Locus 570

Sequence ID	3L_DroMel_CAF1
Location	1,639,284 – 1,639,408
Length	124
Max. P	0.972234

overview

Window 0

Location	1,639,284 – 1,639,383
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	83.92
Mean single sequence MFE	-33.40
Consensus MFE	-27.23
Energy contribution	-26.78
Covariance contribution	-0.44
Combinations/Pair	1.20
Mean z-score	-1.41
Structure conservation index	0.82
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1639284 99 + 23771897
UUUUGUUGGUGUUGAUGGUGAUGAUGAAGGUAGCUAAUACUAUUGGCGGCCACAGCCGCAGCCGCUGCCGCCGCAUUGAAGCUAAUGGGCCCGCCACCA
............((.(((((........((((((.....(....)(((((....)))))....))))))(((.(((((....)))))))).))))).)) ( -33.00)
>DroPse_CAF1 1312 87 + 1
UUCUGUUGC------UGGUGAUGAUGAUGAUAGCUUAUACUAUUGGCUGCCACGGCCGCAGCCGCUGCAGCCGCGUUGAAACUAAUG------CUACCG
.........------.((((........(((((......)))))((((((..((((....))))..))))))((((((....)))))------))))). ( -29.30)
>DroEre_CAF1 1200 99 + 1
UUCUGUUGGUGCUGAUGGUGAUGAUGAUGGUAGCUAAUACUAUUGGCGGCCACGGCCGCAGCCGCUGCCGCCGCAUUGAAGCUAAUGGGACCGCCACCA
...((.((((.(((.((((..(((((((((((.....)))))).((((((..((((....))))..)))))).)))))..)))).))).)))).))... ( -37.90)
>DroWil_CAF1 1439 90 + 1
UUCUGUUGGUUC---UGGUGAUGAUGAUGAUAGCUAAGACUAUUGGCUGCCACGGCUGCGGCCGCUGCAGCCGCAUUAAAACUAAUG------CUACCG
....(.((((..---((((..(((((.((.(((((((.....))))))).))(((((((((...))))))))))))))..))))..)------))).). ( -32.90)
>DroYak_CAF1 1202 99 + 1
UUCUGUUGGUGCUGAUGGUGAUGAUGAUGGUAGCUAAUACUAUUGGCGGCCACGGCUGCAGCCGCUGCCGCCGCAUGGAAGCUAAUGGGACCGCCACCA
...((.((((.(((.((((..(.(((((((((.....)))))).((((((..((((....))))..)))))).))).)..)))).))).)))).))... ( -38.00)
>DroPer_CAF1 1298 87 + 1
UUCUGUUGC------UGGUGAUGAUGAUGAUAGCUUAUACUAUUGGCUGCCACGGCCGCAGCCGCUGCAGCCGCGUUGAAACUAAUG------CUACCG
.........------.((((........(((((......)))))((((((..((((....))))..))))))((((((....)))))------))))). ( -29.30)
>consensus
UUCUGUUGGUGC___UGGUGAUGAUGAUGAUAGCUAAUACUAUUGGCGGCCACGGCCGCAGCCGCUGCAGCCGCAUUGAAACUAAUG______CCACCA
....(.(((((....((((..(((((..(((((......)))))((((((..((((....))))..)))))).)))))..)))).......))))).). (-27.23 = -26.78 +  -0.44)

alignment

secondary structure

dotplot

Window 1

Location	1,639,284 – 1,639,383
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	83.92
Mean single sequence MFE	-34.53
Consensus MFE	-30.25
Energy contribution	-28.87
Covariance contribution	-1.39
Combinations/Pair	1.28
Mean z-score	-2.80
Structure conservation index	0.88
SVM decision value	1.69
SVM RNA-class probability	0.972234
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1639284 99 - 23771897
UGGUGGCGGGCCCAUUAGCUUCAAUGCGGCGGCAGCGGCUGCGGCUGUGGCCGCCAAUAGUAUUAGCUACCUUCAUCAUCACCAUCAACACCAACAAAA
(((((..((......(((((..(((((((((((.(((((....))))).))))))....))))))))))......))..)))))............... ( -36.20)
>DroPse_CAF1 1312 87 - 1
CGGUAG------CAUUAGUUUCAACGCGGCUGCAGCGGCUGCGGCCGUGGCAGCCAAUAGUAUAAGCUAUCAUCAUCAUCACCA------GCAACAGAA
.(((((------(....((......))((((((.(((((....))))).))))))..........)))))).............------......... ( -31.10)
>DroEre_CAF1 1200 99 - 1
UGGUGGCGGUCCCAUUAGCUUCAAUGCGGCGGCAGCGGCUGCGGCCGUGGCCGCCAAUAGUAUUAGCUACCAUCAUCAUCACCAUCAGCACCAACAGAA
(((((..(((.....(((((..(((((((((((.(((((....))))).))))))....)))))))))).....)))..)))))............... ( -38.90)
>DroWil_CAF1 1439 90 - 1
CGGUAG------CAUUAGUUUUAAUGCGGCUGCAGCGGCCGCAGCCGUGGCAGCCAAUAGUCUUAGCUAUCAUCAUCAUCACCA---GAACCAACAGAA
.(((.(------(((((....))))))((((((.(((((....))))).)))))).(((((....)))))..........))).---............ ( -31.60)
>DroYak_CAF1 1202 99 - 1
UGGUGGCGGUCCCAUUAGCUUCCAUGCGGCGGCAGCGGCUGCAGCCGUGGCCGCCAAUAGUAUUAGCUACCAUCAUCAUCACCAUCAGCACCAACAGAA
(((((..(((.....(((((...((((((((((.(((((....))))).))))))....)))).))))).....)))..)))))............... ( -38.30)
>DroPer_CAF1 1298 87 - 1
CGGUAG------CAUUAGUUUCAACGCGGCUGCAGCGGCUGCGGCCGUGGCAGCCAAUAGUAUAAGCUAUCAUCAUCAUCACCA------GCAACAGAA
.(((((------(....((......))((((((.(((((....))))).))))))..........)))))).............------......... ( -31.10)
>consensus
CGGUAG______CAUUAGCUUCAAUGCGGCGGCAGCGGCUGCGGCCGUGGCAGCCAAUAGUAUUAGCUACCAUCAUCAUCACCA___GCACCAACAGAA
.(((((...........((......))((((((.(((((....))))).))))))...........)))))............................ (-30.25 = -28.87 +  -1.39)

