Locus 4836

Sequence ID	2L_DroMel_CAF1
Location	13,758,998 – 13,759,155
Length	157
Max. P	0.809985

overview

Window 3

Location	13,758,998 – 13,759,095
Length	97
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.40
Mean single sequence MFE	-26.27
Consensus MFE	-16.67
Energy contribution	-16.87
Covariance contribution	0.20
Combinations/Pair	1.30
Mean z-score	-1.82
Structure conservation index	0.63
SVM decision value	0.64
SVM RNA-class probability	0.809985
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13758998 97 - 22407834
GAAA---AAAGUCGAGAAGUCGGCCGACUAAUCAAAUUACCGCAAUGG---------------GAAGUUGGCAAUUGAAAGCUUAGGACUUUAGGAUGUAGCCUCAGUCUUGAGU-----
....---.....(((....)))(((((((..(((...........)))---------------..)))))))........((((((((((..(((......))).))))))))))----- ( -25.70)
>DroSec_CAF1 22631 95 - 1
--AA---AAAGUCGAGAAGUCGGCCGACUAAUCAAAUUACCGCAAUGG---------------GAAGUUGGCAAUUGAAAGCUUAGGACUUUAGGAUGUAGCCUUAGUCUUGAGU-----
--..---.....(((....)))(((((((..(((...........)))---------------..)))))))........((((((((((..(((......))).))))))))))----- ( -26.70)
>DroAna_CAF1 43523 120 - 1
GAAAAAAUAAGUUAAAAAGUCGGCCGACUAAUCAAAUUACGGCAAUGAUGCUUGCCACAAAAGGAAAAUGGAGAUAAAAACAUUGUGGGUGUAGGGGCAAGUCUUGGUGGAAAGUUUGAG
.................((((....))))..(((((((.((.(((....((((((((((.......((((..........)))).....)))...))))))).))).))...))))))). ( -22.90)
>DroSim_CAF1 25660 97 - 1
GAAA---AAAGUCGAGAAGUCGGCCGACUAAUCAAAUUACCGCAAUGG---------------GAAGUUGGCAAUUGAAAGCUUAGGACUUUAGGAUGUAGUCUUAGUCUUGAGU-----
....---.....(((....)))(((((((..(((...........)))---------------..)))))))........((((((((((..(((((...)))))))))))))))----- ( -24.60)
>DroEre_CAF1 24295 97 - 1
GAAA---AAAGUCGACAAGCCGGCCGACUAAUCAAAUUACCGCAAUGG---------------GAAGUUGGCAAUUGCAAGCUUAGGACUUUGGGAUGUAGCCUUAGUCUUGAGU-----
....---...........((..(((((((..(((...........)))---------------..)))))))....))..((((((((((..(((......))).))))))))))----- ( -27.60)
>DroYak_CAF1 25745 99 - 1
GAAA-AAAAAGUCGAGAAGUCGGCCGACUAAUCAAAUUACCGCAAUGG---------------AGAGUUGGCAGUUGAAAGCUUAGGACUUUGGGCUGUAGCCUUAGUCUUGAGU-----
....-.......(((....)))(((((((..(((...........)))---------------..)))))))........((((((((((..((((....)))).))))))))))----- ( -30.10)
>consensus
GAAA___AAAGUCGAGAAGUCGGCCGACUAAUCAAAUUACCGCAAUGG_______________GAAGUUGGCAAUUGAAAGCUUAGGACUUUAGGAUGUAGCCUUAGUCUUGAGU_____
......................(((((((....................................)))))))........((((((((((..(((......))).))))))))))..... (-16.67 = -16.87 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	13,759,058 – 13,759,155
Length	97
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.63
Mean single sequence MFE	-30.53
Consensus MFE	-23.63
Energy contribution	-24.22
Covariance contribution	0.59
Combinations/Pair	1.12
Mean z-score	-2.81
Structure conservation index	0.77
SVM decision value	0.55
SVM RNA-class probability	0.778958
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13759058 97 + 22407834
GUAAUUUGAUUAGUCGGCCGACUUCUCGACUUU---UUUCCU---GCUCCUGUCUGCAGGC-----------------UGGCUGACUUGUCUGGGCAAAUUUAUAUAAAUGCCCGCAAAA
((.....(((.((((((((((....))......---...(((---((........))))).-----------------.)))))))).))).(((((............))))))).... ( -31.60)
>DroSec_CAF1 22691 95 + 1
GUAAUUUGAUUAGUCGGCCGACUUCUCGACUUU---UU--CU---CCUGCUGUCUGCAGGC-----------------UGGCUGACUUGUCUGGGCAAAUUUAUAUAAAUGCCCGCAAAA
((.....(((.((((((((((....))......---..--..---(((((.....))))).-----------------.)))))))).))).(((((............))))))).... ( -31.60)
>DroAna_CAF1 43603 120 + 1
GUAAUUUGAUUAGUCGGCCGACUUUUUAACUUAUUUUUUCCUUCAGCUCCUGUCUGCAGGUCGACUUUCUUCUCCCUUUUGCUGACUUGUCUGGGCAAAUUUAUAUAAAUGCCCACAAAA
((((.((((..((((....))))..)))).))))........(((((.((((....))))..((......))........))))).((((..(((((............))))))))).. ( -25.30)
>DroSim_CAF1 25720 97 + 1
GUAAUUUGAUUAGUCGGCCGACUUCUCGACUUU---UUUCCU---GCUGCUGUCUGCAGGC-----------------UGGCUGACUUGUCUGGGCAAAUUUAUAUAAAUGCCCGCAAAA
((.....(((.((((((((((....))......---...(((---((........))))).-----------------.)))))))).))).(((((............))))))).... ( -31.60)
>DroEre_CAF1 24355 97 + 1
GUAAUUUGAUUAGUCGGCCGGCUUGUCGACUUU---UUUCGU---GCUGCUGUCUGCCUGC-----------------UGGCUGACUUGUCUGGGCAAAUUUAUAUAAAUGCCCGCAAAA
((.....(((.(((((((((((..((.(((...---......---......))).))..))-----------------))))))))).))).(((((............))))))).... ( -35.16)
>DroYak_CAF1 25805 99 + 1
GUAAUUUGAUUAGUCGGCCGACUUCUCGACUUUUU-UUUCGU---GCUGAUGUCUGCAGGC-----------------UGGCUGACUUGUCUGGGCAAAUUUAUAUAAAUGCCCGCAAAA
((.....(((.(((((((((.((...(((......-..)))(---((........))))).-----------------))))))))).))).(((((............))))))).... ( -27.90)
>consensus
GUAAUUUGAUUAGUCGGCCGACUUCUCGACUUU___UUUCCU___GCUGCUGUCUGCAGGC_________________UGGCUGACUUGUCUGGGCAAAUUUAUAUAAAUGCCCGCAAAA
((.....(((.((((((((((....))...................((((.....))))....................)))))))).))).(((((............))))))).... (-23.63 = -24.22 +   0.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:49 2006