Locus 6709

Sequence ID	X_DroMel_CAF1
Location	16,734,128 – 16,734,368
Length	240
Max. P	0.977019

overview

Window 3

Location	16,734,128 – 16,734,248
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-29.71
Consensus MFE	-28.74
Energy contribution	-28.78
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.65
Structure conservation index	0.97
SVM decision value	1.78
SVM RNA-class probability	0.977019
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16734128 120 - 22224390
UCGGCCAUUUUGCUUGCAAAUUUUUAUAUGUCUCAGAUUUUGUUUAUGUUUUCGAUUUUGGAGUUCUUCGAACUCGUCGGGGUUUUUGAGAUGUCAUGAAAAAUUGCCCAACCCGCUGAC
(((((....(((...((((.(((((((((((((((((............(..((((....((((((...))))))))))..)..)))))))))).))))))).)))).)))...))))). ( -31.94)
>DroSec_CAF1 21859 120 - 1
UCGGCCAUUUUGCUUGCAAAUUUUUAUAUGUCUCGGAUUUUGUUUAUGUUUUCGAUUUCGGAGUUCUUCGAACUCGUCGGGGUUUUUGAGAUCUCAUGAAAAAUUGCCCAACCCGCUGAC
(((((....(((...((((.(((((((..((((((((............(..((((....((((((...))))))))))..)..))))))))...))))))).)))).)))...))))). ( -28.84)
>DroSim_CAF1 19240 120 - 1
UCGGCCAUUUUGCUUGCAAAUUUUUAUAUGUCUCGGAUUUUGUUUAUGUUUUCGAUUUCGGAGUUCUUCGAACUCGUCGGGGUUUUUGAGAUCUCAUGAAAAAUUGCCCAACCCGCUGAC
(((((....(((...((((.(((((((..((((((((............(..((((....((((((...))))))))))..)..))))))))...))))))).)))).)))...))))). ( -28.84)
>DroEre_CAF1 13252 120 - 1
UCGGCCAUUUUGCUUGCAAAUUUUUAUAUGUCUCGGAUUUUGUUUAUGUUUUCGAUUUCGGAGUUCUUCGAACUCGUCGGGGUUUUUGAGAUCUCAUGAAAAAUUGCUCAACCCGCUGAC
(((((....(((...((((.(((((((..((((((((............(..((((....((((((...))))))))))..)..))))))))...))))))).)))).)))...))))). ( -29.54)
>DroYak_CAF1 13011 120 - 1
UCGGCCAUUUUGCUUGCAAAUUUUUAUAUGUCUCGCAUUUUGUUUAUGUUUUCGAUUUUGGAGUUCUUCGAACUCGUCGGGGUUUUUGAGAUCUCAUGAAAAAUUGCCCAACCCGCUGAC
(((((....(((...((((.(((((((..(((((((((.......))))(..((((....((((((...))))))))))..).....)))))...))))))).)))).)))...))))). ( -29.40)
>consensus
UCGGCCAUUUUGCUUGCAAAUUUUUAUAUGUCUCGGAUUUUGUUUAUGUUUUCGAUUUCGGAGUUCUUCGAACUCGUCGGGGUUUUUGAGAUCUCAUGAAAAAUUGCCCAACCCGCUGAC
(((((....(((...((((.(((((((..((((((((............(..((((....((((((...))))))))))..)..))))))))...))))))).)))).)))...))))). (-28.74 = -28.78 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	16,734,208 – 16,734,328
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.42
Mean single sequence MFE	-32.01
Consensus MFE	-30.14
Energy contribution	-30.58
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	0.94
SVM decision value	1.55
SVM RNA-class probability	0.963221
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16734208 120 + 22224390
AAAUCUGAGACAUAUAAAAAUUUGCAAGCAAAAUGGCCGACAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGCUAAAGCCGUUGCUCGUUGGCCAACUUCCAGUCGGCCGA
....................((((....)))).((((((((.((.(((((((.(((........))).))((((((...(((....)))...)).)))).)))))...)).)))))))). ( -34.90)
>DroSec_CAF1 21939 120 + 1
AAAUCCGAGACAUAUAAAAAUUUGCAAGCAAAAUGGCCGACAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGCUAAAGUCGUUGCUCGUUGGCCAACUUCCAGUCGGCCGA
....................((((....)))).((((((((.((.(((((((.(((........))).))((((((...(((....)))...)).)))).)))))...)).)))))))). ( -32.20)
>DroSim_CAF1 19320 120 + 1
AAAUCCGAGACAUAUAAAAAUUUGCAAGCAAAAUGGCCGACAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGCUAAAGUCGUUGCUCGUUGGCCAACUUCCAGUCGGCCGA
....................((((....)))).((((((((.((.(((((((.(((........))).))((((((...(((....)))...)).)))).)))))...)).)))))))). ( -32.20)
>DroEre_CAF1 13332 120 + 1
AAAUCCGAGACAUAUAAAAAUUUGCAAGCAAAAUGGCCGACAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGUUAAAUUCGCUGCUCGUUGGCCAACUUCGAGUCGGCCGA
....................((((....)))).((((((((.((.(((((.(((..............((.(((((...((......))))))))).))))))))..))..)))))))). ( -29.36)
>DroYak_CAF1 13091 120 + 1
AAAUGCGAGACAUAUAAAAAUUUGCAAGCAAAAUGGCCGACAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGCUAAAGUCGUUGCUCGUUGGCCAACUUCAAGUCGGCCGA
...((((((...........)))))).......(((((((((((((.(((((.(((........))).))((((((...(((....)))...)).)))).))))))))...)))))))). ( -31.40)
>consensus
AAAUCCGAGACAUAUAAAAAUUUGCAAGCAAAAUGGCCGACAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGCUAAAGUCGUUGCUCGUUGGCCAACUUCCAGUCGGCCGA
....................((((....)))).((((((((.((.(((((((.(((........))).))((((((...(((....)))...)).)))).)))))...)).)))))))). (-30.14 = -30.58 +   0.44)

