Locus 8175

Sequence ID	X_DroMel_CAF1
Location	20,339,786 – 20,340,052
Length	266
Max. P	0.978975

overview

Window 7

Location	20,339,786 – 20,339,882
Length	96
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.65
Mean single sequence MFE	-27.86
Consensus MFE	-18.66
Energy contribution	-19.30
Covariance contribution	0.64
Combinations/Pair	1.05
Mean z-score	-2.34
Structure conservation index	0.67
SVM decision value	1.64
SVM RNA-class probability	0.969508
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20339786 96 - 22224390
UGCGUUUGAAUUCUCCAGCAAGCUUUUACUUUAAUUGCCCCAAAAGAACUUGGGAUAUACAAAUAAUAUGGAUCCUAAG-------------AU-------U---U-CGCAAUCGAACAG
...((((((........((((.............)))).......(((((((((((...((.......)).))))))))-------------..-------)---)-)....)))))).. ( -18.02)
>DroSec_CAF1 7680 103 - 1
UGCGUUUGAAUUCUCCAUCAAGCUUUUACUUUAAUUGCCCCAAAAGAACUUGGGGUAUACAAAGUAUAUGGGUCCUGAG-------------AACCAUCUAU---U-CGCAAUCAAAGAG
((((...((.(((((......((((.((((((...((((((((......))))))))...))))))...))))...)))-------------))...))...---.-))))......... ( -27.00)
>DroSim_CAF1 9209 106 - 1
UGCGUUUGAAUUCUCCAUCAAGCUUUUACUUUAAUUGCCCCAAAAGAACUUGGGGUAUACAAAGUAUAUGGAUCCUAAG-------------AACCAUCUAUUUCU-CGCAAUCAAACAG
(((((((((........))))))...((((((...((((((((......))))))))...)))))).((((.((....)-------------).))))........-.)))......... ( -27.00)
>DroEre_CAF1 4003 119 - 1
UGCGUUUGAAUUCUUCAGCAAGCUUUUACUUUAAUUGCCCCAAAACAACUUGGGGUAUACAAAGUGUACGGGCCCUAAGAUCUCGGCGUGAGAACUAACUAUUUUU-UGCAAUCGAGCAG
((((((.((..((((.((...((((.((((((...((((((((......))))))))...))))))...)))).))))))..)))))(..((((........))))-..)......))). ( -30.70)
>DroYak_CAF1 7985 118 - 1
UGCGUUUGAAUUCUCCAGCAAGCUUUUACUUUAAUUGCCCCAACAGAACUCGGGGUAUACAAAGUAUUUGGCUCCUAAGAUAUCGGAGAGAGAACUAUC--UUUUUCUGCAAUCGAACGG
..(((((((..(((..((..((((..((((((...((((((..........))))))...))))))...)))).)).)))...((((((((((....))--))))))))...))))))). ( -36.60)
>consensus
UGCGUUUGAAUUCUCCAGCAAGCUUUUACUUUAAUUGCCCCAAAAGAACUUGGGGUAUACAAAGUAUAUGGAUCCUAAG_____________AACCAUCUAUUU_U_CGCAAUCGAACAG
((((((((..........)))))...((((((...((((((((......))))))))...))))))..........................................)))......... (-18.66 = -19.30 +   0.64)

alignment

secondary structure

dotplot

Window 8

Location	20,339,803 – 20,339,918
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.04
Mean single sequence MFE	-27.90
Consensus MFE	-21.88
Energy contribution	-22.36
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-2.52
Structure conservation index	0.78
SVM decision value	1.83
SVM RNA-class probability	0.978975
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20339803 115 - 22224390
GACUUACAGCCCCUCAC----CCACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAGCAAGCUUUUACUUUAAUUGCCCCAAAAGAACUUGGGAUAUACAAAUAAUAUGGAUCCUAAG-
..((((...........----.....((..(((((....)))))..)).....((((((((.............))))(((((......)))))..............))))...))))- ( -19.62)
>DroSec_CAF1 7704 113 - 1
GACUUACAGC--CUCAC----CCACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAUCAAGCUUUUACUUUAAUUGCCCCAAAAGAACUUGGGGUAUACAAAGUAUAUGGGUCCUGAG-
......(((.--...((----(((.......((((....))))((((((........))))))...((((((...((((((((......))))))))...))))))..))))).)))..- ( -33.40)
>DroSim_CAF1 9236 113 - 1
GACUUACAGC--CUCAC----ACACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAUCAAGCUUUUACUUUAAUUGCCCCAAAAGAACUUGGGGUAUACAAAGUAUAUGGAUCCUAAG-
..((((...(--(....----..........((((....))))((((((........))))))...((((((...((((((((......))))))))...))))))...))....))))- ( -27.40)
>DroEre_CAF1 4042 114 - 1
GACUUACUGC--CUCAC----CCACACACUCGCAUCUCGAUGCGUUUGAAUUCUUCAGCAAGCUUUUACUUUAAUUGCCCCAAAACAACUUGGGGUAUACAAAGUGUACGGGCCCUAAGA
..((((..((--((...----.....((..(((((....)))))..))..................((((((...((((((((......))))))))...))))))...))))..)))). ( -31.90)
>DroYak_CAF1 8023 118 - 1
GACUUACAGC--AUCACCCACCCACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAGCAAGCUUUUACUUUAAUUGCCCCAACAGAACUCGGGGUAUACAAAGUAUUUGGCUCCUAAGA
..((((....--..............((..(((((....)))))..))............((((..((((((...((((((..........))))))...))))))...))))..)))). ( -27.20)
>consensus
GACUUACAGC__CUCAC____CCACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAGCAAGCUUUUACUUUAAUUGCCCCAAAAGAACUUGGGGUAUACAAAGUAUAUGGAUCCUAAG_
..((((....................((..(((((....)))))..))..............((..((((((...((((((((......))))))))...))))))...))....)))). (-21.88 = -22.36 +   0.48)

