Locus 3635

Sequence ID	X_DroMel_CAF1
Location	9,710,537 – 9,710,628
Length	91
Max. P	0.914723

overview

Window 7

Location	9,710,537 – 9,710,628
Length	91
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	90.79
Mean single sequence MFE	-30.92
Consensus MFE	-26.22
Energy contribution	-27.10
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-1.59
Structure conservation index	0.85
SVM decision value	0.88
SVM RNA-class probability	0.874195
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9710537 91 + 22224390
AAAUAGGAAAACCUCGCAAAAUGCUC------CUGCUGAUACCGCUUUUCCUGACCCUUUUGGGGGCUGAGGCCCAGCAAUUUGGCAGUGAGUUUUA
....(((....)))........((((------((((..(....(((...(((.(((((....)))).).)))...)))...)..)))).)))).... ( -26.10)
>DroSec_CAF1 51555 91 + 1
AAAUAGGAAAACCUCGCAAAAUGCUC------CUGCUGAUAGCGCUUUUCCUGGCCCUUUUGGGGGCUGAGGCCCAGCAAUUUGGCAGUGAGUUUUC
......((((((.((((.....))..------((((..(....(((...(((((((((....)))))).)))...)))...)..)))).)))))))) ( -30.10)
>DroSim_CAF1 26305 91 + 1
AAAUAGGAAAACCUCGCAAAAUGCUC------CUGCUGAUAGCGCUUUUCCUGGCCCUUUUGGGGGCUGAGGCCCAGCAAUUUGGCAGUGAGUUCUC
....(((....)))........((((------((((..(....(((...(((((((((....)))))).)))...)))...)..)))).)))).... ( -30.00)
>DroEre_CAF1 28881 97 + 1
AGGAAGGAAAGCCUCGCAAAAUGCUCCUGCUCCUGCUUGUACCGCUUUUCCUGGCCCUCUUGGGGGCUGAGGCCCAGCAGUUUGGCAGUGAGUUUUC
(((((((....))).((.....))))))(((((((((...((.(((...(((((((((....)))))).)))...))).))..))))).)))).... ( -37.10)
>DroYak_CAF1 28490 91 + 1
AGAUGGGAAAACCUCGCAAAAUGCUC------CUGCUUAUACCGCUUUUCCUGGCCCUCUUGGGGGCUGAGGCCCAGCAAUUUGGCAGUGAGUUCUC
.((.((.....)))).......((((------(((((......(((...(((((((((....)))))).)))...))).....))))).)))).... ( -31.30)
>consensus
AAAUAGGAAAACCUCGCAAAAUGCUC______CUGCUGAUACCGCUUUUCCUGGCCCUUUUGGGGGCUGAGGCCCAGCAAUUUGGCAGUGAGUUUUC
......((((((.((((.....))........(((((((....(((...(((((((((....)))))).)))...)))...))))))).)))))))) (-26.22 = -27.10 +   0.88)

alignment

secondary structure

dotplot

Window 8

Location	9,710,537 – 9,710,628
Length	91
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	90.79
Mean single sequence MFE	-29.08
Consensus MFE	-26.72
Energy contribution	-27.04
Covariance contribution	0.32
Combinations/Pair	1.11
Mean z-score	-1.46
Structure conservation index	0.92
SVM decision value	1.10
SVM RNA-class probability	0.914723
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9710537 91 - 22224390
UAAAACUCACUGCCAAAUUGCUGGGCCUCAGCCCCCAAAAGGGUCAGGAAAAGCGGUAUCAGCAG------GAGCAUUUUGCGAGGUUUUCCUAUUU
.....(((.((((...((((((...(((..((((......)))).)))...))))))....))))------..((.....)))))............ ( -25.90)
>DroSec_CAF1 51555 91 - 1
GAAAACUCACUGCCAAAUUGCUGGGCCUCAGCCCCCAAAAGGGCCAGGAAAAGCGCUAUCAGCAG------GAGCAUUUUGCGAGGUUUUCCUAUUU
((((((((.((((.....((((...(((..((((......)))).)))...))))......))))------..((.....)))).))))))...... ( -27.70)
>DroSim_CAF1 26305 91 - 1
GAGAACUCACUGCCAAAUUGCUGGGCCUCAGCCCCCAAAAGGGCCAGGAAAAGCGCUAUCAGCAG------GAGCAUUUUGCGAGGUUUUCCUAUUU
((((((((.((((.....((((...(((..((((......)))).)))...))))......))))------..((.....)))).))))))...... ( -27.80)
>DroEre_CAF1 28881 97 - 1
GAAAACUCACUGCCAAACUGCUGGGCCUCAGCCCCCAAGAGGGCCAGGAAAAGCGGUACAAGCAGGAGCAGGAGCAUUUUGCGAGGCUUUCCUUCCU
((((.(((.((((...((((((...(((..((((......)))).)))...))))))....))))..((((((...)))))))))..))))...... ( -33.80)
>DroYak_CAF1 28490 91 - 1
GAGAACUCACUGCCAAAUUGCUGGGCCUCAGCCCCCAAGAGGGCCAGGAAAAGCGGUAUAAGCAG------GAGCAUUUUGCGAGGUUUUCCCAUCU
(((((((((((((....((.((((.((((.........)))).)))).))..)))))....((((------((...)))))))).))))))...... ( -30.20)
>consensus
GAAAACUCACUGCCAAAUUGCUGGGCCUCAGCCCCCAAAAGGGCCAGGAAAAGCGGUAUCAGCAG______GAGCAUUUUGCGAGGUUUUCCUAUUU
((((((((.((((...((((((...(((..((((......)))).)))...))))))....))))........((.....)))).))))))...... (-26.72 = -27.04 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:17 2006