Locus 81

Sequence ID	sy_ha.0
Location	2,458,081 – 2,458,189
Length	108
Max. P	0.999999

overview

Window 4

Location	2,458,081 – 2,458,187
Length	106
Sequences	2
Columns	120
Reading direction	forward
Mean pairwise identity	68.33
Mean single sequence MFE	-21.35
Consensus MFE	-13.75
Energy contribution	-17.75
Covariance contribution	4.00
Combinations/Pair	1.10
Mean z-score	-2.81
Structure conservation index	0.64
SVM decision value	3.24
SVM RNA-class probability	0.998829
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2458081 106 + 2685015/0-120
AAAUCUCUCCUAUUCUAGU-AAAAGUUAU-UUCAAUAUUAUCUCUCAUGAUAGUUUCUCACCAUCAUGAGAC-AUAAUG------AUUGUUA-GAA----UUCAUAAUUCAUUUAUAAUG
...........((((((((-((..(....-..)..((((((.(((((((((.((.....)).))))))))).-))))))------.))))))-)))----)................... ( -18.40)
>sy_sa.0 2266287 120 + 2516575/0-120
AAAUCUCUCCUAUUCGUUAGAAAAUAAAUUUUUAAAAUUAUCUCUCAUGACAGUUUCUCACCAUCAUGAGAAGAUUGUUUUAUUUUUUGGUAUAAAGGACCAUACAGUACCUUUAUAAUG
........((..(((....)))..........((((((.(((((((((((..((.....))..))))))).)))).))))))......))((((((((((......)).))))))))... ( -24.30)
>consensus
AAAUCUCUCCUAUUCGAGA_AAAAGAAAU_UUCAAAAUUAUCUCUCAUGACAGUUUCUCACCAUCAUGAGAA_AUAAUG______AUUGGUA_AAA____CACACAAUACAUUUAUAAUG
................................(((((((((((((((((((.((.....)).))))))))).))))))))))......((((((((((...........)))))))))). (-13.75 = -17.75 +   4.00)

alignment

secondary structure

dotplot

Window 5

Location	2,458,081 – 2,458,187
Length	106
Sequences	2
Columns	120
Reading direction	reverse
Mean pairwise identity	68.33
Mean single sequence MFE	-30.50
Consensus MFE	-17.05
Energy contribution	-16.80
Covariance contribution	-0.25
Combinations/Pair	1.08
Mean z-score	-4.68
Structure conservation index	0.56
SVM decision value	2.04
SVM RNA-class probability	0.986405
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2458081 106 + 2685015/0-120
CAUUAUAAAUGAAUUAUGAA----UUC-UAACAAU------CAUUAU-GUCUCAUGAUGGUGAGAAACUAUCAUGAGAGAUAAUAUUGAA-AUAACUUUU-ACUAGAAUAGGAGAGAUUU
..((((((.....)))))).----.((-(..((((------.(((((-.((((((((((((.....)))))))))))).)))))))))..-....(((((-(......)))))))))... ( -28.60)
>sy_sa.0 2266287 120 + 2516575/0-120
CAUUAUAAAGGUACUGUAUGGUCCUUUAUACCAAAAAAUAAAACAAUCUUCUCAUGAUGGUGAGAAACUGUCAUGAGAGAUAAUUUUAAAAAUUUAUUUUCUAACGAAUAGGAGAGAUUU
...((((((((.(((....)))))))))))((......(((((..((((.(((((((((((.....)))))))))))))))..)))))..........(((....)))..))........ ( -32.40)
>consensus
CAUUAUAAAGGAACUAUAAA____UUC_UAACAAA______AACAAU_GUCUCAUGAUGGUGAGAAACUAUCAUGAGAGAUAAUAUUAAA_AUAAAUUUU_AAAAGAAUAGGAGAGAUUU
.................................................((((((((((((.....)))))))))))).......................................... (-17.05 = -16.80 +  -0.25) 
# Strand winner: reverse (0.95)

