Locus 6858

Sequence ID	3L_DroMel_CAF1
Location	18,425,690 – 18,425,811
Length	121
Max. P	0.999967

overview

Window 3

Location	18,425,690 – 18,425,784
Length	94
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	69.53
Mean single sequence MFE	-27.52
Consensus MFE	-14.21
Energy contribution	-15.96
Covariance contribution	1.75
Combinations/Pair	1.21
Mean z-score	-3.69
Structure conservation index	0.52
SVM decision value	4.48
SVM RNA-class probability	0.999907
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18425690 94 + 23771897
CCACCACUCACAAGUUUUAGAGGCA----------CUGGUCAUAAGACAGCACCUCCAAAACUUAAAACUGCUUGUUUCGCAAGCUCGUGAACAACAAGCAGUG
...........(((((((.((((..----------(((.((....)))))..)))).)))))))...((((((((((((((......))))..)))))))))). ( -32.10)
>DroSec_CAF1 61673 94 + 1
CUACUAAUCACAAGUUUUAGAAGCA----------CUGGCCAUAAGACAGUCCAUCCAAAACUUGAAACUGCUUGUUUCGCAAGUUCGUGGACGACAAGCAGUA
..........((((((((.((.(.(----------(((.........)))).).)).))))))))..((((((((((((((......))))..)))))))))). ( -29.70)
>DroSim_CAF1 61061 94 + 1
CCACUAAUCACAAGUUUUAGAAGCA----------CUGGCCAUAAGACAGUACAUCCAAAACUUGAAACUGCUUGUUUCGCAAGUUCGUGGACGACAAGCAGUG
..........((((((((.((.(.(----------(((.........)))).).)).))))))))..((((((((((((((......))))..)))))))))). ( -29.70)
>DroAna_CAF1 56880 99 + 1
UUAAUU-UUAUAAGUUUUAAAAGAGUAUGAUACAUUUAGCAAUGUUUCAAUAUCCCUCAGACUGUAAACUGCUU---UAAAAAGGUU-UUUAAAGCAAGCAGUU
......-...............(((..(((.(((((....))))).)))......))).((((((....(((((---(((((....)-))))))))).)))))) ( -18.60)
>consensus
CCACUAAUCACAAGUUUUAGAAGCA__________CUGGCCAUAAGACAGUACAUCCAAAACUUGAAACUGCUUGUUUCGCAAGUUCGUGGACAACAAGCAGUG
..........((((((((.((.................................)).))))))))..((((((((((((((......))))..)))))))))). (-14.21 = -15.96 +   1.75)

alignment

secondary structure

dotplot

Window 4

Location	18,425,690 – 18,425,784
Length	94
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	69.53
Mean single sequence MFE	-32.48
Consensus MFE	-18.10
Energy contribution	-18.48
Covariance contribution	0.37
Combinations/Pair	1.38
Mean z-score	-4.15
Structure conservation index	0.56
SVM decision value	5.00
SVM RNA-class probability	0.999967
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18425690 94 - 23771897
CACUGCUUGUUGUUCACGAGCUUGCGAAACAAGCAGUUUUAAGUUUUGGAGGUGCUGUCUUAUGACCAG----------UGCCUCUAAAACUUGUGAGUGGUGG
(((..(((...........(((((.....))))).....(((((((((((((..(((((....)).)))----------..))))))))))))).)))..))). ( -41.50)
>DroSec_CAF1 61673 94 - 1
UACUGCUUGUCGUCCACGAACUUGCGAAACAAGCAGUUUCAAGUUUUGGAUGGACUGUCUUAUGGCCAG----------UGCUUCUAAAACUUGUGAUUAGUAG
.(((((((((..((((......)).)).)))))))))..(((((((((((.(.((((((....)).)))----------).).))))))))))).......... ( -31.70)
>DroSim_CAF1 61061 94 - 1
CACUGCUUGUCGUCCACGAACUUGCGAAACAAGCAGUUUCAAGUUUUGGAUGUACUGUCUUAUGGCCAG----------UGCUUCUAAAACUUGUGAUUAGUGG
((((((((((..((((......)).)).))))))((((.(((((((((((.((((((((....)).)))----------))).))))))))))).)))))))). ( -35.20)
>DroAna_CAF1 56880 99 - 1
AACUGCUUGCUUUAAA-AACCUUUUUA---AAGCAGUUUACAGUCUGAGGGAUAUUGAAACAUUGCUAAAUGUAUCAUACUCUUUUAAAACUUAUAA-AAUUAA
.((((.((((((((((-(....)))))---))))))....)))).(((((((...(((.(((((....))))).)))...)))))))..........-...... ( -21.50)
>consensus
CACUGCUUGUCGUCCACGAACUUGCGAAACAAGCAGUUUCAAGUUUUGGAGGUACUGUCUUAUGGCCAG__________UGCUUCUAAAACUUGUGAUUAGUAG
.((((((((...((((......)).))..))))))))..((((((((((((((((((((....))).))..........))))))))))))))).......... (-18.10 = -18.48 +   0.37)

