Locus 7971

Sequence ID	3R_DroMel_CAF1
Location	21,374,493 – 21,374,626
Length	133
Max. P	0.994829

overview

Window 2

Location	21,374,493 – 21,374,605
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.27
Mean single sequence MFE	-33.54
Consensus MFE	-17.60
Energy contribution	-18.88
Covariance contribution	1.28
Combinations/Pair	1.08
Mean z-score	-2.82
Structure conservation index	0.52
SVM decision value	2.51
SVM RNA-class probability	0.994829
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21374493 112 - 27905053
UGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCCUUUGGCCGAGGCAUUUAAAUACAGGUGCUGC----C-AGGGAAAUGUUG---CCCAGUUCAGUUGAACAUUUUUCAGUCAA
(((.(.((((((.(((((((((((.((((((((..((((((.....))))))..))))))))((.....)----)-..))))))))))---)...((((....)))))))))).).))). ( -34.90)
>DroSec_CAF1 69024 109 - 1
UGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCCUUUGGCAGAGGCAUUUAAAUACAGGUGCUUCUUAAC-AGAGAACUGUUGCCGCCCAGUUCAGUUGAACAUU----------
((((((((((((......)))))))((((((((..((((((.....))))))..))))))))(((.......(((-((....)))))))))))))((((....))))...---------- ( -34.91)
>DroSim_CAF1 65390 91 - 1
UGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCCUUUGGCCGAGGCAUUUAAAUACAGGUGC-------------------UGCCGGCCAGUUCAGUUGAACAUU----------
.....(((((((......))))))).(((((((.(((...(((((((.(((((((......))))))-------------------)..)))))))..))).))))))).---------- ( -29.20)
>DroEre_CAF1 68516 107 - 1
UGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCUUUUGGCGA-GGCAUUUAAAUACAGGUGCUGC----AAAGGAAAGUGUUG---CC-----CAAUUGACCAUUUUCCAGUCAA
..((((((.....(((((((((((.((((((((..((((((....))-))))..))))))))....((..----..))))))))))))---).-----...))))))............. ( -31.70)
>DroYak_CAF1 67948 107 - 1
UGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUCGCCUUUGGCGGCGGCAUUUAAAUACAGGUGCUGC----C-AGGAAAGUGUUG---CC-----CAAUUGACCAUUUUUCAGUCAC
..((((((.....(((((((((((.(..........(((...)))((((((((((......)))))))))----)-).))))))))))---).-----...))))))............. ( -37.00)
>consensus
UGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCCUUUGGCCGAGGCAUUUAAAUACAGGUGCUGC____C_AGGAAAGUGUUG___CCCAGUUCAGUUGAACAUUUU_CAGUCA_
((((.(((((((......)))))))((((((((..((((((.....))))))..)))))))).............................))))......................... (-17.60 = -18.88 +   1.28)

alignment

secondary structure

dotplot

Window 3

Location	21,374,530 – 21,374,626
Length	96
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	86.12
Mean single sequence MFE	-23.72
Consensus MFE	-17.72
Energy contribution	-18.00
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-2.53
Structure conservation index	0.75
SVM decision value	1.52
SVM RNA-class probability	0.960897
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21374530 96 - 27905053
UUUACUUUGCUUUUU--UUUUUUUGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCCUUUGGCCGAGGCAUUUAAAUACAGGUGCUGC----C-AGGG
...............--....(((((..(((((((......)))))))((((((((..((((((.....))))))..)))))))).......)----)-))). ( -23.40)
>DroSec_CAF1 69054 100 - 1
UUUACUUUCCUUUUU--UUUUUUUGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCCUUUGGCAGAGGCAUUUAAAUACAGGUGCUUCUUAAC-AGAG
...............--....((((.....((((..(((.......(.((((((((..((((((.....))))))..)))))))).)))).))))..)-))). ( -21.71)
>DroSim_CAF1 65414 84 - 1
UUUACUUUCCUUUU------UUAUGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCCUUUGGCCGAGGCAUUUAAAUACAGGUGC-------------
..((((.(((....------....))).(((((((......)))))))((((((((..((((((.....))))))..)))))))))))).------------- ( -21.40)
>DroEre_CAF1 68548 98 - 1
UUUACUUUCCUUCUUUCUUUUUUUGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCUUUUGGCGA-GGCAUUUAAAUACAGGUGCUGC----AAAGGA
.......(((((((..(((.....)))..)))..(((((.((((....((((((((..((((((....))-))))..)))))))))))).)))----)))))) ( -23.40)
>DroYak_CAF1 67980 94 - 1
UUUACUUUCCUUU----UUUUUCUGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUCGCCUUUGGCGGCGGCAUUUAAAUACAGGUGCUGC----C-AGGA
.......((((..----.........(((((((...((((.....))))(((......))))))))))((((((((((......)))))))))----)-)))) ( -28.70)
>consensus
UUUACUUUCCUUUUU__UUUUUUUGGGUCAGAGAUUGCAAUAUUUUUGUGUGUUUAUUUGCCUUUGGCCGAGGCAUUUAAAUACAGGUGCUGC____C_AGGA
..((((......................(((((((......)))))))((((((((..((((((.....))))))..)))))))))))).............. (-17.72 = -18.00 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:15 2006