Locus 1169

Sequence ID	2L_DroMel_CAF1
Location	3,212,684 – 3,212,935
Length	251
Max. P	0.999763

overview

Window 1

Location	3,212,684 – 3,212,794
Length	110
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	91.37
Mean single sequence MFE	-31.98
Consensus MFE	-26.42
Energy contribution	-26.98
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.33
Structure conservation index	0.83
SVM decision value	2.26
SVM RNA-class probability	0.991345
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3212684 110 + 22407834
G---UUCCACCCAUUUCUGGGCAAAGUUAAUGUCACGCACUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUUUUACAAGUCAGCUGGCUGCGUUUUACAU
.---.....((((....))))........((((.(((((...((((.(((((((.((.((((.((.......))..)))).))....))))))).))))..)))))...)))) ( -30.60)
>DroSec_CAF1 46835 105 + 1
--------GCCCAUCUCUGGGCAAAGUUAAUGUCACGCACUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUUUUACAAGUCAGCUGGCUGCGUUUUACAU
--------(((((....))))).......((((.(((((...((((.(((((((.((.((((.((.......))..)))).))....))))))).))))..)))))...)))) ( -34.80)
>DroSim_CAF1 45254 110 + 1
G---CUUCGCCCAUCUCUGGGCAAAGUUAAUGUCACGCACUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUUUUACAAGUCAGCUGGCUGCGUUUUACAU
(---(((.(((((....))))).))))..((((.(((((...((((.(((((((.((.((((.((.......))..)))).))....))))))).))))..)))))...)))) ( -37.10)
>DroEre_CAF1 43439 110 + 1
G---CACCACCAGUCUCUAGGCAAAGUUAAUGUCACGCAUUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUAUUACAAGUCAGCUGGCUGCGUUUUACAU
(---((...(((((.....(((...((.((((.....)))))).)))(((((((.((.((((.((.......))..)))).))....))))))).))))).)))......... ( -28.30)
>DroYak_CAF1 41915 113 + 1
GCUGCACCACCAGACUCUAGGCAAAGUUAAUGUCACGCAUUGCAGCCAGCUUGUUGGCAUGACACUUUUAAUGUCCUCAUCGCUUUCACAAGUCAGCUGGCUGCGUUUUACAU
...........((((....((((.......)))).......((((((((((((..(((((((.((.......))..)))).)))..))......))))))))))))))..... ( -29.10)
>consensus
G___CACCACCCAUCUCUGGGCAAAGUUAAUGUCACGCACUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUUUUACAAGUCAGCUGGCUGCGUUUUACAU
.........((((....))))........((((.(((((...((((.(((((((.((.((((.((.......))..)))).))....))))))).))))..)))))...)))) (-26.42 = -26.98 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	3,212,684 – 3,212,794
Length	110
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	91.37
Mean single sequence MFE	-38.48
Consensus MFE	-32.92
Energy contribution	-33.80
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-3.30
Structure conservation index	0.86
SVM decision value	4.03
SVM RNA-class probability	0.999763
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3212684 110 - 22407834
AUGUAAAACGCAGCCAGCUGACUUGUAAAAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAGUGCGUGACAUUAACUUUGCCCAGAAAUGGGUGGAA---C
((((...(((((..((((((.(((((....((.((...(((((.....))))))).)).))))).))))))...))))).))))....((..((((....))))..)).---. ( -40.90)
>DroSec_CAF1 46835 105 - 1
AUGUAAAACGCAGCCAGCUGACUUGUAAAAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAGUGCGUGACAUUAACUUUGCCCAGAGAUGGGC--------
((((...(((((..((((((.(((((....((.((...(((((.....))))))).)).))))).))))))...))))).)))).......(((((....)))))-------- ( -36.70)
>DroSim_CAF1 45254 110 - 1
AUGUAAAACGCAGCCAGCUGACUUGUAAAAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAGUGCGUGACAUUAACUUUGCCCAGAGAUGGGCGAAG---C
((((...(((((..((((((.(((((....((.((...(((((.....))))))).)).))))).))))))...))))).))))...(((((((((....)))))))))---. ( -43.30)
>DroEre_CAF1 43439 110 - 1
AUGUAAAACGCAGCCAGCUGACUUGUAAUAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAAUGCGUGACAUUAACUUUGCCUAGAGACUGGUGGUG---C
((((...(((((..((((((.(((((....((.((...(((((.....))))))).)).))))).))))))...))))).)))).....(..((........))..)..---. ( -34.10)
>DroYak_CAF1 41915 113 - 1
AUGUAAAACGCAGCCAGCUGACUUGUGAAAGCGAUGAGGACAUUAAAAGUGUCAUGCCAACAAGCUGGCUGCAAUGCGUGACAUUAACUUUGCCUAGAGUCUGGUGGUGCAGC
.........((((((((((...((((....))))....(((((.....))))).........))))))))))..((((...(((((((((......)))).))))).)))).. ( -37.40)
>consensus
AUGUAAAACGCAGCCAGCUGACUUGUAAAAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAGUGCGUGACAUUAACUUUGCCCAGAGAUGGGUGGAG___C
((((...(((((..((((((.(((((....((.((...(((((.....))))))).)).))))).))))))...))))).)))).....(((((((....)))))))...... (-32.92 = -33.80 +   0.88)

