Locus 5032

Sequence ID	2L_DroMel_CAF1
Location	14,425,857 – 14,426,051
Length	194
Max. P	0.999807

overview

Window 4

Location	14,425,857 – 14,425,948
Length	91
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	77.68
Mean single sequence MFE	-31.95
Consensus MFE	-18.69
Energy contribution	-19.31
Covariance contribution	0.61
Combinations/Pair	1.30
Mean z-score	-1.85
Structure conservation index	0.59
SVM decision value	0.70
SVM RNA-class probability	0.827663
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14425857 91 + 22407834
----CCGCCAGUCCGCCUGUCAGCAGUCAAUCGGCUACC-GUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCACAUU-------CGAGUUGACAAUGGG---GA
----(((((.((..(.(((....))).).)).)))..((-((.(((((((...((((.(((((.....))))).)))).-------...))))))))))))---). ( -29.90)
>DroVir_CAF1 33041 100 + 1
AGUAGCUGCUGGCUGGCUGUCAGAAGUCAAUCGGCUGCC-GUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCGAAACUCGAGCGUUGAGUUGGCAAUGGA-----
.......((((..(((((......)))))..))))((((-(....(((((((((..(((((((.....)))))))....))).))))))..))))).....----- ( -38.60)
>DroEre_CAF1 17631 91 + 1
----CCGCCAGUUGGCCUGUCAGCAGUCAAUCGGCUGCC-GUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCACAUU-------CGAGUUGACAAUGGG---GA
----(((((.((((((.((....)))))))).)))..((-((.(((((((...((((.(((((.....))))).)))).-------...))))))))))))---). ( -35.70)
>DroWil_CAF1 115217 73 + 1
------------GCUGCUGUCAGUAGUCAAUCGGCUACC-GUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGC---------------AAUUGACAAUGGC-----
------------(((..(((((((((((....)))))).-..................(((((.....)))))---------------...)))))..)))----- ( -21.90)
>DroAna_CAF1 8474 91 + 1
----CACCCGGACGGCCUGUCAGUAGUCAAUCGGCUGCC-GUCUGUCAACGUCGUGUCGCCUUCAUCAAAGGCCGCAUU-------CGAGUUGACAAUGGG---GA
----..((((((((((..(((.((.....)).))).)))-))))((((((.((((((.(((((.....))))).)))..-------)))))))))...)))---.. ( -38.80)
>DroPer_CAF1 5262 95 + 1
----CCUUCUGUCUGCCUGUCAGUAGUCAAUCGGCUACCGGUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCGCUUU-------CAACUUGACAAUGGGAUGGA
----...((((((((((.....((((((....)))))).))).((((((.((.(.((.(((((.....))))).))...-------).))))))))...))))))) ( -26.80)
>consensus
____CCGCCAGUCCGCCUGUCAGUAGUCAAUCGGCUACC_GUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCACAUU_______CGAGUUGACAAUGGG___GA
...............(((((..((((((....)))))).....(((((((...((((.(((((.....))))).))))...........))))))))))))..... (-18.69 = -19.31 +   0.61)

alignment

secondary structure

dotplot

Window 5

Location	14,425,889 – 14,425,988
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	92.12
Mean single sequence MFE	-29.40
Consensus MFE	-26.93
Energy contribution	-26.70
Covariance contribution	-0.24
Combinations/Pair	1.07
Mean z-score	-1.79
Structure conservation index	0.92
SVM decision value	1.76
SVM RNA-class probability	0.976174
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14425889 99 + 22407834
ACCGUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCACAUUCGAGUUGACAAUGGGGAUAUUGGUUCUGUUUUGUAAUCCGCAAAGGAUACGGAUUUU
.((((.(((((((...((((.(((((.....))))).))))....)))))))))))((((....))))...((((((.(((.....))))))))).... ( -29.00)
>DroSec_CAF1 16385 99 + 1
ACCGUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCACAUUCGAGUUGACAAUGGGGAUAUUGGUUCUGUUUUGUAAUCCGCAAAGGAUACGGAUUUU
.((((.(((((((...((((.(((((.....))))).))))....)))))))))))((((....))))...((((((.(((.....))))))))).... ( -29.00)
>DroSim_CAF1 18057 99 + 1
ACCGUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCACAUUCGAGUUGACAAUGGGGAUAUUGGUUCUGUUUUGUAAUCCGCAAAGGAUACGGAUUUU
.((((.(((((((...((((.(((((.....))))).))))....)))))))))))((((....))))...((((((.(((.....))))))))).... ( -29.00)
>DroEre_CAF1 17663 99 + 1
GCCGUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCACAUUCGAGUUGACAAUGGGGAUAUUGGUUCUGUUUGGUAAUCCGCAAAGGAUACGGAUUUU
.((((.(((((((...((((.(((((.....))))).))))....))))))).((.((((((..(......)..)).)))).))......))))..... ( -30.50)
>DroYak_CAF1 17893 99 + 1
ACCGUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCACAUUCGAGUUGACAAUGGGGAUAUUGGUUCUGUUUUGUAAUCCGCAAAGGAUACGGAUUUU
.((((.(((((((...((((.(((((.....))))).))))....)))))))))))((((....))))...((((((.(((.....))))))))).... ( -29.00)
>DroAna_CAF1 8506 80 + 1
GCCGUCUGUCAACGUCGUGUCGCCUUCAUCAAAGGCCGCAUUCGAGUUGACAAUGGGGA-------------------UCCGCAAAGGAUACGGAUUUU
.((((.(((((((.((((((.(((((.....))))).)))..))))))))))))))(((-------------------((((.........))))))). ( -29.90)
>consensus
ACCGUCUGUCAAUGUCGUGUCGCCUUCAUCAAAGGCCACAUUCGAGUUGACAAUGGGGAUAUUGGUUCUGUUUUGUAAUCCGCAAAGGAUACGGAUUUU
.((((.(((((((.((((((.(((((.....))))).)))..)))))))))).((.((((.................)))).))......))))..... (-26.93 = -26.70 +  -0.24)

