Locus 5523

Sequence ID	X_DroMel_CAF1
Location	14,295,136 – 14,295,269
Length	133
Max. P	0.963244

overview

Window 2

Location	14,295,136 – 14,295,240
Length	104
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	87.34
Mean single sequence MFE	-29.88
Consensus MFE	-22.58
Energy contribution	-24.07
Covariance contribution	1.50
Combinations/Pair	1.04
Mean z-score	-2.73
Structure conservation index	0.76
SVM decision value	1.55
SVM RNA-class probability	0.963244
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14295136 104 + 22224390
UUUCGGAAUAAAAGUGUUGAAUGUAAAUGCGAGAUUUGGGCAGACGAAACUCAAAGAGCUCCUUCCAAAGGGCAACAGGCCCAAGGAUCAAUAUCAGCAUCAUC
.............(((((((..((....))((..(((((((.((......)).....((.(((.....))))).....)))))))..))....))))))).... ( -24.90)
>DroSec_CAF1 8021 104 + 1
CUUCGGAAUAAAAGUGUUGAAUGUGAAUGCGAGAUUUGGGCAGCCGAAAGGCAAAGAGCUCCUUCCAAAGGGCAACAAGCCCAAGGAUCAAUAUCAGCAUCAUC
(....).......(((((((..((....))((..(((((((.(((....))).....((.(((.....))))).....)))))))..))....))))))).... ( -34.70)
>DroSim_CAF1 8566 104 + 1
CUUCGGAAUAAAAGUGUUGAAUGUGAAUGCGAGAUUUGGGCAGCCGAAAGGCAAAGAGCUCCUUCCAAAGGGCAACAAGCCCAAGGAUCAAUAUCAGCAUCAUC
(....).......(((((((..((....))((..(((((((.(((....))).....((.(((.....))))).....)))))))..))....))))))).... ( -34.70)
>DroYak_CAF1 9783 97 + 1
----AAAAUACAAGUGUUGAAUGUG---GCGAGAUUCGGCCAGCCGAAACUAGUAAAGCUCCUUCCAAAGGACAACGAGUCCAAGGAUCAAUAUCAGCAUCAUA
----.........(((((((..((.---((.((.(((((....))))).)).))...))(((((.....((((.....)))))))))......))))))).... ( -25.20)
>consensus
CUUCGGAAUAAAAGUGUUGAAUGUGAAUGCGAGAUUUGGGCAGCCGAAACGCAAAGAGCUCCUUCCAAAGGGCAACAAGCCCAAGGAUCAAUAUCAGCAUCAUC
.............(((((((..((....))((..(((((((.(((....))).....((.(((.....))))).....)))))))..))....))))))).... (-22.58 = -24.07 +   1.50)

alignment

secondary structure

dotplot

Window 3

Location	14,295,161 – 14,295,269
Length	108
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	91.40
Mean single sequence MFE	-28.42
Consensus MFE	-21.77
Energy contribution	-23.27
Covariance contribution	1.50
Combinations/Pair	1.05
Mean z-score	-2.60
Structure conservation index	0.77
SVM decision value	0.93
SVM RNA-class probability	0.884248
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14295161 108 + 22224390
AAUGCGAGAUUUGGGCAGACGAAACUCAAAGAGCUCCUUCCAAAGGGCAACAGGCCCAAGGAUCAAUAUCAGCAUCAUCCCAACCAGAAUUCAAGAUGCAAUU-CCCUU
.....((..(((((((.((......)).....((.(((.....))))).....)))))))..)).......(((((..................)))))....-..... ( -24.07)
>DroSec_CAF1 8046 108 + 1
AAUGCGAGAUUUGGGCAGCCGAAAGGCAAAGAGCUCCUUCCAAAGGGCAACAAGCCCAAGGAUCAAUAUCAGCAUCAUCCCAACCAGAAUUCAAGAUGCAAUU-CCCUU
.....((..(((((((.(((....))).....((.(((.....))))).....)))))))..)).......(((((..................)))))....-..... ( -33.37)
>DroSim_CAF1 8591 108 + 1
AAUGCGAGAUUUGGGCAGCCGAAAGGCAAAGAGCUCCUUCCAAAGGGCAACAAGCCCAAGGAUCAAUAUCAGCAUCAUCCCAACCAGAAUUCAAGAUGCAAUU-CCCUU
.....((..(((((((.(((....))).....((.(((.....))))).....)))))))..)).......(((((..................)))))....-..... ( -33.37)
>DroYak_CAF1 9804 106 + 1
---GCGAGAUUCGGCCAGCCGAAACUAGUAAAGCUCCUUCCAAAGGACAACGAGUCCAAGGAUCAAUAUCAGCAUCAUACCAACCAGAAUUCAAGAUGCAAUUACCCUU
---...((.(((((....))))).)).((((.(.(((((.....((((.....))))))))).).......(((((..................)))))..)))).... ( -22.87)
>consensus
AAUGCGAGAUUUGGGCAGCCGAAACGCAAAGAGCUCCUUCCAAAGGGCAACAAGCCCAAGGAUCAAUAUCAGCAUCAUCCCAACCAGAAUUCAAGAUGCAAUU_CCCUU
.....((..(((((((.(((....))).....((.(((.....))))).....)))))))..)).......(((((..................))))).......... (-21.77 = -23.27 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:02 2006