Locus 4481

Sequence ID	3L_DroMel_CAF1
Location	12,972,264 – 12,972,525
Length	261
Max. P	0.984856

overview

Window 0

Location	12,972,264 – 12,972,366
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.17
Mean single sequence MFE	-30.25
Consensus MFE	-23.38
Energy contribution	-23.62
Covariance contribution	0.24
Combinations/Pair	1.09
Mean z-score	-1.71
Structure conservation index	0.77
SVM decision value	0.43
SVM RNA-class probability	0.731949
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12972264 102 + 23771897
AUUGCGUUGGUGUUUCUGGCUUU---------------UGCCAAUGGCAAACAUGAAAGCAGCUUUGCAUGUGAGCAGAGCGCCAAACAAAAAUCGAA---ACAACAAAUUGAAUGUAAG
.(((((((.(((((((((((...---------------.)))).((((.....((....))(((((((......)))))))))))..........)))---)))......).))))))). ( -30.80)
>DroSec_CAF1 89643 120 + 1
AUUGCGUUGGCGUUUUUGGCUUUUCGAGGUUUGCUGCUUGCCAAUGGCAAACAUGAAAGCAGCUUUGCAUGUGAGCAGAGCGCCAAACAAAAAUCGAAACAACAACAAAUUGAAUGUAAG
.....((((.((((((((((((((....(((((((..........)))))))..)))))).(((((((......)))))))......)))))).))...))))................. ( -34.80)
>DroSim_CAF1 98755 119 + 1
AUUGCGUUGGCGUUUUUGGCUUUUCGAGGUUUGCUGCUUGCCAAUGGCAAACAUGAAAGCAGCUUUGCAUGUGAGCAGAGCGCCAAACAAAAAUC-AAACAACAACAAAUUGAAUGUAAG
.((((((((((.......((((((....(((((((..........)))))))..)))))).(((((((......))))))))))...........-......(((....)))))))))). ( -34.00)
>DroEre_CAF1 95104 114 + 1
AUUGCGUUGGCGUUUCUGGCUUUACGAGGUUUG---CUUGCCAAUGGCAAACAUGAAAGCAGCUCUGCAUGUGAGUAGAACACCAAACAAAAAUCGAA---ACAACAAAUUGAAUGUAAG
.(((((((...(((((..(((((.....(((((---((.......)))))))...))))).(.(((((......))))).)..............)))---))..(.....)))))))). ( -26.40)
>DroYak_CAF1 93666 114 + 1
AUUGCGUUGGCGUUUCUGGCUUUACGAGGUUUG---CUUGCCAAUGGCAAACAUGAAAGCAGCUUUGCAUGUGAGUCGAACACCAAACAAAAAUCGAA---ACAACAAAUUGAAUGUAAG
.(((((((.(((...(((.((((.....(((((---((.......)))))))...)))))))...))).(((...((((..............)))).---)))........))))))). ( -25.24)
>consensus
AUUGCGUUGGCGUUUCUGGCUUUACGAGGUUUG___CUUGCCAAUGGCAAACAUGAAAGCAGCUUUGCAUGUGAGCAGAGCGCCAAACAAAAAUCGAA___ACAACAAAUUGAAUGUAAG
.((((((((((((((...((((...............(((((...)))))(((((((((...)))).))))))))).)))))))..................(((....)))))))))). (-23.38 = -23.62 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	12,972,289 – 12,972,405
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	91.11
Mean single sequence MFE	-27.70
Consensus MFE	-25.57
Energy contribution	-25.90
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.09
Structure conservation index	0.92
SVM decision value	1.99
SVM RNA-class probability	0.984856
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12972289 116 + 23771897
CCAAUGGCAAACAUGAAAGCAGCUUUGCAUGUGAGCAGAGCGCCAAACAAAAAUCGAA---ACAACAAAUUGAAUGUAAGCCAAAGCAACAAUAU-GUAUGUAUGUGGCAACAACAGGUA
((..((((.....((....))(((((((......))))))))))).............---..................((((..(((((.....-)).)))...)))).......)).. ( -25.50)
>DroSec_CAF1 89683 120 + 1
