Locus 409

Sequence ID	3L_DroMel_CAF1
Location	1,193,538 – 1,193,668
Length	130
Max. P	0.996731

overview

Window 8

Location	1,193,538 – 1,193,636
Length	98
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	94.81
Mean single sequence MFE	-37.65
Consensus MFE	-34.39
Energy contribution	-34.45
Covariance contribution	0.06
Combinations/Pair	1.07
Mean z-score	-1.65
Structure conservation index	0.91
SVM decision value	0.48
SVM RNA-class probability	0.753446
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1193538 98 - 23771897
GCCUCUCGGCUCGGU---GGCCCAUUGGCUUCAAUUAGUCUGGGUCUAACAAAGGCCCGAGGCUCAGGGCCCCUCCAUGCCAUUAUUGCCCCAGUGCGGUU
(((....(((..((.---(((((((((....)))).(((((((((((.....)))))).)))))..)))))...))..)))......((......))))). ( -36.10)
>DroSec_CAF1 9180 98 - 1
GCCUCUCGGCUCGGU---GGCCCAUUGGCUUCAAUUAGUCUGGGUCUAACAAAGGCCCGAGGCUCAGGGCCCCUCCAUGCCAUUAUUGCCCCAGUGCGGUU
(((....(((..((.---(((((((((....)))).(((((((((((.....)))))).)))))..)))))...))..)))......((......))))). ( -36.10)
>DroSim_CAF1 8578 98 - 1
GCCUCUCGGCUCGGU---GGCCCAUUGGCUUCAAUUAGUCUGGGUCUAACAAAGGCCCGAAGCUUAGGGGCCCUCCAUGCCAUUAUUGCCCCAGUGCGGUU
(((....(((..((.---(((((...((((((.........((((((.....))))))))))))...)))))..))..)))......((......))))). ( -38.90)
>DroYak_CAF1 8748 101 - 1
GCCCCUCGGCUCGGUGGUGGCCCAUUGGCUUCAAUUAGUCUGGGCCCAACAAAGGCCCGAAGCUCAGGGCCUCUCCAUGCCAUUAUUGCCCCAGUGCGGUU
((((((.(((..((((((((((((..((((......))))))))))......((((((........))))))......))))))...)))..)).).))). ( -39.50)
>consensus
GCCUCUCGGCUCGGU___GGCCCAUUGGCUUCAAUUAGUCUGGGUCUAACAAAGGCCCGAAGCUCAGGGCCCCUCCAUGCCAUUAUUGCCCCAGUGCGGUU
(((....(((..((....(((((...((((((.........((((((.....))))))))))))..)))))...))..)))......((......))))). (-34.39 = -34.45 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	1,193,564 – 1,193,668
Length	104
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	91.79
Mean single sequence MFE	-38.45
Consensus MFE	-33.97
Energy contribution	-33.60
Covariance contribution	-0.37
Combinations/Pair	1.10
Mean z-score	-2.39
Structure conservation index	0.88
SVM decision value	1.80
SVM RNA-class probability	0.977774
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1193564 104 + 23771897
GAGGGGCCCUGAGCCUCGGGCCUUUGUUAGACCCAGACUAAUUGAAGCCAAUGGGCC---ACCGAGCCGAGAGGCUGAAGGGCCAUAAUUGAGAUCUGAGAUCAAAA
....((((((.((((((.(((.((.(((((.......))))).)).)))....(((.---.....)))..))))))..))))))........((((...)))).... ( -39.30)
>DroSec_CAF1 9206 104 + 1
GAGGGGCCCUGAGCCUCGGGCCUUUGUUAGACCCAGACUAAUUGAAGCCAAUGGGCC---ACCGAGCCGAGAGGCUGAAGGGCCAUAAUUGAGAUCUGAGAUCAAAA
....((((((.((((((.(((.((.(((((.......))))).)).)))....(((.---.....)))..))))))..))))))........((((...)))).... ( -39.30)
>DroSim_CAF1 8604 104 + 1
GAGGGCCCCUAAGCUUCGGGCCUUUGUUAGACCCAGACUAAUUGAAGCCAAUGGGCC---ACCGAGCCGAGAGGCUGAAGGGCCAUAAUUGAGAUCUGAGAUCAAAA
((((((((.........))))))))....((.(((((((.((((....)))).((((---....((((....))))....)))).......)).)))).).)).... ( -35.50)
>DroYak_CAF1 8774 100 + 1
GAGAGGCCCUGAGCUUCGGGCCUUUGUUGGGCCCAGACUAAUUGAAGCCAAUGGGCCACCACCGAGCCGAGGGGCUGAAGGGCCAUAAUUGA-------GAUCAAAA
....((((((.((((((.(((.((.((.(((((((..((......))....)))))).).)).)))))..))))))..))))))....(((.-------...))).. ( -39.70)
>consensus
GAGGGGCCCUGAGCCUCGGGCCUUUGUUAGACCCAGACUAAUUGAAGCCAAUGGGCC___ACCGAGCCGAGAGGCUGAAGGGCCAUAAUUGAGAUCUGAGAUCAAAA
....((((((.((((((.(((.((.(((((.......))))).)).)))....(((.........)))..))))))..))))))....((((.........)))).. (-33.97 = -33.60 +  -0.37)

