Locus 81

Sequence ID	4_DroMel_CAF1
Location	577,777 – 577,904
Length	127
Max. P	0.938120

overview

Window 9

Location	577,777 – 577,872
Length	95
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	80.07
Mean single sequence MFE	-23.27
Consensus MFE	-15.50
Energy contribution	-16.81
Covariance contribution	1.31
Combinations/Pair	1.19
Mean z-score	-2.27
Structure conservation index	0.67
SVM decision value	1.10
SVM RNA-class probability	0.914561
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 577777 95 + 1281640
AAUUGAAGC-------------ACUGCUCCUUAACUAGCGUUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCGAAUGUACAUGCAGACAUAUGUAUGUGCAC
((((((((.-------------(((((.(((.....)).)...)))))...(((((.....)))))..)))))))).....((((((((((......)))))))))). ( -25.80)
>DroSec_CAF1 8096 95 + 1
AAUUGAAGC-------------ACUGCUCCUUAACUGGCGUUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCAAAUGUAUAUGCAGACAUAUGUAUGUGCAC
((((((((.-------------(((((.((......)).....)))))...(((((.....)))))..)))))))).....((((((((((......)))))))))). ( -25.00)
>DroSim_CAF1 7963 95 + 1
AAUUGAAGC-------------ACUGCUCCUUAACUGGCGUUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCAAAUGUACAUGCAGACAUAUGUAUGUGCAC
((((((((.-------------(((((.((......)).....)))))...(((((.....)))))..)))))))).....((((((((((......)))))))))). ( -26.90)
>DroEre_CAF1 9688 95 + 1
CAUUGAAGC-------------ACUGCUCCUUAACUGGCGUUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCGAAUGUACAUGCAGACAUAUGUAUGUGCAC
.(((((((.-------------(((((.((......)).....)))))...(((((.....)))))..)))))))......((((((((((......)))))))))). ( -26.30)
>DroWil_CAF1 8537 96 + 1
--UUCACACUUUGGCCGUCCAAAUUUAUUUUGUAUUUGUUUUUGCGUUCUAGUACACAUUCUGCAUAAUUUCAAUUUCGUAUGUAU----------ACAUAUGUGCAU
--.....(((..(..(((..((((..((.....))..))))..)))..).)))........((((............((((((...----------.)))))))))). ( -10.90)
>DroYak_CAF1 8743 95 + 1
GAUUGAAGC-------------ACUGCUCCUUAACUGCCGUUCGAAGUAUGAUGCACAUUUUGCAUAAUUUGAAUUUCGAAUGUACAUGCAGACAUAUGUAUGUGCAC
.......((-------------(((((.......((((((((((((((...(((((.....))))).......)))))))))).....))))......))).)))).. ( -24.72)
>consensus
AAUUGAAGC_____________ACUGCUCCUUAACUGGCGUUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCGAAUGUACAUGCAGACAUAUGUAUGUGCAC
..((((((..............(((((................)))))...(((((.....)))))........)))))).((((((((((......)))))))))). (-15.50 = -16.81 +   1.31)

alignment

secondary structure

dotplot

Window 0

Location	577,804 – 577,904
Length	100
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	81.49
Mean single sequence MFE	-23.43
Consensus MFE	-15.20
Energy contribution	-16.28
Covariance contribution	1.08
Combinations/Pair	1.15
Mean z-score	-2.53
Structure conservation index	0.65
SVM decision value	0.86
SVM RNA-class probability	0.867618
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 577804 100 + 1281640
UUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCGAAUGUACAUGCAGACAUAUGUAUGUGCACACAUGUC---GUGUAUGAAUACACACACACC-----CGAA
...((((.(((.....))).))))...........((((..((((((((((......))))))))))....(((.---(((((....))))))))....-----)))) ( -25.30)
>DroSec_CAF1 8123 100 + 1
UUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCAAAUGUAUAUGCAGACAUAUGUAUGUGCACACAUGUC---GUGUAUGAAUACACACACACC-----CGAA
.(((..((((((((((.....)))))...............((((((((((......))))))))))..)))).)---(((((....))))).......-----))). ( -22.30)
>DroSim_CAF1 7990 100 + 1
UUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCAAAUGUACAUGCAGACAUAUGUAUGUGCACACAUGUC---GUGUAUGAAUACACACACACC-----CGAA
.(((..((((((((((.....)))))...............((((((((((......))))))))))..)))).)---(((((....))))).......-----))). ( -24.20)
>DroEre_CAF1 9715 100 + 1
UUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCGAAUGUACAUGCAGACAUAUGUAUGUGCACACAUGUC---GGGUAUGAAUACACACACAGC-----CGCA
...((.((.(((((((.....)))))...((((..(((((.((((((((((......))))))))))......))---)))..))))........))))-----.)). ( -24.40)
>DroWil_CAF1 8575 88 + 1
UUUGCGUUCUAGUACACAUUCUGCAUAAUUUCAAUUUCGUAUGUAU----------ACAUAUGUGCAUACUAGUAUCCGCCCCCGCACUCGCACACAC----------
...(((..(((((((((((..((((((............)))))).----------....)))))..))))))....)))....((....))......---------- ( -16.00)
>DroYak_CAF1 8770 105 + 1
UUCGAAGUAUGAUGCACAUUUUGCAUAAUUUGAAUUUCGAAUGUACAUGCAGACAUAUGUAUGUGCACACAUGUC---GUGUAUGAAUACACACACCACAAACACGCA
((((((((...(((((.....))))).......))))))))((((((((((......))))))))))....(((.---((((.((....)).)))).)))........ ( -28.40)
>consensus
UUCGCAGUAUGAUGCACAUUUUGCAUAAUUUCAAUUUCGAAUGUACAUGCAGACAUAUGUAUGUGCACACAUGUC___GUGUAUGAAUACACACACACC_____CGAA
...........(((((.....)))))...............((((((((((......))))))))))...........(((((....)))))................ (-15.20 = -16.28 +   1.08)

