Locus 6744

Sequence ID	3L_DroMel_CAF1
Location	18,082,411 – 18,082,571
Length	160
Max. P	0.873856

overview

Window 5

Location	18,082,411 – 18,082,531
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.81
Mean single sequence MFE	-41.73
Consensus MFE	-38.75
Energy contribution	-39.75
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.93
SVM decision value	0.88
SVM RNA-class probability	0.873856
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18082411 120 + 23771897
UCUGCGACUUUCGGGCAAGGCAUUUGCAACUAAUUGAAAGUGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUUGAGGCCCUGGGAGGCCAAUCCACCCAACCACGGACGUCUGCAGAC
((((((((.(((((((((((((((.(((....((((......))))....)))(((.....)))...))))))))).((((......))))...........)).)))).))).))))). ( -42.50)
>DroSec_CAF1 8677 120 + 1
UCUGCGACUUUCGGGCAAGGCAUUUGCAACUAAUUGAAAGUGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUUGAGGCCCUGGGAGGCCAAUCCACCCAACCACGGACGUCUGCAGAC
((((((((.(((((((((((((((.(((....((((......))))....)))(((.....)))...))))))))).((((......))))...........)).)))).))).))))). ( -42.50)
>DroEre_CAF1 9420 120 + 1
UCUGCGACUUUGGGGCAAGGCAUUUGCAACUAAUUGAAAGUGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUUGAGGCCCUGGGAGGCCAAUCCACCCAACCACGUACGUCUGCAGAC
((((((((...(((.(((((((((.(((....((((......))))....)))(((.....)))...)))))))))...)))((((.((.....)).)))).........))).))))). ( -40.50)
>DroYak_CAF1 11738 120 + 1
UCUGCGACUUUCGGGCAAGGCAUUUGCAACUAAUUGAAAGUGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUCGAGGCCCUGGGAGGCCAGUACUCCCCACCACGCACGUCUGCAGAC
((((((((....((((.(((((((.(((....((((......))))....)))(((.....)))...)))))))....)))).(((((.......)))))..........))).))))). ( -41.40)
>consensus
UCUGCGACUUUCGGGCAAGGCAUUUGCAACUAAUUGAAAGUGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUUGAGGCCCUGGGAGGCCAAUCCACCCAACCACGGACGUCUGCAGAC
((((((((.(((((((((((((((.(((....((((......))))....)))(((.....)))...))))))))).((((......))))...........)).)))).))).))))). (-38.75 = -39.75 +   1.00)

alignment

secondary structure

dotplot

Window 6

Location	18,082,411 – 18,082,531
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.81
Mean single sequence MFE	-42.88
Consensus MFE	-40.29
Energy contribution	-40.35
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.76
Structure conservation index	0.94
SVM decision value	0.50
SVM RNA-class probability	0.758547
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18082411 120 - 23771897
GUCUGCAGACGUCCGUGGUUGGGUGGAUUGGCCUCCCAGGGCCUCAAGGCAUUAAUUGCAUUCUGCAGCAUCGCAUUGCACUUUCAAUUAGUUGCAAAUGCCUUGCCCGAAAGUCGCAGA
.(((((.(((.........((((.((.....)).))))((((...((((((((..((((.....))))........((((((.......)).))))))))))))))))....)))))))) ( -42.70)
>DroSec_CAF1 8677 120 - 1
GUCUGCAGACGUCCGUGGUUGGGUGGAUUGGCCUCCCAGGGCCUCAAGGCAUUAAUUGCAUUCUGCAGCAUCGCAUUGCACUUUCAAUUAGUUGCAAAUGCCUUGCCCGAAAGUCGCAGA
.(((((.(((.........((((.((.....)).))))((((...((((((((..((((.....))))........((((((.......)).))))))))))))))))....)))))))) ( -42.70)
>DroEre_CAF1 9420 120 - 1
GUCUGCAGACGUACGUGGUUGGGUGGAUUGGCCUCCCAGGGCCUCAAGGCAUUAAUUGCAUUCUGCAGCAUCGCAUUGCACUUUCAAUUAGUUGCAAAUGCCUUGCCCCAAAGUCGCAGA
.(((((.(((.........((((.((.....)).))))(((...(((((((((..((((.....))))........((((((.......)).))))))))))))).)))...)))))))) ( -42.40)
>DroYak_CAF1 11738 120 - 1
GUCUGCAGACGUGCGUGGUGGGGAGUACUGGCCUCCCAGGGCCUCGAGGCAUUAAUUGCAUUCUGCAGCAUCGCAUUGCACUUUCAAUUAGUUGCAAAUGCCUUGCCCGAAAGUCGCAGA
.(((((.(((...((.(((((((....((((....))))..))))((((((((..((((.....))))........((((((.......)).)))))))))))))))))...)))))))) ( -43.70)
>consensus
GUCUGCAGACGUCCGUGGUUGGGUGGAUUGGCCUCCCAGGGCCUCAAGGCAUUAAUUGCAUUCUGCAGCAUCGCAUUGCACUUUCAAUUAGUUGCAAAUGCCUUGCCCGAAAGUCGCAGA
.(((((.(((..........(((.((.....)).))).((((...((((((((..((((.....))))........((((((.......)).))))))))))))))))....)))))))) (-40.29 = -40.35 +   0.06)

alignment

secondary structure

dotplot

Window 7

Location	18,082,451 – 18,082,571
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.81
Mean single sequence MFE	-34.88
Consensus MFE	-31.30
Energy contribution	-31.80
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.90
SVM decision value	0.01
SVM RNA-class probability	0.536703
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18082451 120 + 23771897
UGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUUGAGGCCCUGGGAGGCCAAUCCACCCAACCACGGACGUCUGCAGACGAGAAGUUGCAUUCGAAACCGAAAUGCACAGAAAAAACGA
((((.((((....))))((((((((((...(((....)))..((((.((.....)).))))........((((....))))...))))))))))..........))))............ ( -33.50)
>DroSec_CAF1 8717 120 + 1
UGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUUGAGGCCCUGGGAGGCCAAUCCACCCAACCACGGACGUCUGCAGACGAGAAGUUGCAUUCGAAACCGAAAUGCACAGAAAAAACGA
((((.((((....))))((((((((((...(((....)))..((((.((.....)).))))........((((....))))...))))))))))..........))))............ ( -33.50)
>DroEre_CAF1 9460 120 + 1
UGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUUGAGGCCCUGGGAGGCCAAUCCACCCAACCACGUACGUCUGCAGACGAGAAGUUGCAUUCGAAACCGAAAUGCACAGAAAAAACGA
((((.((((((.(((((((.(((.......(((....)))..((((.((.....)).)))).....)))..))))))).......))))))((((....)))).))))............ ( -34.50)
>DroYak_CAF1 11778 120 + 1
UGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUCGAGGCCCUGGGAGGCCAGUACUCCCCACCACGCACGUCUGCAGACGAGAAGUUGCAUUCGAAACCGAAAUGCACACAAAAAACGA
((((.((((((.(((((((.(((.......(((....)))...(((((.......)))))......)))..))))))).......))))))((((....)))).))))............ ( -38.00)
>consensus
UGCAAUGCGAUGCUGCAGAAUGCAAUUAAUGCCUUGAGGCCCUGGGAGGCCAAUCCACCCAACCACGGACGUCUGCAGACGAGAAGUUGCAUUCGAAACCGAAAUGCACAGAAAAAACGA
((((.((((....))))((((((((((...(((....)))..((((.((.....)).))))........((((....))))...))))))))))..........))))............ (-31.30 = -31.80 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:58 2006