Locus 1971

Sequence ID	X_DroMel_CAF1
Location	5,388,332 – 5,388,490
Length	158
Max. P	0.840225

overview

Window 9

Location	5,388,332 – 5,388,452
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.75
Mean single sequence MFE	-48.41
Consensus MFE	-45.23
Energy contribution	-45.91
Covariance contribution	0.69
Combinations/Pair	1.06
Mean z-score	-1.66
Structure conservation index	0.93
SVM decision value	0.75
SVM RNA-class probability	0.840225
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5388332 120 - 22224390
AAAAGUGGGGCCCAAAGUGCUGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGUUGCUGCCACUUGACGCAAUACAGUCCGCGUUGCCGGCAAUCGAGAUGCCCAGCCAGAU
....((.((((......((((((((((.((........(((((((...((((....))))....)))))))..(((........))))).))))))))))........)))).))..... ( -49.94)
>DroSec_CAF1 69509 120 - 1
AAAAGUGGGGCCCAAAGUGCUGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGUUGCUGCCACUUGACGCAAUACCGUCCGCGUUGCCGGCGAUCGAGAUGCCCAACCAGAU
....((.((((......((((((((((.((........(((((((...((((....))))....)))))))..((((......)))))).))))))))))........)))).))..... ( -50.04)
>DroSim_CAF1 57221 120 - 1
AAAAGUGGGGCCCAAAGUGCUGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGUUGCUGCCACUUGACGCAGUACCGUCCGCGUUGCUGGCGAUCGAGAUGCCCAACCAGAU
....((.((((......(((..(((((.((........(((((((...((((....))))....)))))))..((((......)))))).)))))..)))........)))).))..... ( -47.44)
>DroYak_CAF1 62998 120 - 1
AAAUGAGGGGCCCAAAGAGCAGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGAUGCUGCCACUUGACGCGAUACCGUCCGCGUUGCCGCCGUCUGAGAUGCCCAACCAGAU
.......((((........(((((....(((((..(..(((((((...((((....))))....)))))))..)(((((........))))))))))..)))))....))))........ ( -46.20)
>consensus
AAAAGUGGGGCCCAAAGUGCUGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGUUGCUGCCACUUGACGCAAUACCGUCCGCGUUGCCGGCGAUCGAGAUGCCCAACCAGAU
.......((((......((((((((((.((........(((((((...((((....))))....)))))))..((((......)))))).))))))))))........))))........ (-45.23 = -45.91 +   0.69)

alignment

secondary structure

dotplot

Window 0

Location	5,388,372 – 5,388,490
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.89
Mean single sequence MFE	-42.05
Consensus MFE	-35.90
Energy contribution	-36.40
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.85
SVM decision value	0.22
SVM RNA-class probability	0.639032
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5388372 118 - 22224390
--CAGACGAAAUCGACCAGGCUUGCAGCCUGGGAACCCGAAAAAGUGGGGCCCAAAGUGCUGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGUUGCUGCCACUUGACGCAA
--....((....)).((((((.....))))))...((((......))))((...(((((..((((((((((..(((((((.....)))))))..))))..))))))..)))))...)).. ( -46.30)
>DroSec_CAF1 69549 108 - 1
--CAUA----------CAGUCUUGAAGCCUGGGAACCCGAAAAAGUGGGGCCCAAAGUGCUGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGUUGCUGCCACUUGACGCAA
--....----------..(((........((((..(((......).))..))))(((((..((((((((((..(((((((.....)))))))..))))..))))))..)))))))).... ( -39.70)
>DroSim_CAF1 57261 108 - 1
--CAUA----------CAGUCUUGAAGCCUGGGAACCCGAAAAAGUGGGGCCCAAAGUGCUGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGUUGCUGCCACUUGACGCAG
--....----------..(((........((((..(((......).))..))))(((((..((((((((((..(((((((.....)))))))..))))..))))))..)))))))).... ( -39.70)
>DroYak_CAF1 63038 119 - 1
UACAUAUAAGAUCG-CCGCAUUUCAAGCCUGGGAACCCGAAAAUGAGGGGCCCAAAGAGCAGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGAUGCUGCCACUUGACGCGA
..............-.(((...(((((..((((..(((........))).)))).......((((.((((((.(((((((.....))))))).....))))).).)))).))))).))). ( -42.50)
>consensus
__CAUA__________CAGUCUUGAAGCCUGGGAACCCGAAAAAGUGGGGCCCAAAGUGCUGGCAACUCGGCAGACUUGUGGCAGACAGGUCGACUGGCCGUUGCUGCCACUUGACGCAA
..........................((.((((..(((......).))..))))(((((..(((((..((((.(((((((.....))))))).....)))))))))..)))))...)).. (-35.90 = -36.40 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:12 2006