Locus 1298

Sequence ID	3L_DroMel_CAF1
Location	3,771,510 – 3,771,659
Length	149
Max. P	0.975257

overview

Window 0

Location	3,771,510 – 3,771,630
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.06
Mean single sequence MFE	-43.58
Consensus MFE	-36.20
Energy contribution	-36.88
Covariance contribution	0.68
Combinations/Pair	1.03
Mean z-score	-2.21
Structure conservation index	0.83
SVM decision value	1.75
SVM RNA-class probability	0.975257
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3771510 120 + 23771897
AAAAUUGUGACAAAAAAUUGUUUAUAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGAAUUUGCACCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCGAGAAGAGA
.....((((((((....))).)))))...((.(((((((((.(((((....(((((.....)))))................((((....)))))))))..)))))))))))........ ( -42.90)
>DroSec_CAF1 169017 120 + 1
AAAUUUGUGACAAAAAAUUGUUUAUAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGACAUUGGCCCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCGAGAAGAGA
.....((((((((....))).)))))...((.(((((((((.((((((....((((.....))))((((...(((((...)).)))...))))))))))..)))))))))))........ ( -48.60)
>DroSim_CAF1 163401 120 + 1
AAAUUUGUGACAAAAAAUUGUUUAUAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGACUUUGGCCCGUUUCGCGGCACUUGUCGGCAGCGCGGUCACACUCGAGAAGAGA
.....((((((((....))).)))))...((.(((((((((.((((((....((((.....))))(((....(((((...)).)))....)))))))))..)))))))))))........ ( -46.90)
>DroEre_CAF1 161718 109 + 1
-AAAUUGUGACAAAAAAUUGUUUAUAUGGCGCAGUGUGGCCAGAUACUUGGCGGCCGAUAAGGCCGAGUUGGGCCCGUUUGGCGGCAUUUUUCGGCAGCGCGGUCACACC----------
-....((((((........(((.....)))...((((.(((.((......((.(((((...((((......))))...))))).)).....))))).)))).))))))..---------- ( -39.50)
>DroYak_CAF1 153126 110 + 1
AAAAUUGUGACAAAAAAUUGUUUAUAUGGCGCAGUGUGGCCAGCUACUAGGCGGCCGAUGAGGCCGAGUUUCGCCCGUUUGGCGGCAUUCUUCGGCAGCGCGGUCACACC----------
.....((((((........(((.....)))...((((.(((.(((....)))((((.....))))((((.(((((.....))))).))))...))).)))).))))))..---------- ( -40.00)
>consensus
AAAAUUGUGACAAAAAAUUGUUUAUAUGCCGCAGUGUGGCCAGCUGCUUAGCGGCCGAUAAGGCCGACUUUGGCCCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCGAGAAGAGA
.....((((.((..............)).))))((((((((.((((((....((((.....))))(((....(.(((.....))))....)))))))))..))))))))........... (-36.20 = -36.88 +   0.68)

alignment

secondary structure

dotplot

Window 1

Location	3,771,510 – 3,771,630
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.06
Mean single sequence MFE	-37.10
Consensus MFE	-31.38
Energy contribution	-31.10
Covariance contribution	-0.28
Combinations/Pair	1.08
Mean z-score	-1.73
Structure conservation index	0.85
SVM decision value	0.80
SVM RNA-class probability	0.854547
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3771510 120 - 23771897
UCUCUUCUCGAGUGUGACCGCGCUGCCGACAAAUGCCGCGAAACGGUGCAAAUUCGGCCUUAUCGGCCGCUAAGCAGCUGGCCACACUGCGGCAUAUAAACAAUUUUUUGUCACAAUUUU
.......(((((((((.(((.(((((........((((.....)))).......(((((.....)))))....)))))))).)))))).))).......((((....))))......... ( -36.70)
>DroSec_CAF1 169017 120 - 1
UCUCUUCUCGAGUGUGACCGCGCUGCCGACAAAUGCCGCGAAACGGGCCAAUGUCGGCCUUAUCGGCCGCUAAGCAGCUGGCCACACUGCGGCAUAUAAACAAUUUUUUGUCACAAAUUU
.(((.....)))((((((((......))....((((((((.....(((((.((((((((.....)))))....)))..)))))....))))))))..............))))))..... ( -41.60)
>DroSim_CAF1 163401 120 - 1
UCUCUUCUCGAGUGUGACCGCGCUGCCGACAAGUGCCGCGAAACGGGCCAAAGUCGGCCUUAUCGGCCGCUAAGCAGCUGGCCACACUGCGGCAUAUAAACAAUUUUUUGUCACAAAUUU
.(((.....)))((((((((......))....(((((((((...(((((......)))))..))(((((((....))).)))).....)))))))..............))))))..... ( -41.10)
>DroEre_CAF1 161718 109 - 1
----------GGUGUGACCGCGCUGCCGAAAAAUGCCGCCAAACGGGCCCAACUCGGCCUUAUCGGCCGCCAAGUAUCUGGCCACACUGCGCCAUAUAAACAAUUUUUUGUCACAAUUU-
----------..((((((.(.((.(((((.......((.....))((((......))))...))))).)))...(((.(((((.....).)))).)))...........))))))....- ( -31.60)
>DroYak_CAF1 153126 110 - 1
----------GGUGUGACCGCGCUGCCGAAGAAUGCCGCCAAACGGGCGAAACUCGGCCUCAUCGGCCGCCUAGUAGCUGGCCACACUGCGCCAUAUAAACAAUUUUUUGUCACAAUUUU
----------((((((.(((.(((((..........((((.....)))).....(((((.....)))))....)))))))).))))))...........((((....))))......... ( -34.50)
>consensus
UCUCUUCUCGAGUGUGACCGCGCUGCCGACAAAUGCCGCGAAACGGGCCAAACUCGGCCUUAUCGGCCGCUAAGCAGCUGGCCACACUGCGGCAUAUAAACAAUUUUUUGUCACAAUUUU
..........((((((.(((.(((((.........(((.....)))........(((((.....)))))....)))))))).))))))...........((((....))))......... (-31.38 = -31.10 +  -0.28)

