Locus 7577

Sequence ID	X_DroMel_CAF1
Location	18,849,383 – 18,849,527
Length	144
Max. P	0.912635

overview

Window 5

Location	18,849,383 – 18,849,474
Length	91
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	77.47
Mean single sequence MFE	-28.52
Consensus MFE	-17.61
Energy contribution	-17.58
Covariance contribution	-0.03
Combinations/Pair	1.32
Mean z-score	-1.94
Structure conservation index	0.62
SVM decision value	1.08
SVM RNA-class probability	0.912635
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18849383 91 + 22224390
UUGUUGUUCC-----GCUGUUGCUGUUGUCCG-CGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCA
..........-----...((((((..(..(((-(((.((((.......))))....)))).((((((.........))))))))..)...)))))). ( -25.90)
>DroVir_CAF1 3838 86 + 1
UUGUU----------GUUGCUGUUGUUGUGCG-UGUGUUGAUUUAUAGUCGCAAUUGGGCUGAGGCGCAACUAAUUUGCCUCGAGUGCUAAGUAGCA
....(----------((((((...((((((..-((((......))))..)))))).(.(((((((((.........)))))).))).)..))))))) ( -23.30)
>DroPse_CAF1 118640 87 + 1
--------UC--UGUGCUGCGUUUGUUGUCCGAUGCGUUGAUUUAUAUUCGAAGCUGCGCUGAGGCGCAGCUAAUUUGCCUCGGGUGUUAAGUAGCA
--------..--..((((((......(..((((.(((((((.......))))((((((((....))))))))....))).))))..)....)))))) ( -34.50)
>DroEre_CAF1 83463 71 + 1
-------------------------UUGUCCG-CGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCA
-------------------------.....((-(((.((((.......)))).)).)))((((((((.........))))))))............. ( -19.50)
>DroAna_CAF1 4346 96 + 1
UUGCUGCCACACGAGGCUGUUGCCGCUGUCCG-CGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCA
.(((((((((.((((((.(((((.(((.((.(-(((.((((.......))))....)))).))))))))))......)))))).)))....)))))) ( -37.90)
>DroPer_CAF1 124703 87 + 1
--------UC--UGUGGUGCGUUUGUUGUCCGAUGCGUUGAUUUAUAUUCGAAGCUGCGCUGAGGCGCAGCUAAUUUGCCUCGGGUGUUAAGUAGCA
--------..--..((.(((......(..((((.(((((((.......))))((((((((....))))))))....))).))))..)....))).)) ( -30.00)
>consensus
_________C_____GCUGCUGUUGUUGUCCG_CGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCA
...............(((((..............((.((((.......)))).)).(((((((((((.........)))))).)))))...))))). (-17.61 = -17.58 +  -0.03)

alignment

secondary structure

dotplot

Window 6

Location	18,849,383 – 18,849,474
Length	91
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	77.47
Mean single sequence MFE	-20.93
Consensus MFE	-11.77
Energy contribution	-11.35
Covariance contribution	-0.42
Combinations/Pair	1.23
Mean z-score	-1.80
Structure conservation index	0.56
SVM decision value	0.46
SVM RNA-class probability	0.743421
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18849383 91 - 22224390
UGCUACUUAACACCCGAGGCAAAUUAGUUGCGCCUCGGCGCAGUUUCGAAUAUAAAUCAACACG-CGGACAACAGCAACAGC-----GGAACAACAA
((((.........(((((((...........)))))))(((.((...((.......))...)))-))......)))).....-----.......... ( -18.50)
>DroVir_CAF1 3838 86 - 1
UGCUACUUAGCACUCGAGGCAAAUUAGUUGCGCCUCAGCCCAAUUGCGACUAUAAAUCAACACA-CGCACAACAACAGCAAC----------AACAA
((((...........(((((...........)))))........((((................-)))).......))))..----------..... ( -14.09)
>DroPse_CAF1 118640 87 - 1
UGCUACUUAACACCCGAGGCAAAUUAGCUGCGCCUCAGCGCAGCUUCGAAUAUAAAUCAACGCAUCGGACAACAAACGCAGCACA--GA--------
((((.........((((.((.....((((((((....))))))))..((.......))...)).))))...........))))..--..-------- ( -23.35)
>DroEre_CAF1 83463 71 - 1
UGCUACUUAACACCCGAGGCAAAUUAGUUGCGCCUCGGCGCAGUUUCGAAUAUAAAUCAACACG-CGGACAA-------------------------
.............(((((((...........)))))))(((.((...((.......))...)))-)).....------------------------- ( -14.70)
>DroAna_CAF1 4346 96 - 1
UGCUACUUAACACCCGAGGCAAAUUAGUUGCGCCUCGGCGCAGUUUCGAAUAUAAAUCAACACG-CGGACAGCGGCAACAGCCUCGUGUGGCAGCAA
((((......(((.((((((.......((((((....))))))...................((-(.....)))......)))))).)))..)))). ( -32.40)
>DroPer_CAF1 124703 87 - 1
UGCUACUUAACACCCGAGGCAAAUUAGCUGCGCCUCAGCGCAGCUUCGAAUAUAAAUCAACGCAUCGGACAACAAACGCACCACA--GA--------
(((..........((((.((.....((((((((....))))))))..((.......))...)).)))).........))).....--..-------- ( -22.51)
>consensus
UGCUACUUAACACCCGAGGCAAAUUAGUUGCGCCUCAGCGCAGUUUCGAAUAUAAAUCAACACA_CGGACAACAACAGCAGC_____G_________
((((.(.........).))))....((((((((....)))))))).................................................... (-11.77 = -11.35 +  -0.42)