alignment

secondary structure

dotplot

Window 0

Location	1,193,564 – 1,193,668
Length	104
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	91.79
Mean single sequence MFE	-40.32
Consensus MFE	-37.04
Energy contribution	-37.85
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-3.53
Structure conservation index	0.92
SVM decision value	2.74
SVM RNA-class probability	0.996731
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1193564 104 - 23771897
UUUUGAUCUCAGAUCUCAAUUAUGGCCCUUCAGCCUCUCGGCUCGGU---GGCCCAUUGGCUUCAAUUAGUCUGGGUCUAACAAAGGCCCGAGGCUCAGGGCCCCUC
....((((...))))........((((((..((((((..((((..((---((((((..((((......))))))))))..))...)))).)))))).)))))).... ( -42.30)
>DroSec_CAF1 9206 104 - 1
UUUUGAUCUCAGAUCUCAAUUAUGGCCCUUCAGCCUCUCGGCUCGGU---GGCCCAUUGGCUUCAAUUAGUCUGGGUCUAACAAAGGCCCGAGGCUCAGGGCCCCUC
....((((...))))........((((((..((((((..((((..((---((((((..((((......))))))))))..))...)))).)))))).)))))).... ( -42.30)
>DroSim_CAF1 8604 104 - 1
UUUUGAUCUCAGAUCUCAAUUAUGGCCCUUCAGCCUCUCGGCUCGGU---GGCCCAUUGGCUUCAAUUAGUCUGGGUCUAACAAAGGCCCGAAGCUUAGGGGCCCUC
....((((...))))........(((((((.(((.((..((((..((---((((((..((((......))))))))))..))...)))).)).))).)))))))... ( -38.10)
>DroYak_CAF1 8774 100 - 1
UUUUGAUC-------UCAAUUAUGGCCCUUCAGCCCCUCGGCUCGGUGGUGGCCCAUUGGCUUCAAUUAGUCUGGGCCCAACAAAGGCCCGAAGCUCAGGGCCUCUC
........-------........((((((..(((...((((..(..((..((((((..((((......))))))))))...))..)..)))).))).)))))).... ( -38.60)
>consensus
UUUUGAUCUCAGAUCUCAAUUAUGGCCCUUCAGCCUCUCGGCUCGGU___GGCCCAUUGGCUUCAAUUAGUCUGGGUCUAACAAAGGCCCGAAGCUCAGGGCCCCUC
.......................((((((..((((((..((((..((...((((((..((((......))))))))))..))...)))).)))))).)))))).... (-37.04 = -37.85 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:10 2006