Locus 2169

Sequence ID	2R_DroMel_CAF1
Location	8,052,108 – 8,052,242
Length	134
Max. P	0.941488

overview

Window 1

Location	8,052,108 – 8,052,202
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	95.53
Mean single sequence MFE	-28.94
Consensus MFE	-25.48
Energy contribution	-26.32
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.63
Structure conservation index	0.88
SVM decision value	1.32
SVM RNA-class probability	0.941488
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8052108 94 + 20766785
CUGAGUGCGAAAAUAUCCUUGAGCUGAGAUGAAGCCAUUGUCUGUGCUUGGCUUUUGUUCUCGGGGCCUCAGACAAUGGCAGAUGCAAAUAUGC
((.(((.(((........))).))).)).....(((((((((((.....((((((.......)))))).)))))))))))....(((....))) ( -29.90)
>DroSec_CAF1 17117 94 + 1
CUGAGUGCGAAAAUAUCCUUGAGCUGAGAUGAAGCCAUUGUCUGUGCUUGGCUUUUGUUCUCGGGGCCUCAGACAAUGGCGGAUGCAAAUAUGU
((.(((.(((........))).))).)).....(((((((((((.....((((((.......)))))).))))))))))).............. ( -29.70)
>DroSim_CAF1 313 94 + 1
CUGAGUGCGAAAAUAUCCUUGAGCUGAGAUGAAGCCAUUGUCUGUGCUUGGCUUUUGUUCUCGGGGCCUCAGACAAUGGCAGAUGCAAAUAUGC
((.(((.(((........))).))).)).....(((((((((((.....((((((.......)))))).)))))))))))....(((....))) ( -29.90)
>DroEre_CAF1 15397 93 + 1
CUGAGUACGAAAAUAUCCUUGAGCUGAGAUGAAGCCAUUGUCUGUUCCUGGCUUUUGUUCUCGG-GCCUCAGACAAUGGCAGAUGCAAAUAUGC
((.(((.(((........))).))).)).....(((((((((((.....(((((........))-))).)))))))))))....(((....))) ( -29.70)
>DroYak_CAF1 15261 93 + 1
CUGAGUGCGAAAAUAUCCUUGAGCUGAGUUGAAGCCAUUUUCUGUGCUUGGCUUUUGUUCUCGG-AACUCAGACAAUGGCAGAUGCAAAUAUGC
((((((.(((.((((.....((((..(((.((((....))))...)))..)))).)))).))).-.))))))......((....))........ ( -25.50)
>consensus
CUGAGUGCGAAAAUAUCCUUGAGCUGAGAUGAAGCCAUUGUCUGUGCUUGGCUUUUGUUCUCGGGGCCUCAGACAAUGGCAGAUGCAAAUAUGC
((.(((.(((........))).))).)).....(((((((((((.....((((((.......)))))).)))))))))))....(((....))) (-25.48 = -26.32 +   0.84)

