Locus 2934

Sequence ID	3L_DroMel_CAF1
Location	8,393,168 – 8,393,407
Length	239
Max. P	0.914898

overview

Window 3

Location	8,393,168 – 8,393,287
Length	119
Sequences	3
Columns	119
Reading direction	reverse
Mean pairwise identity	91.53
Mean single sequence MFE	-34.97
Consensus MFE	-28.01
Energy contribution	-27.57
Covariance contribution	-0.44
Combinations/Pair	1.10
Mean z-score	-2.15
Structure conservation index	0.80
SVM decision value	0.10
SVM RNA-class probability	0.584670
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8393168 119 - 23771897
GGCAUCCGAUAGGCAGGAGCCUGCCAGCAAUUCGCUGGAGGCCAGGAAAAUGCACCUGCACUGGGAGAAAUCAGCAGAACAUAUGAACAAAAGGAAAUCAGUAAAUCAGAGGUGUAUUU
(((.(((....(((((....)))))(((.....)))))).)))....((((((((((...(((.((....))..)))......(((...........))).........)))))))))) ( -37.70)
>DroSec_CAF1 400 116 - 1
GGCAUCCGAUAGGCAGGAGCCUGCCAGCAAUUCGCUGGAGGCCAGGAAAAUGCAUCUGCACUGGGAGAAAUCAGCAGAACAUAUGAAGAAAAGUUA---GGCGAAUCAGAGGACUUUUU
(((.(((....(((((....)))))(((.....)))))).)))......(((..(((((.....((....)).))))).))).....((((((((.---..(......)..)))))))) ( -35.30)
>DroSim_CAF1 389 116 - 1
GGCAUCCGAUAGGCAGGAGCCUGCCAGCAAUUCGCUGGAGGCCAGGAAAAUGCACCUACACUGGGAGAAAUCAGCGGAACAUAUGAACAAAAGUUA---AGCAAAUCAGAGGACUUUUU
(((.(((....(((((....)))))(((.....)))))).)))...........(((...((((((....)).((..(((............))).---.))...)))))))....... ( -31.90)
>consensus
GGCAUCCGAUAGGCAGGAGCCUGCCAGCAAUUCGCUGGAGGCCAGGAAAAUGCACCUGCACUGGGAGAAAUCAGCAGAACAUAUGAACAAAAGUUA___AGCAAAUCAGAGGACUUUUU
(((.(((....(((((....)))))(((.....)))))).))).......(((.((......))((....)).)))........................................... (-28.01 = -27.57 +  -0.44)

alignment

secondary structure

dotplot

Window 4

Location	8,393,208 – 8,393,327
Length	119
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	97.19
Mean single sequence MFE	-34.93
Consensus MFE	-34.49
Energy contribution	-34.27
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.77
Structure conservation index	0.99
SVM decision value	0.67
SVM RNA-class probability	0.817370
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8393208 119 + 23771897
UUCUGCUGAUUUCUCCCAGUGCAGGUGCAUUUUCCUGGCCUCCAGCGAAUUGCUGGCAGGCUCCUGCCUAUCGGAUGCCAUCAAUUGCAAAAAAAAAAGGCGAGAGAAAUAAUAAAAGC
.........(((((((((((((....)))))....((((.((((((.....)))(((((....)))))....))).))))..................)).))))))............ ( -35.00)
>DroSec_CAF1 437 118 + 1
UUCUGCUGAUUUCUCCCAGUGCAGAUGCAUUUUCCUGGCCUCCAGCGAAUUGCUGGCAGGCUCCUGCCUAUCGGAUGCCAUCAAUUGCAAAAA-AAAAGGCGAGAGAAAUAAUAAAAGC
.........(((((((((((((....)))))....((((.((((((.....)))(((((....)))))....))).)))).............-....)).))))))............ ( -35.00)
>DroSim_CAF1 426 117 + 1
UUCCGCUGAUUUCUCCCAGUGUAGGUGCAUUUUCCUGGCCUCCAGCGAAUUGCUGGCAGGCUCCUGCCUAUCGGAUGCCAUCAAUUGCAAAA--AAAAGGCGAGAGAAAUAAUAAAAGC
.........((((((((..(.....((((......((((.((((((.....)))(((((....)))))....))).)))).....))))...--.)..)).))))))............ ( -34.80)
>consensus
UUCUGCUGAUUUCUCCCAGUGCAGGUGCAUUUUCCUGGCCUCCAGCGAAUUGCUGGCAGGCUCCUGCCUAUCGGAUGCCAUCAAUUGCAAAAA_AAAAGGCGAGAGAAAUAAUAAAAGC
.........(((((((((((((....)))))....((((.((((((.....)))(((((....)))))....))).))))..................)).))))))............ (-34.49 = -34.27 +  -0.22)