alignment

secondary structure

dotplot

Window 2

Location	1,639,312 – 1,639,408
Length	96
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	77.19
Mean single sequence MFE	-40.30
Consensus MFE	-27.69
Energy contribution	-27.47
Covariance contribution	-0.22
Combinations/Pair	1.37
Mean z-score	-1.46
Structure conservation index	0.69
SVM decision value	0.76
SVM RNA-class probability	0.842850
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1639312 96 - 23771897
UG---GGCCAUCCGUCG---CAUGUCCGGGGUGGUGGCGGGCCCAUUAGCUUCAAUGCGGCGGCAGCGGCUGCGGCUGUGGCCGCCAAUAGUAUUAGCUACC
((---((((..((..((---(.........)))..))..)))))).(((((..(((((((((((.(((((....))))).))))))....)))))))))).. ( -46.40)
>DroEre_CAF1 1228 96 - 1
UG---GGUCAUCCUUCU---CAUAUCCGGGGUGGUGGCGGUCCCAUUAGCUUCAAUGCGGCGGCAGCGGCUGCGGCCGUGGCCGCCAAUAGUAUUAGCUACC
((---((.(..((.(((---(......)))).)).....).)))).(((((..(((((((((((.(((((....))))).))))))....)))))))))).. ( -40.70)
>DroWil_CAF1 1464 93 - 1
UCGGUGGUCAUCCGCAG---CAUGCGCGGGGCGGUAG------CAUUAGUUUUAAUGCGGCUGCAGCGGCCGCAGCCGUGGCAGCCAAUAGUCUUAGCUAUC
..((((((...((((..---.....))))(((....(------(((((....))))))((((((.(((((....))))).))))))....)))...)))))) ( -39.80)
>DroYak_CAF1 1230 96 - 1
UG---GGUCAUCCUUCG---CAUGUCCGGGGUGGUGGCGGUCCCAUUAGCUUCCAUGCGGCGGCAGCGGCUGCAGCCGUGGCCGCCAAUAGUAUUAGCUACC
((---((((((((((((---......))))).)))))....)))).(((((...((((((((((.(((((....))))).))))))....)))).))))).. ( -41.60)
>DroMoj_CAF1 1830 96 - 1
UC---GGCCAUCCGGCUCAGCAUGGGCGCGG---CACUGGCGGCAUCAGCUUCAAUGCGGCUGCAGCGGCCGCUGCGGUGGCGGCCAAUAGUAUUAGCUAUC
..---((((..(((((((.....))))((((---(....(((((....((......)).)))))....)))))..)))....)))).(((((....))))). ( -42.10)
>DroPer_CAF1 1320 90 - 1
UU---AGUCAUCCCCAG---CAUGCGAGGACCGGUAG------CAUUAGUUUCAACGCGGCUGCAGCGGCUGCGGCCGUGGCAGCCAAUAGUAUAAGCUAUC
..---.(((.((.(...---...).)).))).(((((------(....((......))((((((.(((((....))))).))))))..........)))))) ( -31.20)
>consensus
UG___GGUCAUCCGUCG___CAUGUCCGGGGUGGUAGCGG_CCCAUUAGCUUCAAUGCGGCGGCAGCGGCUGCGGCCGUGGCCGCCAAUAGUAUUAGCUACC
................................((((((..........((......))((((((.(((((....))))).))))))..........)))))) (-27.69 = -27.47 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:35 2006