Locus 6307

Sequence ID	3R_DroMel_CAF1
Location	16,479,238 – 16,479,336
Length	98
Max. P	0.923522

overview

Window 8

Location	16,479,238 – 16,479,336
Length	98
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	65.80
Mean single sequence MFE	-29.25
Consensus MFE	-14.76
Energy contribution	-15.37
Covariance contribution	0.61
Combinations/Pair	1.07
Mean z-score	-1.78
Structure conservation index	0.50
SVM decision value	1.16
SVM RNA-class probability	0.923522
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16479238 98 + 27905053
ACGCGUGGAAGGCCUGCCGGAGGCCUCCAUUGUCUGCGAUAUUCUCACCUGAGA-----UAAAUCGUUAGAAAUUAUUAAUACACA--------AUAUAUGAUUGUGACUU-----
....(((((.(((((.....))))))))))..((((((((..((((....))))-----...)))).))))...........((((--------((.....))))))....----- ( -30.30)
>DroPse_CAF1 35475 94 + 1
AAGCGUGGAAGGCCUGCCGCAGGCCGCCAUUAUCCGCAAUGUUUUCCCCUGCCGAACGGAAGAUCUUUUGUGAGGGGAGGAAGAGGGA-----GAGAGA-----------------
....((((..((((((...)))))).))))..(((.(....(((((((((..(((((....)....))))..)))))))))...))))-----......----------------- ( -32.10)
>DroSec_CAF1 35186 83 + 1
ACGCGUGGAAGGCCUGCCGCAGGCCUCCAUUGUCCGCGAUAUUCUCACCUGAGA-----UGAAUCGUUAGAAAUGAUUAAUAUAUGUA----------------------------
.((((((((.((((((...)))))))))).....))))....((((....))))-----..((((((.....))))))..........---------------------------- ( -25.80)
>DroSim_CAF1 36028 101 + 1
ACGCGUGGAAGGCCUGCCGCAGGCCUCCAUUGUCCGCGAUAUUCUCACCUGAGA-----UAAAUCGUUAGAAAUGAUUAAUAUAUGUA-----UAUAUAUGAUUGUGAAGC-----
..(((((((.((((((...)))))))))))....((((((..((((....))))-----..((((((.....)))))).((((((...-----.)))))).))))))..))----- ( -28.40)
>DroEre_CAF1 36641 111 + 1
ACGCAUGGAAGGCCUGCCGCAGGCCUCCAUUGUCCGCGAUAUUCUCACCUGAAG-----UAAGUCAUUAGAAAUUAUAUAUAAAUAUGAUAGCAACAUACAAUGGUGAAAUGGUAU
.((((((((.((((((...))))))))))).....))).((((.((((((((..-----....)))...(..(((((((....)))))))..)..........))))))))).... ( -28.50)
>DroPer_CAF1 36123 94 + 1
AAGCAUGGAAGGCCUGCCGCAGGCCGCCAUUAUCCGCAAUGUUCUCCCCUGCCGAACGGAAGAUCUUUUGUGAGGAGAGGAAGAUGGA-----GAGAGA-----------------
..((((((..((((((...)))))).)))).....))....(((((((((.((..((((((....))))))..))..))).....)))-----)))...----------------- ( -30.40)
>consensus
ACGCGUGGAAGGCCUGCCGCAGGCCUCCAUUGUCCGCGAUAUUCUCACCUGAGA_____UAAAUCGUUAGAAAUGAUAAAUAGAUGUA______AGAUA_________________
.((((((((.((((((...))))))))))).....))).............................................................................. (-14.76 = -15.37 +   0.61)

alignment

secondary structure

dotplot

Window 9

Location	16,479,238 – 16,479,336
Length	98
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	65.80
Mean single sequence MFE	-25.44
Consensus MFE	-14.88
Energy contribution	-14.97
Covariance contribution	0.08
Combinations/Pair	1.18
Mean z-score	-1.25
Structure conservation index	0.59
SVM decision value	0.33
SVM RNA-class probability	0.691384
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16479238 98 - 27905053
-----AAGUCACAAUCAUAUAU--------UGUGUAUUAAUAAUUUCUAACGAUUUA-----UCUCAGGUGAGAAUAUCGCAGACAAUGGAGGCCUCCGGCAGGCCUUCCACGCGU
-----..((((((((.....))--------))).................((((...-----((((....))))..))))..)))..(((((((((.....))))).))))..... ( -24.90)
>DroPse_CAF1 35475 94 - 1
-----------------UCUCUC-----UCCCUCUUCCUCCCCUCACAAAAGAUCUUCCGUUCGGCAGGGGAAAACAUUGCGGAUAAUGGCGGCCUGCGGCAGGCCUUCCACGCUU
-----------------......-----..........(((((((......((........)).).)))))).......(((.....(((.((((((...))))))..)))))).. ( -23.00)
>DroSec_CAF1 35186 83 - 1
----------------------------UACAUAUAUUAAUCAUUUCUAACGAUUCA-----UCUCAGGUGAGAAUAUCGCGGACAAUGGAGGCCUGCGGCAGGCCUUCCACGCGU
----------------------------.......................(((...-----((((....))))..)))(((......(((((((((...)))))))))..))).. ( -23.60)
>DroSim_CAF1 36028 101 - 1
-----GCUUCACAAUCAUAUAUA-----UACAUAUAUUAAUCAUUUCUAACGAUUUA-----UCUCAGGUGAGAAUAUCGCGGACAAUGGAGGCCUGCGGCAGGCCUUCCACGCGU
-----..(((((....((((((.-----...))))))........((....))....-----......))))).....((((......(((((((((...)))))))))..)))). ( -24.90)
>DroEre_CAF1 36641 111 - 1
AUACCAUUUCACCAUUGUAUGUUGCUAUCAUAUUUAUAUAUAAUUUCUAAUGACUUA-----CUUCAGGUGAGAAUAUCGCGGACAAUGGAGGCCUGCGGCAGGCCUUCCAUGCGU
......((((((((((((((((.............)))))))))......(((....-----..))))))))))....(((.....(((((((((((...)))))).)))))))). ( -30.52)
>DroPer_CAF1 36123 94 - 1
-----------------UCUCUC-----UCCAUCUUCCUCUCCUCACAAAAGAUCUUCCGUUCGGCAGGGGAGAACAUUGCGGAUAAUGGCGGCCUGCGGCAGGCCUUCCAUGCUU
-----------------......-----.((((..((((((((((......((........))....))))))).......)))..)))).((((((...)))))).......... ( -25.71)
>consensus
_________________UAUAU______UACAUAUAUUAAUCAUUUCUAACGAUUUA_____CCUCAGGUGAGAAUAUCGCGGACAAUGGAGGCCUGCGGCAGGCCUUCCACGCGU
.................................................(((................((((.....))))......((((((((((...)))))).))))..))) (-14.88 = -14.97 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:17 2006