Locus 9591

Sequence ID	3R_DroMel_CAF1
Location	25,339,571 – 25,339,827
Length	256
Max. P	0.994146

overview

Window 0

Location	25,339,571 – 25,339,662
Length	91
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.16
Mean single sequence MFE	-35.24
Consensus MFE	-21.84
Energy contribution	-21.84
Covariance contribution	-0.00
Combinations/Pair	1.05
Mean z-score	-2.70
Structure conservation index	0.62
SVM decision value	2.45
SVM RNA-class probability	0.994146
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25339571 91 + 27905053
CGGCUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCCAGCGACGAUGUCACCGG-----------------GCAGCAACAAUUG---------CAGUUGC---UG
..(((((((...(((((((((((...((((((....)))))).........))))))))))).....))-----------------))))).......(---------(....))---.. ( -36.60)
>DroPse_CAF1 26276 87 + 1
CGCUUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCAAGCGACGAUGUCAGC------------------------CACAG------CCACUGCCACUGC---CA
.(((((.((...((((((((((....((((((....))))))..........))))))))))..)).------------------------)).))------)............---.. ( -27.04)
>DroSec_CAF1 24539 100 + 1
CGGCUGUCUCAUCUUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCCAGCGACGAUGUCACCGG-----------------GCAGCAACAAUUGCAGCAGUUGCAGUUGC---UC
..(((((((...(.(((((((((...((((((....)))))).........))))))))).).....))-----------------)))))..(((((((((...))))))))).---.. ( -39.80)
>DroSim_CAF1 24924 100 + 1
CGGCUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCCAGCGACGAUGUCACCGG-----------------GCAGCAACAAUUGCAGCAGUUGCAGUUGC---UG
..(((((((...(((((((((((...((((((....)))))).........))))))))))).....))-----------------)))))..(((((((((...))))))))).---.. ( -43.70)
>DroAna_CAF1 30450 120 + 1
CGCCUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCAAGCGACGAUGUCACCAACUGCAAAUGCAACUGCAACAUCACCAGCCGAAGCAGAAGCAGAAGCAGAAG
............((((((((((....((((((....))))))..........)))))))))).......((((...(((..((((..(..........)..))))..)))...))))... ( -37.24)
>DroPer_CAF1 25785 93 + 1
CGCUUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCAAGCGACGAUGUCAGC------------------------CACAGCCACAGCCACUGCCACUGC---CA
.(((((.((...((((((((((....((((((....))))))..........))))))))))..)).------------------------)).)))..................---.. ( -27.04)
>consensus
CGCCUGUCUCAUCGUUGUCGCUGAUGUGGCCAAAAGUGGCCAAUAAAACCCAAGCGACGAUGUCACCGG_________________GCAGCAACAAUUGCAGCAGCUGCAGUUGC___UG
.((.((......((((((((((....((((((....))))))..........)))))))))).))))..................................................... (-21.84 = -21.84 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	25,339,571 – 25,339,662
Length	91
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.16
Mean single sequence MFE	-37.23
Consensus MFE	-21.99
Energy contribution	-21.77
Covariance contribution	-0.22
Combinations/Pair	1.09
Mean z-score	-2.13
Structure conservation index	0.59
SVM decision value	1.65
SVM RNA-class probability	0.969917
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25339571 91 - 27905053
CA---GCAACUG---------CAAUUGUUGCUGC-----------------CCGGUGACAUCGUCGCUGGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAGCCG
..---((....)---------)..((((((((((-----------------((((((((...))))))))).......((((((....))))))...))))))))).............. ( -36.60)
>DroPse_CAF1 26276 87 - 1
UG---GCAGUGGCAGUGG------CUGUG------------------------GCUGACAUCGUCGCUUGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAAGCG
((---.((((.((((...------)))).------------------------)))).))....((((((........((((((....))))))((((.........))))...)))))) ( -29.40)
>DroSec_CAF1 24539 100 - 1
GA---GCAACUGCAACUGCUGCAAUUGUUGCUGC-----------------CCGGUGACAUCGUCGCUGGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAAAGAUGAGACAGCCG
(.---((...((((.....)))).((((((((((-----------------((((((((...))))))))).......((((((....))))))...)))))))))..........))). ( -40.20)
>DroSim_CAF1 24924 100 - 1
CA---GCAACUGCAACUGCUGCAAUUGUUGCUGC-----------------CCGGUGACAUCGUCGCUGGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAGCCG
((---(((........)))))...((((((((((-----------------((((((((...))))))))).......((((((....))))))...))))))))).............. ( -40.10)
>DroAna_CAF1 30450 120 - 1
CUUCUGCUUCUGCUUCUGCUUCGGCUGGUGAUGUUGCAGUUGCAUUUGCAGUUGGUGACAUCGUCGCUUGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAGGCG
..((((..((.(((...((....)).)))(((((..(..((((....))))...)..)))))((((((.((.......((((((....))))))..))))))))......))..)))).. ( -41.40)
>DroPer_CAF1 25785 93 - 1
UG---GCAGUGGCAGUGGCUGUGGCUGUG------------------------GCUGACAUCGUCGCUUGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAAGCG
..---(((((.((((...)))).))))).------------------------(((....((((((.(((.(((....((((((....))))))....)))..)))))))))....))). ( -35.70)
>consensus
CA___GCAACUGCAACUGCUGCAACUGUUGCUGC_________________CCGGUGACAUCGUCGCUGGGGUUUUAUUGGCCACUUUUGGCCACAUCAGCGACAACGAUGAGACAGCCG
.....((....))........................................(((..((((((((((.((.......((((((....))))))..))))))))...)))).....))). (-21.99 = -21.77 +  -0.22)

