Locus 4823

Sequence ID	2L_DroMel_CAF1
Location	13,747,007 – 13,747,131
Length	124
Max. P	0.770314

overview

Window 4

Location	13,747,007 – 13,747,102
Length	95
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	90.59
Mean single sequence MFE	-28.56
Consensus MFE	-21.86
Energy contribution	-23.02
Covariance contribution	1.16
Combinations/Pair	1.04
Mean z-score	-1.61
Structure conservation index	0.77
SVM decision value	0.18
SVM RNA-class probability	0.623440
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13747007 95 + 22407834
----CACACACACUUCUCAUUGUCGCAGCUUCGGCACACGUGCUGCGGAAUGGCUAAAGAAUGGCAAAAAUGGCAGUGAUGUGGCCUUAACACCACUUU
----............(((((((((((((..((.....)).)))))......((((.....))))......)))))))).((((........))))... ( -28.10)
>DroSec_CAF1 10674 99 + 1
CACACACACACACUUCUCAUUGUCGCAGCUUCGGCACACGUGCUGCGGAAUGGCUAAAGAAUGGCAAAAAUGGCAGUGAUGUGGCCUUAACACCACUUU
................(((((((((((((..((.....)).)))))......((((.....))))......)))))))).((((........))))... ( -28.10)
>DroSim_CAF1 12391 99 + 1
CACACACACACACUUCUCAUUGUCGCAGCUUCGGCACACGUGCUGCGGAAUGGCUAAAGAAUGGCAAAAAUGGCAGUGAUGUGGCCUUAACACCACUUU
................(((((((((((((..((.....)).)))))......((((.....))))......)))))))).((((........))))... ( -28.10)
>DroEre_CAF1 12534 90 + 1
---------ACACUUCCCAUUGUCGCAGCUCCGGCACACGUGCUGAAGAAUGGCGAAAGAAUGGCGAAAAUGGCAGGGAUGUGGCCUUAACACCACUUU
---------...(((.(((((.((((..((.(((((....))))).)).....(....)....)))).))))).)))...((((........))))... ( -26.80)
>DroYak_CAF1 13366 95 + 1
----CACACACACUUCCCAUUGUCGCAGCUUCGGCACACGUGCUGAAGAAUGGCGAAAGUAUGGCAGAAAUGGCAGUGAUGUGGCCUUAACUCCACUUU
----..((((((((..((((..((((..((((((((....))))))))....))))....))))((....))..)))).))))................ ( -31.70)
>consensus
____CACACACACUUCUCAUUGUCGCAGCUUCGGCACACGUGCUGCGGAAUGGCUAAAGAAUGGCAAAAAUGGCAGUGAUGUGGCCUUAACACCACUUU
..........((((.((((((.(((((((..((.....)).)))))))))))((((.....))))......)).))))..((((........))))... (-21.86 = -23.02 +   1.16)

alignment

secondary structure

dotplot

Window 5

Location	13,747,036 – 13,747,131
Length	95
Sequences	4
Columns	98
Reading direction	forward
Mean pairwise identity	89.46
Mean single sequence MFE	-29.89
Consensus MFE	-21.72
Energy contribution	-22.97
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.73
SVM decision value	0.53
SVM RNA-class probability	0.770314
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13747036 95 + 22407834
GCACACGUGCUGCGGAAUGGCUAAAGAAUGGCAAAAAUGGCAGUGAUGUGGCCUUAACACCACUUUGGUGGGGGUAAGUUGGUGGUGG---UGGGUAG
...((((((((((.(....((((.....)))).....).))))).)))))((((...(((((((....((....))....))))))).---.)))).. ( -31.00)
>DroSec_CAF1 10707 95 + 1
GCACACGUGCUGCGGAAUGGCUAAAGAAUGGCAAAAAUGGCAGUGAUGUGGCCUUAACACCACUUUGGUGGGGGUGAAUGGGUGGUGG---UGGGUGG
...((((((((((.(....((((.....)))).....).))))).)))))((((...((((((((..............)))))))).---.)))).. ( -31.64)
>DroSim_CAF1 12424 95 + 1
GCACACGUGCUGCGGAAUGGCUAAAGAAUGGCAAAAAUGGCAGUGAUGUGGCCUUAACACCACUUUGGUGGGGGUGAAUGGGUGGUGG---UGGGUGG
...((((((((((.(....((((.....)))).....).))))).)))))((((...((((((((..............)))))))).---.)))).. ( -31.64)
>DroEre_CAF1 12558 91 + 1
GCACACGUGCUGAAGAAUGGCGAAAGAAUGGCGAAAAUGGCAGGGAUGUGGCCUUAACACCACUUUGGUGGGGGUGA-UGGGGGGUGCGUG------G
...((((..((...(.....(....).....).....(.(((....))).)(((((.((((.(((....))))))).-)))))))..))))------. ( -25.30)
>consensus
GCACACGUGCUGCGGAAUGGCUAAAGAAUGGCAAAAAUGGCAGUGAUGUGGCCUUAACACCACUUUGGUGGGGGUGAAUGGGUGGUGG___UGGGUGG
((.((((((((((.(....((((.....)))).....).))))).))))))).....((((((((..............))))))))........... (-21.72 = -22.97 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:20 2006