Locus 1856

Sequence ID	X_DroMel_CAF1
Location	5,127,574 – 5,127,676
Length	102
Max. P	0.937571

overview

Window 6

Location	5,127,574 – 5,127,676
Length	102
Sequences	3
Columns	107
Reading direction	forward
Mean pairwise identity	72.15
Mean single sequence MFE	-31.23
Consensus MFE	-20.24
Energy contribution	-21.13
Covariance contribution	0.89
Combinations/Pair	1.05
Mean z-score	-1.26
Structure conservation index	0.65
SVM decision value	0.06
SVM RNA-class probability	0.562522
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5127574 102 + 22224390
GCUGAGGGUGAGG---GGUGGAAGAGGUCCAGGACAUGC--GACAGUUGGGAACACAGUGGGAGCGGCCGGCUGAAGCCAGCUAAAUUGCAAGUGGGUCACUGGGCC
.............---.........((((((((((.(((--((.((((((.....((((.((.....)).))))...))))))...))))).....))).))))))) ( -33.60)
>DroSec_CAF1 3967 99 + 1
----NN-NNNNNN---NNNNNNNGGAGUCCAGGAGAUGCUGGGAUGUUGGAAAAACAGUGGGAGCGGCCGGCUGAAGCCAGCUAAAUUGCAAGUGGGUCACUGGGCC
----..-......---..........((((((((..(((((.((((((((.....((((.((.....)).))))...)))))...))).).))))..)).)))))). ( -28.90)
>DroYak_CAF1 4636 105 + 1
GAGGAGGGGUAGGGGUAGGGGAUGGAGUCCAGAAGACGC--GACGGGGUGGAAAACACUGGGAGCGGCCGGCUGAAGCCAGCUAAAUUGCAAGUGGGUCAGUGGGCC
..............((...((((...)))).....))((--..(.((((.....)).)).)..))((((.(((((..(((((......))...))).))))).)))) ( -31.20)
>consensus
G__GAGGG__AGG____G_GGA_GGAGUCCAGGAGAUGC__GACAGUUGGGAAAACAGUGGGAGCGGCCGGCUGAAGCCAGCUAAAUUGCAAGUGGGUCACUGGGCC
..........................((((((.....((....(.((((......)))).)..))(((((((....))).((......)).....)))).)))))). (-20.24 = -21.13 +   0.89)

alignment

secondary structure

dotplot

Window 7

Location	5,127,574 – 5,127,676
Length	102
Sequences	3
Columns	107
Reading direction	reverse
Mean pairwise identity	72.15
Mean single sequence MFE	-22.07
Consensus MFE	-16.63
Energy contribution	-16.30
Covariance contribution	-0.33
Combinations/Pair	1.16
Mean z-score	-1.33
Structure conservation index	0.75
SVM decision value	1.26
SVM RNA-class probability	0.937571
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5127574 102 - 22224390
GGCCCAGUGACCCACUUGCAAUUUAGCUGGCUUCAGCCGGCCGCUCCCACUGUGUUCCCAACUGUC--GCAUGUCCUGGACCUCUUCCACC---CCUCACCCUCAGC
((.((((.(((.....(((......((((((....))))))(((.......)))............--))).))))))).)).........---............. ( -26.20)
>DroSec_CAF1 3967 99 - 1
GGCCCAGUGACCCACUUGCAAUUUAGCUGGCUUCAGCCGGCCGCUCCCACUGUUUUUCCAACAUCCCAGCAUCUCCUGGACUCCNNNNNNN---NNNNNN-NN----
...((((.((...............((((((....)))))).(((.....((((.....))))....)))...))))))............---......-..---- ( -19.90)
>DroYak_CAF1 4636 105 - 1
GGCCCACUGACCCACUUGCAAUUUAGCUGGCUUCAGCCGGCCGCUCCCAGUGUUUUCCACCCCGUC--GCGUCUUCUGGACUCCAUCCCCUACCCCUACCCCUCCUC
((((..((((.(((...((......)))))..))))..))))((..(..(((.....)))...)..--))(((.....))).......................... ( -20.10)
>consensus
GGCCCAGUGACCCACUUGCAAUUUAGCUGGCUUCAGCCGGCCGCUCCCACUGUUUUCCCAACAGUC__GCAUCUCCUGGACUCC_UCC_C____CCU__CCCUC__C
((.((((.((......(((......((((((....)))))).((.......))...............)))..)))))).))......................... (-16.63 = -16.30 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:19 2006