Locus 5854

Sequence ID	2R_DroMel_CAF1
Location	18,514,398 – 18,514,488
Length	90
Max. P	0.547980

overview

Window 0

Location	18,514,398 – 18,514,488
Length	90
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	86.01
Mean single sequence MFE	-36.82
Consensus MFE	-24.72
Energy contribution	-25.36
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.81
Structure conservation index	0.67
SVM decision value	0.03
SVM RNA-class probability	0.547980
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18514398 90 + 20766785
AGCAGCUCUGGGGGCACGCCGCACGCCG-------CAUGCUGCAUGCUGCAUGC--UGCAUGUUGCUAGU-UGCUGUUCGCUGGUUGCAAGCUCAGUUCA
((((((.((((.((((.((.(((.((.(-------((((...))))).)).)))--.)).)))).)))).-.)))))).((((((.....)).))))... ( -36.30)
>DroSec_CAF1 13400 90 + 1
AGCAGCUCUGGGGGCACGCCGCACGCCG-------CAUGCUGCAUGCUGCAUGC--UGCAUGUUGCUAGU-UGCUGUUCGCUGGUUGCAAGCUCAGUUUA
((((((.((((.((((.((.(((.((.(-------((((...))))).)).)))--.)).)))).)))).-.)))))).((((((.....)).))))... ( -36.30)
>DroSim_CAF1 11633 83 + 1
AGCAGCUCUGGGGGCACG-------CCG-------CAUGCUGCAUGCUGCAUGC--UGCAUGUUGCUAGU-UGCUGUUCGCUGGUUGCAAGCUCAGUUCA
((((((.((((.((((.(-------(.(-------(((((........))))))--.)).)))).)))).-.)))))).((((((.....)).))))... ( -34.40)
>DroEre_CAF1 16587 96 + 1
AGCAGCUCUGGGGGCACGCCGCACGCCGCAUGCCGCAUGCUGCAUGCAGCAUGUUUUGCUAGUUGCUAGU-UGCUGUUUGCUGGUUGCAAGCUCAGU---
(((((((((((.((((.((.(....).)).))))((((((((....))))))))....)))).....)))-))))((((((.....)))))).....--- ( -39.00)
>DroYak_CAF1 19188 95 + 1
AGCAGCUCUGGGGGCACGCCGCAUGCCGCACGCCGCAUGCCGCAUGCUGCAUGC--UGCAUGUUGCUAGUUUUCUGUUCGCUGGUUGCAAGCUCAGU---
.(((((....(.((((.((.((((((.(....).)))))).)).)))).)..))--))).(((.((((((.........)))))).)))........--- ( -38.10)
>consensus
AGCAGCUCUGGGGGCACGCCGCACGCCG_______CAUGCUGCAUGCUGCAUGC__UGCAUGUUGCUAGU_UGCUGUUCGCUGGUUGCAAGCUCAGUU_A
((((((.((((.(((.........)))........(((((.(((((...)))))...)))))...))))...)))))).((((((.....)).))))... (-24.72 = -25.36 +   0.64)

alignment

secondary structure

dotplot

Window 1

Location	18,514,398 – 18,514,488
Length	90
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	86.01
Mean single sequence MFE	-32.54
Consensus MFE	-22.68
Energy contribution	-23.28
Covariance contribution	0.60
Combinations/Pair	1.12
Mean z-score	-1.69
Structure conservation index	0.70
SVM decision value	0.02
SVM RNA-class probability	0.542149
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18514398 90 - 20766785
UGAACUGAGCUUGCAACCAGCGAACAGCA-ACUAGCAACAUGCA--GCAUGCAGCAUGCAGCAUG-------CGGCGUGCGGCGUGCCCCCAGAGCUGCU
.......(((((((.....)).....(((-....((..(((((.--((((((........)))))-------).)))))..)).))).....)))))... ( -31.10)
>DroSec_CAF1 13400 90 - 1
UAAACUGAGCUUGCAACCAGCGAACAGCA-ACUAGCAACAUGCA--GCAUGCAGCAUGCAGCAUG-------CGGCGUGCGGCGUGCCCCCAGAGCUGCU
.......(((((((.....)).....(((-....((..(((((.--((((((........)))))-------).)))))..)).))).....)))))... ( -31.10)
>DroSim_CAF1 11633 83 - 1
UGAACUGAGCUUGCAACCAGCGAACAGCA-ACUAGCAACAUGCA--GCAUGCAGCAUGCAGCAUG-------CGG-------CGUGCCCCCAGAGCUGCU
.......(((((((.....)).....(((-....((..(((((.--(((((...))))).)))))-------..)-------).))).....)))))... ( -25.80)
>DroEre_CAF1 16587 96 - 1
---ACUGAGCUUGCAACCAGCAAACAGCA-ACUAGCAACUAGCAAAACAUGCUGCAUGCAGCAUGCGGCAUGCGGCGUGCGGCGUGCCCCCAGAGCUGCU
---.......((((.....)))).((((.-....((.....))....((((((((((((.(((((...))))).))))))))))))........)))).. ( -36.70)
>DroYak_CAF1 19188 95 - 1
---ACUGAGCUUGCAACCAGCGAACAGAAAACUAGCAACAUGCA--GCAUGCAGCAUGCGGCAUGCGGCGUGCGGCAUGCGGCGUGCCCCCAGAGCUGCU
---.(((...((((.....)))).)))..............(((--((.((..((((((.((((((.(....).)))))).))))))...))..))))). ( -38.00)
>consensus
U_AACUGAGCUUGCAACCAGCGAACAGCA_ACUAGCAACAUGCA__GCAUGCAGCAUGCAGCAUG_______CGGCGUGCGGCGUGCCCCCAGAGCUGCU
....(((...((((.....)))).))).....((((....((((.....))))((((((.(((((..........))))).)))))).......)))).. (-22.68 = -23.28 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:29 2006