Locus 428

Sequence ID	X_DroMel_CAF1
Location	1,259,321 – 1,259,418
Length	97
Max. P	0.916861

overview

Window 0

Location	1,259,321 – 1,259,418
Length	97
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	76.19
Mean single sequence MFE	-27.46
Consensus MFE	-16.81
Energy contribution	-15.63
Covariance contribution	-1.19
Combinations/Pair	1.24
Mean z-score	-1.63
Structure conservation index	0.61
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1259321 97 + 22224390
----------UUCCAACUUGUACAGUUGGCUUAU---UAGCCAUAUUAUU-----AUCUCCUAUUAGCCCGAUUUCGGCGU-UUGCCUUUAAGCGAGCUGCAUUGCAGCGCACUGA
----------............(((((((((...---.))))).......-----...........(((((....)))(((-(((....)))))).(((((...))))))))))). ( -24.50)
>DroSec_CAF1 13520 94 + 1
----------UUCCAACUGGUG---CUGGCUUAU---AAGCCAUAUUAUU-----AUCUUCUAUUAGCCCGAUUUCGGCGU-UUGCCUUUAAGCGAGCUGCAUUGCAGCGCACUGA
----------........((((---((((((...---.))))).......-----...........(((((....))).))-((((......))))(((((...)))))))))).. ( -25.60)
>DroSim_CAF1 12182 94 + 1
----------UUCCAACUGGUG---CUGGCUUAU---AAGCCAUAUUAUU-----AUCUUCUAUUAGCCCGAUUUCGGCGU-UUGCCUUUAAGCGAGCUGCAUUGCAGCGCACUGG
----------......(..(((---((((((...---.))))).......-----...........(((((....))).))-((((......))))(((((...)))))))))..) ( -27.80)
>DroEre_CAF1 15316 110 + 1
UUGUGAAUUGUUCCAACUGCUC---U-GGCUAAUUUAGAGCCGCAUUAAUCUCCAAUCUCCUAUUAGCCUGAU--GUCGGCGCUGCCUUUAGGCCAGCUGCAGUGCAGCGCAGCGA
(((((...(((....(((((.(---(-((((((..(((.(((((((((..((.............))..))))--).)))).)))...))).)))))..)))))))).)))))... ( -31.92)
>consensus
__________UUCCAACUGGUG___CUGGCUUAU___AAGCCAUAUUAUU_____AUCUCCUAUUAGCCCGAUUUCGGCGU_UUGCCUUUAAGCGAGCUGCAUUGCAGCGCACUGA
.................((((......((((.......))))........................((..........(((.(((....)))))).(((((...))))))))))). (-16.81 = -15.63 +  -1.19)

alignment

secondary structure

dotplot

Window 1

Location	1,259,321 – 1,259,418
Length	97
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	76.19
Mean single sequence MFE	-29.18
Consensus MFE	-17.19
Energy contribution	-17.62
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-2.11
Structure conservation index	0.59
SVM decision value	1.11
SVM RNA-class probability	0.916861
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1259321 97 - 22224390
UCAGUGCGCUGCAAUGCAGCUCGCUUAAAGGCAA-ACGCCGAAAUCGGGCUAAUAGGAGAU-----AAUAAUAUGGCUA---AUAAGCCAACUGUACAAGUUGGAA----------
((((((.(((((...))))).))))....(((..-..))))).....(((((.((..(...-----..)..))))))).---.....((((((.....))))))..---------- ( -26.30)
>DroSec_CAF1 13520 94 - 1
UCAGUGCGCUGCAAUGCAGCUCGCUUAAAGGCAA-ACGCCGAAAUCGGGCUAAUAGAAGAU-----AAUAAUAUGGCUU---AUAAGCCAG---CACCAGUUGGAA----------
...((((((......))((((((......(((..-..))).....))))))..........-----.......(((((.---...))))))---))).........---------- ( -26.40)
>DroSim_CAF1 12182 94 - 1
CCAGUGCGCUGCAAUGCAGCUCGCUUAAAGGCAA-ACGCCGAAAUCGGGCUAAUAGAAGAU-----AAUAAUAUGGCUU---AUAAGCCAG---CACCAGUUGGAA----------
(((((((((......))((((((......(((..-..))).....))))))..........-----.......(((((.---...))))))---)))....)))..---------- ( -27.80)
>DroEre_CAF1 15316 110 - 1
UCGCUGCGCUGCACUGCAGCUGGCCUAAAGGCAGCGCCGAC--AUCAGGCUAAUAGGAGAUUGGAGAUUAAUGCGGCUCUAAAUUAGCC-A---GAGCAGUUGGAACAAUUCACAA
.((((..(((((...)))))..(((....)))))))(((((--.((.(((((((.((((.(((.(......).)))))))..)))))))-.---))...)))))............ ( -36.20)
>consensus
UCAGUGCGCUGCAAUGCAGCUCGCUUAAAGGCAA_ACGCCGAAAUCGGGCUAAUAGAAGAU_____AAUAAUAUGGCUU___AUAAGCCAA___CACCAGUUGGAA__________
(((..(((((((...)))))..(((....)))......(((....))))).......................(((((.......)))))...........)))............ (-17.19 = -17.62 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:23 2006