Locus 1792

Sequence ID	3L_DroMel_CAF1
Location	5,071,528 – 5,071,682
Length	154
Max. P	0.990050

overview

Window 8

Location	5,071,528 – 5,071,647
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.40
Mean single sequence MFE	-24.79
Consensus MFE	-21.00
Energy contribution	-20.92
Covariance contribution	-0.08
Combinations/Pair	1.08
Mean z-score	-1.96
Structure conservation index	0.85
SVM decision value	1.45
SVM RNA-class probability	0.955171
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5071528 119 + 23771897
AGCAAACCAAACCAGUGGGAA-AAAAUUGUUGUUGACGGCAAGAAUUUUCCACAUUCAUACACUGAACCAGCAAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCUUGUGAC
.((...........(((((((-(...((((((....))))))...)))))))).((((.....))))...)).((((.(((((....))))).......((........))))))..... ( -25.70)
>DroSec_CAF1 278046 119 + 1
AGCAAACCAAACCAGUGGGAA-AAAAUUGUUGUUGACGGCAAGAAUUUUCCACAUUCAUACACUGAACCGGCGAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCCUGUGAC
..............(((((((-(...((((((....))))))...))))))))..((((((.((......((((....(((((....))))).....)))).......)).)..))))). ( -24.92)
>DroSim_CAF1 299327 119 + 1
AGCAAACCAAACCAGUGGGAA-AAAAUUGUUGUUGACGGCAAGAAUUUUCCACAUUCAUACACUGAACCGGCGAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCCUGUGAC
..............(((((((-(...((((((....))))))...))))))))..((((((.((......((((....(((((....))))).....)))).......)).)..))))). ( -24.92)
>DroEre_CAF1 284965 120 + 1
AGAAAACCAAACCAGUGCGAAAAAAAUUGUUGUUGACGGCAAGAAUUUUUCACAUUCAUACAGUGAGCCAGCGAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCUUGUGAC
..........((.(((((((((((..((((((....))))))...))))))...........(((((...((...)).(((((....)))))....)))))........))))).))... ( -25.20)
>DroYak_CAF1 288865 119 + 1
AGCAAACCAAACCAGUGGGAA-AAAAUUGUUGUUGACGGCAAGAAUUUUCCACAUUCAUACACUGAACCAGCCAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCCUGUGAC
.((...........(((((((-(...((((((....))))))...)))))))).((((.....))))...))((.((.(((((....))))).......((........)))).)).... ( -23.20)
>consensus
AGCAAACCAAACCAGUGGGAA_AAAAUUGUUGUUGACGGCAAGAAUUUUCCACAUUCAUACACUGAACCAGCGAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCCUGUGAC
..............(((((((.....((((((....))))))....))))))).............((.(((......(((((....))))).......((........))))).))... (-21.00 = -20.92 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	5,071,567 – 5,071,682
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.76
Mean single sequence MFE	-20.62
Consensus MFE	-16.50
Energy contribution	-16.34
Covariance contribution	-0.16
Combinations/Pair	1.12
Mean z-score	-1.98
Structure conservation index	0.80
SVM decision value	1.08
SVM RNA-class probability	0.911346
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5071567 115 + 23771897
AAGAAUUUUCCACAUUCAUACACUGAACCAGCAAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCUUGUGACAGGCAAAAAUGGAAAUGCAAUAAAAUGA-----AUGGCAA
............(((((((...(((.((.(((......(((((....))))).......((........))))).))..)))(((..........)))......))))-----))).... ( -19.50)
>DroSec_CAF1 278085 115 + 1
AAGAAUUUUCCACAUUCAUACACUGAACCGGCGAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCCUGUGACAGGCAAAAAUGGAAAUGCAAUAAAAUGA-----AUGGCGA
............(((((((...........((((....(((((....))))).....))))........(((((((...)))))....((....))))......))))-----))).... ( -22.50)
>DroSim_CAF1 299366 115 + 1
AAGAAUUUUCCACAUUCAUACACUGAACCGGCGAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCCUGUGACAGGCAAAAAUGGAAAUGCAAUAAAAUGA-----AUGGCGA
............(((((((...........((((....(((((....))))).....))))........(((((((...)))))....((....))))......))))-----))).... ( -22.50)
>DroEre_CAF1 285005 115 + 1
AAGAAUUUUUCACAUUCAUACAGUGAGCCAGCGAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCUUGUGACAGGCAAAAAUGGAAAUGCAAUAAAAUGA-----AUGGCGA
............(((((((....((..(((((((....(((((....))))).....))))..........(((((...))))).....))).....)).....))))-----))).... ( -21.60)
>DroYak_CAF1 288904 120 + 1
AAGAAUUUUCCACAUUCAUACACUGAACCAGCCAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCCUGUGACAGGCACAAAUGGAAAUGCAAUAAAAUUAAUAAAAUGAAAA
..............(((((...(((...)))....((((.......(((((........((........))(((((...))))).)))))....))))...............))))).. ( -17.00)
>consensus
AAGAAUUUUCCACAUUCAUACACUGAACCAGCGAAGCAUCAAAACAAUUUGAAAAACUCGCACAAACAAGCGCCUGUGACAGGCAAAAAUGGAAAUGCAAUAAAAUGA_____AUGGCGA
..(...((((((..((((.....))))...((((....(((((....))))).....))))..........(((((...))))).....))))))..)...................... (-16.50 = -16.34 +  -0.16)

