Locus 4286

Sequence ID	3R_DroMel_CAF1
Location	11,410,355 – 11,410,573
Length	218
Max. P	0.656818

overview

Window 2

Location	11,410,355 – 11,410,461
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.39
Mean single sequence MFE	-30.72
Consensus MFE	-28.14
Energy contribution	-28.18
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.16
Structure conservation index	0.92
SVM decision value	0.26
SVM RNA-class probability	0.656818
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11410355 106 - 27905053
CGGGCAUAUCCUGUUGACAGGAGCGCAUCUGACUGCCU--------GCUGGCCUCAGGUCCUUUC-UCUUAUCUUGGCGGUUCUUUCGUCUAACAUGUGUCCUACAAAUGUUCCC-----
.((((((((((((....)))))..(.((((((..(((.--------...))).)))))).)....-.........(((((.....))))).....))))))).............----- ( -30.10)
>DroSec_CAF1 158003 106 - 1
CGGGCAUAUCCUGUUGACAGGAGCGCAUCUGACUGCCU--------GCUGGCCUCAGGUCCUUUC-UCUUAUCUUGGCGGUUCUUUCGUCUAACAUGUGUCCUACAAAUGUUCCC-----
.((((((((((((....)))))..(.((((((..(((.--------...))).)))))).)....-.........(((((.....))))).....))))))).............----- ( -30.10)
>DroSim_CAF1 149471 106 - 1
CGGGCAUAUCCUGUUGACAGGAGCGCAUCUGACUGCCU--------GCUGGCCUCAGGUCCUUUC-UCUUAUCUUGGCGGUUCUUUCGUCUAACAUGUGUCCUACAAAUGUUCCC-----
.((((((((((((....)))))..(.((((((..(((.--------...))).)))))).)....-.........(((((.....))))).....))))))).............----- ( -30.10)
>DroEre_CAF1 145729 107 - 1
CGGGCAUAUCCUGUUGACAGGGGCGCAUCUGACUGCCU--------GCUGGCCUCAGGUCCUUUCUUCUUAUCUUAGCGGUUCCUUCGUCUAACAUGUGUCCUACAAAUGUUGCC-----
.(((((((...(((((((((((((((((((((..(((.--------...))).)))))).................)).))))))..))).))))))))))).............----- ( -29.42)
>DroYak_CAF1 149604 120 - 1
CGGGCAUAUCCUGUUGACAGGAGCGCAUCUGACUGCCUGCUAUCCUGCUGGCCUCAGGUCCUUUCUUCUUAUCUUGGCGGUUCUUUCGUCUAACAUGUGUCCUACAAAUGUUCCCCCGGU
((((....(((((....)))))((((((((((..(((.((......)).))).))))..................(((((.....)))))....))))))..............)))).. ( -33.90)
>consensus
CGGGCAUAUCCUGUUGACAGGAGCGCAUCUGACUGCCU________GCUGGCCUCAGGUCCUUUC_UCUUAUCUUGGCGGUUCUUUCGUCUAACAUGUGUCCUACAAAUGUUCCC_____
.((((((((((((....)))))..(.((((((..(((............))).)))))).)..............(((((.....))))).....))))))).................. (-28.14 = -28.18 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	11,410,461 – 11,410,573
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.24
Mean single sequence MFE	-34.74
Consensus MFE	-25.82
Energy contribution	-27.14
Covariance contribution	1.32
Combinations/Pair	1.07
Mean z-score	-1.77
Structure conservation index	0.74
SVM decision value	0.23
SVM RNA-class probability	0.642905
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11410461 112 + 27905053
AGUGCCGAGAGCACAUUUCACACCUCACAAUGCAACAA--------UGCAACAAUGCGGCAGUGCCACAAAGGGCGGACCAGCACAGGAUAUCAGCUGCUGCCGCAGUCCCAGUUGAAAA
.((((.....)))).((((((.........((((....--------))))....((((((((((((......))))...((((...........))))))))))))......).))))). ( -33.90)
>DroSec_CAF1 158109 120 + 1
AGUGCCGAGAGCACAUUUCACACCUCACAAUGCAACAAUGUAAGAAUGCAACAAUGCGGCAGUGCCACAAAGGGCGGACCAGCACAGGAUAUCAGAUGCUGCCGCAGUCCCAGUUGAAAA
.((((.....))))..................((((..((((....))))....((((((((((((......)))...((......)).........)))))))))......)))).... ( -32.80)
>DroSim_CAF1 149577 120 + 1
AGUGCCGAGAGCACAUUUCACACCUCACAAUGCAACAAUGUGAGAAUGUAACAAUGCGGCAGUGCCACAAAGGGCGGACCAGCACAGGAUAUCAGCUGCUGCCGCAGUCCCAGUUGAAAA
.((((.....)))).((((((..((((((.((...)).))))))..((..((..((((((((((((......))))...((((...........))))))))))))))..))).))))). ( -38.60)
>DroEre_CAF1 145836 120 + 1
AAUGCCGAGAGCACAUUUCACACCUCACAAUGCAACAAUGCAACAAUGCACCAAUGCGGCAGUGGCACAAAGGGCGGACCUGCAGAGGAUAUCAGCUGCUGCCGCAGUCCCUGCUGAAAA
..(((.....)))..(((((..........((((....)))).....(((....((((((((..((....(((.....)))...((.....)).))..)))))))).....)))))))). ( -36.40)
>DroYak_CAF1 149724 112 + 1
AGUGGCGAGAGAACAUUUCACACCUCACAAUGCAACAAUGCAACA--------AUGCGGCAGUGCCACAAAGGGCGGACCAGCACAGGAUAUCAGCUGCUGCCGCAGUCCCUGUUGAAAA
.(((..((((.....)))).))).(((((.((((....))))...--------.((((((((((((......))))...((((...........)))))))))))).....)).)))... ( -32.00)
>consensus
AGUGCCGAGAGCACAUUUCACACCUCACAAUGCAACAAUGCAACAAUGCAACAAUGCGGCAGUGCCACAAAGGGCGGACCAGCACAGGAUAUCAGCUGCUGCCGCAGUCCCAGUUGAAAA
.((((.....)))).((((((.........((((....))))............((((((((((((......)))...((......)).........)))))))))......).))))). (-25.82 = -27.14 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:44 2006