Locus 4042

Sequence ID	3R_DroMel_CAF1
Location	11,034,979 – 11,035,120
Length	141
Max. P	0.985800

overview

Window 1

Location	11,034,979 – 11,035,081
Length	102
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	77.56
Mean single sequence MFE	-32.97
Consensus MFE	-21.08
Energy contribution	-20.92
Covariance contribution	-0.17
Combinations/Pair	1.24
Mean z-score	-2.72
Structure conservation index	0.64
SVM decision value	2.02
SVM RNA-class probability	0.985800
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11034979 102 + 27905053
---AUUA-CGCGA-UAAACAAACCGAA------UUUGGCACC-CGCUCACCGAA---AUGAGUGCAUCGACGAGCACGUCGACGGCGGCGUCCCAGGACGCCUGCUACAUAUCGCUC
---....-.((((-((......(((..------.........-((((((.....---.))))))..((((((....))))))))).((((((....)))))).......)))))).. ( -37.70)
>DroPse_CAF1 8503 100 + 1
AAAAUUG-GGCGA-UAAACAAACCGAA------UUUGUUAGC-AAAUUA--GAAACUAUGAGUACA---ACGAACACC---GCGGCAGCGUCCCAGGACGCCUGCUACAUAUCGCUG
.......-(((((-((.........((------((((....)-))))).--...............---.........---(..((((((((....)))).))))..).))))))). ( -27.50)
>DroGri_CAF1 10319 102 + 1
---AUUA-CGCGA-UAAACAAAACGAAGCCGAUUUUG-UGGCAAAUUAAACGCA---AUGAGUGUG---GCAAACACC---ACAGCAGCAUCCCAGGAUGCCUGCUACAUAUCGCUA
---....-.((((-((.......((....))....((-(((((........((.---.((.((((.---....)))))---)..)).(((((....))))).))))))))))))).. ( -31.80)
>DroSec_CAF1 10241 102 + 1
---AUUA-CGCGA-UAAACAAACCGAA------UUUGGCACC-CGCUCACCGAA---AUGAGUGCAUCGACGAGCACGUCGACGGCGGCGUCCCAGGACGCCUGCUACAUAUCGCUC
---....-.((((-((......(((..------.........-((((((.....---.))))))..((((((....))))))))).((((((....)))))).......)))))).. ( -37.70)
>DroSim_CAF1 10921 101 + 1
---AUUA-CGCGA-UAAACAAACCGAA------UUU-GCACC-CGCUCACCGAA---AUGAGUGCAUCGACGAGCACGUCGACGGCGGCGUCCCAGGACGCCUGCUACAUAUCGCUC
---....-.((((-((......(((..------...-.....-((((((.....---.))))))..((((((....))))))))).((((((....)))))).......)))))).. ( -37.70)
>DroPer_CAF1 9123 102 + 1
AAAAUUGGGGCGAUUAAACAAACCGAA------UUUGUUAGC-AAGUUA--GAAACUAUGAGUACA---ACGAACACC---GCGGCAGCGUCCCAGGACGCCUGCUACAUAUCGCUG
........((((((...........((------((((....)-))))).--...............---.........---(..((((((((....)))).))))..)..)))))). ( -25.40)
>consensus
___AUUA_CGCGA_UAAACAAACCGAA______UUUGGCACC_AACUCACCGAA___AUGAGUGCA___ACGAACACC___ACGGCAGCGUCCCAGGACGCCUGCUACAUAUCGCUC
.........((((................................................((((........))))......(((((((((....)))).))))).....)))).. (-21.08 = -20.92 +  -0.17)

alignment

secondary structure

dotplot

Window 2

Location	11,034,979 – 11,035,081
Length	102
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	77.56
Mean single sequence MFE	-35.55
Consensus MFE	-23.17
Energy contribution	-21.73
Covariance contribution	-1.44
Combinations/Pair	1.33
Mean z-score	-1.79
Structure conservation index	0.65
SVM decision value	1.01
SVM RNA-class probability	0.900546
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11034979 102 - 27905053
GAGCGAUAUGUAGCAGGCGUCCUGGGACGCCGCCGUCGACGUGCUCGUCGAUGCACUCAU---UUCGGUGAGCG-GGUGCCAAA------UUCGGUUUGUUUA-UCGCG-UAAU---
..((((((...((((((((((....))))))((((((((((....)))))))((((((.(---((....))).)-)))))....------...))).))))))-)))).-....--- ( -42.30)
>DroPse_CAF1 8503 100 - 1
CAGCGAUAUGUAGCAGGCGUCCUGGGACGCUGCCGC---GGUGUUCGU---UGUACUCAUAGUUUC--UAAUUU-GCUAACAAA------UUCGGUUUGUUUA-UCGCC-CAAUUUU
..((((((..(((((((((((....))))))((.((---(.....)))---.))............--.....)-))))(((((------(...)))))).))-)))).-....... ( -26.40)
>DroGri_CAF1 10319 102 - 1
UAGCGAUAUGUAGCAGGCAUCCUGGGAUGCUGCUGU---GGUGUUUGC---CACACUCAU---UGCGUUUAAUUUGCCA-CAAAAUCGGCUUCGUUUUGUUUA-UCGCG-UAAU---
..((((((...(((((.((((....)))))))))((---(((....))---)))...((.---.(((........(((.-.......)))..)))..))..))-)))).-....--- ( -32.70)
>DroSec_CAF1 10241 102 - 1
GAGCGAUAUGUAGCAGGCGUCCUGGGACGCCGCCGUCGACGUGCUCGUCGAUGCACUCAU---UUCGGUGAGCG-GGUGCCAAA------UUCGGUUUGUUUA-UCGCG-UAAU---
..((((((...((((((((((....))))))((((((((((....)))))))((((((.(---((....))).)-)))))....------...))).))))))-)))).-....--- ( -42.30)
>DroSim_CAF1 10921 101 - 1
GAGCGAUAUGUAGCAGGCGUCCUGGGACGCCGCCGUCGACGUGCUCGUCGAUGCACUCAU---UUCGGUGAGCG-GGUGC-AAA------UUCGGUUUGUUUA-UCGCG-UAAU---
..((((((...((((((((((....))))))((((((((((....))))))(((((((.(---((....))).)-)))))-)..------..)))).))))))-)))).-....--- ( -43.70)
>DroPer_CAF1 9123 102 - 1
CAGCGAUAUGUAGCAGGCGUCCUGGGACGCUGCCGC---GGUGUUCGU---UGUACUCAUAGUUUC--UAACUU-GCUAACAAA------UUCGGUUUGUUUAAUCGCCCCAAUUUU
((((((..((..((((.((((....))))))))..)---)....))))---))......((((...--......-)))).....------...((..((......))..))...... ( -25.90)
>consensus
GAGCGAUAUGUAGCAGGCGUCCUGGGACGCCGCCGU___CGUGCUCGU___UGCACUCAU___UUCGGUGAGCG_GCUACCAAA______UUCGGUUUGUUUA_UCGCG_UAAU___
..((((.....((((((((((....))))))((((.....((((........))))...............((.....))............)))).))))...))))......... (-23.17 = -21.73 +  -1.44)

