Locus 2500

Sequence ID	2L_DroMel_CAF1
Location	6,896,687 – 6,896,816
Length	129
Max. P	0.915500

overview

Window 1

Location	6,896,687 – 6,896,779
Length	92
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	87.27
Mean single sequence MFE	-32.82
Consensus MFE	-28.70
Energy contribution	-29.10
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.87
SVM decision value	1.10
SVM RNA-class probability	0.915500
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6896687 92 - 22407834
CAAGCAGCCAUAGGAGCAUCG------CCAGAUGCGCCAGUACCACCAGCACUGGCAGCAGCUCCAUAUC--GUUACACUCGCAGAAUGGCGGGCAGUAA------------
...((.(((((.((((((((.------...)))((((((((.(.....).)))))).)).))))).....--((.......))...)))))..)).....------------ ( -31.50)
>DroSec_CAF1 94683 92 - 1
CAAGCAGCCAUAGGAGCAUCG------CCAGAUGCGGCAGUGCCACCAGCACUGGCAGCAGCUCCAUGUC--GUUACACUCGCAGAAUGGCGGGCAGUAA------------
...((.(((((.((((((((.------...)))(((.((((((.....)))))).).)).))))).((.(--(.......))))..)))))..)).....------------ ( -35.10)
>DroSim_CAF1 88843 92 - 1
CAAGCAGCCAUAGGAGCAUCG------CCAGAUGCGGCAGUGCCACCAGCACUGGCAGCAGCUCCAUAUC--GUUACACUCGCAGAAUGGCGGGCAGUAA------------
...((.(((((.((((((((.------...)))(((.((((((.....)))))).).)).))))).....--((.......))...)))))..)).....------------ ( -33.50)
>DroEre_CAF1 95183 103 - 1
CAAGCAGCCAUAGGAGCAUCG------CCAGAUGCGGCAGUGC-ACCAGCACUGGCAGCAGCUCCAUAUC--GUUACACUCGCAAAAUGGCAGGCAGUAAAAGUGAUGUUUC
...((.(((((.((((((((.------...)))(((.((((((-....)))))).).)).))))).....--((.......))...)))))..))................. ( -32.80)
>DroYak_CAF1 93081 107 - 1
CAAGCAGCCAUAGGAGCAUCUCUCCUACCAGAUGCGGCAGUGCCACCAGCAGUGGCAGCAGCUCCAUAUCCAGUUACACUCGCAAAAUGGCAGGCAGUAAAAG-----UUUC
......(((.((((((.....))))))(((..((((((..((((((.....))))))))((((........)))).....))))...)))..)))........-----.... ( -31.20)
>consensus
CAAGCAGCCAUAGGAGCAUCG______CCAGAUGCGGCAGUGCCACCAGCACUGGCAGCAGCUCCAUAUC__GUUACACUCGCAGAAUGGCGGGCAGUAA____________
...((.(((((.((((((((..........)))(((.((((((.....)))))).).)).))))).......((.......))...)))))..))................. (-28.70 = -29.10 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	6,896,715 – 6,896,816
Length	101
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	83.47
Mean single sequence MFE	-33.87
Consensus MFE	-22.58
Energy contribution	-25.13
Covariance contribution	2.56
Combinations/Pair	1.07
Mean z-score	-1.94
Structure conservation index	0.67
SVM decision value	-0.00
SVM RNA-class probability	0.531788
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6896715 101 - 22407834
GUGGCAUCCUUAAAUAGCCUUGGUCAAUGCAUCCGGACAAGCAGCCAUAGGAGCAUCG------CCAGAUGCGCCAGUACCACCAGCACUGGCAGCAGCUCCAUAUC--
(((((...........((....))...(((..........)))))))).((((((((.------...)))((((((((.(.....).)))))).)).))))).....-- ( -30.60)
>DroSec_CAF1 94711 101 - 1
GUGGCAUCCUUAAAUAGCCUUGGUCAAUGCAUCCGGCCAAGCAGCCAUAGGAGCAUCG------CCAGAUGCGGCAGUGCCACCAGCACUGGCAGCAGCUCCAUGUC--
(((((...((.....)).(((((((.........)))))))..))))).((((((((.------...)))(((.((((((.....)))))).).)).))))).....-- ( -38.00)
>DroSim_CAF1 88871 101 - 1
GUGGCAUCCUUAAAUAGCCUUGGUCAAUGCAUCCGGCCAAGCAGCCAUAGGAGCAUCG------CCAGAUGCGGCAGUGCCACCAGCACUGGCAGCAGCUCCAUAUC--
(((((...((.....)).(((((((.........)))))))..))))).((((((((.------...)))(((.((((((.....)))))).).)).))))).....-- ( -38.00)
>DroEre_CAF1 95223 100 - 1
GUGGCAUCCUUAAAUAGCCUUGGUCAAUGCAUCCGGCCAAGCAGCCAUAGGAGCAUCG------CCAGAUGCGGCAGUGC-ACCAGCACUGGCAGCAGCUCCAUAUC--
(((((...((.....)).(((((((.........)))))))..))))).((((((((.------...)))(((.((((((-....)))))).).)).))))).....-- ( -38.50)
>DroYak_CAF1 93116 109 - 1
GUGGCAUCCUUAAAUAGCCUUGGUCAAUGCAUCCGGCCAAGCAGCCAUAGGAGCAUCUCUCCUACCAGAUGCGGCAGUGCCACCAGCAGUGGCAGCAGCUCCAUAUCCA
(((((...((.....)).(((((((.........)))))))..))))).(((((((((........))))))(((.(((((((.....)))))).).))).....))). ( -36.20)
>DroAna_CAF1 89687 80 - 1
AUGGCAUCCUUAAAUAGCCUUGGUCAAUGCAUCCGGCCAAGCAGCAGUGGAAGCAAAG------GCAAAGGCGACUGUGUCUAC---------------------UU--
..(((((.........(((((.(((..(((.(((.((......))...))).)))..)------)).)))))....)))))...---------------------..-- ( -21.92)
>consensus
GUGGCAUCCUUAAAUAGCCUUGGUCAAUGCAUCCGGCCAAGCAGCCAUAGGAGCAUCG______CCAGAUGCGGCAGUGCCACCAGCACUGGCAGCAGCUCCAUAUC__
(((((...((.....)).(((((((.........)))))))..))))).((((((((..........)))))(.((((((.....)))))).)......)))....... (-22.58 = -25.13 +   2.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:21 2006