Locus 3114

Sequence ID	2R_DroMel_CAF1
Location	10,654,056 – 10,654,153
Length	97
Max. P	0.863595

overview

Window 9

Location	10,654,056 – 10,654,153
Length	97
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	81.63
Mean single sequence MFE	-49.90
Consensus MFE	-29.53
Energy contribution	-32.02
Covariance contribution	2.49
Combinations/Pair	1.11
Mean z-score	-2.81
Structure conservation index	0.59
SVM decision value	0.84
SVM RNA-class probability	0.863595
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10654056 97 + 20766785
GGCGGCAGCACCAGCUCCUCCGGCGGAG---GAGGCGGUCGGAAGAAGGCC---GCCCAAGCGGCUGCAGCUGCCGCUGCGGCGAAUGGAGUGCACAUCCAGA
(((((((((..((((((((((...))))---))(((((((.......))))---)))......))))..)))))))))........((((.......)))).. ( -50.40)
>DroSec_CAF1 87670 97 + 1
GGCGGCAGCACCAGCUCCUCCGGCGGAG---GAGGCGGUCGGAAGAAGGCC---GCUCAAGCGGCUGCAGCCGCUGCUGCCGCGAAUGGAGUGCACAUCCAGA
.((((((((.....(((((((...))))---)))((((((.......))))---))...((((((....))))))))))))))...((((.......)))).. ( -55.30)
>DroSim_CAF1 88881 97 + 1
GGCGGCAGCACCAGCUCCUCCGGCGGAG---GAGGCGGUCGGAAGAAGGCC---GCUCAAGCGGCUGCAGCCGCCGCUGCCGCGAAUGGAGUGCACAUCCAGA
.((((((((......((((((...))))---))(((((((....)).((((---((....))))))....)))))))))))))...((((.......)))).. ( -55.20)
>DroEre_CAF1 88549 100 + 1
GGCGGCAGCACCAGCUCCUCCGGCGGAGGAGGAGGCGGUCGGAAGAAGGCU---GCUCAAGCGGCUGCAGCCGCCGCUGCCGCGAAUGGAGUGCACAUCCAGA
.((((((((.....(((((((...)))))))..(((((((....)).((((---((....))))))....)))))))))))))...((((.......)))).. ( -56.20)
>DroWil_CAF1 129264 82 + 1
GGCGGCA------GCUCCUCUGGCG---------GUAGUCGCAAAAAAUCUUCGGCGCAGGCUCAGGCAGCCGCUG------CUAAUGGUGUGCAUAUAGUAA
....(((------.(.((..(((((---------((.((((.((......))))))...((((.....))))))))------)))..)).))))......... ( -24.70)
>DroYak_CAF1 95795 100 + 1
GGCGGCAGCACCAGCUCCUCCGGCGGCGGAGGCGGCGGUCGGAAGAAGGCU---GCUCAAGCGGCUGCGGCCGCCGCUGCCGCGAAUGGAGUGCACAUCCAAA
.((((((((.......((((((....)))))).((((((((......((((---((....)))))).))))))))))))))))...((((.......)))).. ( -57.60)
>consensus
GGCGGCAGCACCAGCUCCUCCGGCGGAG___GAGGCGGUCGGAAGAAGGCC___GCUCAAGCGGCUGCAGCCGCCGCUGCCGCGAAUGGAGUGCACAUCCAGA
.((((((((....(((..((((((.(.........).))))))....)))..........(((((....))))).))))))))...((((.......)))).. (-29.53 = -32.02 +   2.49)

alignment

secondary structure

dotplot

Window 0

Location	10,654,056 – 10,654,153
Length	97
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	81.63
Mean single sequence MFE	-44.87
Consensus MFE	-28.41
Energy contribution	-30.76
Covariance contribution	2.35
Combinations/Pair	1.10
Mean z-score	-1.82
Structure conservation index	0.63
SVM decision value	0.19
SVM RNA-class probability	0.627538
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10654056 97 - 20766785
UCUGGAUGUGCACUCCAUUCGCCGCAGCGGCAGCUGCAGCCGCUUGGGC---GGCCUUCUUCCGACCGCCUC---CUCCGCCGGAGGAGCUGGUGCUGCCGCC
...(((((.......)))))......((((((((....(((((....))---))).........((((.(((---((((...))))))).)))))))))))). ( -46.50)
>DroSec_CAF1 87670 97 - 1
UCUGGAUGUGCACUCCAUUCGCGGCAGCAGCGGCUGCAGCCGCUUGAGC---GGCCUUCUUCCGACCGCCUC---CUCCGCCGGAGGAGCUGGUGCUGCCGCC
...(((((.......)))))((((((((..(((..(..(((((....))---)))...)..)))((((.(((---((((...))))))).)))))))))))). ( -50.40)
>DroSim_CAF1 88881 97 - 1
UCUGGAUGUGCACUCCAUUCGCGGCAGCGGCGGCUGCAGCCGCUUGAGC---GGCCUUCUUCCGACCGCCUC---CUCCGCCGGAGGAGCUGGUGCUGCCGCC
...(((((.......)))))((((((((..(((..(..(((((....))---)))...)..)))((((.(((---((((...))))))).)))))))))))). ( -50.40)
>DroEre_CAF1 88549 100 - 1
UCUGGAUGUGCACUCCAUUCGCGGCAGCGGCGGCUGCAGCCGCUUGAGC---AGCCUUCUUCCGACCGCCUCCUCCUCCGCCGGAGGAGCUGGUGCUGCCGCC
...(((((.......)))))((((((((((((((....)))((....))---.)))........((((.(((((((......))))))).)))))))))))). ( -50.90)
>DroWil_CAF1 129264 82 - 1
UUACUAUAUGCACACCAUUAG------CAGCGGCUGCCUGAGCCUGCGCCGAAGAUUUUUUGCGACUAC---------CGCCAGAGGAGC------UGCCGCC
....................(------(.((((((.((((.((..((((.(((....))).))).)...---------.))))).).)))------))).)). ( -22.40)
>DroYak_CAF1 95795 100 - 1
UUUGGAUGUGCACUCCAUUCGCGGCAGCGGCGGCCGCAGCCGCUUGAGC---AGCCUUCUUCCGACCGCCGCCUCCGCCGCCGGAGGAGCUGGUGCUGCCGCC
...(((((.......)))))((((((((((((((....))))))..(.(---(((..(((((((...((.((....)).))))))))))))).))))))))). ( -48.60)
>consensus
UCUGGAUGUGCACUCCAUUCGCGGCAGCGGCGGCUGCAGCCGCUUGAGC___AGCCUUCUUCCGACCGCCUC___CUCCGCCGGAGGAGCUGGUGCUGCCGCC
...(((((.......)))))(((((((((.((((.((....((....))....))..(((((((.................))))))))))).))))))))). (-28.41 = -30.76 +   2.35)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:53 2006