Locus 8703

Sequence ID	3R_DroMel_CAF1
Location	23,255,989 – 23,256,114
Length	125
Max. P	0.993314

overview

Window 4

Location	23,255,989 – 23,256,081
Length	92
Sequences	3
Columns	95
Reading direction	forward
Mean pairwise identity	72.39
Mean single sequence MFE	-17.97
Consensus MFE	-10.40
Energy contribution	-10.73
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.58
SVM decision value	2.39
SVM RNA-class probability	0.993314
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23255989 92 + 27905053
AAUUUAU---GUUACUAAGUUACAUAUUUUACAUUUGUGAGGUCUCUUUUUUCACAGUGCUUUUAUCUGCUGAUUAUGUGCUAGAUGGUAUGCAU
((..(((---((.((...)).)))))..)).....(((((((.......)))))))((((..((((((((.........)).))))))...)))) ( -17.00)
>DroSec_CAF1 53464 76 + 1
GACUUAA---GUUACUGAGUUACUCA--------------GAAGC--UUUUUUUCAGUGCAUUUAUCUGCUUAUUAUGUGCUAGAUGGUAUGCAU
((...((---(((.(((((...))))--------------).)))--))....)).((((((((((((((.........)).)))))).)))))) ( -20.50)
>DroSim_CAF1 53393 81 + 1
AACAUUACAUUUUACUGAGUUACUCA--------------GAUACAUUUUUUUUCAGUGCAUUUAUCUGCUUAUUAUGUGCUAGAUGGUAUGCAU
..............(((((...))))--------------)...............((((((((((((((.........)).)))))).)))))) ( -16.40)
>consensus
AACUUAA___GUUACUGAGUUACUCA______________GAUAC_UUUUUUUUCAGUGCAUUUAUCUGCUUAUUAUGUGCUAGAUGGUAUGCAU
........................................................((((((((((((((.........)).)))))).)))))) (-10.40 = -10.73 +   0.33)

alignment

secondary structure

dotplot

Window 5

Location	23,256,016 – 23,256,114
Length	98
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	80.29
Mean single sequence MFE	-18.62
Consensus MFE	-12.30
Energy contribution	-12.38
Covariance contribution	0.09
Combinations/Pair	1.11
Mean z-score	-1.61
Structure conservation index	0.66
SVM decision value	0.36
SVM RNA-class probability	0.706392
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23256016 98 + 27905053
ACAUUUGUGAGGUCU--CUUUUUUCACAGUGCUUUUAUCUGCU--GAUUAUGUGCUAGAUGGUAUGCAUUAUGUAUGUGCAUAUUUAUGACAACUGUCGCUC
.(((((((((((...--....))))))((..(....(((....--)))...)..)))))))((((((((.......))))))))....(((....))).... ( -23.00)
>DroSec_CAF1 53487 86 + 1
----------GAAGC----UUUUUUUCAGUGCAUUUAUCUGCU--UAUUAUGUGCUAGAUGGUAUGCAUUAUGUAUGUGCAUAUUUAUGACAACUGUCGCUC
----------..(((----.........((((((((((((((.--........)).)))))).))))))(((((....))))).....(((....)))))). ( -18.50)
>DroSim_CAF1 53419 88 + 1
----------GAUAC--AUUUUUUUUCAGUGCAUUUAUCUGCU--UAUUAUGUGCUAGAUGGUAUGCAUUAUGUAUGUGCAUAUUUAUGACAACUGUCGCUC
----------.((((--((........(((((((((((((((.--........)).)))))).)))))))))))))............(((....))).... ( -17.80)
>DroEre_CAF1 57803 82 + 1
-----------------GAUUUUUUGCCGUGCAC-UAUCUGCU--UAUUAUGUGCUAGAUGGUAUGCAUUAUGUAUGUGCAUAUUUAUGACAACUGUCGCUC
-----------------(((...(((.((((.((-(((((((.--........)).)))))))((((((.......))))))...)))).)))..))).... ( -18.60)
>DroYak_CAF1 53314 81 + 1
-----------------UAUUUUUUGCAGUGCAUUUAUCUGCU--UAUUAUGUGCUAGAUGGUAUGCAUUAUGUAUGUGCAUAUUUAUGACAACUGUCGC--
-----------------........(((((.(((.(((((((.--........)).)))))((((((((.......))))))))..)))...)))))...-- ( -18.00)
>DroAna_CAF1 47391 88 + 1
----------GAAGCCUUUUUUCUUCCUGU----CUAUACUCUUAUAUAAUGUGCUGGAUAUUAUGCAUUAUGUAUGUGCAUAUUUAUGACAACUGUCGCUU
----------.((((............(((----((((((...........))).)))))).(((((((.......))))))).....(((....))))))) ( -15.80)
>consensus
__________GA__C__UUUUUUUUGCAGUGCAUUUAUCUGCU__UAUUAUGUGCUAGAUGGUAUGCAUUAUGUAUGUGCAUAUUUAUGACAACUGUCGCUC
...................................(((((((...........)).)))))((((((((.......))))))))....(((....))).... (-12.30 = -12.38 +   0.09)

