Locus 6103

Sequence ID	3R_DroMel_CAF1
Location	16,003,875 – 16,003,998
Length	123
Max. P	0.953296

overview

Window 0

Location	16,003,875 – 16,003,968
Length	93
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	74.11
Mean single sequence MFE	-36.84
Consensus MFE	-16.22
Energy contribution	-18.00
Covariance contribution	1.78
Combinations/Pair	1.17
Mean z-score	-2.33
Structure conservation index	0.44
SVM decision value	1.43
SVM RNA-class probability	0.953296
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16003875 93 + 27905053
GUCCUUGCCGCCCUGCUCGUCCUUGCUGCC----------UUCCUCUGCUUCUCUGCUGUCA-------GACCGAGGAUGCAGCGGAAAAUGAUUUGUGCG---GGGCAUAAA
.........(((((((((((..(((((((.----------.(((((.(....((((....))-------))).))))).)))))))...)))).....)))---))))..... ( -33.90)
>DroPse_CAF1 4141 87 + 1
GUCCCUCCG---CUACACGUU-UUACUAGG-----------UCCGUGGCUGCUCCGCUGGCU-------G----CUGCUGCAAUGGAACAUGAUUUGUGCGGCGGGGCAUAAA
(((((.(((---(.(((.(((-........-----------(((((.((.((...((.....-------)----).)).)).)))))....))).))))))).)))))..... ( -32.30)
>DroSec_CAF1 20260 93 + 1
GUCCUUGCCGCCCUGCUCCUCCUUGCUACC----------UUCCACUGCUCCUCUCCUGGCA-------GCCCGAGGAUGCAGUGGAAAAUGAUUUGUGCG---GGGCAUAAA
.........(((((((.........(....----------((((((((((((((....((..-------..))))))).)))))))))...)......)))---))))..... ( -35.36)
>DroSim_CAF1 3835 93 + 1
GUCCUUGCCGCCCUGCUCCUCCUUGCUACC----------UUCCACUGCUCCUCUACUGGCA-------GCCCGAGGAUGCAGUGGAAAAUGAUUUGUGCG---GGGCAUAAA
.........(((((((.........(....----------((((((((((((((....((..-------..))))))).)))))))))...)......)))---))))..... ( -35.36)
>DroEre_CAF1 3778 96 + 1
GUCCUUGCCGUCCUGCUCCUCCUUGCUC-C----------UUC--CUGCUCCUCUGCAGGAGGCAGGAGGCAGGAGGAUGCAGUGAAAAAUGAUUUGUGCG----GGCAUAAA
((((.(((.(((((.((((((((.(((.-.----------.((--((((......))))))))))))))).)).))))))))(((.(((....))).))))----)))..... ( -42.00)
>DroYak_CAF1 4713 99 + 1
GUCCUGGCCGCCGUGCUCCUCCCGGCUC-CUCCAGGCUGCUUU--CUGCUCCUCUGCAGGGA-------GCCGGAGGAUGCAGUGGAAAAUGAUUUGUGCG----GGCAUAAA
....((.((((..(((((((((.(((((-((.((((..((...--..))...))))..))))-------))))))))).)))(..((......))..))))----).)).... ( -42.10)
>consensus
GUCCUUGCCGCCCUGCUCCUCCUUGCUACC__________UUCC_CUGCUCCUCUGCUGGCA_______GCCCGAGGAUGCAGUGGAAAAUGAUUUGUGCG___GGGCAUAAA
........................................((((.(((((((((....(((........))).))))).)))).)))).....(((((((......))))))) (-16.22 = -18.00 +   1.78)

alignment

secondary structure

dotplot

Window 1

Location	16,003,905 – 16,003,998
Length	93
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	82.48
Mean single sequence MFE	-32.53
Consensus MFE	-24.03
Energy contribution	-25.98
Covariance contribution	1.95
Combinations/Pair	1.13
Mean z-score	-2.33
Structure conservation index	0.74
SVM decision value	0.74
SVM RNA-class probability	0.836858
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16003905 93 + 27905053
-----UUCCUCUGCUUCUCUGCUGUCA-------GACCGAGGAUGCAGCGGAAAAUGAUUUGUGCG---GGGCAUAAACUGCGUGAAUUCACAGUACAAAUUGACUUG
-----((((.(((((((((.((.....-------).).))))).)))).))))...(((((((((.---..(((.....)))(((....))).)))))))))...... ( -29.80)
>DroPse_CAF1 4167 91 + 1
------UCCGUGGCUGCUCCGCUGGCU-------G----CUGCUGCAAUGGAACAUGAUUUGUGCGGCGGGGCAUAAACUGCGUGAAUUCCCAGUACAAAUUGACUUG
------((((..(.((((((((((..(-------(----(....))).....(((.....))).))))))))))....)..)).)).....((((....))))..... ( -26.60)
>DroSec_CAF1 20290 93 + 1
-----UUCCACUGCUCCUCUCCUGGCA-------GCCCGAGGAUGCAGUGGAAAAUGAUUUGUGCG---GGGCAUAAACUGCGUGAAUUCACAGUACAAAUUGACUUG
-----((((((((((((((....((..-------..))))))).)))))))))...(((((((((.---..(((.....)))(((....))).)))))))))...... ( -36.50)
>DroSim_CAF1 3865 93 + 1
-----UUCCACUGCUCCUCUACUGGCA-------GCCCGAGGAUGCAGUGGAAAAUGAUUUGUGCG---GGGCAUAAACUGCGUGAAUUCACAGUACAAAUUGACUUG
-----((((((((((((((....((..-------..))))))).)))))))))...(((((((((.---..(((.....)))(((....))).)))))))))...... ( -36.50)
>DroEre_CAF1 3807 97 + 1
-----UUC--CUGCUCCUCUGCAGGAGGCAGGAGGCAGGAGGAUGCAGUGAAAAAUGAUUUGUGCG----GGCAUAAACUGCGUGAAUUCACAGUACAAAUUGACUUG
-----(((--((((..(.((((.....)))))..)))))))...............(((((((((.----.(((.....)))(((....))).)))))))))...... ( -33.10)
>DroYak_CAF1 4747 95 + 1
GCUGCUUU--CUGCUCCUCUGCAGGGA-------GCCGGAGGAUGCAGUGGAAAAUGAUUUGUGCG----GGCAUAAACUGCGUGAACUCACAGUACAAAUUGACUUG
(((((.((--((((((((.....))))-------))...)))).))))).......(((((((((.----.(((.....)))(((....))).)))))))))...... ( -32.70)
>consensus
_____UUCC_CUGCUCCUCUGCUGGCA_______GCCCGAGGAUGCAGUGGAAAAUGAUUUGUGCG___GGGCAUAAACUGCGUGAAUUCACAGUACAAAUUGACUUG
.....((((.(((((((((....(((........))).))))).)))).))))...(((((((((......(((.....)))(((....))).)))))))))...... (-24.03 = -25.98 +   1.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:44 2006