Locus 1785

Sequence ID	2R_DroMel_CAF1
Location	6,688,145 – 6,688,241
Length	96
Max. P	0.901214

overview

Window 7

Location	6,688,145 – 6,688,241
Length	96
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	88.29
Mean single sequence MFE	-37.23
Consensus MFE	-28.15
Energy contribution	-28.48
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.06
Structure conservation index	0.76
SVM decision value	0.36
SVM RNA-class probability	0.704581
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6688145 96 + 20766785
GGCGCCAAAGUGUUCGGCACCACGAAUUUCCCCUCCUUCCAGCUUCCAGUUUCGAACUGCUUUCGCA-CUGGAACUGGAA-----GGCCUUCUAGCCGGGCG
..((((...(((((((......))))).......((((((((.(((((((..((((.....)))).)-))))))))))))-----)).......))..)))) ( -35.80)
>DroSec_CAF1 36686 96 + 1
GGCGCCAAAGUGUUCGGCACUUCGAAUUUCCCCUCCUUCCAGCUUCCAGUUUCGAACUGCUUUCGCA-CUGGAACUGGAA-----GGCCUUCUAGCCGGGCG
...........(((((((.....(.....)....((((((((.(((((((..((((.....)))).)-))))))))))))-----)).......))))))). ( -35.60)
>DroSim_CAF1 40340 96 + 1
GGCGCCAAAGUGUUCGGCACUUCGAAUUUCCCCUCCUUCCAGCUUCCAGUUUCGAACUGCUUUCGCA-CUGGAACUGGAA-----GGCCUUCUAGCCGGGCG
...........(((((((.....(.....)....((((((((.(((((((..((((.....)))).)-))))))))))))-----)).......))))))). ( -35.60)
>DroEre_CAF1 34234 101 + 1
GGCGCCAAAGUGUUCGGCACCUCGAAUUUCCCCUACUUCCCGCUUCCAGUUUCGAACUGCUUUCGCA-CUGGAACUGGAAGCAGUGGCUUUCUAGCCGGCUG
...(((.....((((((....))))))..............(((((((((((((...(((....)))-.)))))))))))))...((((....))))))).. ( -36.70)
>DroYak_CAF1 36788 100 + 1
GGCGCCAAAGUUUUCGGAAACCCGAAUUUCCCCUCCUUCCAGCUUCCAGUUUCGAACUGCUUUCGCA-CUGGAACUGGAAGGAA-GGCCUUCUAGCCGGCUA
...(((......(((((....))))).......(((((((((.(((((((..((((.....)))).)-))))))))))))))).-(((......)))))).. ( -42.30)
>DroAna_CAF1 35500 92 + 1
GGCGCCAAACUGUUCGGCUGUUCGAAUUUCCCCUCCUUCCAGUUUCCAGU-GCGAA----UUUCGCGCCUGGAACUGGAA-----GGCCUUCUAGCCGGCAA
...(((.....((((((....)))))).......((((((((((.(((((-(((..----...)))).))))))))))))-----))..........))).. ( -37.40)
>consensus
GGCGCCAAAGUGUUCGGCACCUCGAAUUUCCCCUCCUUCCAGCUUCCAGUUUCGAACUGCUUUCGCA_CUGGAACUGGAA_____GGCCUUCUAGCCGGCCG
((((((.........))).....(((...((.....((((((.((((((...((((.....))))...)))))))))))).....))..)))..)))..... (-28.15 = -28.48 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	6,688,145 – 6,688,241
Length	96
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	88.29
Mean single sequence MFE	-42.25
Consensus MFE	-32.32
Energy contribution	-32.52
Covariance contribution	0.19
Combinations/Pair	1.03
Mean z-score	-3.62
Structure conservation index	0.77
SVM decision value	1.02
SVM RNA-class probability	0.901214
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6688145 96 - 20766785
CGCCCGGCUAGAAGGCC-----UUCCAGUUCCAG-UGCGAAAGCAGUUCGAAACUGGAAGCUGGAAGGAGGGGAAAUUCGUGGUGCCGAACACUUUGGCGCC
..(((((((....))))-----((((((((((((-(.((((.....))))..))))).))))))))...))).........((((((((.....)))))))) ( -42.40)
>DroSec_CAF1 36686 96 - 1
CGCCCGGCUAGAAGGCC-----UUCCAGUUCCAG-UGCGAAAGCAGUUCGAAACUGGAAGCUGGAAGGAGGGGAAAUUCGAAGUGCCGAACACUUUGGCGCC
..(((((((....))))-----((((((((((((-(.((((.....))))..))))).))))))))...)))..........(((((((.....))))))). ( -40.10)
>DroSim_CAF1 40340 96 - 1
CGCCCGGCUAGAAGGCC-----UUCCAGUUCCAG-UGCGAAAGCAGUUCGAAACUGGAAGCUGGAAGGAGGGGAAAUUCGAAGUGCCGAACACUUUGGCGCC
..(((((((....))))-----((((((((((((-(.((((.....))))..))))).))))))))...)))..........(((((((.....))))))). ( -40.10)
>DroEre_CAF1 34234 101 - 1
CAGCCGGCUAGAAAGCCACUGCUUCCAGUUCCAG-UGCGAAAGCAGUUCGAAACUGGAAGCGGGAAGUAGGGGAAAUUCGAGGUGCCGAACACUUUGGCGCC
...((((((....)))).(((((((((((((.(.-(((....))).)..).))))))))))))......))..........((((((((.....)))))))) ( -45.40)
>DroYak_CAF1 36788 100 - 1
UAGCCGGCUAGAAGGCC-UUCCUUCCAGUUCCAG-UGCGAAAGCAGUUCGAAACUGGAAGCUGGAAGGAGGGGAAAUUCGGGUUUCCGAAAACUUUGGCGCC
.....(((..((((.((-((((((((((((((((-(.((((.....))))..))))).))))))))))))))....(((((....)))))..))))...))) ( -47.20)
>DroAna_CAF1 35500 92 - 1
UUGCCGGCUAGAAGGCC-----UUCCAGUUCCAGGCGCGAAA----UUCGC-ACUGGAAACUGGAAGGAGGGGAAAUUCGAACAGCCGAACAGUUUGGCGCC
.....(((.......((-----((((((((((((..(((...----..)))-.)))).))))))))))................(((((.....)))))))) ( -38.30)
>consensus
CGCCCGGCUAGAAGGCC_____UUCCAGUUCCAG_UGCGAAAGCAGUUCGAAACUGGAAGCUGGAAGGAGGGGAAAUUCGAAGUGCCGAACACUUUGGCGCC
.....(((..(((..((.....((((((((((((...((((.....))))...)))).)))))))).....))...))).....(((((.....)))))))) (-32.32 = -32.52 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:06 2006