Locus 1097

Sequence ID	3R_DroMel_CAF1
Location	3,311,375 – 3,311,613
Length	238
Max. P	0.993825

overview

Window 3

Location	3,311,375 – 3,311,495
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.17
Mean single sequence MFE	-34.24
Consensus MFE	-33.92
Energy contribution	-33.68
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-1.24
Structure conservation index	0.99
SVM decision value	0.20
SVM RNA-class probability	0.632726
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3311375 120 - 27905053
CCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUUCCGUUGCACAAAAUUGUUUGAGAAUGCGAUUUCUCGUUU
....((((((((((((((((.(((((((.(....).))))))).)......))))))))))))....................((((((((((....))))....))))))..))).... ( -33.00)
>DroSec_CAF1 15559 120 - 1
CCAGGAGGGGUUAGCGCCCGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUUCCGUUGCACAAAAUUGUUUGAGAAUGCGAUUUCUCGUUU
....((((((((((((((((.(((((((.(....).))))))).......)))))))))))))....................((((((((((....))))....))))))..))).... ( -35.00)
>DroSim_CAF1 19804 120 - 1
CCAGGAGGGGUUAGCGCCCGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUUCCGUUGCACAAAAUUGUUUGAGAAUGCGAUUUCUCGUUU
....((((((((((((((((.(((((((.(....).))))))).......)))))))))))))....................((((((((((....))))....))))))..))).... ( -35.00)
>DroEre_CAF1 10159 120 - 1
CCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUUCCGUUGCACAAAAUUGUUUGGGAAUGCGAUUUCUCGUUU
....((((((((((((((((.(((((((.(....).))))))).)......)))))))))))).........(((((.((((((..(((......))).))))))...)))))))).... ( -35.20)
>DroYak_CAF1 25846 120 - 1
CCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUUCCGUUGCACAAAAUUGUUUGAGAAUGCGAUUUCUCGUUU
....((((((((((((((((.(((((((.(....).))))))).)......))))))))))))....................((((((((((....))))....))))))..))).... ( -33.00)
>consensus
CCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUUCCGUUGCACAAAAUUGUUUGAGAAUGCGAUUUCUCGUUU
....((((((((((((((((.(((((((.(....).))))))).)......))))))))))))....................((((((((((....))))....))))))..))).... (-33.92 = -33.68 +  -0.24)

alignment

secondary structure

dotplot

Window 4

Location	3,311,415 – 3,311,534
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.61
Mean single sequence MFE	-32.60
Consensus MFE	-29.16
Energy contribution	-29.12
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-2.21
Structure conservation index	0.89
SVM decision value	2.43
SVM RNA-class probability	0.993825
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3311415 119 - 27905053
GAUUUUAAGGGGUUCUGAGGGGGGUUUUAGGGUG-GCUUUCCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUU
.......(((((((((((((..((((.......)-)))..)).....(((((((((((((.(((((((.(....).))))))).)......))))))))))))......))))))))))) ( -41.70)
>DroSec_CAF1 15599 103 - 1
-----------------AGGGGAUUUUUAGGGGGUGCUUUCCAGGAGGGGUUAGCGCCCGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUU
-----------------..((((.((((((((((....)))).....(((((((((((((.(((((((.(....).))))))).......)))))))))))))......)))))).)))) ( -32.20)
>DroSim_CAF1 19844 103 - 1
-----------------AGGGGAUUUUUAGGGGGUGCUUUCCAGGAGGGGUUAGCGCCCGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUU
-----------------..((((.((((((((((....)))).....(((((((((((((.(((((((.(....).))))))).......)))))))))))))......)))))).)))) ( -32.20)
>DroEre_CAF1 10199 97 - 1
---------------------GGUUUUUAGGGGG--UGUUCCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUU
---------------------...((((((..((--....)).....(((((((((((((.(((((((.(....).))))))).)......))))))))))))......))))))..... ( -27.90)
>DroYak_CAF1 25886 97 - 1
---------------------GGUUUUUAGGGGG--CCUUCCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUU
---------------------(((((.....)))--)).........(((((((((((((.(((((((.(....).))))))).)......))))))))))))................. ( -29.00)
>consensus
_________________AGGGGGUUUUUAGGGGG_GCUUUCCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUU
........................((((((((((....)))).....(((((((((((((.(((((((.(....).))))))).)......))))))))))))......))))))..... (-29.16 = -29.12 +  -0.04)

alignment

secondary structure

dotplot

Window 5

Location	3,311,495 – 3,311,613
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.21
Mean single sequence MFE	-18.24
Consensus MFE	-12.36
Energy contribution	-13.20
Covariance contribution	0.84
Combinations/Pair	1.06
Mean z-score	-1.58
Structure conservation index	0.68
SVM decision value	-0.04
SVM RNA-class probability	0.513831
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3311495 118 + 27905053
AAAGC-CACCCUAAAACCCCCCUCAGAACCCCUUAAAAUCCCCCAUCCGGUGGUCAUGCCCGGCCGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUGCAAAA-AAAUUGUAU
.....-...........................................((((((((((..(((.....)))...).)))))))))..(((((.......))))).....-......... ( -21.50)
>DroSec_CAF1 15679 103 + 1
AAAGCACCCCCUAAAAAUCCCCU-----------------CCUCCUCCGGUGGUCACGCCCGUGCGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUGCAAAAAAAAUUGUAU
...(((.................-----------------.........(((((((.((..(((.(....)))).))..)))))))..(((((.......)))))..........))).. ( -19.10)
>DroSim_CAF1 19924 103 + 1
AAAGCACCCCCUAAAAAUCCCCU-----------------CCCCCUCCGGUGGUCACGCCCGUGCGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUGCAAAAAAAAUUGUAU
...(((.................-----------------.........(((((((.((..(((.(....)))).))..)))))))..(((((.......)))))..........))).. ( -19.10)
>DroEre_CAF1 10279 93 + 1
AACA--CCCCCUAAAAACC----------------------CCCAUCCGUUGGUCACGCCCG-GCGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUACAAA--AAAUUGUAU
.(((--.............----------------------.......((((((((.((..(-((....)))...))..))))))..))((((.......)))).....--....))).. ( -15.70)
>DroYak_CAF1 25966 94 + 1
AAGG--CCCCCUAAAAACC----------------------CCCAUCCGUUGGUCACGCCCGGGCGCAUGCCGCAGCCAUGACCAUAACACAGUCUAAUUCUGUACAAA--AAAUUCUAU
.(((--...))).......----------------------.......((((((((.((...(((....)))...))..))))))..))((((.......)))).....--......... ( -15.80)
>consensus
AAAGC_CCCCCUAAAAACCCCCU_________________CCCCAUCCGGUGGUCACGCCCGGGCGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUGCAAAA_AAAUUGUAU
.................................................((((((((((....)))...((....))..)))))))..(((((.......)))))............... (-12.36 = -13.20 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:48 2006