Locus 8365

Sequence ID	3R_DroMel_CAF1
Location	22,318,989 – 22,319,127
Length	138
Max. P	0.857285

overview

Window 7

Location	22,318,989 – 22,319,097
Length	108
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	92.33
Mean single sequence MFE	-24.55
Consensus MFE	-21.98
Energy contribution	-22.06
Covariance contribution	0.08
Combinations/Pair	1.11
Mean z-score	-1.38
Structure conservation index	0.90
SVM decision value	0.81
SVM RNA-class probability	0.857285
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22318989 108 + 27905053
GCGAUAUGA-------AAUCCAUCCAACUUCUGUUGCCAAUCCCCUGGGCAGGAAAUAUUUGGAAAAUUCCUAAUCGCAUCCCUAUCUGAGAUAAGACCAAGCCAGGUCCCCGAU
(((((..((-------(.((((......((((((..(((......)))))))))......))))...)))...)))))(((.(.....).)))..((((......))))...... ( -23.40)
>DroSec_CAF1 35801 108 + 1
GCGAUAUGA-------AAUCCAUACAACUCCUGUUGCCAAUCCCCUGGGCAGGAAAUAUUUGGAAAAUUCCAAAUCGCAUCCCUAUCUGAGAUAAGACCAAGCCAGGUCCCCGAU
(((((..((-------(.((((......((((((..(((......)))))))))......))))...)))...)))))(((.(.....).)))..((((......))))...... ( -26.30)
>DroSim_CAF1 35296 108 + 1
GCGAUAUGA-------AAUCCAUCCAACUCCUGUUGCCAAUCCCCUGGGCAGGAAAUAUUUGGAAAAUUCCAAAUCGCAUCCCUAUCUGAGAUAAGACCAAGCCAGGUCCCCGAA
(((((.((.-------(((...(((((.((((((..(((......))))))))).....)))))..))).)).)))))(((.(.....).)))..((((......))))...... ( -26.60)
>DroEre_CAF1 37045 108 + 1
GCAAUAUGA-------AAUCCAUCCAACUCCGGCUGCCAAUCCCUUGGGCAGGAAAUAUUUGGAAAAUUCCAAAUCGCAUCCUUAUCUAAGAUACGACCAAGCCAGGUCCUCGAU
.........-------.....(((.....((((((........((((((.((((...(((((((....)))))))....))))..)))))).........)))).)).....))) ( -21.73)
>DroYak_CAF1 36594 115 + 1
GCAAUAUGAUCCAUCCAAUCCAUUCAACUCCUGCUGCCAAUCCCUUGGGCAGGAAAUAUUUGGAAAAUUCCAAAUCGCAUCCCUAUCUGAGAUAAGACCAAGCCAGGUCCCCGAU
((..........................((((((..((((....))))))))))...(((((((....))))))).))(((.(.....).)))..((((......))))...... ( -24.70)
>consensus
GCGAUAUGA_______AAUCCAUCCAACUCCUGUUGCCAAUCCCCUGGGCAGGAAAUAUUUGGAAAAUUCCAAAUCGCAUCCCUAUCUGAGAUAAGACCAAGCCAGGUCCCCGAU
(((((.......................((((((..(((......))))))))).....(((((....))))))))))(((.(.....).)))..((((......))))...... (-21.98 = -22.06 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	22,318,989 – 22,319,097
Length	108
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	92.33
Mean single sequence MFE	-34.76
Consensus MFE	-28.02
Energy contribution	-27.86
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-1.71
Structure conservation index	0.81
SVM decision value	0.75
SVM RNA-class probability	0.839832
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22318989 108 - 27905053
AUCGGGGACCUGGCUUGGUCUUAUCUCAGAUAGGGAUGCGAUUAGGAAUUUUCCAAAUAUUUCCUGCCCAGGGGAUUGGCAACAGAAGUUGGAUGGAUU-------UCAUAUCGC
....((((((......))))))(((((.....)))))(((((..((((((((((((...(..(((....)))..)(((....)))...))))).)))))-------))..))))) ( -33.70)
>DroSec_CAF1 35801 108 - 1
AUCGGGGACCUGGCUUGGUCUUAUCUCAGAUAGGGAUGCGAUUUGGAAUUUUCCAAAUAUUUCCUGCCCAGGGGAUUGGCAACAGGAGUUGUAUGGAUU-------UCAUAUCGC
