Locus 2661

Sequence ID	2L_DroMel_CAF1
Location	7,463,420 – 7,463,542
Length	122
Max. P	0.733656

overview

Window 8

Location	7,463,420 – 7,463,511
Length	91
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	89.78
Mean single sequence MFE	-19.34
Consensus MFE	-14.04
Energy contribution	-14.00
Covariance contribution	-0.04
Combinations/Pair	1.05
Mean z-score	-1.65
Structure conservation index	0.73
SVM decision value	-0.05
SVM RNA-class probability	0.506971
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7463420 91 + 22407834
AAACCGCACAUAAAUAAAAGA-AAUAAUUGUUG-AUGGCGGAAAAUGGUUUGGAUAAUCGGCAGCUGACCAAAUCCAAAAAUCUACGAGCUCC
...((((.(((.(((((....-.....))))).-)))))))....((((((((....((((...))))))))).)))................ ( -17.50)
>DroSec_CAF1 59035 91 + 1
AAACCGCACAUAAAUAAAAUA-AAUAAUUGUUG-AUGGCGGAAAAUGGUUUGGAUAAUCGGCAGCUGACCGAAUCCACAAAUCUGCGAGCUCC
...((((.(((.(((((....-.....))))).-))))))).....(((((((((..(((((....).)))))))))..)))).......... ( -20.00)
>DroSim_CAF1 61062 91 + 1
AAACCGCACAUAAAUAAAAUA-AAUAAUUGUUG-AUGGCGGAAAAUGGUUUGGAUAAUCGGCAGCUGACCGAAUCCACAAAUCUACGAGCUCC
...((((.(((.(((((....-.....))))).-))))))).....(((((((((..(((((....).)))))))))..)))).......... ( -20.00)
>DroEre_CAF1 62528 83 + 1
AAACCGCACAUAAAUAAAACA-AAUAAUUGUUG-AUGGCGGAAAAUGGUUUGGAUAAUCGGCUGCUGACCGAAUCC--------GCGAGCUCC
...((((.(((......((((-(....))))).-))))))).....(((((((((..(((((....).))))))))--------..))))).. ( -20.40)
>DroYak_CAF1 61949 84 + 1
AAACCGC-CAUAAAUAAAAUAAAAUAAUUGUUGAAUGGCGGAAAAUGGUUUGGAUAAUCGCCAGCUGACCAAAUCC--------ACGAGCUGC
...((((-(((.(((((..........)))))..)))))))....((((((((.......)))...))))).....--------......... ( -18.80)
>consensus
AAACCGCACAUAAAUAAAAUA_AAUAAUUGUUG_AUGGCGGAAAAUGGUUUGGAUAAUCGGCAGCUGACCGAAUCCA_AAAUCUACGAGCUCC
...((((.((..(((((..........)))))...)))))).....(((((((....((((...))))))))))).................. (-14.04 = -14.00 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	7,463,438 – 7,463,542
Length	104
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	80.46
Mean single sequence MFE	-29.62
Consensus MFE	-16.07
Energy contribution	-17.23
Covariance contribution	1.17
Combinations/Pair	1.12
Mean z-score	-2.26
Structure conservation index	0.54
SVM decision value	0.43
SVM RNA-class probability	0.733656
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7463438 104 - 22407834
CU-----UUGGUGGCGAAAAUGUCAGAGGUUUC-UACGGAGCUCGUAGAUUUUUGG-AUUUGGUCAGCUGCCGAUUAUCCAA-ACCAUUUUCCGCCAU-CA---ACAAUUAUU-UCU
..-----(((((((((((((((.........((-((((.....))))))..(((((-(((((((.....)))))..))))))-).)))))).))))))-))---)........-... ( -34.40)
>DroSec_CAF1 59053 104 - 1
CU-----UUGGUGGCCAAAAUGUCAGAGGUUUC-UACGGAGCUCGCAGAUUUGUGG-AUUCGGUCAGCUGCCGAUUAUCCAA-ACCAUUUUCCGCCAU-CA---ACAAUUAUU-UAU
..-----((((((((.((((((...(((..(((-....)))))).........(((-(((((((.....)))))..))))).-..))))))..)))))-))---)........-... ( -29.20)
>DroSim_CAF1 61080 104 - 1
CU-----UUGGUGGCCAAAAUGUCAGAGGUUUC-UACGGAGCUCGUAGAUUUGUGG-AUUCGGUCAGCUGCCGAUUAUCCAA-ACCAUUUUCCGCCAU-CA---ACAAUUAUU-UAU
..-----((((((((.((((((.........((-((((.....))))))....(((-(((((((.....)))))..))))).-..))))))..)))))-))---)........-... ( -30.70)
>DroEre_CAF1 62546 96 - 1
CU-----UUGGUGGCGAAAAUGUCAGAGGUUUC-UGCGGAGCUCGC--------GG-AUUCGGUCAGCAGCCGAUUAUCCAA-ACCAUUUUCCGCCAU-CA---ACAAUUAUU-UGU
..-----(((((((((((((((...(((.((..-....)).)))..--------((-(((((((.....)))))..))))..-..)))))).))))))-))---)........-... ( -32.20)
>DroYak_CAF1 61966 98 - 1
UU-----UUGGUGGCGAAAAUGUCAGAGGUUUC-UGCGCAGCUCGU--------GG-AUUUGGUCAGCUGGCGAUUAUCCAA-ACCAUUUUCCGCCAUUCA---ACAAUUAUUUUAU
..-----(((((((((((((((...(((.(...-.....).))).(--------((-((.(.(((....))).)..))))).-..)))))).))))).)))---)............ ( -24.10)
>DroAna_CAF1 60217 112 - 1
UUUUUUUUUUGCCUCCCAAAUGUCAGAGGUCUUGCUUGGAG---GAUGAUCUUUGGUCUUUGGUCAGCUACCGAUUGUCCAAAAGCAUUUUCCACCAA-CACCGACCAUAUUU-UAU
.................((((((....(((.(((..(((((---((((...(((((.(.(((((.....)))))..).)))))..))))))))).)))-.)))....))))))-... ( -27.10)
>consensus
CU_____UUGGUGGCCAAAAUGUCAGAGGUUUC_UACGGAGCUCGUAGAUUU_UGG_AUUCGGUCAGCUGCCGAUUAUCCAA_ACCAUUUUCCGCCAU_CA___ACAAUUAUU_UAU
........((((((..((((((...(((.(((.....))).)))..........((...(((((.....)))))....)).....)))))))))))).................... (-16.07 = -17.23 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:08 2006