Locus 5939

Sequence ID	2R_DroMel_CAF1
Location	18,737,832 – 18,737,937
Length	105
Max. P	0.976672

overview

Window 6

Location	18,737,832 – 18,737,937
Length	105
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	74.00
Mean single sequence MFE	-25.54
Consensus MFE	-13.20
Energy contribution	-13.87
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.91
Structure conservation index	0.52
SVM decision value	0.88
SVM RNA-class probability	0.874100
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18737832 105 + 20766785
--AUGUCAGUAUGUCGCA---UCUUUAGUAGGUUUUCCUCAGUGUUUUCCACUCAAUUCUCCACC-AAUCCAGUCCAUCUGGACUUGGCAUUGUUCCAGUGGCACGCUCUU
--.....((..((((((.---.........((........((((.....)))).......))..(-((((((((((....)))).))).)))).....))))))..))... ( -25.56)
>DroSec_CAF1 100648 105 + 1
--AUGUCAGUACUUCGCA---UCUGUAGGUAGUUUUCCUCAGUGUUUUCCACUCAAUUCUCCAAC-AAUCCAGUCCAUCUGGACUUGGCAUUGUUCCAGUGGCACGCUCUU
--.(((((.(.....(((---.(((.(((.......))))))))).................(((-((((((((((....)))).))).))))))..).)))))....... ( -25.00)
>DroSim_CAF1 101439 105 + 1
--AUGUGAGUACUUCGCA---UCUGUAGGUAGUUUUCCUUAGUGUUUUCCACUCAAUUCUCCAAC-AAUCCAGUCCAUCUGGACUUGGCAUUGUUCCAGUGGCACGCUCUU
--....((((.....(((---.(((.(((.......)))))))))...(((((.........(((-((((((((((....)))).))).))))))..)))))...)))).. ( -25.40)
>DroEre_CAF1 103279 93 + 1
--------------CACU----UUUUAAGUGGUUUCCCUCAGUGUUUUCCACUCAACUAUCCACUAAAUCCAGUUGAUCUGGACUUGGCAUUGUUCCAGUGGCACGCUCUA
--------------((((----.....)))).........(((((...(((((.(((......((((.(((((.....))))).))))....)))..))))).)))))... ( -21.20)
>DroYak_CAF1 103106 94 + 1
UAAUGUCAA-GCUUCACC----UUUUAGGUAGUUUUCCUCAGUGUUUUCC------------ACUAAAUCCAGUCGAUCUGGACUUGGCAUUGUGCCAGUGGCACGCUCUU
.((((((((-(....(((----.....)))..........((((.....)------------)))...(((((.....))))))))))))))(((((...)))))...... ( -27.00)
>DroAna_CAF1 97676 97 + 1
--A---------CUCGCAGGGUGUCUAUGGGAUUUCCCCAAGUGCACCCCACUCUGUUGACC---GAAUCCCGUCCUUCUGGACUUGGCAUUGUUCCAGUGGCACGCUCUC
--.---------...((.((((((((.((((.....)))))).))))))((((....((.((---((.....((((....)))))))))).......))))))........ ( -29.10)
>consensus
__AUGUCAG_ACUUCGCA___UCUUUAGGUAGUUUUCCUCAGUGUUUUCCACUCAAUUCUCCACC_AAUCCAGUCCAUCUGGACUUGGCAUUGUUCCAGUGGCACGCUCUU
........................................(((((...((((................(((((.....)))))..(((.......))))))).)))))... (-13.20 = -13.87 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	18,737,832 – 18,737,937
Length	105
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	74.00
Mean single sequence MFE	-28.97
Consensus MFE	-15.53
Energy contribution	-15.45
Covariance contribution	-0.08
Combinations/Pair	1.20
Mean z-score	-2.24
Structure conservation index	0.54
SVM decision value	1.78
SVM RNA-class probability	0.976672
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18737832 105 - 20766785
AAGAGCGUGCCACUGGAACAAUGCCAAGUCCAGAUGGACUGGAUU-GGUGGAGAAUUGAGUGGAAAACACUGAGGAAAACCUACUAAAGA---UGCGACAUACUGACAU--
....((((.(((((.((....((((((.(((((.....)))))))-)))).....)).))))).........(((....))).......)---))).............-- ( -26.30)
>DroSec_CAF1 100648 105 - 1
AAGAGCGUGCCACUGGAACAAUGCCAAGUCCAGAUGGACUGGAUU-GUUGGAGAAUUGAGUGGAAAACACUGAGGAAAACUACCUACAGA---UGCGAAGUACUGACAU--
....((((.(((((.(((((((.(((.((((....))))))))))-)).......)).)))))......((((((.......))).))))---))).............-- ( -28.91)
>DroSim_CAF1 101439 105 - 1
AAGAGCGUGCCACUGGAACAAUGCCAAGUCCAGAUGGACUGGAUU-GUUGGAGAAUUGAGUGGAAAACACUAAGGAAAACUACCUACAGA---UGCGAAGUACUCACAU--
..(((..(((..(((.((((((.(((.((((....))))))))))-)))((.......((((.....)))).((.....)).))..))).---.))).....)))....-- ( -26.20)
>DroEre_CAF1 103279 93 - 1
UAGAGCGUGCCACUGGAACAAUGCCAAGUCCAGAUCAACUGGAUUUAGUGGAUAGUUGAGUGGAAAACACUGAGGGAAACCACUUAAAA----AGUG--------------
...((.((.(((((.((....(((.((((((((.....)))))))).))).....)).)))))...)).))..((....))........----....-------------- ( -27.80)
>DroYak_CAF1 103106 94 - 1
AAGAGCGUGCCACUGGCACAAUGCCAAGUCCAGAUCGACUGGAUUUAGU------------GGAAAACACUGAGGAAAACUACCUAAAA----GGUGAAGC-UUGACAUUA
..((((...((((((((.....)))((((((((.....)))))))))))------------))....((((.(((.......)))....----))))..))-))....... ( -30.90)
>DroAna_CAF1 97676 97 - 1
GAGAGCGUGCCACUGGAACAAUGCCAAGUCCAGAAGGACGGGAUUC---GGUCAACAGAGUGGGGUGCACUUGGGGAAAUCCCAUAGACACCCUGCGAG---------U--
..((.((..((..(((.......))).((((....)))).))...)---).))......(..(((((....((((.....))))....)))))..)...---------.-- ( -33.70)
>consensus
AAGAGCGUGCCACUGGAACAAUGCCAAGUCCAGAUGGACUGGAUU_GGUGGAGAAUUGAGUGGAAAACACUGAGGAAAACCACCUAAAGA___UGCGAAGU_CUGACAU__
....((((.(((((((.......)).(((((((.....))))))).............)))))...)).....((....)).............))............... (-15.53 = -15.45 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:32 2006