alignment

secondary structure

dotplot

Window 5

Location	16,734,248 – 16,734,368
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.64
Mean single sequence MFE	-30.00
Consensus MFE	-29.62
Energy contribution	-29.40
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.76
Structure conservation index	0.99
SVM decision value	0.68
SVM RNA-class probability	0.820554
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16734248 120 + 22224390
CAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGCUAAAGCCGUUGCUCGUUGGCCAACUUCCAGUCGGCCGACUGCAGAAACAAUAAUAAUGAAAACAAUAACAAAUACUGG
((((((((((((.(((........))).).)))..(((((((....))).((((..(((((((.((.....)).))))))).))))............))))........))))).))). ( -31.20)
>DroSec_CAF1 21979 117 + 1
CAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGCUAAAGUCGUUGCUCGUUGGCCAACUUCCAGUCGGCCGACUGCAGAAACAAU---AAUGAAAACAAUAACAAAUACUGG
((((((((((((.(((........))).).)))..(((((((....))).((((..(((((((.((.....)).))))))).)))).......---..))))........))))).))). ( -28.50)
>DroYak_CAF1 13131 117 + 1
CAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGCUAAAGUCGUUGCUCGUUGGCCAACUUCAAGUCGGCCGACUGCAGAAACCAU---AAUGAAAACAAUAACAAAUACUGG
((((((((((((.(((........))).).)))(((((.(((....)))..(((..(((((((.((.....)).))))))).)))).))))..---..............))))).))). ( -30.30)
>consensus
CAGGUUUGGCUCAAAUUAUAAACUAUUAGAAGCGGUUCAGGCUAAAGUCGUUGCUCGUUGGCCAACUUCCAGUCGGCCGACUGCAGAAACAAU___AAUGAAAACAAUAACAAAUACUGG
((((((((((((.(((........))).).)))..(((((((....))).((((..(((((((.((.....)).))))))).))))............))))........))))).))). (-29.62 = -29.40 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:27 2006