Locus 806

Sequence ID	2R_DroMel_CAF1
Location	3,815,310 – 3,815,440
Length	130
Max. P	0.946677

overview

Window 1

Location	3,815,310 – 3,815,420
Length	110
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	82.24
Mean single sequence MFE	-25.87
Consensus MFE	-22.05
Energy contribution	-22.16
Covariance contribution	0.11
Combinations/Pair	1.05
Mean z-score	-2.54
Structure conservation index	0.85
SVM decision value	1.36
SVM RNA-class probability	0.946677
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3815310 110 + 20766785
-CUGUCACUUUUUGCCACACCCCCGGUUUUCGGCCAA-AAUAAAAAUAAGAACAAGCUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAUUUCGAGAGUUUCGUAUUCGC--
-.......((((.(((..(((...)))....))).))-))...........((((((((.(((((((((((..............))))))))))).)))))).))......-- ( -22.74)
>DroPse_CAF1 67270 106 + 1
-CCCUCCCGUUUUCUCGCACUC-----UUUCAGCCAAAAAUAAAAAUAAGAACAAGCUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAUUUCGCGAGUUUCGUAUUGUC--
-.......(((((...((....-----.....))..)))))....((((..((((((((((((((((((((..............)))))))))))))))))).)).)))).-- ( -24.14)
>DroWil_CAF1 114006 113 + 1
CCACCCACUUGGGGCCCCACUCUUUCCUCUCGGGGGC-AAAAGAAAUAAGAACAAAAUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAUUUCGCGAAUUUCGUAUUCGUAU
...(((....)))(((((..............)))))-....(((((..........((((((((((((((..............))))))))))))))))))).......... ( -32.18)
>DroYak_CAF1 68781 109 + 1
-CUGUCACUUUUUGCCACACCCCC-AUUUUUGGCCAG-AAUAAAAAUAAGAACAAGCUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAUUUCGCGAGUUUCGUAUUCGC--
-.......((((.((((.......-.....)))).))-))...........((((((((((((((((((((..............)))))))))))))))))).))......-- ( -28.04)
>DroAna_CAF1 68504 109 + 1
-CUGUCACUUUUU-CCAUUCCUCG-UAUUUCGGCCAAAAAUAAAAAUAAGAACAAACUCGCGGAAUUUGUAUGAAAAUGCAAAAUUACGAAUUUCGCGAGUUUCGUAUUCGC--
-............-..........-..........................((((((((((((((((((((..............)))))))))))))))))).))......-- ( -23.84)
>DroPer_CAF1 66688 106 + 1
-CCCUCUCGUUUUCUCGCACUC-----UUUCAGCCAAAAAUAAAAAUAAGAACAAGCUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAUUUCGCGAGUUUCGUAUUGUC--
-...(((..((((.........-----...............))))..)))((((((((((((((((((((..............)))))))))))))))))).))......-- ( -24.30)
>consensus
_CUCUCACUUUUUGCCACACCCC____UUUCGGCCAA_AAUAAAAAUAAGAACAAGCUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAUUUCGCGAGUUUCGUAUUCGC__
...................................................((((((((((((((((((((..............)))))))))))))))))).))........ (-22.05 = -22.16 +   0.11)

alignment

secondary structure

dotplot

Window 2

Location	3,815,348 – 3,815,440
Length	92
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	81.98
Mean single sequence MFE	-21.48
Consensus MFE	-16.37
Energy contribution	-15.62
Covariance contribution	-0.75
Combinations/Pair	1.21
Mean z-score	-2.76
Structure conservation index	0.76
SVM decision value	1.15
SVM RNA-class probability	0.922290
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3815348 92 + 20766785
U------AAAAAUAAGAACAAGCUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAUUUCGAGAGUUUCGUAUUCGCCUCGCAUUGUACACAUGUAC
.------........(.((((((..(((((.(((((((....)))))))..((((((...(....).)))))))))))...)).)))).)........ ( -20.10)
>DroVir_CAF1 84966 89 + 1
UGUUCC-AAAAAUAAGAACAAAAUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAU-UCGCGAUU-------UCGGUUCGCAUUGUAUGUAUGCAC
......-........((((.((((((((.((((((((..............)))))))-))))))))-------)..))))((((.......)))).. ( -23.94)
>DroGri_CAF1 73036 90 + 1
UGUCCCAAAAAAUAAGAACAAAAUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAU-UCGCGAUU-------UCAGCUCGUAUUGUAUGUAUCCAU
.....((...((((.((.(.((((((((.((((((((..............)))))))-))))))))-------)..).)).))))...))....... ( -16.74)
>DroSec_CAF1 71607 91 + 1
U------AAAAAUAAGAACA-GCUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAUUUCGCGAGUUUCGUAUUCGCCUCGCAUUAUACACAUGUAC
.------........(((..-((((((((((((((((..............)))))))))))))))))))((((..((...))...))))........ ( -24.74)
>DroMoj_CAF1 104662 89 + 1
UGUCCA-AAAAAUAAGAACAAAAUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAU-UCGCGAUU-------UCGGCUCGUAUUGUAUGUAUGCAU
......-........((.(.((((((((.((((((((..............)))))))-))))))))-------).)..))((((.......)))).. ( -18.74)
>DroAna_CAF1 68541 91 + 1
U------AAAAAUAAGAACAAACUCGCGGAAUUUGUAUGAAAAUGCAAAAUUACGAAUUUCGCGAGUUUCGUAUUCGCCUCGCAUUGUCCACAUGUA-
.------..........((((((((((((((((((((..............)))))))))))))))))).)).........((((.(....))))).- ( -24.64)
>consensus
U______AAAAAUAAGAACAAAAUCGCGGAAUUUGUAUAAAAAUGCAAAAUUACGAAU_UCGCGAGU_______UCGCCUCGCAUUGUACACAUGCAC
.....................((((((((.(((((((..............))))))).))))))))..............((((.......)))).. (-16.37 = -15.62 +  -0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:51 2006