Locus 3217

Sequence ID	3L_DroMel_CAF1
Location	9,389,891 – 9,390,131
Length	240
Max. P	0.994281

overview

Window 9

Location	9,389,891 – 9,389,995
Length	104
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	77.49
Mean single sequence MFE	-36.05
Consensus MFE	-23.83
Energy contribution	-24.03
Covariance contribution	0.20
Combinations/Pair	1.27
Mean z-score	-1.61
Structure conservation index	0.66
SVM decision value	0.80
SVM RNA-class probability	0.855253
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9389891 104 + 23771897
AGAUUUAAUCA-UUUACUGGACAGGUAAACCGGCAUCGCCGUGUCCAAGUUCCGGGGACCGUACUAAAUAGAUCGUGGUCUGGCAGUUGGGGCAUGUGGUGCACA
...........-((((((.....))))))...(((((((.((((((.(((.(.(....).).)))...(((((....))))).......)))))))))))))... ( -29.10)
>DroEre_CAF1 13174 104 + 1
AGAUUUCAUCA-UUUACUGGACAGGUAAACCGGCAUCGCCAUGUCCAAGUUCCGGGGAGCGUACUAAAUAUAUCGUGGUCUGGCAGUUGGGGCAUGUGGUGCACA
...........-((((((.....))))))...(((((((.((((((((.(.(((((..(((............)))..))))).).)).)))))))))))))... ( -31.20)
>DroWil_CAF1 19869 95 + 1
---------GG-CUUAUUGCACUGGGGAACCAGCAUCACCGUGUCCCAGCUCGGGGGAGCGUACCAAAUAGAUGGUUGUUUGGCAAUUGGGACAAGUGGUGCACA
---------.(-(.....))..(((....)))(((((((..(((((((((((....))))...((((((((....))))))))....))))))).)))))))... ( -40.70)
>DroYak_CAF1 10655 103 + 1
AGAUUU-AUCG-UUUACUGGACUGGUAAGCCGGCAUCGCCAUGUCCCAAUUCCGGGGAGCGUACUAAAUAGAUCGUGGUCUGGCAGUUGGGGCAUGUGGUGCACA
......-...(-((((((.....)))))))..(((((((.((((((((((((((((..(((..((....))..)))..))))).))))))))))))))))))... ( -43.20)
>DroMoj_CAF1 14821 99 + 1
----UUGGUCAU--UAUUGCAUUGGCAUACCAGCAUCGCCAUGGCCCAGCUCAGGUGUGCGCACCAGGUAAAUGGUUGUCUGGCAAUUGGGGCAUGUGGUGCACA
----.((((...--...(((....))).))))(((((((.(((.((((((.((....)).)).((((..((....))..))))....)))).))))))))))... ( -34.60)
>DroAna_CAF1 13373 98 + 1
GGGUU-------UCUACUGUACUGGUGACCCGGCAUCUCCGUGUCCCAGUUCGGGGGAGCGUACCAAGUAAAUAGUGGUCUGGCAGUUGGGGCACGUGGUGCACA
(((((-------.(((......))).))))).(((((..(((((((((((((....))))((((((.........))))...))...))))))))).)))))... ( -37.50)
>consensus
AGAUUU_AUCA_UUUACUGGACUGGUAAACCGGCAUCGCCAUGUCCCAGUUCCGGGGAGCGUACCAAAUAGAUCGUGGUCUGGCAGUUGGGGCAUGUGGUGCACA
.......................((....)).(((((((.((((((((((((....))))...(((.((........)).)))....)))))))))))))))... (-23.83 = -24.03 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	9,389,995 – 9,390,104
Length	109
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	69.64
Mean single sequence MFE	-43.40
Consensus MFE	-22.50
Energy contribution	-23.75
Covariance contribution	1.25
Combinations/Pair	1.23
Mean z-score	-1.63
Structure conservation index	0.52
SVM decision value	0.12
SVM RNA-class probability	0.593441
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9389995 109 + 23771897
UCUCGGCUUCCGCCGGUGCAGCAGAGCCACCAGCGUUUUCUCUGGGUGCAUUACUGCCGCCAGUUGCUCCUGGAGCUGGUGCUGCU---CCUCCUCCGGUGGUUGGCAUAGU
.....(((.(((((((.(.((..(((((((((((......((..((.(((..((((....))))))).))..)))))))))..)))---))).).)))))))..)))..... ( -48.70)
>DroEre_CAF1 13278 112 + 1
UCUCGGCAUCCGCCGGUGCCGCAGAGCCACCAGCGUUUUCCCUGGGCGCAUUACUGCCGCCAGUUGCUCCUGGAGCUGCUGGUGCUGCUGCUCCUCCGGUGGUUGGCAUAGA
....(.((.(((((((.(..(((((((.(((((((..((((..(((.(((..((((....))))))).))))))).)))))))))).))))..).))))))).)).)..... ( -52.90)
>DroWil_CAF1 19964 87 + 1
UUUCAGCAUCCGGUGGGGGAGCAGCACCACCAGCUC------CG---CCAUUAUUGCC------------AGAAGCAGCCGCUGCCGCAGCAUUU----UGAUUAGCAUUGG
.....(((...(((((.(((((..........))))------).---)))))..)))(------------((((...((.((....)).)).)))----))........... ( -24.90)
>DroYak_CAF1 10758 109 + 1
UCUCGGCAUCCGCCGGUGCCGCAGAGCCACCAGCAUUUUCCCUGGGCGCAUUAUUGCCGCCAGUUGCUCCAGGAGCUGCG---GCUGCUCCUCCUCCGGUGGUUGGUGUAGA
(((((.((.(((((((.(((((((..((...((((......(((((.(((....)))).)))).))))...))..)))))---))..........))))))).)).)).))) ( -47.10)
>consensus
UCUCGGCAUCCGCCGGUGCAGCAGAGCCACCAGCGUUUUCCCUGGGCGCAUUACUGCCGCCAGUUGCUCCAGGAGCUGCUGCUGCUGCUCCUCCUCCGGUGGUUGGCAUAGA
..(((((....)))))....((...((((((.............((((((....)).))))..........(((((.((.......)).)))))...))))))..))..... (-22.50 = -23.75 +   1.25)

