Locus 7005

Sequence ID	X_DroMel_CAF1
Location	17,549,467 – 17,549,667
Length	200
Max. P	0.756857

overview

Window 5

Location	17,549,467 – 17,549,575
Length	108
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	85.96
Mean single sequence MFE	-29.52
Consensus MFE	-23.10
Energy contribution	-24.47
Covariance contribution	1.37
Combinations/Pair	1.14
Mean z-score	-1.41
Structure conservation index	0.78
SVM decision value	-0.01
SVM RNA-class probability	0.525972
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17549467 108 - 22224390
UUAUUUGGAUUUGAUUCGUUUGGAUGAUGAUGAUGGUGAUGAUGGCGGAAG--AACAAGUGUUUUGCCAGCCCAAGCCCAAAUGUGAUUCAAUGCGCUGGGAAUUCAAAA
...(((((((((....(((((((((.((.((...(((.....((((((((.--(.....).))))))))......)))...)))).)))))).)))....))))))))). ( -26.20)
>DroSec_CAF1 1334 99 - 1
UUAUUUGGAUUCGAUUCGUAUGGAU---------GGUGAUGAUGGCGGAAG--AACAUGUGUUUUGCCAGCCCAAGCCCAAAUGUGAUUCCAUGCGCUGGGAAUCCAGAA
...(((((((((....((((((((.---------(((.....((((((((.--(.....).))))))))......)))((....))..))))))))....))))))))). ( -33.40)
>DroSim_CAF1 487 99 - 1
UUAUUUGGAUUCGAUUCGUAUGGAC---------GGUGAUGAUGGCGGAAG--AACAAGUGUUUUGCCAGCCGAAGCCCAAAUGUGAUUCCAUGCGCUGGGAAUCCAGAA
...(((((((((....((((((((.---------(((..((.((((((((.--(.....).))))))))..))..)))((....))..))))))))....))))))))). ( -34.20)
>DroEre_CAF1 6004 100 - 1
UUAUUUUGAUUUGAUCCGUUUGGAU---------GG-GCUGAUGGGGGAAGUAAACAAGUGUUCUGGCAGCCCAAGCCCAAAUAUGAUUCAAUGCGCUGGGAAUCCAACA
.................(((.((((---------((-((((..((((.(..(....)..).))))..))))))...((((..(((......)))...)))).))))))). ( -24.30)
>consensus
UUAUUUGGAUUCGAUUCGUAUGGAU_________GGUGAUGAUGGCGGAAG__AACAAGUGUUUUGCCAGCCCAAGCCCAAAUGUGAUUCAAUGCGCUGGGAAUCCAAAA
...(((((((((....((((((((..........(((.....((((((((...........))))))))......)))..........))))))))....))))))))). (-23.10 = -24.47 +   1.37)

alignment

secondary structure

dotplot

Window 6

Location	17,549,575 – 17,549,667
Length	92
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	90.05
Mean single sequence MFE	-16.41
Consensus MFE	-12.61
Energy contribution	-12.42
Covariance contribution	-0.19
Combinations/Pair	1.06
Mean z-score	-1.72
Structure conservation index	0.77
SVM decision value	0.30
SVM RNA-class probability	0.680368
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17549575 92 + 22224390
GUCUGAGCGGAAUGUAAACACAUUUUC-----------------AAAAGCCAAACAAAAGCCAAAUGAAAACAAUUCACACCCGAGGAAUUCGACUAAUAAUCCGCAAA
......(((((.(((.......(((((-----------------(...((.........))....)))))).(((((.(......))))))......))).)))))... ( -12.90)
>DroSec_CAF1 1433 92 + 1
GUCUGAGCGGAAUGUAAACACAUUUUC-----------------AAAAGCCAAACAAAAGCCAAAUGAAAACAAUUCACACCCGAGGAAUUCGACUAACAAUCCGCAAA
......(((((.(((.......(((((-----------------(...((.........))....)))))).(((((.(......))))))......))).)))))... ( -14.80)
>DroSim_CAF1 586 92 + 1
GUCUGAGCGGAAUGUAAACACAUUUUC-----------------AAAAGCCAAACAAAAGCCAAAUGAAAACAAUUCACACCCGAGGAAUUCGACUAACAAUCCGCAAA
......(((((.(((.......(((((-----------------(...((.........))....)))))).(((((.(......))))))......))).)))))... ( -14.80)
>DroEre_CAF1 6104 107 + 1
GUCUGAGCGGAAUGUAAACACAUUUUCACCGGGCCUGCGUAUGCAAAAGCCAAACAAAAGCCAAAUGAAAACAAUUCACACCCGAGGAAUUCGACUAACAAUCCGCA--
......(((((.(((.........(((..((((..(((....)))....................((((.....))))..))))..)))........))).))))).-- ( -23.13)
>consensus
GUCUGAGCGGAAUGUAAACACAUUUUC_________________AAAAGCCAAACAAAAGCCAAAUGAAAACAAUUCACACCCGAGGAAUUCGACUAACAAUCCGCAAA
......(((((.(((..................................................((((.....))))....((((...))))....))).)))))... (-12.61 = -12.42 +  -0.19)

alignment

secondary structure

dotplot

Window 7

Location	17,549,575 – 17,549,667
Length	92
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	90.05
Mean single sequence MFE	-28.30
Consensus MFE	-19.35
Energy contribution	-19.35
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.04
Structure conservation index	0.68
SVM decision value	0.49
SVM RNA-class probability	0.756857
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17549575 92 - 22224390
UUUGCGGAUUAUUAGUCGAAUUCCUCGGGUGUGAAUUGUUUUCAUUUGGCUUUUGUUUGGCUUUU-----------------GAAAAUGUGUUUACAUUCCGCUCAGAC
...(((((.......((((.....))))((((((((((((((((...((((.......))))..)-----------------))))))).)))))))))))))...... ( -25.60)
>DroSec_CAF1 1433 92 - 1
UUUGCGGAUUGUUAGUCGAAUUCCUCGGGUGUGAAUUGUUUUCAUUUGGCUUUUGUUUGGCUUUU-----------------GAAAAUGUGUUUACAUUCCGCUCAGAC
...(((((.......((((.....))))((((((((((((((((...((((.......))))..)-----------------))))))).)))))))))))))...... ( -25.60)
>DroSim_CAF1 586 92 - 1
UUUGCGGAUUGUUAGUCGAAUUCCUCGGGUGUGAAUUGUUUUCAUUUGGCUUUUGUUUGGCUUUU-----------------GAAAAUGUGUUUACAUUCCGCUCAGAC
...(((((.......((((.....))))((((((((((((((((...((((.......))))..)-----------------))))))).)))))))))))))...... ( -25.60)
>DroEre_CAF1 6104 107 - 1
--UGCGGAUUGUUAGUCGAAUUCCUCGGGUGUGAAUUGUUUUCAUUUGGCUUUUGUUUGGCUUUUGCAUACGCAGGCCCGGUGAAAAUGUGUUUACAUUCCGCUCAGAC
--.(((((.......((((.....))))(((((((((((((((((..(((((.(((...((....))..))).)))))..))))))))).)))))))))))))...... ( -36.40)
>consensus
UUUGCGGAUUGUUAGUCGAAUUCCUCGGGUGUGAAUUGUUUUCAUUUGGCUUUUGUUUGGCUUUU_________________GAAAAUGUGUUUACAUUCCGCUCAGAC
...(((((.......((((.....))))(((((((((((((((....((((.......))))....................))))))).)))))))))))))...... (-19.35 = -19.35 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:55 2006