alignment

secondary structure

dotplot

Window 6

Location	23,256,016 – 23,256,114
Length	98
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	80.29
Mean single sequence MFE	-13.50
Consensus MFE	-9.67
Energy contribution	-10.33
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.72
SVM decision value	0.25
SVM RNA-class probability	0.652018
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23256016 98 - 27905053
GAGCGACAGUUGUCAUAAAUAUGCACAUACAUAAUGCAUACCAUCUAGCACAUAAUC--AGCAGAUAAAAGCACUGUGAAAAAAG--AGACCUCACAAAUGU
..(((((....))).....((((((.........))))))..((((.((........--.))))))....))..(((((......--.....)))))..... ( -15.00)
>DroSec_CAF1 53487 86 - 1
GAGCGACAGUUGUCAUAAAUAUGCACAUACAUAAUGCAUACCAUCUAGCACAUAAUA--AGCAGAUAAAUGCACUGAAAAAAA----GCUUC----------
(((((((....))).....((((......)))).(((((...((((.((........--.))))))..)))))..........----)))).---------- ( -14.60)
>DroSim_CAF1 53419 88 - 1
GAGCGACAGUUGUCAUAAAUAUGCACAUACAUAAUGCAUACCAUCUAGCACAUAAUA--AGCAGAUAAAUGCACUGAAAAAAAAU--GUAUC----------
..(((((....))).....((((((.........)))))).......))........--.(((......))).............--.....---------- ( -12.50)
>DroEre_CAF1 57803 82 - 1
GAGCGACAGUUGUCAUAAAUAUGCACAUACAUAAUGCAUACCAUCUAGCACAUAAUA--AGCAGAUA-GUGCACGGCAAAAAAUC-----------------
........((((((((...((((((.........))))))..((((.((........--.)))))).-))).)))))........----------------- ( -13.40)
>DroYak_CAF1 53314 81 - 1
--GCGACAGUUGUCAUAAAUAUGCACAUACAUAAUGCAUACCAUCUAGCACAUAAUA--AGCAGAUAAAUGCACUGCAAAAAAUA-----------------
--(((((....))).....((((((.........)))))).......))........--.((((.........))))........----------------- ( -13.40)
>DroAna_CAF1 47391 88 - 1
AAGCGACAGUUGUCAUAAAUAUGCACAUACAUAAUGCAUAAUAUCCAGCACAUUAUAUAAGAGUAUAG----ACAGGAAGAAAAAAGGCUUC----------
(((((((....))).....((((((.........))))))...(((......((((((....))))))----...))).........)))).---------- ( -12.10)
>consensus
GAGCGACAGUUGUCAUAAAUAUGCACAUACAUAAUGCAUACCAUCUAGCACAUAAUA__AGCAGAUAAAUGCACUGAAAAAAAAA__G__UC__________
..(((((....))).....((((((.........)))))).......))...........(((......))).............................. ( -9.67 = -10.33 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:38 2006