Locus 905

Sequence ID	2R_DroMel_CAF1
Location	4,050,328 – 4,050,528
Length	200
Max. P	0.997228

overview

Window 8

Location	4,050,328 – 4,050,448
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.21
Mean single sequence MFE	-45.98
Consensus MFE	-39.16
Energy contribution	-39.72
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.71
Structure conservation index	0.85
SVM decision value	2.82
SVM RNA-class probability	0.997228
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4050328 120 - 20766785
AAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGUGGUGACGGGGGACGUAACACGCCCCGUGAAUGCCUGAGUGGGUGCCGACAACAAGUUGCAGAGCUGCUCAUUAAAGGCUU
.((((((((..((((((...((((((((((....(((.((..(.((((((..((.....)))))))).)..)).))).)))))).)))).....))))))....))))))))........ ( -43.90)
>DroSec_CAF1 32849 118 - 1
AAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGUGGUGACGGGGGACGUAACACGCCCCGUGAAUGCCUGAGUGGGUGCCGACAACAAGUUGCA--GCUGCUCAUUAAAGGCUU
.((((((((..((((((...((((((((((....(((.((..(.((((((..((.....)))))))).)..)).))).)))))).)))).....))))))--..))))))))........ ( -45.80)
>DroSim_CAF1 37749 118 - 1
AAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGUGGUGACGGGGGACGUAACACGCCCCGUGAAUGCCUGAGUGGGUGCCGACAACAAGUUGCA--GCUGCUCAUUAAAGGCUU
.((((((((..((((((...((((((((((....(((.((..(.((((((..((.....)))))))).)..)).))).)))))).)))).....))))))--..))))))))........ ( -45.80)
>DroEre_CAF1 32292 117 - 1
AAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGUGGUGACGGG-GGCGAAACACGCUCCCUGAAUGCCUGAGUGGUUGCCGACAACAAGUUGCA--GCUGCUCAUUAAAGGCUC
.((((((((..((((((...((((..((.(.((((((...(((..((((-((((.....))).)))))...)))....))))))).))))))..))))))--..))))))))........ ( -46.70)
>DroYak_CAF1 36205 118 - 1
AAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGUGGUGACGGGGGGCGGAACACGCUCCGUGAAUGCCUGAGUGGUUGCCGACAACAAGUUGCA--GCUGCUCAUUAAAGGCUU
.((((((((..((((((...((((..((.(.((((((...(((..((.((((((.....)))))).))...)))....))))))).))))))..))))))--..))))))))........ ( -47.70)
>consensus
AAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGUGGUGACGGGGGACGUAACACGCCCCGUGAAUGCCUGAGUGGGUGCCGACAACAAGUUGCA__GCUGCUCAUUAAAGGCUU
.((((((((..((((((...((((((((((....(((.((..(.((((((..((.....)))))))).)..)).))).)))))).)))).....))))))....))))))))........ (-39.16 = -39.72 +   0.56)

