Locus 2

Sequence ID	3R_DroMel_CAF1
Location	58,824 – 58,932
Length	108
Max. P	0.919711

overview

Window 2

Location	58,824 – 58,932
Length	108
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	76.02
Mean single sequence MFE	-30.80
Consensus MFE	-21.79
Energy contribution	-22.93
Covariance contribution	1.14
Combinations/Pair	1.26
Mean z-score	-1.53
Structure conservation index	0.71
SVM decision value	1.13
SVM RNA-class probability	0.919711
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 58824 108 + 27905053
AAAAUCAGAAAUAUAGAUCGAAUGCUAUGGCGCACGUAAAGCGGUAUCGGAGGUCGUCUAAGUCCUCGGAGGAAGGCGACCUGGACAACGAGGACUACGUGCCAUACG
.........................((((((((.((.....))((.(((.(((((((((...(((.....))))))))))))......)))..))...)))))))).. ( -31.50)
>DroPse_CAF1 1926 102 + 1
----UAAAUAAUUUCGUU--AACAAAAUGGCAAAUGUAAAGAGGUACAGGAGAACUUCAAAGUCAUCCGAUGACGGAGCGGAGGAGAACGAUGACUAUGUACCGUAUG
----...........(((--(......))))...........(((((((((....)))..(((((((((....)))).((........)).))))).))))))..... ( -20.00)
>DroSec_CAF1 1 82 + 1
--------------------------AUGGCGCAGGUAAAGCGGUAUCGGAGGUCGUCUAAGUCCUCGGAGGAAGGCAACCCGGACAACGAGGAGUACGUGCCAUACG
--------------------------(((((((.......((..(.((.((((.(......).)))).))..)..))..((((.....)).)).....)))))))... ( -27.00)
>DroSim_CAF1 3854 108 + 1
AAAAUCAGAAAUAUAGAUCGAAUGGUAUGGCGCAGGUAAAGCGGUAUCGGAGGUCGUCUAAGUCCUCGGAGGAAGGCGACCCAGACAACGAGGAGUACGUGCCAUACG
........................(((((((((..(((...((...((.(.((((((((...(((.....)))))))))))).))...)).....)))))))))))). ( -34.20)
>DroEre_CAF1 1976 108 + 1
AAAGUCAGAAAUAUAGAUCGACUGGUAUGGCGCAAGUAAAGCGGUAUCGGAGGUCGUCCAAGUCCUCCGAGGAAGGCGACCAGGACAACGAGGAGUACGUGCCGUACG
..((((.((........)))))).(((((((((.......((..(.(((((((.(......).)))))))..)..))..((.(.....)..)).....))))))))). ( -35.90)
>DroYak_CAF1 3841 108 + 1
AAAGUCAGAAAUAUAGAUCGACUUGUAUGGCGUUUGUAAAGCGGUAUCGGAGGUCGUCUAACUCCUCCGAGGAAGGCGACCAGGACAACGAGGAGUACGUGCCGUACG
.(((((.((........)))))))((((((((..((((...((...((...((((((((..(((....)))..))))))))..))...)).....)))))))))))). ( -36.20)
>consensus
AAA_UCAGAAAUAUAGAUCGAAUGGUAUGGCGCAGGUAAAGCGGUAUCGGAGGUCGUCUAAGUCCUCCGAGGAAGGCGACCAGGACAACGAGGAGUACGUGCCAUACG
........................(((((((((..(((...((...((...((((((((...(((.....)))))))))))..))...)).....)))))))))))). (-21.79 = -22.93 +   1.14)

alignment

secondary structure

dotplot

Window 3

Location	58,824 – 58,932
Length	108
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	76.02
Mean single sequence MFE	-26.42
Consensus MFE	-16.20
Energy contribution	-15.79
Covariance contribution	-0.41
Combinations/Pair	1.43
Mean z-score	-1.46
Structure conservation index	0.61
SVM decision value	0.35
SVM RNA-class probability	0.700127
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 58824 108 - 27905053
CGUAUGGCACGUAGUCCUCGUUGUCCAGGUCGCCUUCCUCCGAGGACUUAGACGACCUCCGAUACCGCUUUACGUGCGCCAUAGCAUUCGAUCUAUAUUUCUGAUUUU
..((((((((((((....((.((((.((((((.(((((.....)))...)).))))))..)))).))..))))))..))))))......((((.........)))).. ( -28.90)
>DroPse_CAF1 1926 102 - 1
CAUACGGUACAUAGUCAUCGUUCUCCUCCGCUCCGUCAUCGGAUGACUUUGAAGUUCUCCUGUACCUCUUUACAUUUGCCAUUUUGUU--AACGAAAUUAUUUA----
.....((((((.(((((((((........))..((....))))))))).)).........((((......))))..))))((((((..--..))))))......---- ( -16.80)
>DroSec_CAF1 1 82 - 1
CGUAUGGCACGUACUCCUCGUUGUCCGGGUUGCCUUCCUCCGAGGACUUAGACGACCUCCGAUACCGCUUUACCUGCGCCAU--------------------------
...(((((..(((.((...((((((..(((..((((.....)))))))..))))))....))))).((.......)))))))-------------------------- ( -22.70)
>DroSim_CAF1 3854 108 - 1
CGUAUGGCACGUACUCCUCGUUGUCUGGGUCGCCUUCCUCCGAGGACUUAGACGACCUCCGAUACCGCUUUACCUGCGCCAUACCAUUCGAUCUAUAUUUCUGAUUUU
.(((((((..(((.((...(((((((((((..((((.....)))))))))))))))....))))).((.......))))))))).....((((.........)))).. ( -30.60)
>DroEre_CAF1 1976 108 - 1
CGUACGGCACGUACUCCUCGUUGUCCUGGUCGCCUUCCUCGGAGGACUUGGACGACCUCCGAUACCGCUUUACUUGCGCCAUACCAGUCGAUCUAUAUUUCUGACUUU
.(((.(((..(((.((...(((((((.((((.((......))..)))).)))))))....))))).((.......))))).))).((((((........)).)))).. ( -30.70)
>DroYak_CAF1 3841 108 - 1
CGUACGGCACGUACUCCUCGUUGUCCUGGUCGCCUUCCUCGGAGGAGUUAGACGACCUCCGAUACCGCUUUACAAACGCCAUACAAGUCGAUCUAUAUUUCUGACUUU
.(((.(((..........((.((((..(((((.((..(((....)))..)).)))))...)))).))..........))).)))(((((((........)).))))). ( -28.85)
>consensus
CGUACGGCACGUACUCCUCGUUGUCCUGGUCGCCUUCCUCCGAGGACUUAGACGACCUCCGAUACCGCUUUACAUGCGCCAUACCAUUCGAUCUAUAUUUCUGA_UUU
.....(((.((.......((.((((..(((((.(((((.....)))...)).)))))...)))).)).......)).)))............................ (-16.20 = -15.79 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:29:47 2006