Locus 9235

Sequence ID	3R_DroMel_CAF1
Location	24,628,368 – 24,628,464
Length	96
Max. P	0.766289

overview

Window 3

Location	24,628,368 – 24,628,464
Length	96
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	68.90
Mean single sequence MFE	-26.52
Consensus MFE	-8.97
Energy contribution	-9.72
Covariance contribution	0.75
Combinations/Pair	1.18
Mean z-score	-1.90
Structure conservation index	0.34
SVM decision value	0.26
SVM RNA-class probability	0.658425
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24628368 96 + 27905053
GGCUAAUAAAGCGUACGUC---UUUUUG-GCAA----CAAAAUGGCGGCGUUGGAGACAACGACACCAAAUCAAUGCUCAAA-------UAGAGCUCGGGCU--CUCAAA--AUC--
.........(((((.((((---.(((((-....----))))).)))).(((((....)))))...........)))))....-------.(((((....)))--))....--...-- ( -30.00)
>DroSec_CAF1 108495 96 + 1
GGCUAAUAAAGCGUAUGUC---UUUUUG-GCAA----CAAAAUGGCGGCGUUGGAGACAACGACACCAAAUCAAUGCUCAAA-------UAGAGCGCGGGCU--CUCAAG--CUC--
((((.....(((((..(((---.(((((-....----))))).)))(((((((....)))))...))......)))))....-------.(((((....)))--))..))--)).-- ( -31.20)
>DroEre_CAF1 115449 96 + 1
GGCUAAUAAAGCGUACGUC---UUUUUG-GCAA----CGAAAUGGCGGCGUUGGAGACAACGACACCAAAUCAAUGCUCAAC-------UAGAGUUUGGGCU--CUUAAA--AUC--
.........(((((.((((---.(((((-....----))))).)))).(((((....))))))).((((......((((...-------..)))))))))))--......--...-- ( -27.90)
>DroWil_CAF1 119903 111 + 1
AGCUAAUAAAGCGUAAGUCUCCUUUUUG-GUGCCAGCCAAAAUGCCAAUGCUGG---CAACGACACCAAAUCAAUGCGCCGACUUCCUCUUUACUUUGGCUUCCCUUUUGUCCUU--
(((((((((((.(.(((((....(((((-((....)))))))(((((....)))---)).....................))))).).)))))..))))))..............-- ( -26.40)
>DroYak_CAF1 110744 96 + 1
GGCUAAUAAAGCGUACGAC---CUUUUG-GCAA----CGAAAUGGCGGCGUUGGAGACAACGACACCAAAUCAAUGCUCAAA-------UAGAGUUUGGGCU--UUUAAA--AUC--
.......(((((((.((.(---((((((-....----))))).)))).(((((....))))))).((((......((((...-------..)))))))))))--))....--...-- ( -27.90)
>DroMoj_CAF1 130695 85 + 1
AGCUAAUAAAGCGUGCGCC---UUUUCGUGCCU----CAAAGUGGUAGCC----GAACGACGACUUCAAAUCAAUGCGCCCU-------UCG--------------ACUAUCUGUCU
.(((.....)))(.((((.---..((((((((.----......))))..)----))).((.....))........)))).).-------..(--------------((.....))). ( -15.70)
>consensus
GGCUAAUAAAGCGUACGUC___UUUUUG_GCAA____CAAAAUGGCGGCGUUGGAGACAACGACACCAAAUCAAUGCUCAAA_______UAGAGUUUGGGCU__CUUAAA__AUC__
.(((.....)))..............................(((...(((((....)))))...)))................................................. ( -8.97 =  -9.72 +   0.75)

alignment

secondary structure

dotplot

Window 4

Location	24,628,368 – 24,628,464
Length	96
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	68.90
Mean single sequence MFE	-28.34
Consensus MFE	-10.04
Energy contribution	-10.82
Covariance contribution	0.78
Combinations/Pair	1.20
Mean z-score	-1.94
Structure conservation index	0.35
SVM decision value	0.52
SVM RNA-class probability	0.766289
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24628368 96 - 27905053
--GAU--UUUGAG--AGCCCGAGCUCUA-------UUUGAGCAUUGAUUUGGUGUCGUUGUCUCCAACGCCGCCAUUUUG----UUGC-CAAAAA---GACGUACGCUUUAUUAGCC
--...--....((--(((....))))).-------((((.(((..((..(((((.(((((....))))).)))))..)).----.)))-))))..---.......(((.....))). ( -28.00)
>DroSec_CAF1 108495 96 - 1
--GAG--CUUGAG--AGCCCGCGCUCUA-------UUUGAGCAUUGAUUUGGUGUCGUUGUCUCCAACGCCGCCAUUUUG----UUGC-CAAAAA---GACAUACGCUUUAUUAGCC
--..(--((..((--(((......(((.-------((((.(((..((..(((((.(((((....))))).)))))..)).----.)))-)))).)---)).....)))))...))). ( -30.60)
>DroEre_CAF1 115449 96 - 1
--GAU--UUUAAG--AGCCCAAACUCUA-------GUUGAGCAUUGAUUUGGUGUCGUUGUCUCCAACGCCGCCAUUUCG----UUGC-CAAAAA---GACGUACGCUUUAUUAGCC
--...--....((--(((....(((((.-------.(((.(((.(((..(((((.(((((....))))).)))))..)))----.)))-)))..)---)).))..)))))....... ( -29.10)
>DroWil_CAF1 119903 111 - 1
--AAGGACAAAAGGGAAGCCAAAGUAAAGAGGAAGUCGGCGCAUUGAUUUGGUGUCGUUG---CCAGCAUUGGCAUUUUGGCUGGCAC-CAAAAAGGAGACUUACGCUUUAUUAGCU
--..........((....))..(((((((...((((((((((.........)))))(.((---(((((............))))))).-)........)))))...))))))).... ( -31.50)
>DroYak_CAF1 110744 96 - 1
--GAU--UUUAAA--AGCCCAAACUCUA-------UUUGAGCAUUGAUUUGGUGUCGUUGUCUCCAACGCCGCCAUUUCG----UUGC-CAAAAG---GUCGUACGCUUUAUUAGCC
--...--....((--(((.......((.-------((((.(((.(((..(((((.(((((....))))).)))))..)))----.)))-)))).)---)......)))))....... ( -27.92)
>DroMoj_CAF1 130695 85 - 1
AGACAGAUAGU--------------CGA-------AGGGCGCAUUGAUUUGAAGUCGUCGUUC----GGCUACCACUUUG----AGGCACGAAAA---GGCGCACGCUUUAUUAGCU
...((((((((--------------(((-------(.((((.(((.......))))))).)))----)))))....))))----.(((..((.((---(((....))))).)).))) ( -22.90)
>consensus
__GAU__UUUAAG__AGCCCAAACUCUA_______UUUGAGCAUUGAUUUGGUGUCGUUGUCUCCAACGCCGCCAUUUUG____UUGC_CAAAAA___GACGUACGCUUUAUUAGCC
.............................................((..(((((.(((((....))))).)))))..))..........................(((.....))). (-10.04 = -10.82 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:29:30 2006