alignment

secondary structure

dotplot

Window 3

Location	3,212,714 – 3,212,832
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	98.14
Mean single sequence MFE	-33.90
Consensus MFE	-31.80
Energy contribution	-31.84
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.63
Structure conservation index	0.94
SVM decision value	1.45
SVM RNA-class probability	0.955172
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3212714 118 + 22407834
CACGCACUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUUUUACAAGUCAGCUGGCUGCGUUUUACAUGCGCUUACUGCAGUCAAGUGUAAAAUGGAAAAUGAGUU
.....((((((((((((((((.((.((((.((.......))..)))).))....)))....))))))))))(((((((((((((.....)).))...)))))))))........))). ( -32.80)
>DroSec_CAF1 46860 118 + 1
CACGCACUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUUUUACAAGUCAGCUGGCUGCGUUUUACAUGCGCUUACUGCAGUCAAGUGUAAAAUGGAAAAUGAGUU
.....((((((((((((((((.((.((((.((.......))..)))).))....)))....))))))))))(((((((((((((.....)).))...)))))))))........))). ( -32.80)
>DroSim_CAF1 45284 118 + 1
CACGCACUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUUUUACAAGUCAGCUGGCUGCGUUUUACAUGCGCUUACUGCAGUCAAGUGUAAAAUGGAAAAUGAGUU
.....((((((((((((((((.((.((((.((.......))..)))).))....)))....))))))))))(((((((((((((.....)).))...)))))))))........))). ( -32.80)
>DroEre_CAF1 43469 118 + 1
CACGCAUUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUAUUACAAGUCAGCUGGCUGCGUUUUACAUGCGCUUACUGCAGUCAAGUGUAAAAUGGAAAAUGAGUU
.((.(((((((((((((((((.((.((((.((.......))..)))).))....)))....))))))))))(((((((((((((.....)).))...)))))))))....)))).)). ( -34.80)
>DroYak_CAF1 41948 118 + 1
CACGCAUUGCAGCCAGCUUGUUGGCAUGACACUUUUAAUGUCCUCAUCGCUUUCACAAGUCAGCUGGCUGCGUUUUACAUGCGCUUACUGCAGUCAAGUGUAAAAUGGAAAAUGAGUU
.((.((((((((((((((((..(((((((.((.......))..)))).)))..))......))))))))))(((((((((((((.....)).))...)))))))))....)))).)). ( -36.30)
>consensus
CACGCACUGCAGCCGGCUUGUUGCCAUGACACUUUUAAUGUCCUCAUCGCUUUUACAAGUCAGCUGGCUGCGUUUUACAUGCGCUUACUGCAGUCAAGUGUAAAAUGGAAAAUGAGUU
.((.((..(((((((((((((.((.((((.((.......))..)))).))....)))....))))))))))(((((((((((((.....)).))...)))))))))......)).)). (-31.80 = -31.84 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	3,212,714 – 3,212,832
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	98.14
Mean single sequence MFE	-33.34
Consensus MFE	-31.90
Energy contribution	-31.66
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-1.53
Structure conservation index	0.96
SVM decision value	1.33
SVM RNA-class probability	0.942441
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3212714 118 - 22407834
AACUCAUUUUCCAUUUUACACUUGACUGCAGUAAGCGCAUGUAAAACGCAGCCAGCUGACUUGUAAAAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAGUGCGUG
.((.((((.....(((((((..((.((......))))..))))))).((((((.(((..((..(.......)..))(((((.....))))).((....))))).)))))))))).)). ( -32.40)
>DroSec_CAF1 46860 118 - 1
AACUCAUUUUCCAUUUUACACUUGACUGCAGUAAGCGCAUGUAAAACGCAGCCAGCUGACUUGUAAAAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAGUGCGUG
.((.((((.....(((((((..((.((......))))..))))))).((((((.(((..((..(.......)..))(((((.....))))).((....))))).)))))))))).)). ( -32.40)
