Locus 5637

Sequence ID	X_DroMel_CAF1
Location	14,570,392 – 14,570,500
Length	108
Max. P	0.987093

overview

Window 5

Location	14,570,392 – 14,570,500
Length	108
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	73.96
Mean single sequence MFE	-30.48
Consensus MFE	-13.41
Energy contribution	-15.73
Covariance contribution	2.31
Combinations/Pair	1.19
Mean z-score	-3.11
Structure conservation index	0.44
SVM decision value	2.07
SVM RNA-class probability	0.987093
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14570392 108 + 22224390
UGCAUUCCUCAUUAAAUUGGAGUCUGUAUGAAAGCCCACACCCACCCAUGUGUA--UGUAUG-----UG--UAUGUAUAUAGAAUCUGUGUGGAUAUAGCCAC--ACAUGCAGGCUUGC
.(((..((((((......(((.((((((((...((..(((..(((....)))..--)))..)-----).--....)))))))).)))((((((......))))--))))).)))..))) ( -31.30)
>DroSec_CAF1 46055 100 + 1
UGCAUUCCUCAUUAAAUUGGAGUCUGUAUGAAAGCGCACACCCAACGAUGUG-------------------UGUGUAUAUAACAUCUGUGUAGAUAUAGCCACACACAUGCAGGCUAUC
.....(((..........)))(((((((((...((((((((........)))-------------------)))))..........(((((.(......).)))))))))))))).... ( -29.20)
>DroEre_CAF1 40341 113 + 1
UGCAUUCCUCAUUAAAUUGGAGUCUGCAUGAAAGCUCACACCCACCGAUGUGUACAUAUAUAGUGUGUAUAUAGCUAUGUAAUAUCUGUGUGGAUAUAUGCACACA------UGCUUGC
((((..(..((......))..)..))))...((((..((((........)))).........(((((((((((.(((..((.....))..))).))))))))))).------.)))).. ( -30.70)
>DroYak_CAF1 42362 110 + 1
UGCAUUCCUCAUUAAAUUGGAGUCUGCAUGGAAACCCACACCCACA----UGUACAUACAUA-----UAUAUGUAUAUAUAAUAUCUUGGUAGAUAUAUUCACACACAUGCAGGCUCGC
...................(((((((((((...............(----((((((((....-----..)))))))))...((((((....)))))).........))))))))))).. ( -30.70)
>consensus
UGCAUUCCUCAUUAAAUUGGAGUCUGCAUGAAAGCCCACACCCACCGAUGUGUA__UAUAUA_____UA__UAUGUAUAUAAUAUCUGUGUAGAUAUAGCCACACACAUGCAGGCUUGC
...................(((((((((((.......((((........))))............................((((((....)))))).........))))))))))).. (-13.41 = -15.73 +   2.31)

alignment

secondary structure

dotplot

Window 6

Location	14,570,392 – 14,570,500
Length	108
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	73.96
Mean single sequence MFE	-29.89
Consensus MFE	-14.06
Energy contribution	-18.00
Covariance contribution	3.94
Combinations/Pair	1.18
Mean z-score	-2.32
Structure conservation index	0.47
SVM decision value	0.74
SVM RNA-class probability	0.837319
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14570392 108 - 22224390
GCAAGCCUGCAUGU--GUGGCUAUAUCCACACAGAUUCUAUAUACAUA--CA-----CAUACA--UACACAUGGGUGGGUGUGGGCUUUCAUACAGACUCCAAUUUAAUGAGGAAUGCA
(((((((..(((((--((((......))))))................--((-----(...((--(....))).))).)))..))))...........(((..........))).))). ( -29.10)
>DroSec_CAF1 46055 100 - 1
GAUAGCCUGCAUGUGUGUGGCUAUAUCUACACAGAUGUUAUAUACACA-------------------CACAUCGUUGGGUGUGCGCUUUCAUACAGACUCCAAUUUAAUGAGGAAUGCA
.(((.((.(((((((((((...((((((....))))))......))))-------------------))))).)).)).)))(((.((((((...............))))))..))). ( -25.96)
>DroEre_CAF1 40341 113 - 1
GCAAGCA------UGUGUGCAUAUAUCCACACAGAUAUUACAUAGCUAUAUACACACUAUAUAUGUACACAUCGGUGGGUGUGAGCUUUCAUGCAGACUCCAAUUUAAUGAGGAAUGCA
(((.(((------((...((.(((((((((...(((..((((((..((((.......))))))))))...))).))))))))).))...)))))....(((..........))).))). ( -32.10)
>DroYak_CAF1 42362 110 - 1
GCGAGCCUGCAUGUGUGUGAAUAUAUCUACCAAGAUAUUAUAUAUACAUAUA-----UAUGUAUGUACA----UGUGGGUGUGGGUUUCCAUGCAGACUCCAAUUUAAUGAGGAAUGCA
(.(((((..(((.((..((...((((((....))))))..(((((((((...-----.)))))))))))----..)).)))..))))).).((((..(((.........)))...)))) ( -32.40)
>consensus
GCAAGCCUGCAUGUGUGUGGAUAUAUCCACACAGAUAUUAUAUACACA__UA_____UAUAUA__UACACAUCGGUGGGUGUGGGCUUUCAUACAGACUCCAAUUUAAUGAGGAAUGCA
(.(((((((((((((((((...(((((......)))))..)))))))....................(((....))).)))))))))).).((((..(((.........)))...)))) (-14.06 = -18.00 +   3.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:52 2006