alignment

secondary structure

dotplot

Window 3

Location	11,035,005 – 11,035,120
Length	115
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	74.14
Mean single sequence MFE	-44.40
Consensus MFE	-26.73
Energy contribution	-26.18
Covariance contribution	-0.55
Combinations/Pair	1.42
Mean z-score	-1.64
Structure conservation index	0.60
SVM decision value	0.88
SVM RNA-class probability	0.873378
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11035005 115 - 27905053
CGGCGGCUGCGAGGUGCGGAAGUACUCCGCCAGGCCAAGGAGCGAUAUGUAGCAGGCGUCCUGGGACGCCGCCGUCGACGUGCUCGUCGAUGCACUCAU---UUCGGUGAGCG-GGUGC
.((((((((((..((((....))))..)))..)))).....((........)).((((((....)))))))))(((((((....)))))))((((((.(---((....))).)-))))) ( -56.80)
>DroVir_CAF1 7861 106 - 1
UGGCGGCUGUGAGGUACGGAAGUAUUCGGCGAGUCCGAGCAGCGAUAUAUAGCAGGCAUCCUGUGAUGCUGCUGU---GGUAUUAAC---UCCACUCAU---UGCGUUUAAUU-GC---
(((.((((((...((((....))))((((.....)))))))))((((((((((((.((((....)))))))))))---.)))))..)---.))).....---.(((......)-))--- ( -34.10)
>DroPse_CAF1 8532 110 - 1
UGGCGGCUGGGAGGUUCGAAAGUAUUCGGCCAGGCCGAGCAGCGAUAUGUAGCAGGCGUCCUGGGACGCUGCCGC---GGUGUUCGU---UGUACUCAUAGUUUC--UAAUUU-GCUAA
((((((((.((.((..(....)...))..)).))))(((((((((..((..((((.((((....))))))))..)---)....))))---))..)))........--......-)))). ( -41.90)
>DroGri_CAF1 10351 109 - 1
UGGCGGCUGGGAGGUACGAAAGUAUUCGGCAAGUCCGAGUAGCGAUAUGUAGCAGGCAUCCUGGGAUGCUGCUGU---GGUGUUUGC---CACACUCAU---UGCGUUUAAUUUGCCA-
.(((((((.((((((((....))))).......))).))).(((((..(((((((.((((....)))))))))((---(((....))---)))))..))---)))........)))).- ( -42.51)
>DroAna_CAF1 8119 107 - 1
CGGCGGCUGCGAUGUGCGGAAGUACUCCGCCAGACCGAGCAGCGAUAUGUAGCAGGCGUCUUGCGAGGCCGCUGCCGUCGUGCUCGUCGAUGCGCUCAUAU-UUCA-----------CC
(((((((((((..((((....))))..)).))).))(((((.((((..(((((.(((.((....)).)))))))).)))))))))))))............-....-----------.. ( -48.10)
>DroPer_CAF1 9154 110 - 1
UGGCGGCUGGGAGGUUCGAAAGUAUUCGGCCAGGCCGAGCAGCGAUAUGUAGCAGGCGUCCUGGGACGCUGCCGC---GGUGUUCGU---UGUACUCAUAGUUUC--UAACUU-GCUAA
.......(((.(((((.((((.((((((((...)))))(((((((..((..((((.((((....))))))))..)---)....))))---)))....))).))))--.)))))-.))). ( -43.00)
>consensus
UGGCGGCUGGGAGGUACGAAAGUAUUCGGCCAGGCCGAGCAGCGAUAUGUAGCAGGCGUCCUGGGACGCUGCCGC___GGUGUUCGU___UGCACUCAU___UUCG_UAAAUU_GCUA_
((((.((((....((((....))))((((.....)))).))))...........((((((....)))))))))).....((((........))))........................ (-26.73 = -26.18 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:33 2006