>DroSim_CAF1 45284 118 - 1
AACUCAUUUUCCAUUUUACACUUGACUGCAGUAAGCGCAUGUAAAACGCAGCCAGCUGACUUGUAAAAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAGUGCGUG
.((.((((.....(((((((..((.((......))))..))))))).((((((.(((..((..(.......)..))(((((.....))))).((....))))).)))))))))).)). ( -32.40)
>DroEre_CAF1 43469 118 - 1
AACUCAUUUUCCAUUUUACACUUGACUGCAGUAAGCGCAUGUAAAACGCAGCCAGCUGACUUGUAAUAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAAUGCGUG
.((.((((.....(((((((..((.((......))))..))))))).((((((.((((........))))......(((((.....)))))..(((.....))))))))))))).)). ( -32.60)
>DroYak_CAF1 41948 118 - 1
AACUCAUUUUCCAUUUUACACUUGACUGCAGUAAGCGCAUGUAAAACGCAGCCAGCUGACUUGUGAAAGCGAUGAGGACAUUAAAAGUGUCAUGCCAACAAGCUGGCUGCAAUGCGUG
.((.((((.....(((((((..((.((......))))..))))))).((((((((((...((((....))))....(((((.....))))).........)))))))))))))).)). ( -36.90)
>consensus
AACUCAUUUUCCAUUUUACACUUGACUGCAGUAAGCGCAUGUAAAACGCAGCCAGCUGACUUGUAAAAGCGAUGAGGACAUUAAAAGUGUCAUGGCAACAAGCCGGCUGCAGUGCGUG
.((.((((.....(((((((..((.((......))))..))))))).((((((.(((..((..(.......)..))(((((.....))))).((....))))).)))))))))).)). (-31.90 = -31.66 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	3,212,832 – 3,212,935
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	92.62
Mean single sequence MFE	-33.14
Consensus MFE	-24.28
Energy contribution	-27.04
Covariance contribution	2.76
Combinations/Pair	1.06
Mean z-score	-1.84
Structure conservation index	0.73
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3212832 103 - 22407834
GCCUGGCGAUAAGCCCGAGGCGAGUUGCCUUCGCCAACAAUCUUGGCUAAGUGCAGUUGCAUUCGGGCUCCUCUCAUGUUUACAGAUUUUAAUCUAAAGUGCG
((((.(.((..((((((((((((.(((((((.(((((.....))))).))).)))))))).))))))))..)).)........((((....))))..)).)). ( -36.80)
>DroSec_CAF1 46978 103 - 1
GCCUGGCGAUAAGCCCGAGGCGAGUUGCCUUCGCCAACAAUCUUGGCUAAGUGCAGUUGCAUUCGGGCUCCUCUCAUGUUUACAGAUUUUAAUCUAAAGUGCG
((((.(.((..((((((((((((.(((((((.(((((.....))))).))).)))))))).))))))))..)).)........((((....))))..)).)). ( -36.80)
>DroSim_CAF1 45402 103 - 1
GCCUGGCGAUAAGCCCGAGGCGAGUUGCCUUCGCCAACAAUCUUGGCUAAGUGCAGUUGCAUUCGGGCUCCUCUCAUGUUUACAGAUUUUAAUCUAAAGUGCG
((((.(.((..((((((((((((.(((((((.(((((.....))))).))).)))))))).))))))))..)).)........((((....))))..)).)). ( -36.80)
>DroEre_CAF1 43587 89 - 1
GCCUGGCGAUAAGCCCGAGGCGAGUUGCCAUCGCCAACAAUCUUGGCUAAGUG--------------CUCCGCUCAUGUUUACAGAUUUUAAUCUAAAGUGCG
(((((((.....)))..))))((((.(((...(((((.....)))))...).)--------------)...))))..((....((((....)))).....)). ( -22.90)
>DroYak_CAF1 42066 103 - 1
GCCUGGCGAUAAGCUCGAGGCAAGUUGCCAUCGCCAACAAUCUUGGCUAAGUGCAGUUGCAUUCGGGCUCCGCUCAUGUUUACAGAUUUUAAUCUAAAGUGCG
((((((((...((((((((((((.(((((...(((((.....)))))...).)))))))).)))))))).)))).........((((....))))..)).)). ( -32.40)
>consensus
GCCUGGCGAUAAGCCCGAGGCGAGUUGCCUUCGCCAACAAUCUUGGCUAAGUGCAGUUGCAUUCGGGCUCCUCUCAUGUUUACAGAUUUUAAUCUAAAGUGCG
((((...(((.((((((((((((.(((((((.(((((.....))))).))).)))))))).))))))))....((.((....)))).....)))...)).)). (-24.28 = -27.04 +   2.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:20 2006