alignment

secondary structure

dotplot

Window 2

Location	3,771,550 – 3,771,659
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.37
Mean single sequence MFE	-41.04
Consensus MFE	-29.24
Energy contribution	-30.82
Covariance contribution	1.58
Combinations/Pair	1.04
Mean z-score	-1.77
Structure conservation index	0.71
SVM decision value	0.70
SVM RNA-class probability	0.826904
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3771550 109 + 23771897
CAGCUGCUUAGCGGCCGAUAAGGCCGAAUUUGCACCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCGAGAAGAGAGCGGCUG---------GAAA-UUCAAA-AUUUAAUUUGGC
((((((((..(.(((((.....(((((...(((..((...))..)))....)))))....))))).).(((.....)))))))))))---------....-.(((((-......))))). ( -39.80)
>DroSec_CAF1 169057 110 + 1
CAGCUGCUUAGCGGCCGAUAAGGCCGACAUUGGCCCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCGAGAAGAGAGCGGCUG---------GAAA-UUCAAAAAUGUAAUUUGGC
((((((((..(.(((((.....(((((((...(((((...)).)))...)))))))....))))).).(((.....)))))))))))---------....-................... ( -45.10)
>DroSim_CAF1 163441 109 + 1
CAGCUGCUUAGCGGCCGAUAAGGCCGACUUUGGCCCGUUUCGCGGCACUUGUCGGCAGCGCGGUCACACUCGAGAAGAGAGCGGCUG---------GAAA-UUCAAA-AUUUAAUUUGGC
((((((((..(.(((((.....((((((....(((((...)).)))....))))))....))))).).(((.....)))))))))))---------....-.(((((-......))))). ( -43.90)
>DroEre_CAF1 161757 104 + 1
CAGAUACUUGGCGGCCGAUAAGGCCGAGUUGGGCCCGUUUGGCGGCAUUUUUCGGCAGCGCGGUCACACC----------GCGGCUGUAGUGAGCGGAAU-UUCAAA-AU----UUUGGC
....((((..((.(((((...((((......))))...))))).))........(((((((((.....))----------)).)))))))))..((((((-(....)-))----)))).. ( -38.20)
>DroYak_CAF1 153166 104 + 1
CAGCUACUAGGCGGCCGAUGAGGCCGAGUUUCGCCCGUUUGGCGGCAUUCUUCGGCAGCGCGGUCACACC----------GCGGCUGUA-UGAAUGAAAUUUUCAAA-AU----UUUGGC
..((((.....(((((.....)))))....(((((.....)))))(((((....(((((((((.....))----------)).))))).-.)))))...........-..----..)))) ( -38.20)
>consensus
CAGCUGCUUAGCGGCCGAUAAGGCCGACUUUGGCCCGUUUCGCGGCAUUUGUCGGCAGCGCGGUCACACUCGAGAAGAGAGCGGCUG_________GAAA_UUCAAA_AU_UAAUUUGGC
(((((((...(.(((((.....((((((....(.(((.....))))....))))))....))))).).(((.....))).)))))))................................. (-29.24 = -30.82 +   1.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:14 2006