alignment

secondary structure

dotplot

Window 5

Location	18,425,715 – 18,425,811
Length	96
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	67.88
Mean single sequence MFE	-27.43
Consensus MFE	-15.05
Energy contribution	-15.91
Covariance contribution	0.87
Combinations/Pair	1.48
Mean z-score	-2.22
Structure conservation index	0.55
SVM decision value	2.14
SVM RNA-class probability	0.988915
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18425715 96 + 23771897
-------CUGGUCA----UAAGACAGCACCUCCAAAACUUAAAACUGCUUGUUUCGCAAGCUCGUGAACAACAAGCAGUGCUGAUAGUGGUUGGUGUAUUGGAUAAA
-------...(((.----...))).(((((.(((....(((..((((((((((((((......))))..))))))))))..)))...)))..))))).......... ( -31.30)
>DroSec_CAF1 61698 96 + 1
-------CUGGCCA----UAAGACAGUCCAUCCAAAACUUGAAACUGCUUGUUUCGCAAGUUCGUGGACGACAAGCAGUACUCACAGUGGUUGGUGUAUUGGAUAGA
-------(((.(((----....(((..(((.(((.....(((.((((((((((((((......))))..))))))))))..)))...))).))))))..))).))). ( -30.00)
>DroSim_CAF1 61086 96 + 1
-------CUGGCCA----UAAGACAGUACAUCCAAAACUUGAAACUGCUUGUUUCGCAAGUUCGUGGACGACAAGCAGUGCUCACAGUGGUUGGUGUGUUGGAUAGA
-------.......----.....(((((((.((((.((((((.((((((((((((((......))))..))))))))))..))).)))..)))))))))))...... ( -31.20)
>DroEre_CAF1 68914 93 + 1
-------CAGGCCGUUGGUAAGACAGUGCAUCUAAAACAUUGAACUGCUUGUCUGGCAAGA------ACGGCAAGCAGUCUUUAUAAUGGUUGAUGUAUUGGAUAG-
-------...(((...)))....(((((((((.....(((((.((((((((.(((......------.))))))))))).....)))))...))))))))).....- ( -28.40)
>DroYak_CAF1 70497 95 + 1
-------CAGGCCGUUUGUAAAACAGUGAGUCCAAAACUUUAAACUGCUUGUCUCGAAAGUUCGUUUACAACAAGCAGU----GCAAUGGUUGAUGUAUUGGAUAA-
-------...((.(((.....))).))..((((((((((....(((((((((..(((....)))......)))))))))----.....))))......))))))..- ( -20.70)
>DroAna_CAF1 56907 97 + 1
GAUACAUUUAGCAA----UGUUUCAAUAUCCCUCAGACUGUAAACUGCUU---UAAAAAGGUU-UUUAAAGCAAGCAGUUUGUA-AAUGGCUUAUAACUUGGCUUA-
((.(((((....))----))).)).........((((((((....(((((---(((((....)-))))))))).))))))))..-...((((........))))..- ( -23.00)
>consensus
_______CUGGCCA____UAAGACAGUACAUCCAAAACUUUAAACUGCUUGUUUCGCAAGUUCGUGGACAACAAGCAGUGCUCACAAUGGUUGAUGUAUUGGAUAA_
.......................(((((((((((.........((((((((((...((......))...))))))))))........)))...))))))))...... (-15.05 = -15.91 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:31 2006