Locus 986

Sequence ID	2R_DroMel_CAF1
Location	4,139,135 – 4,139,254
Length	119
Max. P	0.740500

overview

Window 1

Location	4,139,135 – 4,139,254
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	90.48
Mean single sequence MFE	-50.90
Consensus MFE	-39.16
Energy contribution	-40.48
Covariance contribution	1.31
Combinations/Pair	1.16
Mean z-score	-1.87
Structure conservation index	0.77
SVM decision value	0.45
SVM RNA-class probability	0.740500
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4139135 119 + 20766785
CCUCGGGCAGGUAGGGCUGUGCGAUGGAUUGGCCGGCAUUUGCCAACCAGGUCCUCCGCAUCGCGUUCCUCUCAUCGGCAUUGUGCGGUGCGCUUAGCACCAACACCAUGAGGAAGAGG
(((((((.(((.((.((.(((((..(((((((..(((....)))..))).))))..))))).)).)))))))).((..(((.(((.(((((.....)))))..))).)))..)).)))) ( -51.80)
>DroSec_CAF1 4262 119 + 1
CCUCGGGCAGGUAGGGCUGUGUGAGGGAUUGGCCGGCAUUUGCCAGCCAGGUGCUCCGCAUCGCGUUCCUCUCAUCGGAAUUGUGCGGUGCGCUGAGCACCAACACCAUAAGGAAGAGU
(((((.((((......)))).)))))...((((.(((....))).))))((((((((((((((((((((.......)))))...))))))))..)))))))....((....))...... ( -57.20)
>DroEre_CAF1 4254 119 + 1
CCUCGGGAAGAUAGGGCUGUGCGAGGGAUUGGCCCGCACUCGCCAGCCAGGUGCUCCGCAUCGCUUGCCUCUCCUCUGCAUUGUGUGGUGCGCUGAGCACCAACACCAUAAGGAAGAGG
((((..........(((((.(((((((......))...)))))))))).(((((((((((((((.(((.........)))....))))))))..)))))))....((....))..)))) ( -50.70)
>DroYak_CAF1 4156 119 + 1
CCUCGGGAAAAUAGGGCUGUGCAAGAGAUUGGCCCGCAUUUGCCAGCCAGGUGCUCCGCAUCGCGUUCCUCUCAUCUGCAUUGUGUGGUGCGCUGAGCACCAACACCAUAAGGAAGAGG
((((((((....((.((.((((..(((.(((((..((....))..)))))...))).)))).)).))..)))).(((..((.(((((((((.....))))).)))).))..))).)))) ( -43.90)
>consensus
CCUCGGGAAGAUAGGGCUGUGCGAGGGAUUGGCCCGCAUUUGCCAGCCAGGUGCUCCGCAUCGCGUUCCUCUCAUCGGCAUUGUGCGGUGCGCUGAGCACCAACACCAUAAGGAAGAGG
(((..((.......(((((.(((((((.....)))....))))))))).((((((((((((((((((((.......)))))...))))))))..)))))))....))...)))...... (-39.16 = -40.48 +   1.31)

alignment

secondary structure

dotplot

Window 2

Location	4,139,135 – 4,139,254
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	90.48
Mean single sequence MFE	-47.25
Consensus MFE	-38.35
Energy contribution	-38.60
Covariance contribution	0.25
Combinations/Pair	1.14
Mean z-score	-1.71
Structure conservation index	0.81
SVM decision value	0.44
SVM RNA-class probability	0.739172
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4139135 119 - 20766785
CCUCUUCCUCAUGGUGUUGGUGCUAAGCGCACCGCACAAUGCCGAUGAGAGGAACGCGAUGCGGAGGACCUGGUUGGCAAAUGCCGGCCAAUCCAUCGCACAGCCCUACCUGCCCGAGG
((((...((((((((((((((((.....)))))....)))))).)))))(((...((..((((..(((..((((((((....)))))))).)))..))))..))....)))....)))) ( -52.10)
>DroSec_CAF1 4262 119 - 1
ACUCUUCCUUAUGGUGUUGGUGCUCAGCGCACCGCACAAUUCCGAUGAGAGGAACGCGAUGCGGAGCACCUGGCUGGCAAAUGCCGGCCAAUCCCUCACACAGCCCUACCUGCCCGAGG
.(((.........((((.(((((((..((((.(((....((((.......)))).))).)))))))))))((((((((....)))))))).......)))).((.......))..))). ( -47.00)
>DroEre_CAF1 4254 119 - 1
CCUCUUCCUUAUGGUGUUGGUGCUCAGCGCACCACACAAUGCAGAGGAGAGGCAAGCGAUGCGGAGCACCUGGCUGGCGAGUGCGGGCCAAUCCCUCGCACAGCCCUAUCUUCCCGAGG
((((.........((((.(((((.....)))))))))......(((((..(((..((((.(.(((.....(((((.((....)).))))).))))))))...)))...)))))..)))) ( -47.20)
>DroYak_CAF1 4156 119 - 1
CCUCUUCCUUAUGGUGUUGGUGCUCAGCGCACCACACAAUGCAGAUGAGAGGAACGCGAUGCGGAGCACCUGGCUGGCAAAUGCGGGCCAAUCUCUUGCACAGCCCUAUUUUCCCGAGG
((((((.(((((.((((.(((((.....))))))))).))).))..))))))...((..(((((((....(((((.((....)).)))))..))).))))..))............... ( -42.70)
>consensus
CCUCUUCCUUAUGGUGUUGGUGCUCAGCGCACCACACAAUGCAGAUGAGAGGAACGCGAUGCGGAGCACCUGGCUGGCAAAUGCCGGCCAAUCCCUCGCACAGCCCUACCUGCCCGAGG
((((((((((...((((.(((((.....)))))))))....(....).)))))).((..((((..(....((((((((....))))))))...)..))))..))...........)))) (-38.35 = -38.60 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:26 2006