Locus 6811

Sequence ID	X_DroMel_CAF1
Location	16,954,214 – 16,954,318
Length	104
Max. P	0.998796

overview

Window 4

Location	16,954,214 – 16,954,318
Length	104
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.71
Mean single sequence MFE	-45.02
Consensus MFE	-36.20
Energy contribution	-38.08
Covariance contribution	1.87
Combinations/Pair	1.19
Mean z-score	-3.44
Structure conservation index	0.80
SVM decision value	3.23
SVM RNA-class probability	0.998796
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16954214 104 + 22224390
G--UGGGAAAAAUGGGGGCGUGGUGCCAAAAGUGGGUUGCAUUUUGAUAUGCACAAGGCA------------CCACUUUUCACCACUCCCCCCCUGUGUCCCAGCA--AAUUUAUUUAUG
.--(((((.....(((((.((((((..(((((((((((((((......)))))....)).------------)))))))))))))).)))))......)))))...--............ ( -44.60)
>DroSec_CAF1 31397 114 + 1
G--UGGGAA-AAUGGGGGCGUGGUACCAAAAGUGGGUUGCAUUUUGAUAUGCACAAGGCAUGGGCGUGCGACCCCCUUUUCACCACUCCCCGC---UGUCCCAGCAUAAAUUUAUUUACG
.--(((((.-..((((((.(((((...(((((.(((((((((.....(((((.....)))))...))))))))).))))).))))))))))).---..)))))................. ( -48.60)
>DroEre_CAF1 18701 114 + 1
GGGGGGAGA-AAUGGGGGCGUGGUGGCAAAAGUGGGUUGCAUUUUGAUAUGCACAAGGCAUGGGCGUGCGACCCCCUUUUCAGCACUUCCCAC---UGUGUUUGCU--AAUUUAUUUAUG
.((.(((.(-..((((((.(((.(((..((((.(((((((((.....(((((.....)))))...))))))))).))))))).))))))))).---..).))).))--............ ( -39.00)
>DroYak_CAF1 18172 114 + 1
GUGGGGGGA-AACGGGGGCGUGGUGCCAAAAGUGGGUUGCAUUUUGAUAUGCACAAGACAUGGGCGUGCGACCCCCUUUUCACCACUCCCCGC---UGUCUCUGCU--AAUUUAUUUAUG
..(.(((((-..((((((.((((((..(((((.(((((((((.....(((((....).))))...))))))))).))))))))))))))))).---..))))).).--............ ( -47.90)
>consensus
G__GGGGAA_AAUGGGGGCGUGGUGCCAAAAGUGGGUUGCAUUUUGAUAUGCACAAGGCAUGGGCGUGCGACCCCCUUUUCACCACUCCCCGC___UGUCCCAGCA__AAUUUAUUUAUG
...(((((....((((((.((((((..(((((.(((((((((.....(((((.....)))))...))))))))).)))))))))))))))))......)))))................. (-36.20 = -38.08 +   1.87)

alignment

secondary structure

dotplot

Window 5

Location	16,954,214 – 16,954,318
Length	104
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.71
Mean single sequence MFE	-37.60
Consensus MFE	-25.88
Energy contribution	-27.50
Covariance contribution	1.62
Combinations/Pair	1.07
Mean z-score	-2.94
Structure conservation index	0.69
SVM decision value	2.23
SVM RNA-class probability	0.990710
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16954214 104 - 22224390
CAUAAAUAAAUU--UGCUGGGACACAGGGGGGGAGUGGUGAAAAGUGG------------UGCCUUGUGCAUAUCAAAAUGCAACCCACUUUUGGCACCACGCCCCCAUUUUUCCCA--C
............--...(((((......(((((.((((((.(((((((------------.(.....(((((......))))).))))))))...)))))).))))).....)))))--. ( -42.60)
>DroSec_CAF1 31397 114 - 1
CGUAAAUAAAUUUAUGCUGGGACA---GCGGGGAGUGGUGAAAAGGGGGUCGCACGCCCAUGCCUUGUGCAUAUCAAAAUGCAACCCACUUUUGGUACCACGCCCCCAUU-UUCCCA--C
((((((....)))))).(((((.(---(.((((.((((((.(((((((((.(((.....((((.....)))).......))).)))).)))))..))))))..)))).))-.)))))--. ( -42.10)
>DroEre_CAF1 18701 114 - 1
CAUAAAUAAAUU--AGCAAACACA---GUGGGAAGUGCUGAAAAGGGGGUCGCACGCCCAUGCCUUGUGCAUAUCAAAAUGCAACCCACUUUUGCCACCACGCCCCCAUU-UCUCCCCCC
............--.........(---(((((..(((.((.(((((((((.(((.....((((.....)))).......))).)))).)))))..)).)))...))))))-......... ( -27.20)
>DroYak_CAF1 18172 114 - 1
CAUAAAUAAAUU--AGCAGAGACA---GCGGGGAGUGGUGAAAAGGGGGUCGCACGCCCAUGUCUUGUGCAUAUCAAAAUGCAACCCACUUUUGGCACCACGCCCCCGUU-UCCCCCCAC
............--....(((((.---(.((((.((((((.(((((((((.(((.....((((.....)))).......))).)))).)))))..)))))).))))))))-))....... ( -38.50)
>consensus
CAUAAAUAAAUU__AGCAGAGACA___GCGGGGAGUGGUGAAAAGGGGGUCGCACGCCCAUGCCUUGUGCAUAUCAAAAUGCAACCCACUUUUGGCACCACGCCCCCAUU_UCCCCA__C
...........................(.((((.(((((((((((.((((.(((.....((((.....)))).......))).)))).)))))..)))))).)))))............. (-25.88 = -27.50 +   1.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:32 2006