Locus 1834

Sequence ID	2R_DroMel_CAF1
Location	6,883,173 – 6,883,319
Length	146
Max. P	0.893178

overview

Window 2

Location	6,883,173 – 6,883,279
Length	106
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	94.55
Mean single sequence MFE	-29.00
Consensus MFE	-23.80
Energy contribution	-24.47
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.82
SVM decision value	0.14
SVM RNA-class probability	0.601931
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6883173 106 + 20766785
UAUAUGU----ACCUGAAAGCGGACAAACUCAAACCGCCCGGCCUGAUAUUUUUCGUACGCUGGUACAUAUACAUAUGUAUAUAGAAACUGUACGUUCAUAUGUGUGU--GU
(((((((----(((.(...(((((.((..(((..((....))..)))..)).)))))...).))))))))))((((..(((((.(((........))))))))..)))--). ( -28.70)
>DroSim_CAF1 2829 108 + 1
UAUAUGU----ACCUGAAAGCGGCCAAACUCAAACCGCCCGGCCUGAUAUUUUUCGUACGCUGGUACAUAUACAUAUGUAUAUAGAAACUGUACGUACAUAUGUGUGUGUGU
.......----........((((...........))))(((((.(((......)))...)))))(((((((((((((((((((((...))))..))))))))))))))))). ( -32.00)
>DroEre_CAF1 4058 110 + 1
UAUAUGUACAUACCUGAAAGCGGCCAAACUCAAACCGCCCGGCCUGAUAUUUUUCGUACGCUGGUACAUAUACAUAUGUAUAUAGAAACUGUACGUACACAUGUGUGU--GU
...................((((...........))))(((((.(((......)))...))))).((((((((((.(((((((((...))))..))))).))))))))--)) ( -26.30)
>consensus
UAUAUGU____ACCUGAAAGCGGCCAAACUCAAACCGCCCGGCCUGAUAUUUUUCGUACGCUGGUACAUAUACAUAUGUAUAUAGAAACUGUACGUACAUAUGUGUGU__GU
...................((((...........))))(((((.(((......)))...)))))...((((((((((((((((((...))))..)))))))))))))).... (-23.80 = -24.47 +   0.67)

alignment

secondary structure

dotplot

Window 3

Location	6,883,173 – 6,883,279
Length	106
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	94.55
Mean single sequence MFE	-35.53
Consensus MFE	-29.09
Energy contribution	-29.20
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-4.04
Structure conservation index	0.82
SVM decision value	0.98
SVM RNA-class probability	0.893178
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6883173 106 - 20766785
AC--ACACACAUAUGAACGUACAGUUUCUAUAUACAUAUGUAUAUGUACCAGCGUACGAAAAAUAUCAGGCCGGGCGGUUUGAGUUUGUCCGCUUUCAGGU----ACAUAUA
..--....((((((((((.....)))........)))))))(((((((((((((.(((((.....(((((((....))))))).))))).))))....)))----)))))). ( -33.00)
>DroSim_CAF1 2829 108 - 1
ACACACACACAUAUGUACGUACAGUUUCUAUAUACAUAUGUAUAUGUACCAGCGUACGAAAAAUAUCAGGCCGGGCGGUUUGAGUUUGGCCGCUUUCAGGU----ACAUAUA
........(((((((((..((.......))..)))))))))(((((((((((((..((((.....(((((((....))))))).))))..))))....)))----)))))). ( -37.20)
>DroEre_CAF1 4058 110 - 1
AC--ACACACAUGUGUACGUACAGUUUCUAUAUACAUAUGUAUAUGUACCAGCGUACGAAAAAUAUCAGGCCGGGCGGUUUGAGUUUGGCCGCUUUCAGGUAUGUACAUAUA
..--......((((((((((((......(((((((....)))))))....((((..((((.....(((((((....))))))).))))..)))).....)))))))))))). ( -36.40)
>consensus
AC__ACACACAUAUGUACGUACAGUUUCUAUAUACAUAUGUAUAUGUACCAGCGUACGAAAAAUAUCAGGCCGGGCGGUUUGAGUUUGGCCGCUUUCAGGU____ACAUAUA
........(((((((((..((.......))..)))))))))(((((((((((((..((((.....(((((((....))))))).))))..))))....)))....)))))). (-29.09 = -29.20 +   0.11)

alignment

secondary structure

dotplot

Window 4

Location	6,883,209 – 6,883,319
Length	110
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	97.01
Mean single sequence MFE	-33.77
Consensus MFE	-27.92
Energy contribution	-28.37
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-2.19
Structure conservation index	0.83
SVM decision value	-0.00
SVM RNA-class probability	0.532272
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6883209 110 + 20766785
GGCCUGAUAUUUUUCGUACGCUGGUACAUAUACAUAUGUAUAUAGAAACUGUACGUUCAUAUGUGUGU--GUGUAUGUCAGUUGGAGUGCGGUCGGCAAAUUGCAGCGAGAA
((((.((......))((((.((..((((((((((((..(((((.(((........))))))))..)))--))))))))..)..)).)))))))).((.....))........ ( -33.00)
>DroSim_CAF1 2865 112 + 1
GGCCUGAUAUUUUUCGUACGCUGGUACAUAUACAUAUGUAUAUAGAAACUGUACGUACAUAUGUGUGUGUGUGUGUGUCAGUUGGAGUGCGGUCGGCAAAUUGCAGCGAGAA
((((.((......))((((((((..(((((((((((..(((((....((.....))..)))))..)))))))))))..))))....)))))))).((.....))........ ( -35.50)
>DroEre_CAF1 4098 110 + 1
GGCCUGAUAUUUUUCGUACGCUGGUACAUAUACAUAUGUAUAUAGAAACUGUACGUACACAUGUGUGU--GUGUGUGUCAGUUGGAGUGCGGUCGGCAAAUUGCAGCGAGAA
((((.((......))((((((((..(((((((((((((((((.......)))))(....)..))))))--))))))..))))....)))))))).((.....))........ ( -32.80)
>consensus
GGCCUGAUAUUUUUCGUACGCUGGUACAUAUACAUAUGUAUAUAGAAACUGUACGUACAUAUGUGUGU__GUGUGUGUCAGUUGGAGUGCGGUCGGCAAAUUGCAGCGAGAA
.(((((((((.....((((....))))((((((((((((((((((...))))..))))))))))))))......)))))))......((((((......))))))))..... (-27.92 = -28.37 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:17 2006