	1.28
Mean z-score	-2.42
Structure conservation index	0.58
SVM decision value	2.77
SVM RNA-class probability	0.996950
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3579300 100 - 22407834
-----------AUCCAAGUGCGUGCCUCUGCCCUCCAUUGGCACCGUUAGUGCUGCAGUGGCGGCUGCUGCGGCUGCCGCAGCAGCUGCUGCGAGCCAACAGGCGGCGCUG
-----------.....((((((((((..((.....))..)))))(((..((...((.(..(((((((((((((...)))))))))))))..)..))..))..)))))))). ( -54.30)
>DroPse_CAF1 51548 111 - 1
ACUUCAUGUGCCACCAAGUGCCUGCCACUGCCUUCGAUUGGAACUGUGAGUGCUGCUGUGGCAGCAGCUGCUGCCGCCGCUGCGGCCGCGGCCAAUCAACAAGCGGCCCUC
.........(((....((((.....))))((....((((((..(((((..(((.((.((((((((....)))))))).)).)))..))))))))))).....))))).... ( -44.20)
>DroSec_CAF1 47050 100 - 1
-----------AUCCAAGUGCCUGCCUCUGCCCUCCAUUGGCACCGUUAGUGCUGCAGUGGCGGCUGCUGCGGCUGCCGCAGCAGCUGCUGCGAGCCAACAGGCAGCGCUG
-----------.....(((((.(((((.....(((....(((((.....)))))...(..(((((((((((((...)))))))))))))..)))).....)))))))))). ( -54.30)
>DroWil_CAF1 73930 82 - 1
-----------AACAAAUCGAACAAAAUUACCCUCAAUCGGUACAGUGAGUGCGG------------------CAGCUGCUGCAGUUGCUGCCAAUCAACAGGCAGCAUUA
-----------.................((((.......))))....((.(((((------------------(....)))))).))((((((........)))))).... ( -24.60)
>DroPer_CAF1 51655 111 - 1
ACUUCAUGUGCCACCAAGUGCCUGCCACUGCCUUCGAUUGGAACUGUGAGUGCUGCUGUGGCAGCAGCUGCUGCCGCCGCUGCGGCCGCGGCCAAUCAACAAGCGGCCCUC
.........(((....((((.....))))((....((((((..(((((..(((.((.((((((((....)))))))).)).)))..))))))))))).....))))).... ( -44.20)
>consensus
___________AACCAAGUGCCUGCCACUGCCCUCCAUUGGAACCGUGAGUGCUGCAGUGGCAGCAGCUGCGGCCGCCGCUGCAGCUGCUGCCAAUCAACAGGCGGCCCUC
............................((((.......))))....(((((((((.(((((.((....)).))))).(((((....)))))..........))))))))) (-25.49 = -26.72 +   1.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:16 2006