alignment

secondary structure

dotplot

Window 6

Location	2,458,081 – 2,458,189
Length	108
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	70.39
Mean single sequence MFE	-21.67
Consensus MFE	-10.90
Energy contribution	-11.23
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.96
Structure conservation index	0.50
SVM decision value	3.19
SVM RNA-class probability	0.998696
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2458081 108 + 2685015/40-160
UCUCUCAUGAUAGUUUCUCACCAUCAUGAGAC-AUAAUG------AUUGUUA-GAA----UUCAUAAUUCAUUUAUAAUGCAUUUUCAGUAAAAAAUCAAUUCAUAAAGAUGUUCGCUUA
..(((((((((.((.....)).))))))))).-....((------(((....-(((----(.....))))........(((.......)))...)))))..................... ( -15.10)
>sy_au.0 2191269 118 - 2809422/40-160
UCUCUCAUGAUAGUUUCUCACCAUCAUGAGAA-AUUAUUUAUAGCGAUGCAA-AAAGAAUUUUACAAUUCUUUUAUAAUGCAUUCACCCCAAAAAAUCAAACUAUAAAGAUGAUAGCUUA
..(((((((((.((.....)).))))))))).-.........((((((((((-((((((((....)))))))))....))))))...........((((..((....)).)))).))).. ( -24.10)
>sy_sa.0 2266287 120 + 2516575/40-160
UCUCUCAUGACAGUUUCUCACCAUCAUGAGAAGAUUGUUUUAUUUUUUGGUAUAAAGGACCAUACAGUACCUUUAUAAUGCAUUUUUCCCAAAAAAUCAAUUAAUAAAACUACAAGCCAC
((((((((((..((.....))..))))))).)))..((((((((..(((.((((((((((......)).))))))))....((((((....)))))))))..)))))))).......... ( -25.80)
>consensus
UCUCUCAUGAUAGUUUCUCACCAUCAUGAGAA_AUUAUUU_____AUUGCUA_AAAG_A_UUUACAAUUCAUUUAUAAUGCAUUUUCCCCAAAAAAUCAAUUAAUAAAGAUGAUAGCUUA
..(((((((((.((.....)).)))))))))......................................................................................... (-10.90 = -11.23 +   0.33)

alignment

secondary structure

dotplot

Window 7

Location	2,458,081 – 2,458,189
Length	108
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	70.39
Mean single sequence MFE	-31.30
Consensus MFE	-19.56
Energy contribution	-19.23
Covariance contribution	-0.32
Combinations/Pair	1.19
Mean z-score	-3.86
Structure conservation index	0.62
SVM decision value	6.63
SVM RNA-class probability	0.999999
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2458081 108 + 2685015/40-160
UAAGCGAACAUCUUUAUGAAUUGAUUUUUUACUGAAAAUGCAUUAUAAAUGAAUUAUGAA----UUC-UAACAAU------CAUUAU-GUCUCAUGAUGGUGAGAAACUAUCAUGAGAGA
..........(((((((((..((((((((....)))))).))))))))).))........----...-.......------......-.((((((((((((.....)))))))))))).. ( -22.30)
>sy_au.0 2191269 118 - 2809422/40-160
UAAGCUAUCAUCUUUAUAGUUUGAUUUUUUGGGGUGAAUGCAUUAUAAAAGAAUUGUAAAAUUCUUU-UUGCAUCGCUAUAAAUAAU-UUCUCAUGAUGGUGAGAAACUAUCAUGAGAGA
((((((((.......))))))))....((((.(((((.((((....(((((((((....))))))))-)))))))))).))))...(-(((((((((((((.....)))))))))))))) ( -38.40)
>sy_sa.0 2266287 120 + 2516575/40-160
GUGGCUUGUAGUUUUAUUAAUUGAUUUUUUGGGAAAAAUGCAUUAUAAAGGUACUGUAUGGUCCUUUAUACCAAAAAAUAAAACAAUCUUCUCAUGAUGGUGAGAAACUGUCAUGAGAGA
..........((((((((..(((((((((....))))))....((((((((.(((....))))))))))).)))..))))))))....(((((((((((((.....))))))))))))). ( -33.20)
>consensus
UAAGCUAACAUCUUUAUAAAUUGAUUUUUUGGGGAAAAUGCAUUAUAAAAGAAUUGUAAA_U_CUUU_UAACAAA_____AAAUAAU_UUCUCAUGAUGGUGAGAAACUAUCAUGAGAGA
............(((((((..((((((((....)))))).)))))))))........................................((((((((((((.....)))))))))))).. (-19.56 = -19.23 +  -0.32) 
# Strand winner: reverse (1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:56:22 2006