Locus 9031

Sequence ID	3R_DroMel_CAF1
Location	24,181,093 – 24,181,205
Length	112
Max. P	0.934834

overview

Window 6

Location	24,181,093 – 24,181,205
Length	112
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	72.98
Mean single sequence MFE	-23.69
Consensus MFE	-2.66
Energy contribution	-2.34
Covariance contribution	-0.32
Combinations/Pair	1.50
Mean z-score	-1.74
Structure conservation index	0.11
SVM decision value	0.72
SVM RNA-class probability	0.833283
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24181093 112 + 27905053
CGA-GCAUUCCGGCCAUUUUUUAUUGCCAAAUGUCCGUUCAACUCGACCGAUUGAAUCACCGCCACAG--GACGCUU-UCUCAUUUUUG-CUUCUCUUUGCGUCGGCUUAAAUUUUU
((.-.((((..(((.((.....)).))).))))..))(((((.((....))))))).....(((....--(((((..-...........-.........)))))))).......... ( -20.85)
>DroSec_CAF1 4140 99 + 1
CGA-GCGUUCCGGCCAUUUUUUAUUGCCAAAUGGCCAUUCAGCUCGAC------------CACCACAG--GACGCUC-UCUCAUU-UUG-CUUUCCUUUGCGACGGCUUAAAUUUUU
.((-((((((.((((((((.........))))))))..((.....)).------------.......)--)))))))-.......-..(-((.((......)).))).......... ( -25.30)
>DroSim_CAF1 3159 99 + 1
CGA-GCGUUCCGGCCAUUUUUUAUUGCCAAAUGGCCAUUCAGCUCGAC------------CACCACAG--GACGCUC-UCUCAUU-UUG-CUUUCCUUUGCGACGGCUUAAAUUUUU
.((-((((((.((((((((.........))))))))..((.....)).------------.......)--)))))))-.......-..(-((.((......)).))).......... ( -25.30)
>DroEre_CAF1 7111 102 + 1
CGA-GCAUUCCGGCCAUUUUUUAUGGCCAAAUGACCGUUCGACUCGAC------------CGAUUGAGCAGCCGCUUUUCUAAUU-UUG-CUCCUUUUUGCGGUGGCUUACAUUUUC
...-.......((((((.....))))))(((((...((((((.((...------------.))))))))(((((((.........-..(-(........)))))))))..))))).. ( -27.60)
>DroPer_CAF1 3326 94 + 1
CGAGGCAUUCCGUUCAUUUUUUAUUGUAA-CGCUCCAUUGAAUCCGG----------------GG-CG--GACGCUU-UCUAAUU-UUGGGUUUCUUUUUUGGUUCCUUACAUUUU-
.(((((..((((((((........)).))-)(((((.........))----------------))-))--)).))))-)......-..(((..((......))..)))........- ( -19.40)
>consensus
CGA_GCAUUCCGGCCAUUUUUUAUUGCCAAAUGGCCAUUCAACUCGAC____________CACCACAG__GACGCUU_UCUCAUU_UUG_CUUUCCUUUGCGACGGCUUAAAUUUUU
.........................(((...((......))...............................(((........................)))..))).......... ( -2.66 =  -2.34 +  -0.32)

alignment

secondary structure

dotplot

Window 7

Location	24,181,093 – 24,181,205
Length	112
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	72.98
Mean single sequence MFE	-26.48
Consensus MFE	-9.06
Energy contribution	-9.94
Covariance contribution	0.88
Combinations/Pair	1.29
Mean z-score	-2.06
Structure conservation index	0.34
SVM decision value	1.24
SVM RNA-class probability	0.934834
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24181093 112 - 27905053
AAAAAUUUAAGCCGACGCAAAGAGAAG-CAAAAAUGAGA-AAGCGUC--CUGUGGCGGUGAUUCAAUCGGUCGAGUUGAACGGACAUUUGGCAAUAAAAAAUGGCCGGAAUGC-UCG
..........(((((.((........)-).....((((.-.(.((((--....)))).)..)))).)))))(((((....(((.(((((.........))))).)))....))-))) ( -27.70)
>DroSec_CAF1 4140 99 - 1
AAAAAUUUAAGCCGUCGCAAAGGAAAG-CAA-AAUGAGA-GAGCGUC--CUGUGGUG------------GUCGAGCUGAAUGGCCAUUUGGCAAUAAAAAAUGGCCGGAACGC-UCG
..........(((..((((..(((..(-(..-.......-..)).))--)))))..)------------))(((((....(((((((((.........)))))))))....))-))) ( -32.20)
>DroSim_CAF1 3159 99 - 1
AAAAAUUUAAGCCGUCGCAAAGGAAAG-CAA-AAUGAGA-GAGCGUC--CUGUGGUG------------GUCGAGCUGAAUGGCCAUUUGGCAAUAAAAAAUGGCCGGAACGC-UCG
..........(((..((((..(((..(-(..-.......-..)).))--)))))..)------------))(((((....(((((((((.........)))))))))....))-))) ( -32.20)
>DroEre_CAF1 7111 102 - 1
GAAAAUGUAAGCCACCGCAAAAAGGAG-CAA-AAUUAGAAAAGCGGCUGCUCAAUCG------------GUCGAGUCGAACGGUCAUUUGGCCAUAAAAAAUGGCCGGAAUGC-UCG
..........((....))......(((-((.-.....((....((((((......))------------))))..)).........(((((((((.....))))))))).)))-)). ( -28.00)
>DroPer_CAF1 3326 94 - 1
-AAAAUGUAAGGAACCAAAAAAGAAACCCAA-AAUUAGA-AAGCGUC--CG-CC----------------CCGGAUUCAAUGGAGCG-UUACAAUAAAAAAUGAACGGAAUGCCUCG
-....(((((.(..(((.....(.....)..-.......-..(.(((--((-..----------------.))))).)..)))..).-))))).............((....))... ( -12.30)
>consensus
AAAAAUUUAAGCCGCCGCAAAGGAAAG_CAA_AAUGAGA_AAGCGUC__CUGUGGCG____________GUCGAGUUGAAUGGACAUUUGGCAAUAAAAAAUGGCCGGAAUGC_UCG
.......................................................................(((((....(((((((((.........)))))))))....)).))) ( -9.06 =  -9.94 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:25:09 2006