Locus 5440

Sequence ID	2L_DroMel_CAF1
Location	15,495,449 – 15,495,580
Length	131
Max. P	0.800764

overview

Window 7

Location	15,495,449 – 15,495,546
Length	97
Sequences	3
Columns	102
Reading direction	forward
Mean pairwise identity	78.98
Mean single sequence MFE	-36.23
Consensus MFE	-20.69
Energy contribution	-21.37
Covariance contribution	0.67
Combinations/Pair	1.17
Mean z-score	-2.32
Structure conservation index	0.57
SVM decision value	0.62
SVM RNA-class probability	0.800764
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15495449 97 + 22407834
CAAAAAU---GUGGUUCCAUAGCUGGUUCCAUUCACCCUCUCGCUCGCUCUUCCAGCCGGCGAAUUAUUGAUUUUGUGUGAGAGCGAGGGAG--CGCGCAUA
.....((---((((((((......(((.......)))..((((((((((.....)))..(((((........)))))....)))))))))))--).))))). ( -30.30)
>DroEre_CAF1 260 94 + 1
CAAAAAUCGCGUGGUGCCACUGCUCG---CGCUCUCCCUCUCGCUCGCUCCUCCAGCCGGCGAACCAUUGAUUUUGCGCGAGAGCGUGUGAG--UGCGA---
........(((((....))).))(((---(((((.(((((((((..(((.....)))..(((((........)))))))))))).).).)))--)))))--- ( -36.70)
>DroYak_CAF1 304 93 + 1
CUAAAAU---GUGGUUCCAUUGCUCG---CGCUCACCCUCUCGCUCGCUCUUCCAGCCGGCGAACCAUUCAUUUUGUGGGAGAGCGAGCGAGAGUGAGA---
.......---(((((......)).))---).(((((..((((((((((((((((.....(((((........)))))))))))))))))))))))))).--- ( -41.70)
>consensus
CAAAAAU___GUGGUUCCAUUGCUCG___CGCUCACCCUCUCGCUCGCUCUUCCAGCCGGCGAACCAUUGAUUUUGUGCGAGAGCGAGCGAG__UGCGA___
..........(((....)))...................(((((((((((((...((..(((((........)))))))))))))))))))).......... (-20.69 = -21.37 +   0.67)

alignment

secondary structure

dotplot

Window 8

Location	15,495,471 – 15,495,580
Length	109
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	63.04
Mean single sequence MFE	-39.90
Consensus MFE	-14.64
Energy contribution	-14.45
Covariance contribution	-0.19
Combinations/Pair	1.47
Mean z-score	-2.31
Structure conservation index	0.37
SVM decision value	0.09
SVM RNA-class probability	0.576798
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15495471 109 + 22407834
GUUCCAUUCACCCUCUCGCUCGCUCUUCCAGCCGGCGAAUUAUUGAUUUUGUGUGAGAGCGAGGGAG--CGCGCAUAAGAGAGAGGGAGAGAGAGUGAGAGUGAAGGCGUG
...((.(((((..((((((((.(((((((.(....)......((..(((((((((...((......)--).)))))))))..))))))))).))))))))))))))).... ( -42.80)
>DroEre_CAF1 285 90 + 1
G---CGCUCUCCCUCUCGCUCGCUCCUCCAGCCGGCGAACCAUUGAUUUUGCGCGAGAGCGUGUGAG--UGCGA------GAGAG------A----GAGCGAGAGGGCGUG
(---(((((((((((((.(((((..(((((....(((((........)))))((....)).)).)))--.))))------)...)------)----))).).)))))))). ( -42.00)
>DroYak_CAF1 326 91 + 1
G---CGCUCACCCUCUCGCUCGCUCUUCCAGCCGGCGAACCAUUCAUUUUGUGGGAGAGCGAGCGAGAGUGAGA------GAGAG------C----GAGCGAGAG-GCGUG
.---....((((((((((((((((((..(..((.(((((........))))).)).......((....))..).------.))))------)----)))))))))-).))) ( -45.10)
>DroMoj_CAF1 374 94 + 1
-------UCUGCUUCUUGUUCU--CCUCGUGCCGGUGCUUCAUUGAUUUUGCUUGCAAGUAUGUGU--GUGUGCGA----GAGAG--CAAGUCCAUGAAUAAGCAGGCGUG
-------(((((((((((((((--(.(((..(((((((((((...........)).))))))...)--).)..)))----)))))--)))).........))))))).... ( -29.70)
>consensus
G___CGCUCACCCUCUCGCUCGCUCCUCCAGCCGGCGAACCAUUGAUUUUGCGUGAGAGCGAGUGAG__UGCGA______GAGAG______A____GAGCGAGAAGGCGUG
........(.(((((((((((............((....))......(((((......))))).................................))))))))))).).. (-14.64 = -14.45 +  -0.19)

alignment

secondary structure

dotplot

Window 9

Location	15,495,471 – 15,495,580
Length	109
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	63.04
Mean single sequence MFE	-32.50
Consensus MFE	-13.39
Energy contribution	-15.70
Covariance contribution	2.31
Combinations/Pair	1.21
Mean z-score	-2.04
Structure conservation index	0.41
SVM decision value	0.44
SVM RNA-class probability	0.736649
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15495471 109 - 22407834
CACGCCUUCACUCUCACUCUCUCUCCCUCUCUCUUAUGCGCG--CUCCCUCGCUCUCACACAAAAUCAAUAAUUCGCCGGCUGGAAGAGCGAGCGAGAGGGUGAAUGGAAC
......(((.(..((((((((((...(((.(((((....(((--......))).......................((....))))))).))).))))))))))..)))). ( -29.00)
>DroEre_CAF1 285 90 - 1
CACGCCCUCUCGCUC----U------CUCUC------UCGCA--CUCACACGCUCUCGCGCAAAAUCAAUGGUUCGCCGGCUGGAGGAGCGAGCGAGAGGGAGAGCG---C
..(.(((((((((((----.------(((.(------((.((--..(...(((....)))..........((....)))..)))))))).))))))))))).)....---. ( -39.10)
>DroYak_CAF1 326 91 - 1
CACGC-CUCUCGCUC----G------CUCUC------UCUCACUCUCGCUCGCUCUCCCACAAAAUGAAUGGUUCGCCGGCUGGAAGAGCGAGCGAGAGGGUGAGCG---C
.....-....(((((----(------((...------.....((((((((((((((.(((.........(((....)))..))).))))))))))))))))))))))---. ( -43.00)
>DroMoj_CAF1 374 94 - 1
CACGCCUGCUUAUUCAUGGACUUG--CUCUC----UCGCACAC--ACACAUACUUGCAAGCAAAAUCAAUGAAGCACCGGCACGAGG--AGAACAAGAAGCAGA-------
.....((((((.((....))((((--.((((----(((.....--........(((....)))..........((....)).))).)--))).)))))))))).------- ( -18.90)
>consensus
CACGCCCUCUCGCUC____U______CUCUC______GCGCA__CUCACACGCUCUCACACAAAAUCAAUGAUUCGCCGGCUGGAAGAGCGAGCGAGAGGGAGAGCG___C
..(((((((((((((......................................................(((....)))(((.....))))))))))))))))........ (-13.39 = -15.70 +   2.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:16 2006