alignment

secondary structure

dotplot

Window 9

Location	4,050,408 – 4,050,528
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.83
Mean single sequence MFE	-42.79
Consensus MFE	-40.30
Energy contribution	-41.34
Covariance contribution	1.04
Combinations/Pair	1.02
Mean z-score	-1.82
Structure conservation index	0.94
SVM decision value	2.15
SVM RNA-class probability	0.989089
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4050408 120 + 20766785
ACUUGAUUGUCAGAUGCAACCGCGCUGCAUUCGCUCAUUUCGCAUUCCGCAGUGUUUGUUUGCAUAAACUUGAGCGACAGGCGGGCGGAUUGGGUGGAUGGUUUUGAAUGACAGCGCAGA
....(.((((.....)))).)((((((((((((.(((((((.((.(((((..((((((((.((..........)))))))))).))))).)).).))))))...)))))).))))))... ( -42.60)
>DroSec_CAF1 32927 120 + 1
ACUUGAUUGUCAGAUGCAACCGCGCUGCAUUCGCUCAUUUCGCAUUCCGCAGUGUUUGUUUGCAUAAACUUGAGCGACAGGCGGGCGGAUUGGGUGGAUGGUUUUGAAUGACAGCGCGGA
......((((.....))))((((((((((((((.(((((((.((.(((((..((((((((.((..........)))))))))).))))).)).).))))))...)))))).)))))))). ( -47.60)
>DroSim_CAF1 37827 120 + 1
ACUUGAUUGUCAGAUGCAACCGCGCUGCAUUCGCUCAUUUCGCAUUCCGCAGUGUUUGUUUGCAUAAACUUGAGCGACAGGCGGGCGGAUUGGGUGGAUGGUUUUGAAUGACAGCGCAGA
....(.((((.....)))).)((((((((((((.(((((((.((.(((((..((((((((.((..........)))))))))).))))).)).).))))))...)))))).))))))... ( -42.60)
>DroEre_CAF1 32369 120 + 1
ACUUGAUUGUCAGAUGCAACCGCGCUGCAUUCGCUCAUUUCGCAUUCCACAGUGUUUGUUUGCAUAAACUUGAGCGACAGGCGGACGGAUUGGGUGGAUGGUUUUGAAUGACAGCGCGCA
......((((.....)))).((((((((((((((.......))..(((((...((((((((((.................))))))))))...))))).......))))).))))))).. ( -37.93)
>DroYak_CAF1 36283 120 + 1
ACUUGAUUGUCAGAUGCAACCGCGCUGCAUUCGCUCAUUUCGCAUUCCGCAGUGUUUGUUUGCAUAAACUUGAGCGACAGGCGGGCGGAUUGGGUAGAUGGUUUUGAAUGACAGCACGGA
......((((.....))))(((.((((((((((.(((((((.((.(((((..((((((((.((..........)))))))))).))))).)).).))))))...)))))).)))).))). ( -43.20)
>consensus
ACUUGAUUGUCAGAUGCAACCGCGCUGCAUUCGCUCAUUUCGCAUUCCGCAGUGUUUGUUUGCAUAAACUUGAGCGACAGGCGGGCGGAUUGGGUGGAUGGUUUUGAAUGACAGCGCGGA
......((((.....))))((((((((((((((.(((((((.((.(((((..((((((((.((..........)))))))))).))))).)).).))))))...)))))).)))))))). (-40.30 = -41.34 +   1.04)

alignment

secondary structure

dotplot

Window 0

Location	4,050,408 – 4,050,528
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-32.58
Consensus MFE	-31.74
Energy contribution	-31.26
Covariance contribution	-0.48
Combinations/Pair	1.10
Mean z-score	-1.38
Structure conservation index	0.97
SVM decision value	1.01
SVM RNA-class probability	0.899276
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4050408 120 - 20766785
UCUGCGCUGUCAUUCAAAACCAUCCACCCAAUCCGCCCGCCUGUCGCUCAAGUUUAUGCAAACAAACACUGCGGAAUGCGAAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGU
...((((((.(((((................(((((..((.....))....((((....)))).......)))))..((.......)))))))))))))((((((....).))))).... ( -32.80)
>DroSec_CAF1 32927 120 - 1
UCCGCGCUGUCAUUCAAAACCAUCCACCCAAUCCGCCCGCCUGUCGCUCAAGUUUAUGCAAACAAACACUGCGGAAUGCGAAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGU
.((((((((.(((((................(((((..((.....))....((((....)))).......)))))..((.......)))))))))))))))................... ( -33.80)
>DroSim_CAF1 37827 120 - 1
UCUGCGCUGUCAUUCAAAACCAUCCACCCAAUCCGCCCGCCUGUCGCUCAAGUUUAUGCAAACAAACACUGCGGAAUGCGAAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGU
...((((((.(((((................(((((..((.....))....((((....)))).......)))))..((.......)))))))))))))((((((....).))))).... ( -32.80)
>DroEre_CAF1 32369 120 - 1
UGCGCGCUGUCAUUCAAAACCAUCCACCCAAUCCGUCCGCCUGUCGCUCAAGUUUAUGCAAACAAACACUGUGGAAUGCGAAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGU
...((((((.(((((.......(((((...........((.....))....((((....)))).......)))))..((.......)))))))))))))((((((....).))))).... ( -31.60)
>DroYak_CAF1 36283 120 - 1
UCCGUGCUGUCAUUCAAAACCAUCUACCCAAUCCGCCCGCCUGUCGCUCAAGUUUAUGCAAACAAACACUGCGGAAUGCGAAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGU
.((((((((.(((((................(((((..((.....))....((((....)))).......)))))..((.......)))))))))))))))................... ( -31.90)
>consensus
UCCGCGCUGUCAUUCAAAACCAUCCACCCAAUCCGCCCGCCUGUCGCUCAAGUUUAUGCAAACAAACACUGCGGAAUGCGAAAUGAGCGAAUGCAGCGCGGUUGCAUCUGACAAUCAAGU
...((((((.(((((................(((((..((.....))....((((....)))).......)))))..((.......)))))))))))))((((((....).))))).... (-31.74 = -31.26 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:50 2006