alignment

secondary structure

dotplot

Window 6

Location	14,425,889 – 14,425,988
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	92.12
Mean single sequence MFE	-28.90
Consensus MFE	-27.12
Energy contribution	-27.62
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.88
Structure conservation index	0.94
SVM decision value	4.13
SVM RNA-class probability	0.999807
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14425889 99 - 22407834
AAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACGACAUUGACAGACGGU
..((((((((.....))))))))...................((..(((((((.(((..(((.((((((...)))))).))))))..)))))))..)). ( -29.20)
>DroSec_CAF1 16385 99 - 1
AAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACGACAUUGACAGACGGU
..((((((((.....))))))))...................((..(((((((.(((..(((.((((((...)))))).))))))..)))))))..)). ( -29.20)
>DroSim_CAF1 18057 99 - 1
AAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACGACAUUGACAGACGGU
..((((((((.....))))))))...................((..(((((((.(((..(((.((((((...)))))).))))))..)))))))..)). ( -29.20)
>DroEre_CAF1 17663 99 - 1
AAAAUCCGUAUCCUUUGCGGAUUACCAAACAGAACCAAUAUCCCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACGACAUUGACAGACGGC
..((((((((.....))))))))...................((..(((((((.(((..(((.((((((...)))))).))))))..)))))))..)). ( -29.00)
>DroYak_CAF1 17893 99 - 1
AAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACGACAUUGACAGACGGU
..((((((((.....))))))))...................((..(((((((.(((..(((.((((((...)))))).))))))..)))))))..)). ( -29.20)
>DroAna_CAF1 8506 80 - 1
AAAAUCCGUAUCCUUUGCGGA-------------------UCCCCAUUGUCAACUCGAAUGCGGCCUUUGAUGAAGGCGACACGACGUUGACAGACGGC
...(((((((.....))))))-------------------).((..(((((((((((..((..((((((...))))))..))))).))))))))..)). ( -27.60)
>consensus
AAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACGACAUUGACAGACGGU
..((((((((.....))))))))...................((..(((((((.(((..(((.((((((...)))))).))))))..)))))))..)). (-27.12 = -27.62 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	14,425,948 – 14,426,051
Length	103
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	84.34
Mean single sequence MFE	-20.22
Consensus MFE	-17.96
Energy contribution	-17.80
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.14
Structure conservation index	0.89
SVM decision value	1.71
SVM RNA-class probability	0.973446
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14425948 103 - 22407834
AAUUGCAUUCAAGUAUGUUCCAUCCAGCCACGUAGCUCUUCUUGCC-AGACUUGAGCACUUUCAAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUA
...(((..((((((.((........(((......)))........)-).)))))))))........((((((((.....))))))))................. ( -19.49)
>DroSec_CAF1 16444 104 - 1
AAUUGCAUUCAACUAUGUUCCCUCCAGCCACGUAGCUCUUCUUGCCAAGACUUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUA
................((((...........((.((((.(((.....)))...)))))).......((((((((.....))))))))........))))..... ( -18.70)
>DroSim_CAF1 18116 104 - 1
AAUUGCAUUCAACUAUGUUCCCUCCAGCCACGUAGCUCUUCUGGCCAAGACUUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUA
................((((...........((.((((.(((.....)))...)))))).......((((((((.....))))))))........))))..... ( -19.80)
>DroEre_CAF1 17722 80 - 1
AAUUGCAUUC-----------------------AGCUCUUCUUGCC-GGAGCUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACCAAACAGAACCAAUA
...(((..((-----------------------((((((.......-)))))))))))........((((((((.....))))))))................. ( -22.80)
>DroYak_CAF1 17952 88 - 1
AAUUGCAUUCAACUAUG---------------CAGCUCUUCUUGCC-AGACUUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUA
...(((((......)))---------------))((((.(((....-)))...)))).........((((((((.....))))))))................. ( -20.30)
>consensus
AAUUGCAUUCAACUAUGUUCC_UCCAGCCACGUAGCUCUUCUUGCC_AGACUUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUA
.((((..(((........................((((.(((.....)))...)))).........((((((((.....))))))))........))).)))). (-17.96 = -17.80 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:05 2006