Locus 852

Sequence ID	2L_DroMel_CAF1
Location	2,425,378 – 2,425,525
Length	147
Max. P	0.869007

overview

Window 3

Location	2,425,378 – 2,425,495
Length	117
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	91.85
Mean single sequence MFE	-21.64
Consensus MFE	-17.11
Energy contribution	-17.27
Covariance contribution	0.16
Combinations/Pair	1.14
Mean z-score	-1.67
Structure conservation index	0.79
SVM decision value	0.51
SVM RNA-class probability	0.763886
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2425378 117 + 22407834
GAAGUUAUAGAAAUUGAUUUCUCUUUCAAGCAAG-UCUUUAAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUUCCACAAAGCUCUUAGCUCCUCACAA-ACCUUUUCCGAUCU
.........(((((((((....(((......)))-...........((((......)))).)))))))))(((((((((......(((.....)))......))-)))))))....... ( -16.50)
>DroSec_CAF1 4873 117 + 1
GGGGUUAUAAAAAUUGAUUUCUCUUUCAAGCAAG-GCUUUGAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUUCCACAAAGCUCUUAGCUCCACACAA-ACCUUUUCCGAUCU
.(((((...(((((((((.....((((((((...-)).))))))..((((......)))).)))))))))(((((((((......(((.....)))......))-)))))))..))))) ( -23.40)
>DroSim_CAF1 4894 117 + 1
GGGGUUAUAAAAAUUGAUUUCUCUUUCAAGCAGG-GCUUUGAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUGCCACAAAGCUCUUAGCUCCACACAA-ACCUUUUCCGAUCU
(((((((......((((........))))..(((-((((((.....((((......))))...((((((....))))))...))))))))))))))))......-.............. ( -25.10)
>DroEre_CAF1 4893 118 + 1
GAGGUUAUAAAAAUUGAUUUCUCUUUUAAGCAAGAUGCCUGAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUUCCACAAAGCUCUCAGCUCGCCGCAA-ACCUUUUCCGAUCU
.(((((...(((((((((...........(((((((((.(....).)))))).....))).)))))))))(((((((((.(....(((.....)))....).))-)))))))..))))) ( -23.70)
>DroYak_CAF1 4984 118 + 1
GGGGUUAUAAAAAUUGAUUUCUCUUUUAACCAAG-UCUUUGGAAAUGCAUCUAACAAUGCCAUCAAAUUUAAAAGGUUUUCACAAAGCUCUUAGCUCGCCACAAAACCUUUUCCGAUCU
(..((((.......))))..).............-...((((((..((((......))))............((((((((.....(((.....)))......))))))))))))))... ( -19.50)
>consensus
GGGGUUAUAAAAAUUGAUUUCUCUUUCAAGCAAG_UCUUUGAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUUCCACAAAGCUCUUAGCUCCACACAA_ACCUUUUCCGAUCU
.(((((...(((((((((.....(((((((.......)))))))..((((......)))).)))))))))(((((((........(((.....))).........)))))))..))))) (-17.11 = -17.27 +   0.16)

alignment

secondary structure

dotplot

Window 4

Location	2,425,378 – 2,425,495
Length	117
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	91.85
Mean single sequence MFE	-29.76
Consensus MFE	-22.04
Energy contribution	-22.52
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.74
SVM decision value	0.27
SVM RNA-class probability	0.661216
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2425378 117 - 22407834
AGAUCGGAAAAGGU-UUGUGAGGAGCUAAGAGCUUUGUGGAAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUUAAAGA-CUUGCUUGAAAGAGAAAUCAAUUUCUAUAACUUC
.......(((((((-((.((..((((.....))))..)).))))))))).((((((((.(((((....)))))...........-....(((....)))..)))))))).......... ( -27.10)
>DroSec_CAF1 4873 117 - 1
AGAUCGGAAAAGGU-UUGUGUGGAGCUAAGAGCUUUGUGGAAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUCAAAGC-CUUGCUUGAAAGAGAAAUCAAUUUUUAUAACCCC
.....(((((((((-((.((..((((.....))))..)).)))))))))(((((((((.(((((....))))).(((((((.((-...)))))))))....))))))))).....)).. ( -34.80)
>DroSim_CAF1 4894 117 - 1
AGAUCGGAAAAGGU-UUGUGUGGAGCUAAGAGCUUUGUGGCAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUCAAAGC-CCUGCUUGAAAGAGAAAUCAAUUUUUAUAACCCC
.....(((((((((-(..((..((((.....))))..))..))))))))(((((((((.(((((....))))).(((((((.((-...)))))))))....))))))))).....)).. ( -30.80)
>DroEre_CAF1 4893 118 - 1
AGAUCGGAAAAGGU-UUGCGGCGAGCUGAGAGCUUUGUGGAAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUCAGGCAUCUUGCUUAAAAGAGAAAUCAAUUUUUAUAACCUC
.....(((((((((-((.(.((((((.....)).)))).))))))))))(((((((((.(((((....))))).(((((((((.....))))....)))))))))))))).....)).. ( -31.90)
>DroYak_CAF1 4984 118 - 1
AGAUCGGAAAAGGUUUUGUGGCGAGCUAAGAGCUUUGUGAAAACCUUUUAAAUUUGAUGGCAUUGUUAGAUGCAUUUCCAAAGA-CUUGGUUAAAAGAGAAAUCAAUUUUUAUAACCCC
.....((((((((((((...((((((.....)).)))).))))))).............(((((....))))).))))).....-...((((((((((........))))).))))).. ( -24.20)
>consensus
AGAUCGGAAAAGGU_UUGUGGGGAGCUAAGAGCUUUGUGGAAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUCAAAGA_CUUGCUUGAAAGAGAAAUCAAUUUUUAUAACCCC
.....(((((((((.((.((..((((.....))))..)).)))))))))(((((((((.(((((....)))))................(((....)))..))))))))).....)).. (-22.04 = -22.52 +   0.48)