alignment

secondary structure

dotplot

Window 5

Location	8,393,208 – 8,393,327
Length	119
Sequences	3
Columns	119
Reading direction	reverse
Mean pairwise identity	97.19
Mean single sequence MFE	-38.48
Consensus MFE	-37.40
Energy contribution	-37.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.97
SVM decision value	1.10
SVM RNA-class probability	0.914898
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8393208 119 - 23771897
GCUUUUAUUAUUUCUCUCGCCUUUUUUUUUUGCAAUUGAUGGCAUCCGAUAGGCAGGAGCCUGCCAGCAAUUCGCUGGAGGCCAGGAAAAUGCACCUGCACUGGGAGAAAUCAGCAGAA
(((......((((((((((((...................))).......(((((((.((((.(((((.....)))))))))((......))..))))).))))))))))).))).... ( -38.71)
>DroSec_CAF1 437 118 - 1
GCUUUUAUUAUUUCUCUCGCCUUUU-UUUUUGCAAUUGAUGGCAUCCGAUAGGCAGGAGCCUGCCAGCAAUUCGCUGGAGGCCAGGAAAAUGCAUCUGCACUGGGAGAAAUCAGCAGAA
(((......((((((((((......-....((((.((..((((.(((....(((((....)))))(((.....)))))).))))...)).)))).......)))))))))).))).... ( -38.43)
>DroSim_CAF1 426 117 - 1
GCUUUUAUUAUUUCUCUCGCCUUUU--UUUUGCAAUUGAUGGCAUCCGAUAGGCAGGAGCCUGCCAGCAAUUCGCUGGAGGCCAGGAAAAUGCACCUACACUGGGAGAAAUCAGCGGAA
(((......((((((((((......--...((((.((..((((.(((....(((((....)))))(((.....)))))).))))...)).)))).......)))))))))).))).... ( -38.29)
>consensus
GCUUUUAUUAUUUCUCUCGCCUUUU_UUUUUGCAAUUGAUGGCAUCCGAUAGGCAGGAGCCUGCCAGCAAUUCGCUGGAGGCCAGGAAAAUGCACCUGCACUGGGAGAAAUCAGCAGAA
(((......((((((((((...........((((.((..((((.(((....(((((....)))))(((.....)))))).))))...)).)))).......)))))))))).))).... (-37.40 = -37.40 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	8,393,247 – 8,393,367
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-25.91
Consensus MFE	-25.91
Energy contribution	-25.91
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.38
Structure conservation index	1.00
SVM decision value	0.06
SVM RNA-class probability	0.562230
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8393247 120 + 23771897
CUCCAGCGAAUUGCUGGCAGGCUCCUGCCUAUCGGAUGCCAUCAAUUGCAAAAAAAAAAGGCGAGAGAAAUAAUAAAAGCAGCCACCGUAUAAUUUUCAAAAGUGGAAAAAUCCAGCAAC
..(((((.....)))))..((((((........))).))).....((((..........(((...................)))...................((((....)))))))). ( -25.91)
>DroSec_CAF1 476 119 + 1
CUCCAGCGAAUUGCUGGCAGGCUCCUGCCUAUCGGAUGCCAUCAAUUGCAAAAA-AAAAGGCGAGAGAAAUAAUAAAAGCAGCCACCGUAUAAUUUUCAAAAGUGGAAAAAUCCAGCAAC
..(((((.....)))))..((((((........))).))).....((((.....-....(((...................)))...................((((....)))))))). ( -25.91)
>DroSim_CAF1 465 118 + 1
CUCCAGCGAAUUGCUGGCAGGCUCCUGCCUAUCGGAUGCCAUCAAUUGCAAAA--AAAAGGCGAGAGAAAUAAUAAAAGCAGCCACCGUAUAAUUUUCAAAAGUGGAAAAAUCCAGCAAC
..(((((.....)))))..((((((........))).))).....((((....--....(((...................)))...................((((....)))))))). ( -25.91)
>consensus
CUCCAGCGAAUUGCUGGCAGGCUCCUGCCUAUCGGAUGCCAUCAAUUGCAAAAA_AAAAGGCGAGAGAAAUAAUAAAAGCAGCCACCGUAUAAUUUUCAAAAGUGGAAAAAUCCAGCAAC
..(((((.....)))))..((((((........))).))).....((((..........(((...................)))...................((((....)))))))). (-25.91 = -25.91 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	8,393,287 – 8,393,407
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-25.18
Consensus MFE	-24.84
Energy contribution	-24.84
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.99
SVM decision value	0.62
SVM RNA-class probability	0.802041
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8393287 120 + 23771897
AUCAAUUGCAAAAAAAAAAGGCGAGAGAAAUAAUAAAAGCAGCCACCGUAUAAUUUUCAAAAGUGGAAAAAUCCAGCAACCAACGCACUGCACUGCUGGGCAGGGACUUUUGCAUGAUAU
((((..(((((((......(((...................))).((......((((((....))))))..(((((((..((......))...)))))))..))...))))))))))).. ( -25.11)
>DroSec_CAF1 516 119 + 1
AUCAAUUGCAAAAA-AAAAGGCGAGAGAAAUAAUAAAAGCAGCCACCGUAUAAUUUUCAAAAGUGGAAAAAUCCAGCAACCAACGCACUGCACUGCUGGGCAGGGACUUUUGCAUGAUAU
((((..(((((((.-....(((...................))).((......((((((....))))))..(((((((..((......))...)))))))..))...))))))))))).. ( -25.11)
>DroSim_CAF1 505 118 + 1
AUCAAUUGCAAAA--AAAAGGCGAGAGAAAUAAUAAAAGCAGCCACCGUAUAAUUUUCAAAAGUGGAAAAAUCCAGCAACCAAUGCACUGCACUGCUGGGCAGGGACUUUUGCAUGAUAU
((((..(((((((--....(((...................))).((......((((((....))))))..(((((((.....(((...))).)))))))..))...))))))))))).. ( -25.31)
>consensus
AUCAAUUGCAAAAA_AAAAGGCGAGAGAAAUAAUAAAAGCAGCCACCGUAUAAUUUUCAAAAGUGGAAAAAUCCAGCAACCAACGCACUGCACUGCUGGGCAGGGACUUUUGCAUGAUAU
((((..(((((((......(((...................))).((......((((((....))))))..(((((((..((......))...)))))))..))...))))))))))).. (-24.84 = -24.84 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:31 2006