alignment

secondary structure

dotplot

Window 9

Location	20,339,842 – 20,339,958
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.36
Mean single sequence MFE	-19.97
Consensus MFE	-18.48
Energy contribution	-18.32
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.11
Structure conservation index	0.93
SVM decision value	0.07
SVM RNA-class probability	0.568937
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20339842 116 - 22224390
UCCUGCGCUGCCCUCUGUCUGCGUGUAAUUAAAUAAAAACGACUUACAGCCCCUCAC----CCACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAGCAAGCUUUUACUUUAAUUGCCC
....((((.((.....))..))))((((((((((((((...................----..........((((....))))(((((..........)))))))))).))))))))).. ( -18.30)
>DroSec_CAF1 7743 114 - 1
UCCUGCGCUGUCCUCUGUCUGCGUGUAAUUAAGUAAAAACGACUUACAGC--CUCAC----CCACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAUCAAGCUUUUACUUUAAUUGCCC
....((((.(........).))))((((((((((((((............--.....----..........((((....))))((((((........)))))))))))).)))))))).. ( -22.80)
>DroSim_CAF1 9275 114 - 1
UCCUGCGCUGCCCUCUGUCUGCGUGUAAUUAAAUAAAAACGACUUACAGC--CUCAC----ACACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAUCAAGCUUUUACUUUAAUUGCCC
....((((.((.....))..))))((((((((((((((............--.....----..........((((....))))((((((........))))))))))).))))))))).. ( -20.60)
>DroEre_CAF1 4082 114 - 1
UCCUGCGCUGCCCUCUGUCUGCGUGUAAUUAAAUAAAAACGACUUACUGC--CUCAC----CCACACACUCGCAUCUCGAUGCGUUUGAAUUCUUCAGCAAGCUUUUACUUUAAUUGCCC
....((((.((.....))..))))((((((((((((((..(.(((.(((.--.....----.....((..(((((....)))))..)).......))).))))))))).))))))))).. ( -19.07)
>DroYak_CAF1 8063 118 - 1
UCCUGCGCUGCCCUCUGUCUGCGUGUAAUUAAAUAAAAACGACUUACAGC--AUCACCCACCCACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAGCAAGCUUUUACUUUAAUUGCCC
....((((.((.....))..))))((((((((((((((..........((--(((.......................)))))(((((..........)))))))))).))))))))).. ( -19.10)
>consensus
UCCUGCGCUGCCCUCUGUCUGCGUGUAAUUAAAUAAAAACGACUUACAGC__CUCAC____CCACACACUCGCAUCUCGAUGCGUUUGAAUUCUCCAGCAAGCUUUUACUUUAAUUGCCC
....((((............))))((((((((((((((.................................((((....))))(((((..........)))))))))).))))))))).. (-18.48 = -18.32 +  -0.16)

alignment

secondary structure

dotplot

Window 0

Location	20,339,958 – 20,340,052
Length	94
Sequences	3
Columns	94
Reading direction	forward
Mean pairwise identity	98.58
Mean single sequence MFE	-12.27
Consensus MFE	-11.63
Energy contribution	-11.63
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.95
SVM decision value	0.29
SVM RNA-class probability	0.669065
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20339958 94 + 22224390
AAAAGGACAUUUGAAGCGUUGUACAUAAAUGAAAAUGAAAUAAAUUAAAAUAAGUGUCGAAGCUGAAGGCAAAGGCAAAGGCAAAAAGGACCAA
.....((((((((...((((.......))))..(((.......)))....))))))))...(((....((....))...)))............ ( -12.20)
>DroSec_CAF1 7857 94 + 1
AAAAGGACAUUUGAAGCGUUGUGCAUAAAUGAAAAUGAAAUAAAUUAAAAUAAGUGUCGAAGCUAAAGGCAAAGGCAAAGGCAAAAAGGACCAA
.....((((((((..((.....))....((....))..............))))))))...(((....((....))...)))............ ( -12.30)
>DroSim_CAF1 9389 94 + 1
AAAAGGACAUUUGAAGCGUUGUGCAUAAAUGAAAAUGAAAUAAAUUAAAAUAAGUGUCGAAGCUAAAGGCAAAGGCAAAGGCAAAAAGGACCAA
.....((((((((..((.....))....((....))..............))))))))...(((....((....))...)))............ ( -12.30)
>consensus
AAAAGGACAUUUGAAGCGUUGUGCAUAAAUGAAAAUGAAAUAAAUUAAAAUAAGUGUCGAAGCUAAAGGCAAAGGCAAAGGCAAAAAGGACCAA
.....((((((((.....((((.(((........)))..)))).......))))))))...(((....((....))...)))............ (-11.63 = -11.63 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:34 2006