Locus 244

Sequence ID	X_DroMel_CAF1
Location	835,638 – 835,776
Length	138
Max. P	0.741401

overview

Window 6

Location	835,638 – 835,755
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	82.29
Mean single sequence MFE	-34.74
Consensus MFE	-24.70
Energy contribution	-26.14
Covariance contribution	1.44
Combinations/Pair	1.06
Mean z-score	-1.65
Structure conservation index	0.71
SVM decision value	0.17
SVM RNA-class probability	0.615559
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 835638 117 + 22224390
CACAUUAUGCUAAUGUCGUGUAAUUUUGUGUGCACAAGGAGCGGCAUUAGGGAUCCAAAGGGGGCUUUCGGAGGGAGUUCUCGGUGGGUUCUCGGUGGGUAGGACCCAUUUGAGAAC
.......(.((((((((((....((((((....)))))).)))))))))).)..(((..(((((((((.....)))))))))..)))((((((((((((.....)))).)))))))) ( -45.90)
>DroSec_CAF1 36539 93 + 1
CACAUUAUGCUAAUGUCGUGUAAUUUUGUGUGCACAAGGAGCGGCAUUAGGGAUCCAAAGGGGG-------------UUCU-----------CGGUGGGUAGGACACAUUUGAGGAC
.......(.((((((((((....((((((....)))))).)))))))))).).(((....)))(-------------((((-----------(.(((.......)))....)))))) ( -25.60)
>DroSim_CAF1 32943 104 + 1
CACAUUAUGCUAAUGUCGUGUAAUUUUGUGUGCACAAGGAGCGGCAUUAGGGAUCCAAAGGGGG-------------UUCUCGGUGGGUUCUCGGUGGGUAGGACACAUUUGAGGAC
(((......((((((((((....((((((....)))))).))))))))))((((((.....)))-------------)))...))).((((((.(((.......)))....)))))) ( -33.00)
>DroEre_CAF1 36032 105 + 1
CACAUUAUGCUAAUGUCGUGUAAUUUUGUGUGCACAAGGAGCGGCAUUAGGGAUGCGAAGG-GGCUUUCAG-----------GGGAGGUUCUCGUUGGGUAGGACCCAUUUGAGGAC
(.((((...((((((((((....((((((....)))))).)))))))))).)))).)....-..((((...-----------.))))(((((((.((((.....))))..))))))) ( -33.10)
>DroYak_CAF1 33295 109 + 1
CACAUUAUGCUAAUGUCGUGUAAUUUUGUGUGCACAAGGAGCGGCAUUAGGGUUGCGAGGGCGGCUUUCAGAGG--------GGGGGGUUCUCGGUGGGUAAAACCCAUUUGAGGAC
.........((((((((((....((((((....)))))).))))))))))((((((....))))))........--------.....((((((((((((.....)))).)))))))) ( -36.10)
>consensus
CACAUUAUGCUAAUGUCGUGUAAUUUUGUGUGCACAAGGAGCGGCAUUAGGGAUCCAAAGGGGGCUUUC_G______UUCU_GGGGGGUUCUCGGUGGGUAGGACCCAUUUGAGGAC
.......(.((((((((((....((((((....)))))).)))))))))).).(((....)))........................((((((((((((.....)))).)))))))) (-24.70 = -26.14 +   1.44)

alignment

secondary structure

dotplot

Window 7

Location	835,678 – 835,776
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	78.70
Mean single sequence MFE	-16.90
Consensus MFE	-9.72
Energy contribution	-10.48
Covariance contribution	0.76
Combinations/Pair	1.07
Mean z-score	-1.91
Structure conservation index	0.58
SVM decision value	0.45
SVM RNA-class probability	0.741401
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 835678 98 - 22224390
ACCACCCACCACUUGGCAUACGUUCUCAAAUGGGUCCUACCCACCGAGAACCCACCGAGAACUCCCUCCGAAAGCCCCCUUUGGAUCCCUAAUGCCGC
..............(((((..((((((...(((((.((........)).)))))..))))))....((((((.......))))))......))))).. ( -27.00)
>DroSec_CAF1 36579 74 - 1
ACCACCCACCACUUGGCAUACGUCCUCAAAUGUGUCCUACCCACCG-----------AGAA-------------CCCCCUUUGGAUCCCUAAUGCCGC
..............(((((((((......))))..........(((-----------((..-------------.....))))).......))))).. ( -10.50)
>DroSim_CAF1 32983 85 - 1
ACCACCCACCACUUGGCAUACGUCCUCAAAUGUGUCCUACCCACCGAGAACCCACCGAGAA-------------CCCCCUUUGGAUCCCUAAUGCCGC
..............(((((..((.(((....(((.......))).))).))...(((((..-------------.....))))).......))))).. ( -13.10)
>DroEre_CAF1 36072 86 - 1
ACCACCCACCACUUGGCAUACGUCCUCAAAUGGGUCCUACCCAACGAGAACCUCCC-----------CUGAAAGCC-CCUUCGCAUCCCUAAUGCCGC
..............(((((..((.(((...((((.....))))..))).)).....-----------......((.-.....)).......))))).. ( -17.00)
>DroYak_CAF1 33335 90 - 1
ACCACCCACCACUUGGCAUACGUCCUCAAAUGGGUUUUACCCACCGAGAACCCCCC--------CCUCUGAAAGCCGCCCUCGCAACCCUAAUGCCGC
..............(((((..((.(((...((((.....))))..))).)).....--------............((....)).......))))).. ( -16.90)
>consensus
ACCACCCACCACUUGGCAUACGUCCUCAAAUGGGUCCUACCCACCGAGAACCCACC_AGAA______C_GAAAGCCCCCUUUGGAUCCCUAAUGCCGC
..............(((((.....(((...((((.....))))..)))............................((....)).......))))).. ( -9.72 = -10.48 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:48 2006