Locus 243

Sequence ID	2L_DroMel_CAF1
Location	715,262 – 715,388
Length	126
Max. P	0.988539

overview

Window 8

Location	715,262 – 715,364
Length	102
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	89.29
Mean single sequence MFE	-30.72
Consensus MFE	-23.82
Energy contribution	-24.70
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-2.82
Structure conservation index	0.78
SVM decision value	2.12
SVM RNA-class probability	0.988539
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 715262 102 + 22407834
CUAUCUGUCUAUAGCU-----GCUCUCCCGCUCCGAGAGCGACCCGCUAUAACUACUAUAACUACCUAUUGUUUUUGUGGCGAUGCCAGGCUCUUCUGGCAUGUAAA
...............(-----((((((.......)))))))...((((((((..((.(((......))).))..))))))))((((((((....))))))))..... ( -30.60)
>DroSec_CAF1 94006 102 + 1
CUAUCUGUCUAUAGCU-----GCUCUCCCGCUCCGAGAGCGGCCCGCUAUAACUACUAUAGCUACCCAUUGUUUUUGUGGCGAUGCCAGGCUCUUCUGGCAUGUAAA
.............(((-----((((((.......))))))))).((((((((..((..............))..))))))))((((((((....))))))))..... ( -35.44)
>DroSim_CAF1 99183 102 + 1
CUAUCUGUCUAUAGCU-----GCUCUCCCGCUCCGAGAGCGACCCGCUAUAACUACUAUAACUACCCAUUGUUUUUGUGGCCAUGCCAGGCUCUUCUGGCAUGUAAA
.........(((((((-----((((((.......)))))))....)))))).((((...(((........)))...)))).(((((((((....))))))))).... ( -31.90)
>DroEre_CAF1 103760 99 + 1
CUAUCUGUCUGUAGCUCUCUCGCU--------CCGAGAGCGGCCCGCUAUAACUACUAUAACUGCCCAUUGUUUUUGUGGCGAUUCCAGGCUCUUGUGGCAUGUAAA
.(((.((((....((((((.....--------..))))))((((((((((((..((..............))..))))))))......)))).....)))).))).. ( -26.14)
>DroYak_CAF1 99780 107 + 1
CUAUCUGUCUAUAGCUCUCUCGCUCUCUCAGUCCGAGAGCGAACCGCUAUAACUACUAUAACUGCCCAUUGUUUUUGUGGCGAUUCCAGGCUCUUCUGGCAUGUAAA
.(((.((((...((((...((((((((.......))))))))..((((((((..((..............))..))))))))......)))).....)))).))).. ( -29.54)
>consensus
CUAUCUGUCUAUAGCU_____GCUCUCCCGCUCCGAGAGCGACCCGCUAUAACUACUAUAACUACCCAUUGUUUUUGUGGCGAUGCCAGGCUCUUCUGGCAUGUAAA
.........((((((......((((((.......)))))).....)))))).((((...(((........)))...))))..((((((((....))))))))..... (-23.82 = -24.70 +   0.88)

