Locus 842

Sequence ID	3R_DroMel_CAF1
Location	2,877,048 – 2,877,192
Length	144
Max. P	0.844151

overview

Window 1

Location	2,877,048 – 2,877,152
Length	104
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.12
Mean single sequence MFE	-24.07
Consensus MFE	-20.29
Energy contribution	-20.10
Covariance contribution	-0.19
Combinations/Pair	1.06
Mean z-score	-1.73
Structure conservation index	0.84
SVM decision value	0.59
SVM RNA-class probability	0.793715
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2877048 104 - 27905053
UGCUGGCCCAUGUUCGCAAUGGAACUUCACUCCAUGCACUCGAGCCUAGCAGGUGGCCCCAGUAUCCGGCCACUCCC---------------C-AUUUUCUCCUCCCUCCUUCUUCGUUC
(((((((.(..((..(((.((((.......)))))))))..).))).))))(((((((.........)))))))...---------------.-.......................... ( -26.70)
>DroSec_CAF1 8191 92 - 1
UGCUGGCCCAUGUUCGCAAUGGAACUUCACUCCAUGCACUCGAGCCUAGCAGGUGGCCCCAGCAUCCG----------------------------UUUCUCCUCCCUCCAUCUUCAUUC
((((((.((......(((.((((.......)))))))......(((.....)))))..))))))....----------------------------........................ ( -20.60)
>DroSim_CAF1 10590 105 - 1
UGCUGGCCCAUGUUCGCAAUGGAACUUCACUCCAUGCACUCGAGCCUAGCAGGUGGCCCCAGCAUCCGGCCACUCCC---------------CCCAUUUCUCCUCCCUCCAUCUUCAUUC
(((((((.(..((..(((.((((.......)))))))))..).))).))))(((((((.........)))))))...---------------............................ ( -26.70)
>DroEre_CAF1 9209 120 - 1
UGCUGGCCCAUGUUCGCAAUGGAACUUCACUCCAUGCACUCGAGCCUAGCAGGUGGCCCCAGCAUCCGGCGACUCCCCUAAUCCUCCAUUCCCCCAUUCCUGCUCCCUCCUUCUUCAUUC
(((((((.(..((..(((.((((.......)))))))))..).))).))))(((.(((.........))).))).............................................. ( -22.30)
>consensus
UGCUGGCCCAUGUUCGCAAUGGAACUUCACUCCAUGCACUCGAGCCUAGCAGGUGGCCCCAGCAUCCGGCCACUCCC_______________C_CAUUUCUCCUCCCUCCAUCUUCAUUC
((((((.((......(((.((((.......)))))))......(((.....)))))..))))))........................................................ (-20.29 = -20.10 +  -0.19)

alignment

secondary structure

dotplot

Window 2

Location	2,877,075 – 2,877,192
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.81
Mean single sequence MFE	-40.98
Consensus MFE	-38.35
Energy contribution	-38.35
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.94
SVM decision value	0.76
SVM RNA-class probability	0.844151
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2877075 117 + 27905053
---GGGAGUGGCCGGAUACUGGGGCCACCUGCUAGGCUCGAGUGCAUGGAGUGAAGUUCCAUUGCGAACAUGGGCCAGCAUGUCGCUCCAUUAAUUUGCCAUAAAACAGAAGUGGACUAA
---....(((((..(.((.((((((.((.((((.((((((..(((((((((.....))))).))))....)))))))))).)).)))))).)).)..))))).................. ( -42.40)
>DroSec_CAF1 8215 108 + 1
------------CGGAUGCUGGGGCCACCUGCUAGGCUCGAGUGCAUGGAGUGAAGUUCCAUUGCGAACAUGGGCCAGCAUGUCGCUCCAUUAAUUUGCCAUAAAACAGAAGUGGACUUA
------------(((((..((((((.((.((((.((((((..(((((((((.....))))).))))....)))))))))).)).))))))...)))))((((.........))))..... ( -38.40)
>DroSim_CAF1 10618 117 + 1
---GGGAGUGGCCGGAUGCUGGGGCCACCUGCUAGGCUCGAGUGCAUGGAGUGAAGUUCCAUUGCGAACAUGGGCCAGCAUGUCGCUCCAUUAAUUUGCCAUAAAACAGAAGUGGACUAA
---....(((((.((((..((((((.((.((((.((((((..(((((((((.....))))).))))....)))))))))).)).))))))...))))))))).................. ( -42.70)
>DroEre_CAF1 9249 120 + 1
UAGGGGAGUCGCCGGAUGCUGGGGCCACCUGCUAGGCUCGAGUGCAUGGAGUGAAGUUCCAUUGCGAACAUGGGCCAGCAUGUCGCUCCAUUAAUUUGCCAUAAAACAGAAGUGGACUAA
......(((((.(((((..((((((.((.((((.((((((..(((((((((.....))))).))))....)))))))))).)).))))))...))))).).....((....)).)))).. ( -40.40)
>consensus
___GGGAGUGGCCGGAUGCUGGGGCCACCUGCUAGGCUCGAGUGCAUGGAGUGAAGUUCCAUUGCGAACAUGGGCCAGCAUGUCGCUCCAUUAAUUUGCCAUAAAACAGAAGUGGACUAA
............(((((..((((((.((.((((.((((((..(((((((((.....))))).))))....)))))))))).)).))))))...)))))((((.........))))..... (-38.35 = -38.35 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:32 2006