Locus 3154

Sequence ID	X_DroMel_CAF1
Location	8,381,863 – 8,381,962
Length	99
Max. P	0.967500

overview

Window 0

Location	8,381,863 – 8,381,962
Length	99
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	74.00
Mean single sequence MFE	-15.62
Consensus MFE	-8.88
Energy contribution	-10.16
Covariance contribution	1.28
Combinations/Pair	1.11
Mean z-score	-2.09
Structure conservation index	0.57
SVM decision value	1.61
SVM RNA-class probability	0.967500
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8381863 99 + 22224390
GGGAAAAAAAAAAGGGAAAACAAAAUGUUGGGAAAAACUGCAACUGAAC---AAUUCGGUUCUUAAGUAGUCCGAUUAAAAUCCGGAAAUUGCAACCCCA-AA------------
(((..........(......).....((((.((....((((....((((---......))))....))))((((.........))))..)).))))))).-..------------ ( -18.60)
>DroSec_CAF1 10732 91 + 1
GGGAAAA-------GGCAAACAAAAUGUAGGGAAAAACUGCAACUGAAC---AAUUCAGU-CUUAAGUAGUCCGAUUAAAAUCCGGAAAUUGCAACCCCA-AA------------
(((....-------.((((((....(((((.......)))))(((((..---...)))))-.....))..((((.........))))..))))...))).-..------------ ( -20.40)
>DroEre_CAF1 11962 93 + 1
GGGAAAA-------GGCAAACAGAAUAAAGGGAAAAACUGCAACUGAAC---AAUUUAGUUCUUAAGUAGUCCGAUUAAAAUCCGGAAAUUGCAACCCCAAAA------------
(((....-------.((((..................((((....((((---......))))....))))((((.........))))..))))...)))....------------ ( -18.90)
>DroYak_CAF1 10772 81 + 1
------------------UACAAAAUCAAGGGAAAAACUGCAACUGAAC---AAUUCAGUUCUUAAGUAGUCCGAUUAAAAUCCCGAAAUUGCAACCCCA-AA------------
------------------...........(((....(((((....((((---......))))....))))).(((((..........)))))....))).-..------------ ( -12.40)
>DroAna_CAF1 22198 103 + 1
---AAAAUAUAAA--------GGAAUAAUAAUAAAAACUGCAACUGAACAACAAUUCAAUCGUUAAGUAGUCCGAUUAAAAUCCGAAUCUUUCAACCCCA-AAAACCAAAAAAGA
---..........--------(((....((((....((((((((((((......))))...)))..)))))...))))...)))................-.............. (  -7.80)
>consensus
GGGAAAA_______GG_AAACAAAAUAAAGGGAAAAACUGCAACUGAAC___AAUUCAGUUCUUAAGUAGUCCGAUUAAAAUCCGGAAAUUGCAACCCCA_AA____________
.............................(((.....(((((((((((......))))))).....))))((((.........)))).........)))................ ( -8.88 = -10.16 +   1.28)

alignment

secondary structure

dotplot

Window 1

Location	8,381,863 – 8,381,962
Length	99
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	74.00
Mean single sequence MFE	-17.76
Consensus MFE	-11.38
Energy contribution	-11.82
Covariance contribution	0.44
Combinations/Pair	1.24
Mean z-score	-1.36
Structure conservation index	0.64
SVM decision value	-0.05
SVM RNA-class probability	0.510257
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8381863 99 - 22224390
------------UU-UGGGGUUGCAAUUUCCGGAUUUUAAUCGGACUACUUAAGAACCGAAUU---GUUCAGUUGCAGUUUUUCCCAACAUUUUGUUUUCCCUUUUUUUUUUCCC
------------.(-((((((((((((((((((.......)))))........((((......---))))))))))))....))))))........................... ( -19.60)
>DroSec_CAF1 10732 91 - 1
------------UU-UGGGGUUGCAAUUUCCGGAUUUUAAUCGGACUACUUAAG-ACUGAAUU---GUUCAGUUGCAGUUUUUCCCUACAUUUUGUUUGCC-------UUUUCCC
------------..-(((((((((....(((((.......)))))........(-(((((...---..)))))))))).....))))).............-------....... ( -17.60)
>DroEre_CAF1 11962 93 - 1
------------UUUUGGGGUUGCAAUUUCCGGAUUUUAAUCGGACUACUUAAGAACUAAAUU---GUUCAGUUGCAGUUUUUCCCUUUAUUCUGUUUGCC-------UUUUCCC
------------....(((((((((((((((((.......)))))........((((......---))))))))))))....))))...............-------....... ( -18.80)
>DroYak_CAF1 10772 81 - 1
------------UU-UGGGGUUGCAAUUUCGGGAUUUUAAUCGGACUACUUAAGAACUGAAUU---GUUCAGUUGCAGUUUUUCCCUUGAUUUUGUA------------------
------------..-.((((((((((((((((........)))))........((((......---)))).)))))))....))))...........------------------ ( -16.70)
>DroAna_CAF1 22198 103 - 1
UCUUUUUUGGUUUU-UGGGGUUGAAAGAUUCGGAUUUUAAUCGGACUACUUAACGAUUGAAUUGUUGUUCAGUUGCAGUUUUUAUUAUUAUUCC--------UUUAUAUUUU---
..............-..(((((....)))))(((...((((..((..(((...(((((((((....))))))))).)))..))...)))).)))--------..........--- ( -16.10)
>consensus
____________UU_UGGGGUUGCAAUUUCCGGAUUUUAAUCGGACUACUUAAGAACUGAAUU___GUUCAGUUGCAGUUUUUCCCUUCAUUUUGUUU_CC_______UUUUCCC
................((((((((....(((((.......))))).........((((((((....))))))))))))....))))............................. (-11.38 = -11.82 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:25 2006