Locus 1360

Sequence ID	3L_DroMel_CAF1
Location	3,966,792 – 3,966,890
Length	98
Max. P	0.999818

overview

Window 6

Location	3,966,792 – 3,966,890
Length	98
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	96.47
Mean single sequence MFE	-41.32
Consensus MFE	-37.38
Energy contribution	-38.02
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-3.07
Structure conservation index	0.90
SVM decision value	4.16
SVM RNA-class probability	0.999818
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3966792 98 + 23771897
CAAGAGGCAAGAGCCGCGAGCCCCAAGCCGAAAAAGUUCCAAAAGGGCCAAAGAGCCAUGAGCCAAUUCUCAGGUAUGGCUGGGGGUCCGGUGCCUCC---
...(((((....((((.((.(((((.((((.....(..((....))..).....(((.((((......))))))).))))))))).))))))))))).--- ( -42.50)
>DroSec_CAF1 39141 98 + 1
CAAGAGGCAAGAGCCGCGAGCCCCGAGCCGAAAAAGUUCCAAAAGGGCCAAAGAGCCAUGAGCCAAUUCUCAGGUAUGGCUGGGGGUCCGGUGCCUCC---
...(((((....((((.((.((((.(((((.....(..((....))..).....(((.((((......))))))).))))).))))))))))))))).--- ( -42.60)
>DroSim_CAF1 42634 98 + 1
CAAGAGGCAAGAGCCGCGAGCCCCGAGCCGAAAAAGUUCCAAAAGGGCCAAAGAGCCAUGAGCCAAUUCUCAGGUAUGGCUGGGGGUCCGGUGCCUCC---
...(((((....((((.((.((((.(((((.....(..((....))..).....(((.((((......))))))).))))).))))))))))))))).--- ( -42.60)
>DroEre_CAF1 40212 98 + 1
CAAGAGCCAAGAGCCGCGAGCCCCCAGCCGAAAAAGUUCCAAAAGGGCCAAAGAGCCAUGAGCCAAUUCUCAGGUAUGGCUGGGGGUCCGGUGCCCCC---
............((((.((.((((((((((.....(..((....))..).....(((.((((......))))))).))))))))))))))))......--- ( -39.40)
>DroYak_CAF1 42279 101 + 1
CAAGAGCCAAGAGCCGCGAGCCCCGAGCCGAAAAAGUUCCAAAAGGGCCAAAGAGCCAUGAGCCAAUUCUCAGGUAUGGCUGGGGGUCCGGUGCUCCCUCC
...(((....(((((.((..((((.(((((.....(..((....))..).....(((.((((......))))))).))))).))))..))).)))).))). ( -39.50)
>consensus
CAAGAGGCAAGAGCCGCGAGCCCCGAGCCGAAAAAGUUCCAAAAGGGCCAAAGAGCCAUGAGCCAAUUCUCAGGUAUGGCUGGGGGUCCGGUGCCUCC___
...(((((....((((.((.((((.(((((.....(..((....))..).....(((.((((......))))))).))))))))).))))))))))).... (-37.38 = -38.02 +   0.64)

alignment

secondary structure

dotplot

Window 7

Location	3,966,792 – 3,966,890
Length	98
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	96.47
Mean single sequence MFE	-39.40
Consensus MFE	-34.84
Energy contribution	-35.20
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.79
Structure conservation index	0.88
SVM decision value	1.64
SVM RNA-class probability	0.969315
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3966792 98 - 23771897
---GGAGGCACCGGACCCCCAGCCAUACCUGAGAAUUGGCUCAUGGCUCUUUGGCCCUUUUGGAACUUUUUCGGCUUGGGGCUCGCGGCUCUUGCCUCUUG
---((((((((((((((((.((((.....((((......)))).((((....))))................)))).)))).)).)))....))))))).. ( -38.60)
>DroSec_CAF1 39141 98 - 1
---GGAGGCACCGGACCCCCAGCCAUACCUGAGAAUUGGCUCAUGGCUCUUUGGCCCUUUUGGAACUUUUUCGGCUCGGGGCUCGCGGCUCUUGCCUCUUG
---((((((((((((((((.((((.....((((......)))).((((....))))................)))).)))).)).)))....))))))).. ( -38.60)
>DroSim_CAF1 42634 98 - 1
---GGAGGCACCGGACCCCCAGCCAUACCUGAGAAUUGGCUCAUGGCUCUUUGGCCCUUUUGGAACUUUUUCGGCUCGGGGCUCGCGGCUCUUGCCUCUUG
---((((((((((((((((.((((.....((((......)))).((((....))))................)))).)))).)).)))....))))))).. ( -38.60)
>DroEre_CAF1 40212 98 - 1
---GGGGGCACCGGACCCCCAGCCAUACCUGAGAAUUGGCUCAUGGCUCUUUGGCCCUUUUGGAACUUUUUCGGCUGGGGGCUCGCGGCUCUUGGCUCUUG
---((((((..((..(((((((((.....((((......)))).((((....))))................)))))))))..))..))))))........ ( -42.50)
>DroYak_CAF1 42279 101 - 1
GGAGGGAGCACCGGACCCCCAGCCAUACCUGAGAAUUGGCUCAUGGCUCUUUGGCCCUUUUGGAACUUUUUCGGCUCGGGGCUCGCGGCUCUUGGCUCUUG
(((((((((..((..((((.((((.....((((......)))).((((....))))................)))).))))..))..)))))...)))).. ( -38.70)
>consensus
___GGAGGCACCGGACCCCCAGCCAUACCUGAGAAUUGGCUCAUGGCUCUUUGGCCCUUUUGGAACUUUUUCGGCUCGGGGCUCGCGGCUCUUGCCUCUUG
...((((((((((((((((.((((.....((((......)))).((((....))))................)))).)))).)).)))....))))))).. (-34.84 = -35.20 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:35 2006