Locus 5115

Sequence ID	3R_DroMel_CAF1
Location	13,472,072 – 13,472,165
Length	93
Max. P	0.876615

overview

Window 2

Location	13,472,072 – 13,472,165
Length	93
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	80.04
Mean single sequence MFE	-33.50
Consensus MFE	-28.05
Energy contribution	-29.05
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.84
SVM decision value	0.90
SVM RNA-class probability	0.876615
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13472072 93 + 27905053
AUCAAAUGC-CGUUAUAUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAG-----G
.........-.......(((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))))..-----. ( -33.80)
>DroVir_CAF1 21935 94 + 1
GCGAACCAAUUUUCCGACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAUA-----A
..................((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))...-----. ( -33.10)
>DroPse_CAF1 30685 97 + 1
ACCAGGUGC-CGUUAUGUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGAA-UAGA
.........-..((((.(((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))))..)-))). ( -34.40)
>DroWil_CAF1 22510 93 + 1
GUGAAACAC-C-----AUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAACUUUGGA
........(-(-----((((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))))....))). ( -35.60)
>DroMoj_CAF1 20446 94 + 1
GUUGGGCAUUUCAUCGAAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAG-----C
(((((((....((((......))))..((((........))))....)))))))...((.(((((.(((((.......))))).)))))))..-----. ( -33.50)
>DroAna_CAF1 24404 94 + 1
AUCUGAUAC-GUUUAUACGGGGAUGUAGCUCAGAUGGUAGAACGCUCCCUUAUCAUGUGAGACGUACUGCUAUCGAUACCGCGCAUCUCCAACU----G
.........-........((((((((.((...((((((((.((((((.(.......).))).))).))))))))......))))))))))....----. ( -30.60)
>consensus
AUCAAACAC_CGUUAUAUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAA_____A
..................((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))......... (-28.05 = -29.05 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	13,472,072 – 13,472,165
Length	93
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	80.04
Mean single sequence MFE	-27.77
Consensus MFE	-19.25
Energy contribution	-19.95
Covariance contribution	0.70
Combinations/Pair	1.05
Mean z-score	-1.43
Structure conservation index	0.69
SVM decision value	0.34
SVM RNA-class probability	0.693960
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13472072 93 - 27905053
C-----CUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCAUAUAACG-GCAUUUGAU
.-----....(((.(((((((.......))))))).)))(((.(((((..(....)((((........))))................)-)))).))). ( -27.10)
>DroVir_CAF1 21935 94 - 1
U-----UAUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUCGGAAAAUUGGUUCGC
.-----(((((((((((((((.......)))))))..)))).))))....((((((((((........))))....(((.....)))......)))))) ( -33.40)
>DroPse_CAF1 30685 97 - 1
UCUA-UUCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCACAUAACG-GCACCUGGU
....-....((((.(((((((.......))))))).))))((..((((..(....)((((........))))................)-)))..)).. ( -25.00)
>DroWil_CAF1 22510 93 - 1
UCCAAAGUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCAU-----G-GUGUUUCAC
......((.((((.(((((((.......))))))).)))).))..(((.....)))((((........)))).(((((.....-----)-))))..... ( -28.50)
>DroMoj_CAF1 20446 94 - 1
G-----CUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCUUCGAUGAAAUGCCCAAC
(-----(.(((((((((((((.......)))))))..)))).)).)).....(.((((((........))))..((((......))))....)).)... ( -29.30)
>DroAna_CAF1 24404 94 - 1
C----AGUUGGAGAUGCGCGGUAUCGAUAGCAGUACGUCUCACAUGAUAAGGGAGCGUUCUACCAUCUGAGCUACAUCCCCGUAUAAAC-GUAUCAGAU
.----...((((((((..(.((.......)).)..)))))).))(((((.((((..((((........))))....))))(((....))-))))))... ( -23.30)
>consensus
U_____CUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCAUAUAAAG_GUAUCUGAC
........(((((((((((((.......)))))))..)))).)).(((.....)))((((........))))........................... (-19.25 = -19.95 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:38 2006