Locus 4084

Sequence ID	2R_DroMel_CAF1
Location	13,461,469 – 13,461,563
Length	94
Max. P	0.871640

overview

Window 4

Location	13,461,469 – 13,461,563
Length	94
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	82.13
Mean single sequence MFE	-20.87
Consensus MFE	-11.38
Energy contribution	-11.58
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.55
SVM decision value	0.31
SVM RNA-class probability	0.683732
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13461469 94 + 20766785
UUAAUUUUCCACACAUUAAAGUCAGUGUGGAAAAAAUAGAAGGCAGCCGUAACUCAUUU-----UUCGCUGCAUAUUUUAUUUAUUUGUUUGAU----ACAAC
.....(((((((((..........)))))))))((((((((.(((((............-----...)))))...))))))))..((((.....----)))). ( -23.46)
>DroSec_CAF1 10260 98 + 1
UUAAUUUUCCACACAUUAAAGUCAGUGUGGAAAAACUAGAACGCAGGCGUAACUCAUUU-----UUCGCCGCAUAUUUUAUUUAUUGGUUUAAUUACCCCAGC
....((((((((((..........))))))))))........((.((((..........-----..))))))..............(((......)))..... ( -22.20)
>DroSim_CAF1 10422 98 + 1
UUAAUUUUCCACACAUUAAAGUCAGUGUGGAAAAACUAGAACGCAGGCGUAACUCAUUU-----UUCGCCGCAUAUUUUAUUUAUUGGUUUAAUUACCCCAGC
....((((((((((..........))))))))))........((.((((..........-----..))))))..............(((......)))..... ( -22.20)
>DroEre_CAF1 10683 94 + 1
UUAAUUUUCCACACAUUAAAGUCAGUGUUGAAAAACCAGCAGG----CGUACUUCGUUU-----CUCAGUGUAUAUUUUAUUUAUUGGUCUAAUUACCCCAAC
.(((((..(((.....((((((..(..((((.((((....((.----....))..))))-----.))))..)..)))))).....)))...)))))....... ( -11.70)
>DroYak_CAF1 11159 99 + 1
UUAAUUUUCCACACAUUAAAGUCUGUGUGGAAAAAGUAGAACG----AGAACUACGGUUCAGUUUUCGUUGCAUAUUUUAUUUAUUGGUUUAAUUACUUCAAC
....(((((((((((........)))))))))))(((((((((----((((((.......))))))))))...((..(((.....)))..)).)))))..... ( -24.80)
>consensus
UUAAUUUUCCACACAUUAAAGUCAGUGUGGAAAAACUAGAACGCAG_CGUAACUCAUUU_____UUCGCUGCAUAUUUUAUUUAUUGGUUUAAUUACCCCAAC
....((((((((((..........))))))))))..................................................................... (-11.38 = -11.58 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	13,461,469 – 13,461,563
Length	94
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	82.13
Mean single sequence MFE	-22.63
Consensus MFE	-12.75
Energy contribution	-12.47
Covariance contribution	-0.28
Combinations/Pair	1.29
Mean z-score	-2.46
Structure conservation index	0.56
SVM decision value	0.87
SVM RNA-class probability	0.871640
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13461469 94 - 20766785
GUUGU----AUCAAACAAAUAAAUAAAAUAUGCAGCGAA-----AAAUGAGUUACGGCUGCCUUCUAUUUUUUCCACACUGACUUUAAUGUGUGGAAAAUUAA
(((..----....)))...............(((((...-----............)))))........((((((((((..........)))))))))).... ( -20.06)
>DroSec_CAF1 10260 98 - 1
GCUGGGGUAAUUAAACCAAUAAAUAAAAUAUGCGGCGAA-----AAAUGAGUUACGCCUGCGUUCUAGUUUUUCCACACUGACUUUAAUGUGUGGAAAAUUAA
((((((((......)))............((((((((.(-----(......)).)))).)))).)))))((((((((((..........)))))))))).... ( -27.60)
>DroSim_CAF1 10422 98 - 1
GCUGGGGUAAUUAAACCAAUAAAUAAAAUAUGCGGCGAA-----AAAUGAGUUACGCCUGCGUUCUAGUUUUUCCACACUGACUUUAAUGUGUGGAAAAUUAA
((((((((......)))............((((((((.(-----(......)).)))).)))).)))))((((((((((..........)))))))))).... ( -27.60)
>DroEre_CAF1 10683 94 - 1
GUUGGGGUAAUUAGACCAAUAAAUAAAAUAUACACUGAG-----AAACGAAGUACG----CCUGCUGGUUUUUCAACACUGACUUUAAUGUGUGGAAAAUUAA
((..((((......)))..................((((-----((((..((((..----..)))).))))))))...)..)).................... ( -15.90)
>DroYak_CAF1 11159 99 - 1
GUUGAAGUAAUUAAACCAAUAAAUAAAAUAUGCAACGAAAACUGAACCGUAGUUCU----CGUUCUACUUUUUCCACACAGACUUUAAUGUGUGGAAAAUUAA
(((.((....)).))).................(((((.(((((.....))))).)----)))).....(((((((((((........))))))))))).... ( -22.00)
>consensus
GUUGGGGUAAUUAAACCAAUAAAUAAAAUAUGCAGCGAA_____AAAUGAGUUACG_CUGCGUUCUAGUUUUUCCACACUGACUUUAAUGUGUGGAAAAUUAA
((((............................)))).................................((((((((((..........)))))))))).... (-12.75 = -12.47 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:21 2006