Locus 3989

Sequence ID	X_DroMel_CAF1
Location	10,566,431 – 10,566,542
Length	111
Max. P	0.888097

overview

Window 1

Location	10,566,431 – 10,566,542
Length	111
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	91.61
Mean single sequence MFE	-25.25
Consensus MFE	-20.49
Energy contribution	-21.05
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.76
Structure conservation index	0.81
SVM decision value	0.42
SVM RNA-class probability	0.731142
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10566431 111 + 22224390
CAGACAAAGACGAAUAGAACUGGUUAAUAACCUGCGCA--CGCCAUGGCUUCCUUGGCAUCUGUUGCUCAUUCUUGGCCACU--UCCAUUGCCGUUUUCCGUUUCUUUCUCUUCU-
.((((.(((((((((.(((.(((((((......(((((--.((((.((...)).))))...)).)))......))))))).)--)).)))..))))))..))))...........- ( -23.20)
>DroSec_CAF1 6594 113 + 1
CAGACAAAGACGAAUAGAACUGGUUAAUAACCUGCGCACACACCAUGGCUUCUUCGGCAUCUGUUGCUCAUUCUUGAGCACU--UCCAUUGCCGUUAUCCGUUUCUUUCUCUUCU-
......((((.(((.((((.(((.((((.......((.((.....))))......((((.....((((((....))))))..--.....)))))))).))).)))))))))))..- ( -25.90)
>DroEre_CAF1 6542 108 + 1
CAGACAAAGACGAAUAGAACUGGUUAAUAACCUGC------ACCAUGGCUUCUUUGGCAUCUGUUGCUCAUUCUUGAGCACU--UCCAUUGCCGUUUUCCGUUUCUUUCUCUUCUG
((((...(((.(((.((((.(((..(((..((...------.....)).......((((.....((((((....))))))..--.....)))))))..))).)))))))))))))) ( -26.20)
>DroYak_CAF1 7202 110 + 1
CAGACAAAGACGAAUAGAACUGGUUAAUAACCUGC------AGCAUGGCUUCUUUGGCAUCUGUUGCUCAUUCUUGAGCACUUUUCCAUUGCCGUUUUCCGCUUCUUUCUCUUCUU
.(((.(((((.(...(((((.(((.........((------((.(((.(......).)))))))((((((....))))))..........))))))))...).))))).))).... ( -25.70)
>consensus
CAGACAAAGACGAAUAGAACUGGUUAAUAACCUGC______ACCAUGGCUUCUUUGGCAUCUGUUGCUCAUUCUUGAGCACU__UCCAUUGCCGUUUUCCGUUUCUUUCUCUUCU_
......((((.(((..((((.(((.....)))............(((((.....(((.....((.(((((....)))))))....)))..))))).....))))..)))))))... (-20.49 = -21.05 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	10,566,431 – 10,566,542
Length	111
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	91.61
Mean single sequence MFE	-31.00
Consensus MFE	-24.73
Energy contribution	-24.85
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-2.27
Structure conservation index	0.80
SVM decision value	0.95
SVM RNA-class probability	0.888097
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10566431 111 - 22224390
-AGAAGAGAAAGAAACGGAAAACGGCAAUGGA--AGUGGCCAAGAAUGAGCAACAGAUGCCAAGGAAGCCAUGGCG--UGCGCAGGUUAUUAACCAGUUCUAUUCGUCUUUGUCUG
-...(((.(((((..((.....))(.((((((--(.(((.....(((((.(..(..((((((.((...)).)))))--)..)..).)))))..))).)))))))).))))).))). ( -30.40)
>DroSec_CAF1 6594 113 - 1
-AGAAGAGAAAGAAACGGAUAACGGCAAUGGA--AGUGCUCAAGAAUGAGCAACAGAUGCCGAAGAAGCCAUGGUGUGUGCGCAGGUUAUUAACCAGUUCUAUUCGUCUUUGUCUG
-...(((.(((((..((((((.(((((.((..--..((((((....)))))).))..)))))..((((((((.....))).)).(((.....)))..)))))))))))))).))). ( -35.30)
>DroEre_CAF1 6542 108 - 1
CAGAAGAGAAAGAAACGGAAAACGGCAAUGGA--AGUGCUCAAGAAUGAGCAACAGAUGCCAAAGAAGCCAUGGU------GCAGGUUAUUAACCAGUUCUAUUCGUCUUUGUCUG
....(((.(((((..((((....((((.((..--..((((((....)))))).))..))))..((((....((((------...........)))).)))).))))))))).))). ( -29.70)
>DroYak_CAF1 7202 110 - 1
AAGAAGAGAAAGAAGCGGAAAACGGCAAUGGAAAAGUGCUCAAGAAUGAGCAACAGAUGCCAAAGAAGCCAUGCU------GCAGGUUAUUAACCAGUUCUAUUCGUCUUUGUCUG
....(((.(((((.((((.....(((..(((.....((((((....)))))).......))).....)))...))------)).(((.....)))...........))))).))). ( -28.60)
>consensus
_AGAAGAGAAAGAAACGGAAAACGGCAAUGGA__AGUGCUCAAGAAUGAGCAACAGAUGCCAAAGAAGCCAUGGU______GCAGGUUAUUAACCAGUUCUAUUCGUCUUUGUCUG
....(((.((((..(((((....((((.((......((((((....)))))).))..))))..((((((............)).(((.....)))..)))).))))))))).))). (-24.73 = -24.85 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:43 2006