alignment

secondary structure

dotplot

Window 7

Location	18,849,402 – 18,849,492
Length	90
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	88.11
Mean single sequence MFE	-27.03
Consensus MFE	-23.75
Energy contribution	-23.00
Covariance contribution	-0.75
Combinations/Pair	1.21
Mean z-score	-1.69
Structure conservation index	0.88
SVM decision value	0.58
SVM RNA-class probability	0.787365
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18849402 90 + 22224390
G----UUGUCCGCGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAAUAAACGCAACG
(----((((.(((((((((....((((((((...(((((....))))).(......)..))))))))....)))))))))........))))). ( -27.20)
>DroVir_CAF1 3852 82 + 1
G----UUGUGCGUGUGUUGAUUUAUAGUCGCAAUUGGGCUGAGGCGCAACUAAUUUGCCUCGAGUGCUAAGUAGCAUGCGAAACA--------G
(----((.(((((((....(((((((.((((......)).((((((.........)))))))).)).))))).))))))).))).--------. ( -24.80)
>DroSec_CAF1 85971 90 + 1
G----UUGUCCGCGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAAUAAACGCAACG
(----((((.(((((((((....((((((((...(((((....))))).(......)..))))))))....)))))))))........))))). ( -27.20)
>DroEre_CAF1 83463 89 + 1
-----UUGUCCGCGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGCGAAAUAAACGCAACG
-----.....(((((((((....((((((((...(((((....))))).(......)..))))))))....))))))))).............. ( -27.20)
>DroYak_CAF1 83757 94 + 1
GUUGGUUGUCCGCGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAAUAAACGCAACG
(((((((...(((((((((....((((((((...(((((....))))).(......)..))))))))....))))))))).....))).)))). ( -30.50)
>DroAna_CAF1 4370 80 + 1
G----CUGUCCGCGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAAU----------
.----.....(((((((((....((((((((...(((((....))))).(......)..))))))))....)))))))))....---------- ( -25.30)
>consensus
G____UUGUCCGCGUGUUGAUUUAUAUUCGAAACUGCGCCGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAAUAAACGCAACG
..........((((((((((.......))...((((((((((((((.........)))))).)))))..))))))))))).............. (-23.75 = -23.00 +  -0.75)

alignment

secondary structure

dotplot

Window 8

Location	18,849,437 – 18,849,527
Length	90
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	72.71
Mean single sequence MFE	-22.52
Consensus MFE	-14.98
Energy contribution	-14.48
Covariance contribution	-0.50
Combinations/Pair	1.20
Mean z-score	-0.98
Structure conservation index	0.67
SVM decision value	0.02
SVM RNA-class probability	0.541370
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18849437 90 + 22224390
CGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAAUAAACGC----AACG-------GGA---GAAAGCCAAACAC--UCAGGAGUGUAGAGAUGGG
...(((((((.....))))((((.(((((....)))))(((.......)))----..))-------)).---....)))..((((--(....)))))......... ( -20.20)
>DroVir_CAF1 3887 78 + 1
UGAGGCGCAACUAAUUUGCCUCGAGUGCUAAGUAGCAUGCGAAACA------------G-------GGAGACGACAGCCAAAAGC--AUGUGAGUGCAG-------
.((((((.........))))))..(..((.....((((((......------------.-------(....)(.....)....))--)))).))..)..------- ( -21.70)
>DroSec_CAF1 86006 88 + 1
CGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAAUAAACGC----AACG-------GGA---GAAAGCCAAACAC--UCAGGAGUGCGGUG--GGG
.((((((.........))))))(((((((........((((.......)))----)...-------((.---.....)).)))))--))............--... ( -20.00)
>DroEre_CAF1 83497 80 + 1
CGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGCGAAAUAAACGC----AACG-------GGA---GAAAGCCAAACAC--UGGAGAGUG----------
(((((((.........)))))))((((((........((((.......)))----)...-------((.---.....)).)))))--)........---------- ( -20.70)
>DroYak_CAF1 83796 82 + 1
CGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAAUAAACGC----AACG-------GGA---GAAAGCCAAACACAUGGGAGAGUG----------
(((((((.........))))))).(((((........((((.......)))----)...-------((.---.....)).)))))...........---------- ( -17.80)
>DroPer_CAF1 124753 91 + 1
UGAGGCGCAGCUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAGUAAACGGUGGCAGCGCAGGGCAGGG---CAGAGCCC------------AGUGCCGAAAGAGA
....((((.((((.(((((.(((.(((((....))))).))).)))))...)))).))))..(((((((---(...))))------------..))))........ ( -34.70)
>consensus
CGAGGCGCAACUAAUUUGCCUCGGGUGUUAAGUAGCAUGUGAAAUAAACGC____AACG_______GGA___GAAAGCCAAACAC__UCGAGAGUGC_G_______
...(((((((.....)))).(((.(((((....))))).)))..................................)))........................... (-14.98 = -14.48 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:28 2006