....((((((......))))))(((((.....)))))(((((.(((((...((((.(((.((((((.((((....))))...)))))).))).))))))-------))).))))) ( -36.40)
>DroSim_CAF1 35296 108 - 1
UUCGGGGACCUGGCUUGGUCUUAUCUCAGAUAGGGAUGCGAUUUGGAAUUUUCCAAAUAUUUCCUGCCCAGGGGAUUGGCAACAGGAGUUGGAUGGAUU-------UCAUAUCGC
....((((((......))))))(((((.....)))))(((((.(((((((((((((....((((((.((((....))))...))))))))))).)))))-------))).))))) ( -37.60)
>DroEre_CAF1 37045 108 - 1
AUCGAGGACCUGGCUUGGUCGUAUCUUAGAUAAGGAUGCGAUUUGGAAUUUUCCAAAUAUUUCCUGCCCAAGGGAUUGGCAGCCGGAGUUGGAUGGAUU-------UCAUAUUGC
......((((......))))(((((((.....)))))))(((.(((((((((((((....((((.((((((....))))..)).))))))))).)))))-------))).))).. ( -32.10)
>DroYak_CAF1 36594 115 - 1
AUCGGGGACCUGGCUUGGUCUUAUCUCAGAUAGGGAUGCGAUUUGGAAUUUUCCAAAUAUUUCCUGCCCAAGGGAUUGGCAGCAGGAGUUGAAUGGAUUGGAUGGAUCAUAUUGC
....((((((......))))))(((((.....)))))(((((.(((.((((((((.....(((((((((((....))))..))))))).....))))..))))...))).))))) ( -34.00)
>consensus
AUCGGGGACCUGGCUUGGUCUUAUCUCAGAUAGGGAUGCGAUUUGGAAUUUUCCAAAUAUUUCCUGCCCAGGGGAUUGGCAACAGGAGUUGGAUGGAUU_______UCAUAUCGC
....((((((......))))))(((((.....)))))(((((.(((.....((((..((.((((((.((((....))))...)))))).))..)))).........))).))))) (-28.02 = -27.86 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	22,319,020 – 22,319,127
Length	107
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	93.06
Mean single sequence MFE	-37.88
Consensus MFE	-33.96
Energy contribution	-34.15
Covariance contribution	0.19
Combinations/Pair	1.09
Mean z-score	-1.56
Structure conservation index	0.90
SVM decision value	0.42
SVM RNA-class probability	0.728356
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22319020 107 - 27905053
CCACAGGCG-------ACUGGGAGUCUUGGUUGUCGGAUCGGGGACCUGGCUUGGUCUUAUCUCAGAUAGGGAUGCGAUUAGGAAUUUUCCAAAUAUUUCCUGCCCAGGGGAUU
.....((((-------((..((...))..))))))(((((((....))))(((((((.((((((.....)))))).))))))).....)))....((..(((....)))..)). ( -34.30)
>DroSec_CAF1 35832 107 - 1
CCACAGGCG-------ACUGGGAGUCUUGGUUGUCGGAUCGGGGACCUGGCUUGGUCUUAUCUCAGAUAGGGAUGCGAUUUGGAAUUUUCCAAAUAUUUCCUGCCCAGGGGAUU
((...(((.-------.((((((..(((((((....)))))))((((......))))...))))))...((((....(((((((....)))))))...)))))))...)).... ( -36.70)
>DroEre_CAF1 37076 114 - 1
CCACAGGCGACUGGCGACUGGGAGUCUUGGUUGUCGGAUCGAGGACCUGGCUUGGUCGUAUCUUAGAUAAGGAUGCGAUUUGGAAUUUUCCAAAUAUUUCCUGCCCAAGGGAUU
((.(((((((((((((((..((...))..)))))))).)))....)))).((((((((((((((.....)))))))))((((((....))))))..........)))))))... ( -43.30)
>DroYak_CAF1 36632 107 - 1
CCACAGGCG-------ACUGGGAGUCUUGCCUGUCGGAUCGGGGACCUGGCUUGGUCUUAUCUCAGAUAGGGAUGCGAUUUGGAAUUUUCCAAAUAUUUCCUGCCCAAGGGAUU
(((((((((-------((.....)))..)))))).))...(((((((......))))..........((((((....(((((((....)))))))..)))))))))........ ( -37.20)
>consensus
CCACAGGCG_______ACUGGGAGUCUUGGUUGUCGGAUCGGGGACCUGGCUUGGUCUUAUCUCAGAUAGGGAUGCGAUUUGGAAUUUUCCAAAUAUUUCCUGCCCAAGGGAUU
((...(((.........((((((..(((((((....)))))))((((......))))...))))))...((((....(((((((....)))))))...)))))))...)).... (-33.96 = -34.15 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:46 2006