Locus 4410

Sequence ID	3L_DroMel_CAF1
Location	12,904,140 – 12,904,248
Length	108
Max. P	0.995480

overview

Window 5

Location	12,904,140 – 12,904,248
Length	108
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	93.79
Mean single sequence MFE	-39.08
Consensus MFE	-36.42
Energy contribution	-36.26
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.79
Structure conservation index	0.93
SVM decision value	2.58
SVM RNA-class probability	0.995480
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12904140 108 + 23771897
AAGGAGCCGGUGGCAAUUGAGUCGAGUGUGCAUUAGAGGACGUGGAUUUAAUGCACUCAGGCGGACCGUGUUCGACUCCUGGCCAAGGUUC------UAUGUAGCCCAACGA-AA
..((((((..((((....((((((((.((((((((((.........)))))))))).).((....))....)))))))...)))).)))))------)..............-.. ( -39.80)
>DroSec_CAF1 25002 108 + 1
AAGGAGCCGGUGGCAAUUGAGUCGAGUGUGCAUUAGAGGACGUGGAUUUAAUGCACUCAGGCGGACCGUGUUCGACUCCUGGCCAAGGUUC------UAUGUAGCCCAACGA-AA
..((((((..((((....((((((((.((((((((((.........)))))))))).).((....))....)))))))...)))).)))))------)..............-.. ( -39.80)
>DroSim_CAF1 22719 108 + 1
AAGGAGCCGGUGGCAAUUGAGUCGAGUGUGCAUUAGAGGACGUGGAUUUAAUGCACUCAGGCGGACCGUGUUCGACUCCUGGCCAAGGUUC------UAUGCAGCCCAACGA-AA
..((((((..((((....((((((((.((((((((((.........)))))))))).).((....))....)))))))...)))).)))))------)..............-.. ( -39.80)
>DroEre_CAF1 30087 109 + 1
AAGGAGCCGGUGGCAAUUGAGUCGAGUGUGCAUUAGAGGACGUGGAUUUAAUGCACUCAAGCGGACCGUGUUCGACUCCUGGCCAAGGUUU------UAUGUAGCCCGACACAAA
..((((((..((((....((((((((.((((((((((.........)))))))))).)..(((...)))..)))))))...)))).)))))------)................. ( -36.10)
>DroYak_CAF1 27316 115 + 1
AUGGAGCCGGUGGCAAUUGAGUCGAGUGUGCAUUAGAGGACGUGGAUUUAAUGCACUCAAGCGGACCGUGUUCGACUCCUGGCCAAGGUUCUGCUUGUAUGUAGCCCGACCAAAC
..((((((..((((....((((((((.((((((((((.........)))))))))).)..(((...)))..)))))))...)))).))))))(((.......))).......... ( -39.90)
>consensus
AAGGAGCCGGUGGCAAUUGAGUCGAGUGUGCAUUAGAGGACGUGGAUUUAAUGCACUCAGGCGGACCGUGUUCGACUCCUGGCCAAGGUUC______UAUGUAGCCCAACGA_AA
...(((((..((((....((((((((.((((((((((.........)))))))))).)..(((...)))..)))))))...)))).)))))........................ (-36.42 = -36.26 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	12,904,140 – 12,904,248
Length	108
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	93.79
Mean single sequence MFE	-32.59
Consensus MFE	-30.65
Energy contribution	-30.17
Covariance contribution	-0.48
Combinations/Pair	1.07
Mean z-score	-1.71
Structure conservation index	0.94
SVM decision value	2.40
SVM RNA-class probability	0.993518
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12904140 108 - 23771897
UU-UCGUUGGGCUACAUA------GAACCUUGGCCAGGAGUCGAACACGGUCCGCCUGAGUGCAUUAAAUCCACGUCCUCUAAUGCACACUCGACUCAAUUGCCACCGGCUCCUU
..-..(((((.((....)------).....((((...(((((((.((.((....)))).((((((((.............))))))))..)))))))....)))))))))..... ( -32.42)
>DroSec_CAF1 25002 108 - 1
UU-UCGUUGGGCUACAUA------GAACCUUGGCCAGGAGUCGAACACGGUCCGCCUGAGUGCAUUAAAUCCACGUCCUCUAAUGCACACUCGACUCAAUUGCCACCGGCUCCUU
..-..(((((.((....)------).....((((...(((((((.((.((....)))).((((((((.............))))))))..)))))))....)))))))))..... ( -32.42)
>DroSim_CAF1 22719 108 - 1
UU-UCGUUGGGCUGCAUA------GAACCUUGGCCAGGAGUCGAACACGGUCCGCCUGAGUGCAUUAAAUCCACGUCCUCUAAUGCACACUCGACUCAAUUGCCACCGGCUCCUU
..-.....((((((....------......((((...(((((((.((.((....)))).((((((((.............))))))))..)))))))....)))).))))))... ( -32.52)
>DroEre_CAF1 30087 109 - 1
UUUGUGUCGGGCUACAUA------AAACCUUGGCCAGGAGUCGAACACGGUCCGCUUGAGUGCAUUAAAUCCACGUCCUCUAAUGCACACUCGACUCAAUUGCCACCGGCUCCUU
.....(((((........------......((((...(((((((.((.((....)))).((((((((.............))))))))..)))))))....)))))))))..... ( -29.95)
>DroYak_CAF1 27316 115 - 1
GUUUGGUCGGGCUACAUACAAGCAGAACCUUGGCCAGGAGUCGAACACGGUCCGCUUGAGUGCAUUAAAUCCACGUCCUCUAAUGCACACUCGACUCAAUUGCCACCGGCUCCAU
....(((((((((.......))).......((((...(((((((.((.((....)))).((((((((.............))))))))..)))))))....)))))))))).... ( -35.62)
>consensus
UU_UCGUUGGGCUACAUA______GAACCUUGGCCAGGAGUCGAACACGGUCCGCCUGAGUGCAUUAAAUCCACGUCCUCUAAUGCACACUCGACUCAAUUGCCACCGGCUCCUU
.....(((((....................((((...(((((((.((.((....)))).((((((((.............))))))))..)))))))....)))))))))..... (-30.65 = -30.17 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:55 2006