Locus 1502

Sequence ID	3R_DroMel_CAF1
Location	4,316,398 – 4,316,557
Length	159
Max. P	0.777817

overview

Window 4

Location	4,316,398 – 4,316,517
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.66
Mean single sequence MFE	-35.83
Consensus MFE	-32.12
Energy contribution	-31.90
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.82
Structure conservation index	0.90
SVM decision value	0.09
SVM RNA-class probability	0.576222
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4316398 119 - 27905053
UGACAACAUUGACAAAAUGUCAAUGCUUUUCGC-CGGGCCGAGGAAAACUGGUUUUCUGGAGAAUGCUCCGCAUAAUUAGCCUCAAACUCUUGACAGUUGUUUCGCAAGAGGGGGCAUUU
.((.(((((((((.....))))))).)).))((-(...((((((....((((((...(((((....)))))...))))))))))...((((((...(......).))))))))))).... ( -35.90)
>DroSec_CAF1 3796 120 - 1
UGACAACAUUGACAAAAUGUCAAUGCCUUUCGUGCGGGCCGAGGAAAACUGGUUUUCUGGAGAAUGCUCCGCAUAAUUAGCCUCAAACUCUUGACAGUUGUUUCGCAAGAGGGGACAUUU
......(((((((.....)))))))((((((.(((((..(((((....((((((...(((((....)))))...)))))))))).((((......)))))..))))).))))))...... ( -37.70)
>DroEre_CAF1 3788 118 - 1
UGACAACAUUGACAAAAUGUCAAUGCUUUUCGC-CGGGCCGAGGA-AACUGGUUUUCUGGAGAAUCCUCCGCAUAAUUAGCCUCAAACUCUUGACAGUUGUUUCGCAAGAGGGGACAUUU
.((.(((((((((.....))))))).)).))..-.(..((((((.-..((((((...(((((....)))))...))))))))))...((((((...(......).))))))))..).... ( -33.90)
>consensus
UGACAACAUUGACAAAAUGUCAAUGCUUUUCGC_CGGGCCGAGGAAAACUGGUUUUCUGGAGAAUGCUCCGCAUAAUUAGCCUCAAACUCUUGACAGUUGUUUCGCAAGAGGGGACAUUU
...((((((((((.....)))))))..........(((..((((....((((((...(((((....)))))...))))))))))...))))))...(((.((((....)))).))).... (-32.12 = -31.90 +  -0.22)

alignment

secondary structure

dotplot

Window 5

Location	4,316,438 – 4,316,557
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	94.99
Mean single sequence MFE	-32.17
Consensus MFE	-28.81
Energy contribution	-28.82
Covariance contribution	0.01
Combinations/Pair	1.10
Mean z-score	-2.12
Structure conservation index	0.90
SVM decision value	0.55
SVM RNA-class probability	0.777817
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4316438 119 + 27905053
CUAAUUAUGCGGAGCAUUCUCCAGAAAACCAGUUUUCCUCGGCCCG-GCGAAAAGCAUUGACAUUUUGUCAAUGUUGUCAGCAUAAAAUCCCGAGCAAGAGUGUCAUAAACUCCGACAAC
.......(((((((((((((...(((((....)))))(((((....-((....(((((((((.....)))))))))....))........)))))..)))))).......))))).)).. ( -33.81)
>DroSec_CAF1 3836 120 + 1
CUAAUUAUGCGGAGCAUUCUCCAGAAAACCAGUUUUCCUCGGCCCGCACGAAAGGCAUUGACAUUUUGUCAAUGUUGUCAGCAUAAAAUCCCGAGCAAGAGUGUCAUAAACUUCGACAAC
....(((((.((((....)))).......((.((((.(((((......(....)((((((((.....))))))))...............))))).)))).)).)))))........... ( -28.90)
>DroEre_CAF1 3828 118 + 1
CUAAUUAUGCGGAGGAUUCUCCAGAAAACCAGUU-UCCUCGGCCCG-GCGAAAAGCAUUGACAUUUUGUCAAUGUUGUCAGCAUAAAAUCCCGAGCAAAAGUGUCAUAAACUCCGGGAAC
....((((((.(((((..((..........))..-))))).....(-(((....((((((((.....)))))))))))).))))))..(((((.(....(((.......))))))))).. ( -33.80)
>consensus
CUAAUUAUGCGGAGCAUUCUCCAGAAAACCAGUUUUCCUCGGCCCG_GCGAAAAGCAUUGACAUUUUGUCAAUGUUGUCAGCAUAAAAUCCCGAGCAAGAGUGUCAUAAACUCCGACAAC
.........(((((..(((....)))...((.((((.(((((.....((....(((((((((.....)))))))))....))........))))).)))).)).......)))))..... (-28.81 = -28.82 +   0.01)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:11 2006