Locus 7522

Sequence ID	3R_DroMel_CAF1
Location	20,129,410 – 20,129,543
Length	133
Max. P	0.989333

overview

Window 8

Location	20,129,410 – 20,129,515
Length	105
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	90.88
Mean single sequence MFE	-42.58
Consensus MFE	-41.24
Energy contribution	-40.44
Covariance contribution	-0.80
Combinations/Pair	1.13
Mean z-score	-1.65
Structure conservation index	0.97
SVM decision value	2.16
SVM RNA-class probability	0.989333
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20129410 105 + 27905053
------UCC-AAGUCCCCUGAGCACCUUCUAAGCUCGUGGCUACCAUGGGUCAGGGCAGCCCAAAGGGCACAGCGGACCACAGACGGGUUCAUCGGAGCCAGGAGGUGCUAA
------...-..........((((((((((..((((((((...))))))))...(((.((((...)))).....(((((.......)))))......))))))))))))).. ( -42.80)
>DroSec_CAF1 17670 105 + 1
------UCC-AAGUCCCGCAAGCACCUUCUAAGCUCGUGGCUGCCAUGGGUCAGGGCAGCCCAAAGGGCACAGCGGACCACCGACGGGUUCAUCGGAGCCAGGAGGUGCUAA
------...-..........((((((((((..((((..(((((((.((...)).)))))))....))))...((((....))).).(((((....))))))))))))))).. ( -45.00)
>DroSim_CAF1 13449 105 + 1
------UCC-AAGUCCCGCAAGCACCUUCUAAGCUCGUGGCUGCCAUGGGUCAGGGCAGCCCAAAGGGCACAGCGGACCACAGACAGGUUCAUCGGAGCCAGGAGGUGCUAA
------...-..........((((((((((..((((..(((((((.((...)).)))))))....)))).................(((((....))))))))))))))).. ( -42.90)
>DroEre_CAF1 13721 111 + 1
AAGUCUUCC-AAGUCCCCCAAGCGCUUUCUAAGCUCGUGGCUGCCAUGGGUCAGGGCAGCCCAAAGGGCACAGCGGAUCACAGACGGGUUCACCGGAGCCAGGAGGUGCUAA
.........-..........((((((((((..((((((((((((.....((....)).((((...))))...)))).))))...(((.....))))))).)))))))))).. ( -40.00)
>DroYak_CAF1 13772 112 + 1
AAGUACCCCAAAGUCCCCCAAGCGCUUUCUAAGCUCGUGGCUGCCAUGGGUCAGGGCAGCCCAAAGGGCACAGCGGACCACAGACGGGUUCAUUGGAGUCAGGAGGUGCUAA
.((((((((..(.(((.....(((((((....((((((((...)))))))).))))).((((...))))...))(((((.......)))))...))).)..)).)))))).. ( -42.20)
>consensus
______UCC_AAGUCCCCCAAGCACCUUCUAAGCUCGUGGCUGCCAUGGGUCAGGGCAGCCCAAAGGGCACAGCGGACCACAGACGGGUUCAUCGGAGCCAGGAGGUGCUAA
....................((((((((((..((((((((...))))))))...(((.((((...)))).....(((((.......)))))......))))))))))))).. (-41.24 = -40.44 +  -0.80)

alignment

secondary structure

dotplot

Window 9

Location	20,129,439 – 20,129,543
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	93.94
Mean single sequence MFE	-34.92
Consensus MFE	-31.34
Energy contribution	-31.34
Covariance contribution	-0.00
Combinations/Pair	1.17
Mean z-score	-1.79
Structure conservation index	0.90
SVM decision value	2.14
SVM RNA-class probability	0.988935
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20129439 104 - 27905053
GCACUUCCCCCACAAAGACGAGAUCAUUUUAGCACCUCCUGGCUCCGAUGAACCCGUCUGUGGUCCGCUGUGCCCUUUGGGCUGCCCUGACCCAUGGUAGCCAC
((((.....(((((..((((.(.(((((..(((........)))..))))).).)))))))))......))))......(((((((.((...)).))))))).. ( -36.40)
>DroSec_CAF1 17699 104 - 1
GCACUUCCCACACAAAGACGAGAUCAUUUUAGCACCUCCUGGCUCCGAUGAACCCGUCGGUGGUCCGCUGUGCCCUUUGGGCUGCCCUGACCCAUGGCAGCCAC
((((...((((.....((((.(.(((((..(((........)))..))))).).)))).))))......))))......(((((((.((...)).))))))).. ( -37.00)
>DroSim_CAF1 13478 104 - 1
GCACUUUCCACGCAAAGACGAGAUCAUUUUAGCACCUCCUGGCUCCGAUGAACCUGUCUGUGGUCCGCUGUGCCCUUUGGGCUGCCCUGACCCAUGGCAGCCAC
((((...((((....(((((.(.(((((..(((........)))..))))).).)))))))))......))))......(((((((.((...)).))))))).. ( -35.70)
>DroEre_CAF1 13756 104 - 1
GCACUACCCACACGGAGAAGAGAUCAUUUUAGCACCUCCUGGCUCCGGUGAACCCGUCUGUGAUCCGCUGUGCCCUUUGGGCUGCCCUGACCCAUGGCAGCCAC
........((((((((..(.((((((((..(((........)))..))))).....))).)..)))).)))).......(((((((.((...)).))))))).. ( -32.80)
>DroYak_CAF1 13808 104 - 1
GCACUUCCCACACGCAGAAGAGAUCAUUUUAGCACCUCCUGACUCCAAUGAACCCGUCUGUGGUCCGCUGUGCCCUUUGGGCUGCCCUGACCCAUGGCAGCCAC
((((..(..((.((((((.(.(.(((((..((((.....)).))..))))).).).))))))))..)..))))......(((((((.((...)).))))))).. ( -32.70)
>consensus
GCACUUCCCACACAAAGACGAGAUCAUUUUAGCACCUCCUGGCUCCGAUGAACCCGUCUGUGGUCCGCUGUGCCCUUUGGGCUGCCCUGACCCAUGGCAGCCAC
((((......(((..(((((.(.(((((..(((........)))..))))).).)))))))).......))))......(((((((.((...)).))))))).. (-31.34 = -31.34 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:01 2006