alignment

secondary structure

dotplot

Window 2

Location	8,052,108 – 8,052,202
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	95.53
Mean single sequence MFE	-22.67
Consensus MFE	-20.10
Energy contribution	-20.18
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-1.24
Structure conservation index	0.89
SVM decision value	0.20
SVM RNA-class probability	0.632018
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8052108 94 - 20766785
GCAUAUUUGCAUCUGCCAUUGUCUGAGGCCCCGAGAACAAAAGCCAAGCACAGACAAUGGCUUCAUCUCAGCUCAAGGAUAUUUUCGCACUCAG
.......(((....(((((((((((.(((.............))).....)))))))))))...((((........))))......)))..... ( -23.62)
>DroSec_CAF1 17117 94 - 1
ACAUAUUUGCAUCCGCCAUUGUCUGAGGCCCCGAGAACAAAAGCCAAGCACAGACAAUGGCUUCAUCUCAGCUCAAGGAUAUUUUCGCACUCAG
.......(((....(((((((((((.(((.............))).....)))))))))))...((((........))))......)))..... ( -23.92)
>DroSim_CAF1 313 94 - 1
GCAUAUUUGCAUCUGCCAUUGUCUGAGGCCCCGAGAACAAAAGCCAAGCACAGACAAUGGCUUCAUCUCAGCUCAAGGAUAUUUUCGCACUCAG
.......(((....(((((((((((.(((.............))).....)))))))))))...((((........))))......)))..... ( -23.62)
>DroEre_CAF1 15397 93 - 1
GCAUAUUUGCAUCUGCCAUUGUCUGAGGC-CCGAGAACAAAAGCCAGGAACAGACAAUGGCUUCAUCUCAGCUCAAGGAUAUUUUCGUACUCAG
(((....)))....(((((((((((.(((-............))).....)))))))))))...((((........)))).............. ( -23.30)
>DroYak_CAF1 15261 93 - 1
GCAUAUUUGCAUCUGCCAUUGUCUGAGUU-CCGAGAACAAAAGCCAAGCACAGAAAAUGGCUUCAACUCAGCUCAAGGAUAUUUUCGCACUCAG
(((....)))...(((...((((((((((-..(((.....((((((...........))))))...))))))))..))))).....)))..... ( -18.90)
>consensus
GCAUAUUUGCAUCUGCCAUUGUCUGAGGCCCCGAGAACAAAAGCCAAGCACAGACAAUGGCUUCAUCUCAGCUCAAGGAUAUUUUCGCACUCAG
.......(((....(((((((((((.(((.............))).....)))))))))))...............(((....))))))..... (-20.10 = -20.18 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	8,052,137 – 8,052,242
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	85.69
Mean single sequence MFE	-28.41
Consensus MFE	-20.58
Energy contribution	-21.50
Covariance contribution	0.92
Combinations/Pair	1.08
Mean z-score	-2.45
Structure conservation index	0.72
SVM decision value	0.01
SVM RNA-class probability	0.539030
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8052137 105 - 20766785
AGCGAGAGAACUUGUAUUUUACCACCUCAUUACAAGAUUUGCAUAUUUGCAUCUGCCAUUGUCUGAGGCC-CCGAGAACAAAAGCCAAGCACAGACAAUGGCUUCA--------------
...((((((.((((((..............))))))...((((....)))))))(((((((((((.(((.-............))).....)))))))))))))).-------------- ( -29.56)
>DroSec_CAF1 17146 105 - 1
AGCGAGAGAACUUGUAUUUUACCACCUCAUUACAAGAUUUACAUAUUUGCAUCCGCCAUUGUCUGAGGCC-CCGAGAACAAAAGCCAAGCACAGACAAUGGCUUCA--------------
.((((((((.((((((..............)))))).))).....)))))....(((((((((((.(((.-............))).....)))))))))))....-------------- ( -27.36)
>DroSim_CAF1 342 105 - 1
AGCGAGAGAACUUGUAUUUUACCACCUCAUUACAAGAUUUGCAUAUUUGCAUCUGCCAUUGUCUGAGGCC-CCGAGAACAAAAGCCAAGCACAGACAAUGGCUUCA--------------
...((((((.((((((..............))))))...((((....)))))))(((((((((((.(((.-............))).....)))))))))))))).-------------- ( -29.56)
>DroEre_CAF1 15426 104 - 1
AGCGAGAGAACUUGUAUUUUACCACCUCAUUACAAGAUUUGCAUAUUUGCAUCUGCCAUUGUCUGAGGC--CCGAGAACAAAAGCCAGGAACAGACAAUGGCUUCA--------------
...((((((.((((((..............))))))...((((....)))))))(((((((((((.(((--............))).....)))))))))))))).-------------- ( -29.64)
>DroYak_CAF1 15290 104 - 1
AGCGAGAGAACUUGUAUUUUACCACCUCAUUACAAGAUUUGCAUAUUUGCAUCUGCCAUUGUCUGAGUU--CCGAGAACAAAAGCCAAGCACAGAAAAUGGCUUCA--------------
...((((((.((((((..............))))))...((((....)))))))((((((.((((.(((--(...))))....((...)).)))).))))))))).-------------- ( -24.94)
>DroAna_CAF1 18562 117 - 1
A---CGACAACUUGUACCUUACCACCUCAUUACUACAUUUGCAUAUUUGCAUCUGCCAUUGUCUGUGGCAGCCGAACAAAGAGGUGCAACUCAGACAAUGACAACAAUAGCCUGGUUGGU
.---((((...(((((((((...................((((....)))).(((((((.....))))))).........)))))))))..(((.(.((.......)).).))))))).. ( -29.40)
>consensus
AGCGAGAGAACUUGUAUUUUACCACCUCAUUACAAGAUUUGCAUAUUUGCAUCUGCCAUUGUCUGAGGCC_CCGAGAACAAAAGCCAAGCACAGACAAUGGCUUCA______________
..........((((((..............))))))...((((....))))...(((((((((((.(((..............))).....))))))))))).................. (-20.58 = -21.50 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:58 2006