Locus 1697

Sequence ID	X_DroMel_CAF1
Location	4,731,822 – 4,731,946
Length	124
Max. P	0.972333

overview

Window 7

Location	4,731,822 – 4,731,918
Length	96
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	75.60
Mean single sequence MFE	-25.89
Consensus MFE	-3.08
Energy contribution	-4.36
Covariance contribution	1.28
Combinations/Pair	1.31
Mean z-score	-1.57
Structure conservation index	0.12
SVM decision value	0.38
SVM RNA-class probability	0.713416
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4731822 96 + 22224390
ACACCAACGGACCAGAAGAAGUCGAAGGAAAUGUGCAACCUUUGGCU--G-CACAUAUUG-ACGAAGCUGAUAG----GAUGGCAAAUAUUCCGUACAUACGGA
...(((.(..(.(((.....(((((.....(((((((.((...)).)--)-))))).)))-))....))).)..----).))).......(((((....))))) ( -23.20)
>DroSec_CAF1 24741 96 + 1
ACACCAACGGACCAGAAGAAGUCGAAGGAAAUGUGCAACCUUUGGCU--G-CACAUAUUG-ACGAAGCUGAUGG----GAUGGCAAAUAUUCCGCACAUGCGGA
.......((..(((..((..(((((.....(((((((.((...)).)--)-))))).)))-))....))..)))----..))........(((((....))))) ( -29.30)
>DroEre_CAF1 28155 97 + 1
ACACCAACGGACCAGAAGAAGUCGAAGGAAAUGUGCAACCUUAGGCU--G-CACAUAUUGGUCGAAGCAGAUGG----GAUGGCAAAUAUUUCGCUCGUAGGGA
...((.(((((((((......((....)).(((((((.((...)).)--)-))))).)))))).....((.((.----.(((.....)))..))))))).)).. ( -28.10)
>DroYak_CAF1 25974 96 + 1
ACACCAACGGACCAGAAGAAGUCGAAGGAAAUGUGCAACCCUAGGUU--G-CACAUAUUG-ACGAAGCAGAUGG----GAUGGCAAAUAUGCCGCACAUGGGGC
...(((.....(((......(((((.....((((((((((...))))--)-))))).)))-))........)))----(.(((((....))))))...)))... ( -28.94)
>DroAna_CAF1 27824 95 + 1
ACAGCAUCCGAACAGAACCAGAAGCUGGAAAAGUGCAAACCAAGAUGUAGCCAGAACGUG-GCUCAGCUGACACGUAAGAU-CCGAAUACCCUGCAC-------
.((((.((.(........).)).)))).....(((((.....((.((.(((((.....))-))))).))....(....)..-..........)))))------- ( -19.90)
>consensus
ACACCAACGGACCAGAAGAAGUCGAAGGAAAUGUGCAACCUUAGGCU__G_CACAUAUUG_ACGAAGCUGAUGG____GAUGGCAAAUAUUCCGCACAUACGGA
..............................((((((........(((........((((..........))))........))).........))))))..... ( -3.08 =  -4.36 +   1.28)