alignment

secondary structure

dotplot

Window 2

Location	25,339,640 – 25,339,735
Length	95
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	76.97
Mean single sequence MFE	-31.97
Consensus MFE	-20.46
Energy contribution	-21.78
Covariance contribution	1.31
Combinations/Pair	1.10
Mean z-score	-2.15
Structure conservation index	0.64
SVM decision value	1.50
SVM RNA-class probability	0.959032
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25339640 95 + 27905053
GCAGCAACAAUUG---------CAGUUGCUGUUGCAGUUGCAGCAGCGAUGACGACGAAUUAUAGCAAAGUAAUCGCAGUGGACUCUCCAGUUGCCAGUGCAUC
((((((((.((((---------(.(((((((((((....)))))))))))......((.((((......)))))))))))((.....)).)))))...)))... ( -33.70)
>DroPse_CAF1 26343 83 + 1
-----CACAG------CCACUGCCACUGCCACAGCAGCAGCUCCAGCGAUGACGACGAAUUAUAGCAAAGUAAUCGCACUGGACUCUGUAGU----------GC
-----.....------.((((((..((((....)))).((.(((((((((.((................)).)))))..))))))..)))))----------). ( -20.59)
>DroSec_CAF1 24608 104 + 1
GCAGCAACAAUUGCAGCAGUUGCAGUUGCUCUUGCAGUUGCAGCAGCGAUGACGACGAAUUAUAGCAAAGUAAUCGCAGUGGACUCUCCAGUUGCCAGUGCAUC
((((((((.(((((.((.((((((..(((....)))..)))))).))(((.((................)).))))))))((.....)).)))))...)))... ( -34.39)
>DroSim_CAF1 24993 104 + 1
GCAGCAACAAUUGCAGCAGUUGCAGUUGCUGUUGCAGUUGCAGCAGCGAUGACGACGAAUUAUAGCAAAGUAAUCGCAGUGGACUCUCCAGUUGCCAGUGCAUC
((((((((.(((((....((((..(((((((((((....)))))))))))..))))((.((((......)))))))))))((.....)).)))))...)))... ( -39.20)
>consensus
GCAGCAACAAUUG___CAGUUGCAGUUGCUGUUGCAGUUGCAGCAGCGAUGACGACGAAUUAUAGCAAAGUAAUCGCAGUGGACUCUCCAGUUGCCAGUGCAUC
((((((((................(((((((((((....)))))))))))...(.(((.((((......))))))))..(((.....))))))))...)))... (-20.46 = -21.78 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	25,339,735 – 25,339,827
Length	92
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	71.34
Mean single sequence MFE	-22.44
Consensus MFE	-11.14
Energy contribution	-12.14
Covariance contribution	1.00
Combinations/Pair	1.33
Mean z-score	-1.83
Structure conservation index	0.50
SVM decision value	0.71
SVM RNA-class probability	0.830929
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25339735 92 - 27905053
---------GAUAU-GAUUGUAAUACUUAUAUAUA-AAUGGUAGUUCAGAGUUGGCUUUGGCAUAUCCUACUCCUUGAAAGGGUAUGAUCCAGGUGGACAAAG
---------.....-..(((...((((........-...))))...))).(((.((((.((((((((((..........)))))))).)).)))).))).... ( -19.10)
>DroSec_CAF1 24712 95 - 1
AUUG-----CAUAU-AUUUAUAAUACUUAUAUAGC-AA-GGUAAAUCAAAAUUGGCUUUGGCAUAUCCUCUUCCUUGAAAGGGUAUUAUCAAGGUGGACAAAG
.(((-----(((((-(...........))))).))-))-............((.(((((((.(((((((.(((...))))))))))..))))))).))..... ( -17.70)
>DroSim_CAF1 25097 95 - 1
AUUG-----CAUAU-AUUUAUAAUACUUAUAUAUC-AA-GGUAUAUAAGAGUUGGCUUUGGCAUAUCCUACUCCUUGAAAGGGUAUUAUCAAGGUGGACAAAG
....-----.....-..........(((((((((.-..-.))))))))).(((.(((((((.(((((((..........)))))))..))))))).))).... ( -24.40)
>DroEre_CAF1 24943 95 - 1
GCUGCAUUUAAUAA-AUU--UUAUACUG---AAUAAAU-GGUAAACUAGCGCUAC-UUCGGUAUAUCCUGCUCCUCGAAAGGGUAUGCUCGAGGUGGACAAAG
((((..((((....-..(--((((....---.))))).-..)))).))))(((((-(((((((((((((..........))))))))).)))))))).).... ( -26.20)
>DroYak_CAF1 27380 89 - 1
AUUG-----AAUGGCAUU--U--UACUU---UAUU-AG-GGUAAAGUAGAGUUAAUUUUGGUAUAUCGUCUUCCUGGAAAGGGUAUGCCUGAGCUGGACAAAG
.(((-----..(((((((--(--(((((---(((.-..-.)))))))))))).......((((((((.(((....)))...))))))))...))))..))).. ( -24.80)
>consensus
AUUG_____AAUAU_AUUU_UAAUACUUAUAUAUA_AA_GGUAAAUCAGAGUUGGCUUUGGCAUAUCCUACUCCUUGAAAGGGUAUGAUCAAGGUGGACAAAG
..................................................(((.(((((((((((((((..........)))))))).))))))).))).... (-11.14 = -12.14 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:37:48 2006