CCAAUGGCAAACAUGAAAGCAGCUUUGCAUGUGAGCAGAGCGCCAAACAAAAAUCGAAACAACAACAAAUUGAAUGUAAGCCACAGCAACAAUACCAUAUGUAUGUGGCAACUACAGGUA
((..((((.....((....))(((((((......))))))))))).............................((((.((((((...(((........))).))))))...)))))).. ( -29.20)
>DroSim_CAF1 98795 113 + 1
CCAAUGGCAAACAUGAAAGCAGCUUUGCAUGUGAGCAGAGCGCCAAACAAAAAUC-AAACAACAACAAAUUGAAUGUAAGCCACAGCAA-----CCAUAUGUAUGUGGCAACAACAGGC-
((..((((.....((....))(((((((......)))))))))))..........-.......................(((((((((.-----.....))).)))))).......)).- ( -28.40)
>consensus
CCAAUGGCAAACAUGAAAGCAGCUUUGCAUGUGAGCAGAGCGCCAAACAAAAAUCGAAACAACAACAAAUUGAAUGUAAGCCACAGCAACAAUACCAUAUGUAUGUGGCAACAACAGGUA
((..((((.....((....))(((((((......)))))))))))..................................(((((((((...........))).)))))).......)).. (-25.57 = -25.90 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	12,972,405 – 12,972,525
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-34.64
Consensus MFE	-29.92
Energy contribution	-31.20
Covariance contribution	1.28
Combinations/Pair	1.05
Mean z-score	-1.54
Structure conservation index	0.86
SVM decision value	1.00
SVM RNA-class probability	0.897449
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12972405 120 - 23771897
UCCGAGCAAGUAACGUUAGAGGCUAGAGGCCAUGUUAAAGUUUUGUCCUCGUCGCCUUCAUCAAGUGUUUCUACACGCCCCGUGCAAUUAAGGUAAUUAGCUUUACGUUGCCAUUGCUCU
...(((((((((((((..(((((((((((.((...........)).))))...(((((......((((....))))((.....))....)))))...))))))))))))))..)))))). ( -37.80)
>DroSec_CAF1 89803 120 - 1
UCCGAGCAAGUAACGUUAGAGGCUAGAGGCCAAGUUAAAGUUUUGUCCUCGUCGCCUUCAUCAAGUGUUUCUACACGCCCCGUGCAAUUAAGGUAAUUAGCGUUACGUUGCCAUUGCUCU
...(((((((((((((..((.((((((((.((((.......)))).))))...(((((......((((....))))((.....))....)))))...)))).)))))))))..)))))). ( -38.30)
>DroSim_CAF1 98908 120 - 1
UCCGAGCAAGUUACGUUUGGAGGUUGAGGCCAAGUUAAAGUUUUGUGCUCGUCGCCUUCAUCAAGUGUUUCUACACGCCCCGUGCAAAUAAGGUAAUUAGCGUUACGUUGCCAUUGCUCU
...((((((((.(((..(((((((((((..((((.......))))..))))..)))))))....((((....))))....)))))......((((((.........)))))).)))))). ( -32.70)
>DroEre_CAF1 95249 120 - 1
UACGAGCCAGUAAUGUUAGAGGCUAAAGGCCAAGUUAAAGUUUUGUCCUCGUCGCCUUCAUCAAGUGUUCAUACACGCCCAGUGCAAUUAAGGUAAUUAGCGUUACGUUGCCAUUGCUCU
...((((..(((((((..((.((((((((.((((.......)))).)))....(((((......((((....))))((.....))....)))))..))))).)))))))))....)))). ( -30.40)
>DroYak_CAF1 93811 120 - 1
UCCGAGCAAGUAACAUUAGAGGCUAGAGGCCAAGCUAAAGUUUUGUCCUCGUCGCCUUCAUCAAGUGUUCCUACACGCCCAGUGCAAUUAAGGUAAUUAGCGUUACGUUGCCAUUGCUCU
...(((((((((((....((.(((((((((.((((....)))).).))))...(((((......((((....))))((.....))....)))))...)))).))..)))))..)))))). ( -34.00)
>consensus
UCCGAGCAAGUAACGUUAGAGGCUAGAGGCCAAGUUAAAGUUUUGUCCUCGUCGCCUUCAUCAAGUGUUUCUACACGCCCCGUGCAAUUAAGGUAAUUAGCGUUACGUUGCCAUUGCUCU
...(((((((((((((..((.((((((((.((((.......)))).))))...(((((......((((....))))((.....))....)))))...)))).)))))))))..)))))). (-29.92 = -31.20 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:27 2006