alignment

secondary structure

dotplot

Window 8

Location	4,731,822 – 4,731,918
Length	96
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	75.60
Mean single sequence MFE	-28.52
Consensus MFE	-8.16
Energy contribution	-7.28
Covariance contribution	-0.88
Combinations/Pair	1.40
Mean z-score	-2.27
Structure conservation index	0.29
SVM decision value	1.69
SVM RNA-class probability	0.972333
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4731822 96 - 22224390
UCCGUAUGUACGGAAUAUUUGCCAUC----CUAUCAGCUUCGU-CAAUAUGUG-C--AGCCAAAGGUUGCACAUUUCCUUCGACUUCUUCUGGUCCGUUGGUGU
(((((....)))))......((((.(----..(((((..(((.-....(((((-(--((((...))))))))))......)))......)))))..).)))).. ( -29.10)
>DroSec_CAF1 24741 96 - 1
UCCGCAUGUGCGGAAUAUUUGCCAUC----CCAUCAGCUUCGU-CAAUAUGUG-C--AGCCAAAGGUUGCACAUUUCCUUCGACUUCUUCUGGUCCGUUGGUGU
(((((....)))))............----.(((((((.....-....(((((-(--((((...)))))))))).......((((......)))).))))))). ( -32.70)
>DroEre_CAF1 28155 97 - 1
UCCCUACGAGCGAAAUAUUUGCCAUC----CCAUCUGCUUCGACCAAUAUGUG-C--AGCCUAAGGUUGCACAUUUCCUUCGACUUCUUCUGGUCCGUUGGUGU
......((((((..............----.....))).)))(((((((((((-(--((((...)))))))))).......((((......)))).)))))).. ( -25.91)
>DroYak_CAF1 25974 96 - 1
GCCCCAUGUGCGGCAUAUUUGCCAUC----CCAUCUGCUUCGU-CAAUAUGUG-C--AACCUAGGGUUGCACAUUUCCUUCGACUUCUUCUGGUCCGUUGGUGU
((((.(((..(((((....))))...----.........(((.-....(((((-(--((((...))))))))))......))).........)..))).)).)) ( -28.10)
>DroAna_CAF1 27824 95 - 1
-------GUGCAGGGUAUUCGG-AUCUUACGUGUCAGCUGAGC-CACGUUCUGGCUACAUCUUGGUUUGCACUUUUCCAGCUUCUGGUUCUGUUCGGAUGCUGU
-------((((((((((..(((-(....(((((.(......).-)))))))))..))).......))))))).....((((.(((((......))))).)))). ( -26.81)
>consensus
UCCCCAUGUGCGGAAUAUUUGCCAUC____CCAUCAGCUUCGU_CAAUAUGUG_C__AGCCUAAGGUUGCACAUUUCCUUCGACUUCUUCUGGUCCGUUGGUGU
...................(((((......(((......(((......(((((....((((...)))).)))))......))).......))).....))))). ( -8.16 =  -7.28 +  -0.88)

alignment

secondary structure

dotplot

Window 9

Location	4,731,846 – 4,731,946
Length	100
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	82.29
Mean single sequence MFE	-28.73
Consensus MFE	-17.35
Energy contribution	-17.10
Covariance contribution	-0.25
Combinations/Pair	1.27
Mean z-score	-2.66
Structure conservation index	0.60
SVM decision value	1.30
SVM RNA-class probability	0.939179
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4731846 100 - 22224390
AUCUCCAAGUUGCCGA------UGCUACCACGCAUCCGUAUGUACGGAAUAUUUGCCAUCCUAUCAGCUUCGU-CAAUAUGUGCAGCCAAAGGUUGCACAUUUCCUU
........((((.(((------.(((.....((((((((....))))).....))).........))).))).-))))((((((((((...))))))))))...... ( -27.34)
>DroSec_CAF1 24765 100 - 1
AUGUCCAAGUCGCCGU------UGCUACCACGCAUCCGCAUGUGCGGAAUAUUUGCCAUCCCAUCAGCUUCGU-CAAUAUGUGCAGCCAAAGGUUGCACAUUUCCUU
........(.((..((------((.......((((((((....))))).....)))........))))..)).-)...((((((((((...))))))))))...... ( -27.26)
>DroEre_CAF1 28179 101 - 1
UACUGCACGUCGCCGA------CGAUACCUCGCAUCCCUACGAGCGAAAUAUUUGCCAUCCCAUCUGCUUCGACCAAUAUGUGCAGCCUAAGGUUGCACAUUUCCUU
....(((((((...))------)).....((((.((.....))))))..................)))..........((((((((((...))))))))))...... ( -23.20)
>DroYak_CAF1 25998 106 - 1
UACUCAAAGUCGCCGACGACGACGAUGCCACACAGCCCCAUGUGCGGCAUAUUUGCCAUCCCAUCUGCUUCGU-CAAUAUGUGCAACCUAGGGUUGCACAUUUCCUU
........((((....))))(((((.((..((((......)))).((((....)))).........)).))))-)...((((((((((...))))))))))...... ( -37.10)
>consensus
AACUCCAAGUCGCCGA______CGAUACCACGCAUCCCCAUGUGCGGAAUAUUUGCCAUCCCAUCAGCUUCGU_CAAUAUGUGCAGCCAAAGGUUGCACAUUUCCUU
..................................(((((....)))))..............................((((((((((...))))))))))...... (-17.35 = -17.10 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:54 2006