Locus 7142

Sequence ID	3R_DroMel_CAF1
Location	18,822,962 – 18,823,104
Length	142
Max. P	0.905840

overview

Window 7

Location	18,822,962 – 18,823,052
Length	90
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	91.10
Mean single sequence MFE	-35.92
Consensus MFE	-26.06
Energy contribution	-26.22
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-2.18
Structure conservation index	0.73
SVM decision value	0.43
SVM RNA-class probability	0.732063
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18822962 90 + 27905053
GUGCUGAAG--------UGCAUAUGUGCAUAUCUGAGCACGCAUUGUGCACUU-------GGCUGUCGGAGCCACUUCGCUUGGCUGGCCAACAAAGCGUUGGCA
..(((.(((--------(((((((((((........)))))...)))))))))-------)))......(((((.......))))).((((((.....)))))). ( -35.20)
>DroSec_CAF1 48203 90 + 1
GUGCUGAAG--------UGCAUAUGCGCAUAUCUGAGCACGCAUUGUGCACUU-------GGCUGUCGGAGCCACUUCGCUUGGCUGGCCAACAAAGCGUUGGCA
..(((.(((--------((((((((((............)))).)))))))))-------)))......(((((.......))))).((((((.....)))))). ( -34.00)
>DroSim_CAF1 51381 90 + 1
GUGCUGAAG--------UGCAUAUGCGCAUAUCUGAGCACGCAUUGUGCACUU-------GGCUGUCGGAGCCACUUCGCUUGGCUGGCCAACAAAGCGUUGGCA
..(((.(((--------((((((((((............)))).)))))))))-------)))......(((((.......))))).((((((.....)))))). ( -34.00)
>DroEre_CAF1 48374 89 + 1
GUGCUG---------UGUGCAUAUGUGCAUAUCUGAGCACGCAUUGUGCACUU-------GGCUGUCGGAGCCACUUCGCUUGGCUGGCCAACAAAGCGUUGGCA
((((((---------((((((....)))))))...)))))((...(((....(-------((((.....)))))...)))...))..((((((.....)))))). ( -34.40)
>DroYak_CAF1 51600 105 + 1
GUGCUGAAGUGCAUAUGUGCAAAUGUGCAUAUCUGAGCACGCAUUGUGCACUUGGCUCUUGGCUGUCGGAGCCACUUCGCUUGGCUGGCCAACAAAGCGUUGGCA
(((((((.((((((((......)))))))).))..)))))((...(((....(((((((........)))))))...)))...))..((((((.....)))))). ( -42.00)
>consensus
GUGCUGAAG________UGCAUAUGUGCAUAUCUGAGCACGCAUUGUGCACUU_______GGCUGUCGGAGCCACUUCGCUUGGCUGGCCAACAAAGCGUUGGCA
..(((((..........((((((((((............)))).))))))..........((((.....)))).......)))))..((((((.....)))))). (-26.06 = -26.22 +   0.16)

alignment

secondary structure

dotplot

Window 8

Location	18,822,962 – 18,823,052
Length	90
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	91.10
Mean single sequence MFE	-31.04
Consensus MFE	-24.58
Energy contribution	-24.34
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-1.94
Structure conservation index	0.79
SVM decision value	1.04
SVM RNA-class probability	0.905840
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18822962 90 - 27905053
UGCCAACGCUUUGUUGGCCAGCCAAGCGAAGUGGCUCCGACAGCC-------AAGUGCACAAUGCGUGCUCAGAUAUGCACAUAUGCA--------CUUCAGCAC
(((....((((((((((....)).))))))))((((.....))))-------(((((((...((((((......))))))....))))--------)))..))). ( -29.30)
>DroSec_CAF1 48203 90 - 1
UGCCAACGCUUUGUUGGCCAGCCAAGCGAAGUGGCUCCGACAGCC-------AAGUGCACAAUGCGUGCUCAGAUAUGCGCAUAUGCA--------CUUCAGCAC
(((....((((((((((....)).))))))))((((.....))))-------(((((((..((((((..........)))))).))))--------)))..))). ( -31.50)
>DroSim_CAF1 51381 90 - 1
UGCCAACGCUUUGUUGGCCAGCCAAGCGAAGUGGCUCCGACAGCC-------AAGUGCACAAUGCGUGCUCAGAUAUGCGCAUAUGCA--------CUUCAGCAC
(((....((((((((((....)).))))))))((((.....))))-------(((((((..((((((..........)))))).))))--------)))..))). ( -31.50)
>DroEre_CAF1 48374 89 - 1
UGCCAACGCUUUGUUGGCCAGCCAAGCGAAGUGGCUCCGACAGCC-------AAGUGCACAAUGCGUGCUCAGAUAUGCACAUAUGCACA---------CAGCAC
.((((((.....)))))).......((....(((((.....))))-------).(((((...((((((......))))))....))))).---------..)).. ( -28.30)
>DroYak_CAF1 51600 105 - 1
UGCCAACGCUUUGUUGGCCAGCCAAGCGAAGUGGCUCCGACAGCCAAGAGCCAAGUGCACAAUGCGUGCUCAGAUAUGCACAUUUGCACAUAUGCACUUCAGCAC
.((((((.....)))))).......((((((((((((..........)))))..(((((.(((..((((........))))))))))))......))))).)).. ( -34.60)
>consensus
UGCCAACGCUUUGUUGGCCAGCCAAGCGAAGUGGCUCCGACAGCC_______AAGUGCACAAUGCGUGCUCAGAUAUGCACAUAUGCA________CUUCAGCAC
.......(((.((((((..(((((.......)))))))))))((............((.....))((((........))))....)).............))).. (-24.58 = -24.34 +  -0.24)