alignment

secondary structure

dotplot

Window 9

Location	715,262 – 715,364
Length	102
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	89.29
Mean single sequence MFE	-30.28
Consensus MFE	-24.18
Energy contribution	-25.34
Covariance contribution	1.16
Combinations/Pair	1.04
Mean z-score	-1.64
Structure conservation index	0.80
SVM decision value	0.49
SVM RNA-class probability	0.755971
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 715262 102 - 22407834
UUUACAUGCCAGAAGAGCCUGGCAUCGCCACAAAAACAAUAGGUAGUUAUAGUAGUUAUAGCGGGUCGCUCUCGGAGCGGGAGAGC-----AGCUAUAGACAGAUAG
.(((((((((((......))))))).(((............))).......))))(((((((.....((((((.......))))))-----.)))))))........ ( -28.40)
>DroSec_CAF1 94006 102 - 1
UUUACAUGCCAGAAGAGCCUGGCAUCGCCACAAAAACAAUGGGUAGCUAUAGUAGUUAUAGCGGGCCGCUCUCGGAGCGGGAGAGC-----AGCUAUAGACAGAUAG
.....(((((((......))))))).(((.((.......))))).(((((((...))))))).(((.((((((.......))))))-----.)))............ ( -31.70)
>DroSim_CAF1 99183 102 - 1
UUUACAUGCCAGAAGAGCCUGGCAUGGCCACAAAAACAAUGGGUAGUUAUAGUAGUUAUAGCGGGUCGCUCUCGGAGCGGGAGAGC-----AGCUAUAGACAGAUAG
....((((((((......))))))))(((.((.......)))))...(((.....(((((((.....((((((.......))))))-----.)))))))....))). ( -32.30)
>DroEre_CAF1 103760 99 - 1
UUUACAUGCCACAAGAGCCUGGAAUCGCCACAAAAACAAUGGGCAGUUAUAGUAGUUAUAGCGGGCCGCUCUCGG--------AGCGAGAGAGCUACAGACAGAUAG
..............(.((((......(((.((.......))))).(((((((...))))))))))))((((((..--------.....))))))............. ( -24.10)
>DroYak_CAF1 99780 107 - 1
UUUACAUGCCAGAAGAGCCUGGAAUCGCCACAAAAACAAUGGGCAGUUAUAGUAGUUAUAGCGGUUCGCUCUCGGACUGAGAGAGCGAGAGAGCUAUAGACAGAUAG
.((((...((((......))))....(((.((.......))))).......))))(((((((..(((((((((.......)))))))))...)))))))........ ( -34.90)
>consensus
UUUACAUGCCAGAAGAGCCUGGCAUCGCCACAAAAACAAUGGGUAGUUAUAGUAGUUAUAGCGGGUCGCUCUCGGAGCGGGAGAGC_____AGCUAUAGACAGAUAG
.(((((((((((......))))))).(((............))).......))))(((((((.....((((((.......))))))......)))))))........ (-24.18 = -25.34 +   1.16)

alignment

secondary structure

dotplot

Window 0

Location	715,293 – 715,388
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	94.95
Mean single sequence MFE	-29.71
Consensus MFE	-24.88
Energy contribution	-25.68
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.84
SVM decision value	0.75
SVM RNA-class probability	0.839712
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 715293 95 + 22407834
GAGCGACCCGCUAUAACUACUAUAACUACCUAUUGUUUUUGUGGCGAUGCCAGGCUCUUCUGGCAUGUAAAUUAGCUGCUCUCCGUGAGAGAGAG
.(((....((((((((..((.(((......))).))..))))))))((((((((....))))))))........))).((((((....).))))) ( -33.10)
>DroSec_CAF1 94037 95 + 1
GAGCGGCCCGCUAUAACUACUAUAGCUACCCAUUGUUUUUGUGGCGAUGCCAGGCUCUUCUGGCAUGUAAAUUAGCUGCUCUCCGUGAGAGAGAG
..(((((.((((((((..((..............))..))))))))((((((((....))))))))........)))))(((((....).)))). ( -34.64)
>DroSim_CAF1 99214 95 + 1
GAGCGACCCGCUAUAACUACUAUAACUACCCAUUGUUUUUGUGGCCAUGCCAGGCUCUUCUGGCAUGUAAAUUAGCUGCUCUCCGUGAGAGAGAG
.(((.....(((((((..((..............))..)))))))(((((((((....))))))))).......))).((((((....).))))) ( -31.54)
>DroEre_CAF1 103788 95 + 1
GAGCGGCCCGCUAUAACUACUAUAACUGCCCAUUGUUUUUGUGGCGAUUCCAGGCUCUUGUGGCAUGUAAAUUAGCUGCUCUCGGCGAGAGAGAG
(((((((.((((((((..((..............))..))))))))....((.(((.....))).)).......)))))))((..(....).)). ( -24.54)
>DroYak_CAF1 99816 95 + 1
GAGCGAACCGCUAUAACUACUAUAACUGCCCAUUGUUUUUGUGGCGAUUCCAGGCUCUUCUGGCAUGUAAAUUAGCUGCUCUCCGCGAGAGAGAG
(((((((.((((((((..((..............))..)))))))).)))...))))....(((..........))).((((((....).))))) ( -24.74)
>consensus
GAGCGACCCGCUAUAACUACUAUAACUACCCAUUGUUUUUGUGGCGAUGCCAGGCUCUUCUGGCAUGUAAAUUAGCUGCUCUCCGUGAGAGAGAG
.(((....((((((((..((..............))..))))))))((((((((....))))))))........))).(((((.....))))).. (-24.88 = -25.68 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:01 2006