alignment

secondary structure

dotplot

Window 1

Location	577,804 – 577,904
Length	100
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	81.49
Mean single sequence MFE	-29.89
Consensus MFE	-17.78
Energy contribution	-18.62
Covariance contribution	0.84
Combinations/Pair	1.21
Mean z-score	-3.36
Structure conservation index	0.59
SVM decision value	1.29
SVM RNA-class probability	0.938120
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 577804 100 - 1281640
UUCG-----GGUGUGUGUGUAUUCAUACAC---GACAUGUGUGCACAUACAUAUGUCUGCAUGUACAUUCGAAAUUGAAAUUAUGCAAAAUGUGCAUCAUACUGCGAA
.(((-----((((((((..((((.......---((((((((((....))))))))))((((((....((((....))))..)))))).))))..)).)))))).))). ( -31.40)
>DroSec_CAF1 8123 100 - 1
UUCG-----GGUGUGUGUGUAUUCAUACAC---GACAUGUGUGCACAUACAUAUGUCUGCAUAUACAUUUGAAAUUGAAAUUAUGCAAAAUGUGCAUCAUACUGCGAA
((((-----((((((((((((.........---((((((((((....))))))))))))))))))))))))))..........((((..(((.....)))..)))).. ( -30.80)
>DroSim_CAF1 7990 100 - 1
UUCG-----GGUGUGUGUGUAUUCAUACAC---GACAUGUGUGCACAUACAUAUGUCUGCAUGUACAUUUGAAAUUGAAAUUAUGCAAAAUGUGCAUCAUACUGCGAA
.(((-----((((((((((....)))))))---((((((((((....))))))))))((.((((((((((...((.......))...)))))))))))).))).))). ( -32.40)
>DroEre_CAF1 9715 100 - 1
UGCG-----GCUGUGUGUGUAUUCAUACCC---GACAUGUGUGCACAUACAUAUGUCUGCAUGUACAUUCGAAAUUGAAAUUAUGCAAAAUGUGCAUCAUACUGCGAA
.(((-----(.((((((..((((.......---((((((((((....))))))))))((((((....((((....))))..)))))).))))..)).))))))))... ( -31.10)
>DroWil_CAF1 8575 88 - 1
----------GUGUGUGCGAGUGCGGGGGCGGAUACUAGUAUGCACAUAUGU----------AUACAUACGAAAUUGAAAUUAUGCAGAAUGUGUACUAGAACGCAAA
----------.....((((..(((....)))....((((((((((....(((----------(((((........))....))))))...))))))))))..)))).. ( -21.50)
>DroYak_CAF1 8770 105 - 1
UGCGUGUUUGUGGUGUGUGUAUUCAUACAC---GACAUGUGUGCACAUACAUAUGUCUGCAUGUACAUUCGAAAUUCAAAUUAUGCAAAAUGUGCAUCAUACUUCGAA
(((((((.....(((((((....)))))))---((((((((((....)))))))))).)))))))..((((((.........(((((.....))))).....)))))) ( -32.14)
>consensus
UUCG_____GGUGUGUGUGUAUUCAUACAC___GACAUGUGUGCACAUACAUAUGUCUGCAUGUACAUUCGAAAUUGAAAUUAUGCAAAAUGUGCAUCAUACUGCGAA
............(((((((....)))))))...((((((((((....))))))))))...(((((((((....((.......))....)))))))))........... (-17.78 = -18.62 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:05 2006