alignment

secondary structure

dotplot

Window 9

Location	18,823,013 – 18,823,104
Length	91
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	78.11
Mean single sequence MFE	-31.92
Consensus MFE	-14.80
Energy contribution	-14.36
Covariance contribution	-0.44
Combinations/Pair	1.25
Mean z-score	-2.10
Structure conservation index	0.46
SVM decision value	0.15
SVM RNA-class probability	0.608712
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18823013 91 - 27905053
-CAGGACGGCAAAAAGGA-------UGCUGAAGACAGAGACAUCCAGU------GGAACA--------GCUCCAUGCCAACGCU-UUGUUGGCCAGCCAAGCGAAGUGGCUCCG
-..(((((((.....(((-------((((........)).))))).((------(((...--------..))))))))..((((-(((((((....)).)))))))))).))). ( -34.00)
>DroSec_CAF1 48254 91 - 1
-CAGGACGGCAAAAUGGA-------UGCUGAAGACAGAGACAUCCAGA------GGAACA--------GCUCCAUGCCAACGCU-UUGUUGGCCAGCCAAGCGAAGUGGCUCCG
-..((((((((...((((-------((((........)).))))))..------(((...--------..))).))))..((((-(((((((....)).)))))))))).))). ( -33.70)
>DroSim_CAF1 51432 91 - 1
-CAGGACGGCAAAAUGGA-------UGCUGAAGACAGAGACAUCCAGA------GGAACA--------GCUCCAUGCCAACGCU-UUGUUGGCCAGCCAAGCGAAGUGGCUCCG
-..((((((((...((((-------((((........)).))))))..------(((...--------..))).))))..((((-(((((((....)).)))))))))).))). ( -33.70)
>DroEre_CAF1 48424 83 - 1
---------CAAAGAGGA-------UGCUGAAGACAGAGACAUCCAGC------GGCACA--------GCUUCAUGCCAACGCU-UUGUUGGCCAGCCAAGCGAAGUGGCUCCG
---------......(((-------((((........)).)))))(((------((((..--------......))))..((((-(((((((....)).))))))))))))... ( -28.30)
>DroYak_CAF1 51666 98 - 1
ACAGGCGGGCAAAAAGGA-------UGCUGAAGACAGAGACAUCCAGAGGCAGAGGCACA--------GCUUCAUGCCAACGCU-UUGUUGGCCAGCCAAGCGAAGUGGCUCCG
.....(((((.....(((-------((((........)).)))))...(((((((((...--------))))).))))..((((-(((((((....)).))))))))))).))) ( -37.80)
>DroPer_CAF1 62832 107 - 1
-CAGAGGACCAAAAAGAGAGAGGGAGAGACAAGAGUAAGACAUUCAAA------UGCACAUAGUUUCCGCACAACGUCAACGCUUUUGUUGGCCAACCAAGCGAAGUUGGUCUG
-....(((((((...(......((...(((((((((..(.(((....)------))).....(((..((.....))..))))))))))))..)).......)....))))))). ( -24.02)
>consensus
_CAGGACGGCAAAAAGGA_______UGCUGAAGACAGAGACAUCCAGA______GGAACA________GCUCCAUGCCAACGCU_UUGUUGGCCAGCCAAGCGAAGUGGCUCCG
...............(((.........(((....))).....))).........((...................(((((((....))))))).(((((.......))))))). (-14.80 = -14.36 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:31 2006