Locus 2786

Sequence ID	2R_DroMel_CAF1
Location	9,728,485 – 9,728,589
Length	104
Max. P	0.929517

overview

Window 2

Location	9,728,485 – 9,728,589
Length	104
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	89.44
Mean single sequence MFE	-30.57
Consensus MFE	-24.00
Energy contribution	-24.33
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.33
Structure conservation index	0.79
SVM decision value	1.02
SVM RNA-class probability	0.902464
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9728485 104 + 20766785
UUGGGGCCAAGCUGAUUGGUAUCCAACUGGAGAUAAGCAGCCAAAUUGCAUAUUGCAACAACUGCUGCCAGCGAACCGCACA---GCCAAGCCCAAAAAAUAAAAAA
...((((...((((..((((.((...((((.....(((((.....((((.....))))...))))).)))).))))))..))---))...))))............. ( -31.90)
>DroSec_CAF1 46613 103 + 1
UUGGGGCCAAGCUGAUUGGUAUCCAACUGGAGAUAAGCAGCCAAAUUGCAUAUUGCAACAACUGCUGCCAGCGAACCGCACA---GCCAAGCCCAAAAAAUAAA-AA
...((((...((((..((((.((...((((.....(((((.....((((.....))))...))))).)))).))))))..))---))...))))..........-.. ( -31.90)
>DroSim_CAF1 37917 103 + 1
UUGGGGCCAAGCUGAUUGGUAUCCAACUGGAGAUAAGCAGCCAAAUUGCAUAUUGCAAGAACUGCUGCCAGCGAACCGCACA---GCCAAGCCCAAAAAAUAAA-AA
...((((...((((..((((.((...((((.....(((((.....((((.....))))...))))).)))).))))))..))---))...))))..........-.. ( -33.00)
>DroEre_CAF1 39441 95 + 1
UUGGGGCCAAGCUGAUUGCUAUCCAACUGGAGAUAAGCAGCCAAAUUGCAUAUUGCAACAACUGCUGCCAGCGAACCGCACA---GCCAAGCCCAAA---------A
...((((...((((..(((..(((....))).....(((((....((((.....)))).....))))).........)))))---))...))))...---------. ( -29.90)
>DroYak_CAF1 45678 96 + 1
UUGGGGCCAAGCUGAUUGGUAUCCAACUGAAGAUAAGCAGCCAAAUUGCAUAUUGCAACAACUGCUGCCAGCGAACCGCACA---GCCAAGCCCAAA--------AA
...((((...((((..(((((((........))).(((((.....((((.....))))...)))))))))(((...))).))---))...))))...--------.. ( -28.60)
>DroAna_CAF1 43448 102 + 1
UAGGGGCCAAGCUGAUUGGUAUCCAGUGGAAGAUAAGCACCCAAAUUGCAUAUUGCAACAACUGCUGGCAGCCAAGAGCCAAGAUGCCAAGCCCAAAA--UAAA---
...((((........((((((((((((....((((.(((.......))).))))......)))).((((........)))).))))))))))))....--....--- ( -28.10)
>consensus
UUGGGGCCAAGCUGAUUGGUAUCCAACUGGAGAUAAGCAGCCAAAUUGCAUAUUGCAACAACUGCUGCCAGCGAACCGCACA___GCCAAGCCCAAAA__UAAA_AA
...((((...((((.....((((........)))).(((((....((((.....)))).....))))))))).....((......))...))))............. (-24.00 = -24.33 +   0.33)

alignment

secondary structure

dotplot

Window 3

Location	9,728,485 – 9,728,589
Length	104
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	89.44
Mean single sequence MFE	-37.70
Consensus MFE	-28.78
Energy contribution	-29.87
Covariance contribution	1.09
Combinations/Pair	1.06
Mean z-score	-3.83
Structure conservation index	0.76
SVM decision value	1.20
SVM RNA-class probability	0.929517
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9728485 104 - 20766785
UUUUUUAUUUUUUGGGCUUGGC---UGUGCGGUUCGCUGGCAGCAGUUGUUGCAAUAUGCAAUUUGGCUGCUUAUCUCCAGUUGGAUACCAAUCAGCUUGGCCCCAA
.............(((((.(((---((...((((((((((.((((((((((((.....)))))..))))))).....)))))..)).)))...))))).)))))... ( -39.50)
>DroSec_CAF1 46613 103 - 1
UU-UUUAUUUUUUGGGCUUGGC---UGUGCGGUUCGCUGGCAGCAGUUGUUGCAAUAUGCAAUUUGGCUGCUUAUCUCCAGUUGGAUACCAAUCAGCUUGGCCCCAA
..-..........(((((.(((---((...((((((((((.((((((((((((.....)))))..))))))).....)))))..)).)))...))))).)))))... ( -39.50)
>DroSim_CAF1 37917 103 - 1
UU-UUUAUUUUUUGGGCUUGGC---UGUGCGGUUCGCUGGCAGCAGUUCUUGCAAUAUGCAAUUUGGCUGCUUAUCUCCAGUUGGAUACCAAUCAGCUUGGCCCCAA
..-..........(((((.(((---((...((((((((((.(((((((.((((.....))))...))))))).....)))))..)).)))...))))).)))))... ( -37.80)
>DroEre_CAF1 39441 95 - 1
U---------UUUGGGCUUGGC---UGUGCGGUUCGCUGGCAGCAGUUGUUGCAAUAUGCAAUUUGGCUGCUUAUCUCCAGUUGGAUAGCAAUCAGCUUGGCCCCAA
.---------...(((((.(((---(((((.(((((((((.((((((((((((.....)))))..))))))).....)))).))))).)))..))))).)))))... ( -42.00)
>DroYak_CAF1 45678 96 - 1
UU--------UUUGGGCUUGGC---UGUGCGGUUCGCUGGCAGCAGUUGUUGCAAUAUGCAAUUUGGCUGCUUAUCUUCAGUUGGAUACCAAUCAGCUUGGCCCCAA
..--------...(((((.(((---((...(((...(..((((((((((((((.....)))))..)))))))........))..)..)))...))))).)))))... ( -37.60)
>DroAna_CAF1 43448 102 - 1
---UUUA--UUUUGGGCUUGGCAUCUUGGCUCUUGGCUGCCAGCAGUUGUUGCAAUAUGCAAUUUGGGUGCUUAUCUUCCACUGGAUACCAAUCAGCUUGGCCCCUA
---....--....(((((.(((....((((........))))(((.(((((((.....)))))..)).))).(((((......))))).......))).)))))... ( -29.80)
>consensus
UU_UUUA__UUUUGGGCUUGGC___UGUGCGGUUCGCUGGCAGCAGUUGUUGCAAUAUGCAAUUUGGCUGCUUAUCUCCAGUUGGAUACCAAUCAGCUUGGCCCCAA
.............(((((.(((.....((..(((((((((.((((((((((((.....)))))..))))))).....))))).))))..))....))).)))))... (-28.78 = -29.87 +   1.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:28 2006