alignment

secondary structure

dotplot

Window 0

Location	5,071,567 – 5,071,682
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.76
Mean single sequence MFE	-27.10
Consensus MFE	-23.24
Energy contribution	-22.80
Covariance contribution	-0.44
Combinations/Pair	1.11
Mean z-score	-2.05
Structure conservation index	0.86
SVM decision value	2.19
SVM RNA-class probability	0.990050
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5071567 115 - 23771897
UUGCCAU-----UCAUUUUAUUGCAUUUCCAUUUUUGCCUGUCACAAGCGCUUGUUUGUGCGAGUUUUUCAAAUUGUUUUGAUGCUUUGCUGGUUCAGUGUAUGAAUGUGGAAAAUUCUU
.(((.((-----.......)).)))(((((((...((((((...((.((((......))))((((...(((((....))))).))))...))...))).))).....)))))))...... ( -24.60)
>DroSec_CAF1 278085 115 - 1
UCGCCAU-----UCAUUUUAUUGCAUUUCCAUUUUUGCCUGUCACAGGCGCUUGUUUGUGCGAGUUUUUCAAAUUGUUUUGAUGCUUCGCCGGUUCAGUGUAUGAAUGUGGAAAAUUCUU
((..(((-----((((..(((((.....((......(((((...)))))........(.((((((...(((((....))))).)).)))))))..))))).)))))))..))........ ( -28.20)
>DroSim_CAF1 299366 115 - 1
UCGCCAU-----UCAUUUUAUUGCAUUUCCAUUUUUGCCUGUCACAGGCGCUUGUUUGUGCGAGUUUUUCAAAUUGUUUUGAUGCUUCGCCGGUUCAGUGUAUGAAUGUGGAAAAUUCUU
((..(((-----((((..(((((.....((......(((((...)))))........(.((((((...(((((....))))).)).)))))))..))))).)))))))..))........ ( -28.20)
>DroEre_CAF1 285005 115 - 1
UCGCCAU-----UCAUUUUAUUGCAUUUCCAUUUUUGCCUGUCACAAGCGCUUGUUUGUGCGAGUUUUUCAAAUUGUUUUGAUGCUUCGCUGGCUCACUGUAUGAAUGUGAAAAAUUCUU
((((.((-----((((......(((..........)))..(((((((((....))))))((((((...(((((....))))).)).)))).))).......))))))))))......... ( -24.50)
>DroYak_CAF1 288904 120 - 1
UUUUCAUUUUAUUAAUUUUAUUGCAUUUCCAUUUGUGCCUGUCACAGGCGCUUGUUUGUGCGAGUUUUUCAAAUUGUUUUGAUGCUUGGCUGGUUCAGUGUAUGAAUGUGGAAAAUUCUU
.........................(((((((..(((((((...)))))))..(((..(((((((...(((((....))))).)))).((((...)))))))..))))))))))...... ( -30.00)
>consensus
UCGCCAU_____UCAUUUUAUUGCAUUUCCAUUUUUGCCUGUCACAGGCGCUUGUUUGUGCGAGUUUUUCAAAUUGUUUUGAUGCUUCGCUGGUUCAGUGUAUGAAUGUGGAAAAUUCUU
.........................((((((((..((((((.....(((((((((....))))))...(((((....)))))......)))....))).)))..)))).))))....... (-23.24 = -22.80 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:35 2006