alignment

secondary structure

dotplot

Window 1

Location	9,390,032 – 9,390,131
Length	99
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	73.52
Mean single sequence MFE	-40.43
Consensus MFE	-17.34
Energy contribution	-19.39
Covariance contribution	2.06
Combinations/Pair	1.11
Mean z-score	-2.79
Structure conservation index	0.43
SVM decision value	2.47
SVM RNA-class probability	0.994281
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9390032 99 - 23771897
CCGCCGAAUGCGGUUGCUCCGCAGGCAACUAU---GCCAACCACCGGAGGAGG---AGCAGCACCAGCUCCAGGAGCAACUGGCGGCAGUAAUGCACCCAGAGAA
((((.....))))(((((((...((((....)---)))..((......)).((---(((.......))))).)))))))((((..(((....)))..)))).... ( -43.50)
>DroSec_CAF1 12932 102 - 1
CCGCCGAAUGCGGUUGCUCCGCAGGCAACUAU---GCCAACCACCGGAGGAGCAGGAGCAGCACCAGCUCCAGGAGCAACUGGCGGCAGUAAUGCACCCAGAGAA
((((.....))))(((((((((.((((....)---)))..((......)).)).(((((.......))))).)))))))((((..(((....)))..)))).... ( -46.60)
>DroSim_CAF1 12430 102 - 1
CCGCCGAAUGCGGUUGCUCCGCAGGCAACUAU---GCCAACCACCGGAGGAGGAGCAGCAGCACAAGCUCCAGGAGCAACUGGCGGCAGUAAUGCACCCAGAGAA
((((.....))))(((((((...((((....)---)))..((......)).(((((..........))))).)))))))((((..(((....)))..)))).... ( -42.90)
>DroEre_CAF1 13315 96 - 1
CCGCCAAAU------GCUCCGCAGGCAUCUAU---GCCAACCACCGGAGGAGCAGCAGCACCAGCAGCUCCAGGAGCAACUGGCGGCAGUAAUGCGCCCAGGGAA
.(((((..(------(((((...((((....)---)))..........(((((.((.......)).))))).))))))..)))))(((....))).......... ( -41.40)
>DroYak_CAF1 10795 93 - 1
CCUCCAAAC------GCUCCACAGACAUCUAC---ACCAACCACCGGAGGAGGAGCAGC---CGCAGCUCCUGGAGCAACUGGCGGCAAUAAUGCGCCCAGGGAA
..(((....------(((((............---.....((......))((((((...---....)))))))))))..((((.((((....))).)))))))). ( -32.50)
>DroAna_CAF1 13508 94 - 1
-GGCCGGAGGAAGU-------CAGGCAGCUGGAGCACCAUCAAGUGGCGGACUAGGAGCCGGU---GCAGCAGGAGGAGCCGGCAAUGCCGCUGCACCACGAGAG
-(((........))-------).(((..((((..(.((((...)))).)..))))..)))(((---(((((.((.....))(((...)))))))))))....... ( -35.70)
>consensus
CCGCCGAAUGCGGU_GCUCCGCAGGCAACUAU___GCCAACCACCGGAGGAGGAGCAGCAGCACCAGCUCCAGGAGCAACUGGCGGCAGUAAUGCACCCAGAGAA
...............(((((...(((.........)))..........((((...............)))).)))))..((((..(((....)))..)))).... (-17.34 = -19.39 +   2.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:19 2006