alignment

secondary structure

dotplot

Window 5

Location	2,425,417 – 2,425,525
Length	108
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	95.20
Mean single sequence MFE	-19.15
Consensus MFE	-15.89
Energy contribution	-16.09
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.83
SVM decision value	0.86
SVM RNA-class probability	0.869007
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2425417 108 + 22407834
AAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUUCCACAAAGCUCUUAGCUCCUCACAA-ACCUUUUCCGAUCUUGCAACACUCGAGUACCGAUGCUCAUCGCA
.....(((.........(((.....(((..(((((((((......(((.....)))......))-)))))))..)))...)))......(((((....)))))...))) ( -18.80)
>DroSec_CAF1 4912 108 + 1
GAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUUCCACAAAGCUCUUAGCUCCACACAA-ACCUUUUCCGAUCUUGCAACACUCGAGUACCGAUGCUCAUCGCA
.....(((.........(((.....(((..(((((((((......(((.....)))......))-)))))))..)))...)))......(((((....)))))...))) ( -18.80)
>DroSim_CAF1 4933 108 + 1
GAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUGCCACAAAGCUCUUAGCUCCACACAA-ACCUUUUCCGAUCUUGCAACACUCGAGUACCGAUGCUCAUCGCA
.....(((.........(((.....(((..((((((((.......(((.....))).......)-)))))))..)))...)))......(((((....)))))...))) ( -18.84)
>DroEre_CAF1 4933 108 + 1
GAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUUCCACAAAGCUCUCAGCUCGCCGCAA-ACCUUUUCCGAUCUUGCAACACUUGAGUACCGAUGCUCAUCGCA
.....(((.........(((.....(((..(((((((((.(....(((.....)))....).))-)))))))..)))...))).....((((((....))))))..))) ( -19.20)
>DroYak_CAF1 5023 109 + 1
GGAAAUGCAUCUAACAAUGCCAUCAAAUUUAAAAGGUUUUCACAAAGCUCUUAGCUCGCCACAAAACCUUUUCCGAUCUUGCAACACUUGAGUACCGAUGCUCAUCGCA
((((..((((......))))............((((((((.....(((.....)))......)))))))))))).....(((......((((((....))))))..))) ( -20.10)
>consensus
GAAAAUGCAUCUAACAAUGCCAUCAAUUUUAAAAGGUUUCCACAAAGCUCUUAGCUCCACACAA_ACCUUUUCCGAUCUUGCAACACUCGAGUACCGAUGCUCAUCGCA
.....(((.........(((.....(((..(((((((........(((.....))).........)))))))..)))...)))......(((((....)))))...))) (-15.89 = -16.09 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	2,425,417 – 2,425,525
Length	108
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	95.20
Mean single sequence MFE	-29.08
Consensus MFE	-24.30
Energy contribution	-24.34
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.32
Structure conservation index	0.84
SVM decision value	-0.06
SVM RNA-class probability	0.505204
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2425417 108 - 22407834
UGCGAUGAGCAUCGGUACUCGAGUGUUGCAAGAUCGGAAAAGGU-UUGUGAGGAGCUAAGAGCUUUGUGGAAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUU
.((((((..(((((((..((((...........))))(((((((-((.((..((((.....))))..)).)))))))))...))))))).))))))............. ( -28.60)
>DroSec_CAF1 4912 108 - 1
UGCGAUGAGCAUCGGUACUCGAGUGUUGCAAGAUCGGAAAAGGU-UUGUGUGGAGCUAAGAGCUUUGUGGAAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUC
.((((((..(((((((..((((...........))))(((((((-((.((..((((.....))))..)).)))))))))...))))))).))))))............. ( -31.60)
>DroSim_CAF1 4933 108 - 1
UGCGAUGAGCAUCGGUACUCGAGUGUUGCAAGAUCGGAAAAGGU-UUGUGUGGAGCUAAGAGCUUUGUGGCAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUC
.((((((..(((((((....(((.(((((.(((((......)))-))..(..((((.....))))..).)))))))).....))))))).))))))............. ( -28.50)
>DroEre_CAF1 4933 108 - 1
UGCGAUGAGCAUCGGUACUCAAGUGUUGCAAGAUCGGAAAAGGU-UUGCGGCGAGCUGAGAGCUUUGUGGAAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUC
........(((((...((...((((((((((......(((((((-((.(.((((((.....)).)))).))))))))))....))).)))))))))..)))))...... ( -28.70)
>DroYak_CAF1 5023 109 - 1
UGCGAUGAGCAUCGGUACUCAAGUGUUGCAAGAUCGGAAAAGGUUUUGUGGCGAGCUAAGAGCUUUGUGAAAACCUUUUAAAUUUGAUGGCAUUGUUAGAUGCAUUUCC
........((((((((..(((...((..(((((((......)))))))..))((((.....))))..)))..))).........((((......)))))))))...... ( -28.00)
>consensus
UGCGAUGAGCAUCGGUACUCGAGUGUUGCAAGAUCGGAAAAGGU_UUGUGGGGAGCUAAGAGCUUUGUGGAAACCUUUUAAAAUUGAUGGCAUUGUUAGAUGCAUUUUC
........(((((...((...((((((((((......(((((((.((.((..((((.....))))..)).)))))))))....))).)))))))))..)))))...... (-24.30 = -24.34 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:12 2006