Locus 1752

Sequence ID	2L_DroMel_CAF1
Location	4,789,689 – 4,789,781
Length	92
Max. P	0.860551

overview

Window 2

Location	4,789,689 – 4,789,781
Length	92
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	70.50
Mean single sequence MFE	-14.86
Consensus MFE	-3.45
Energy contribution	-3.49
Covariance contribution	0.04
Combinations/Pair	1.14
Mean z-score	-1.96
Structure conservation index	0.23
SVM decision value	0.83
SVM RNA-class probability	0.860551
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4789689 92 + 22407834
UAUUU-UUUAUGG-----CUUUUAUACCUUUGUCAAAAAAGGUAGAACCACAAAACAGCACUUAUCCUAUGUCUACUUUUUACCACUCUAAAACUAAA
....(-(((.(((-----.(((..(((((((......))))))))))))).))))........................................... ( -10.10)
>DroSec_CAF1 237907 77 + 1
UAUUU-UUUAUAG-----CUUUUAUACCUUUGUCAAA-AAGGUAGAACCACAGAGUAGAG--------------GCUUCUUACCACUCUAAAACUAAA
.....-....(((-----.((((.(((((((.....)-)))))).......(((((.(((--------------....)))...)))))))))))).. ( -12.20)
>DroSim_CAF1 215091 77 + 1
UAUUU-UUUAUAG-----CUUUUAUACCUUUGUCAAA-AAGGUAGAACCACAGAGUAGUG--------------GCUUUUUACCACUCUAAAACUAAA
.....-....(((-----.((((.(((((((.....)-)))))).......(((((.(((--------------(....)))).)))))))))))).. ( -14.50)
>DroEre_CAF1 232337 94 + 1
CAUUU-UUAACGGCAGAGGAGAUAU--UUUU-CCACCAAAGGUGGAACCACAAAGAAGCACUUAUCUCAUGUCGUAUUUUUACCACUCUAAAACUAAA
.....-...((((((...(((((..--..((-(((((...))))))).....(((.....)))))))).))))))....................... ( -21.50)
>DroYak_CAF1 225950 93 + 1
UAUUUUUUAACUGCAGAGCAGUUAU--U-UU-CCACCAAAGGUAGAACCACAAAAGAGCACUUAUCUUA-GUCGGCUUUUUACCACUCCAAAACUAAA
.......(((((((...))))))).--.-..-........(((((((((((..((((.......)))).-)).))..))))))).............. ( -16.00)
>consensus
UAUUU_UUUAUAG_____CUUUUAUACCUUUGUCAAAAAAGGUAGAACCACAAAGUAGCACUUAUC__A_GUC_GCUUUUUACCACUCUAAAACUAAA
........................................(((((((..............................))))))).............. ( -3.45 =  -3.49 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	4,789,689 – 4,789,781
Length	92
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	70.50
Mean single sequence MFE	-19.18
Consensus MFE	-4.63
Energy contribution	-4.79
Covariance contribution	0.16
Combinations/Pair	1.42
Mean z-score	-1.76
Structure conservation index	0.24
SVM decision value	0.22
SVM RNA-class probability	0.641686
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4789689 92 - 22407834
UUUAGUUUUAGAGUGGUAAAAAGUAGACAUAGGAUAAGUGCUGUUUUGUGGUUCUACCUUUUUUGACAAAGGUAUAAAAG-----CCAUAAA-AAAUA
....(((((...(((((..........(((((((((.....)))))))))....(((((((......))))))).....)-----))))..)-)))). ( -17.70)
>DroSec_CAF1 237907 77 - 1
UUUAGUUUUAGAGUGGUAAGAAGC--------------CUCUACUCUGUGGUUCUACCUU-UUUGACAAAGGUAUAAAAG-----CUAUAAA-AAAUA
..((((((((((((((........--------------..))))))).......((((((-(.....)))))))..))))-----)))....-..... ( -17.20)
>DroSim_CAF1 215091 77 - 1
UUUAGUUUUAGAGUGGUAAAAAGC--------------CACUACUCUGUGGUUCUACCUU-UUUGACAAAGGUAUAAAAG-----CUAUAAA-AAAUA
..(((((((((((((((.......--------------.)))))))).......((((((-(.....)))))))..))))-----)))....-..... ( -19.10)
>DroEre_CAF1 232337 94 - 1
UUUAGUUUUAGAGUGGUAAAAAUACGACAUGAGAUAAGUGCUUCUUUGUGGUUCCACCUUUGGUGG-AAAA--AUAUCUCCUCUGCCGUUAA-AAAUG
(((((...(((((.((((......(.(((.((((........))))))).)(((((((...)))))-))..--.))))..)))))...))))-).... ( -20.20)
>DroYak_CAF1 225950 93 - 1
UUUAGUUUUGGAGUGGUAAAAAGCCGAC-UAAGAUAAGUGCUCUUUUGUGGUUCUACCUUUGGUGG-AA-A--AUAACUGCUCUGCAGUUAAAAAAUA
((((..(.(((((..((.....((((..-.((((.......))))...))))((((((...)))))-).-.--...))..))))).)..))))..... ( -21.70)
>consensus
UUUAGUUUUAGAGUGGUAAAAAGC_GAC_U__GAUAAGUGCUACUUUGUGGUUCUACCUUUUUUGACAAAGGUAUAAAAG_____CCAUAAA_AAAUA
........((((((((((....................)))))))))).((.....))........................................ ( -4.63 =  -4.79 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:15 2006