Locus 1825

Sequence ID 3R_DroMel_CAF1
Location 5,222,491 – 5,222,611
Length 120
Max. P 0.837600
window3001 window3002 window3003

overview

Window 1

Location 5,222,491 – 5,222,590
Length 99
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 71.49
Mean single sequence MFE -26.72
Consensus MFE -12.28
Energy contribution -11.73
Covariance contribution -0.55
Combinations/Pair 1.52
Mean z-score -1.88
Structure conservation index 0.46
SVM decision value 0.74
SVM RNA-class probability 0.837600
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5222491 99 + 27905053
GAAGUUCAACAU---GGGUCUGAACUCAUGGAUA-UAUGUACAUGCACAUAUAUCUAUGUUCGGUUUAUAUAGCUGGUUGGCCCGGAAUUAUUCG-GCAAUGGG
(((........(---(((((......((((((((-(((((......))))))))))))).((((((.....))))))..))))))......))).-........ ( -28.64)
>DroSec_CAF1 5878 97 + 1
GAAGUUCAACAU---GGGUCUGAACUCAUGGAUA-UAUGUACAA--ACAUAUAUCUACGUUCGGUUUAUAUAGCUGGUUGGGCCGGAAUUAUUCG-GCAAUGGA
.....(((((((---((((....))))))(((((-(((((....--)))))))))).....(((((.....))))))))))((((((....))))-))...... ( -29.50)
>DroSim_CAF1 11213 97 + 1
GAAGUUCAACAU---GGGUCUGAACCCAUGGAUA-UAUGUACAU--ACAUAUAUCUACGUUCGGUUUAUAUAGCUGGUUGGGCCGGAAUUAUUCG-GCAAUGGA
.....(((((((---((((....))))))(((((-(((((....--)))))))))).....(((((.....))))))))))((((((....))))-))...... ( -32.50)
>DroEre_CAF1 11991 95 + 1
GAAGUUCAACAU---GGGUCUGAACUCACAGAUA-UAUGUAGCUAUAUA----UCUGCGUUCGGCUUAUAUAGCUGGCUAGGCCGGAAUUAUUCG-GCAGUGGG
........((((---(.(((((......))))).-)))))(((((((((----...((.....)).)))))))))..(((.((((((....))))-))..))). ( -30.00)
>DroYak_CAF1 6271 89 + 1
GAAGUUUAGCAU---GGGUGUGAACCCAUAGAUA-CAUGUAGUCAUAUAUCUAUCUACGUUCGGUUUAUAUAGCUCGCUGGGCCGGAAUUAUU-----------
...(((((((..---(.((((((((((.((((((-.(((((....))))).)))))).)...)))))))))..)..)))))))..........----------- ( -23.60)
>DroAna_CAF1 6011 85 + 1
GAAGUUCAAGAAGUGGGGUCGGAACCUCAGAGUAAAUUGUAUAUAUACGGAUGUCU-----UGG--------------UCUUUCGGAAUUGUUCGGGUAAUGGG
((((..(((((..((((((....)))))).......(((((....)))))...)))-----)).--------------.))))((((....))))......... ( -16.10)
>consensus
GAAGUUCAACAU___GGGUCUGAACCCAUGGAUA_UAUGUACAUAUACAUAUAUCUACGUUCGGUUUAUAUAGCUGGUUGGGCCGGAAUUAUUCG_GCAAUGGG
..(((((........((((....)))).((((((...(((......)))..))))))....(((((((..........)))))))))))).............. (-12.28 = -11.73 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,222,518 – 5,222,611
Length 93
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 86.02
Mean single sequence MFE -24.01
Consensus MFE -18.77
Energy contribution -19.65
Covariance contribution 0.88
Combinations/Pair 1.09
Mean z-score -1.84
Structure conservation index 0.78
SVM decision value 0.65
SVM RNA-class probability 0.812156
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5222518 93 + 27905053
GAUAUAUGUACAUGCACAUAUAUCUAUGUUCGGUUUAUAUAGCUGGUUGGCCCGGAAUUAUUCGGCAAUGGGAACUUGAUGAACAA---UAGAUGA
(((((((((......)))))))))..((((((..........((.((((..(((((....))))))))).)).......)))))).---....... ( -22.53)
>DroSec_CAF1 5905 91 + 1
GAUAUAUGUACAA--ACAUAUAUCUACGUUCGGUUUAUAUAGCUGGUUGGGCCGGAAUUAUUCGGCAAUGGAAACUCGAGGAACAA---UAGAUGA
(((((((((....--)))))))))..(((((((((.....)))))((((.((((((....))))))...(....)........)))---).)))). ( -24.40)
>DroSim_CAF1 11240 91 + 1
GAUAUAUGUACAU--ACAUAUAUCUACGUUCGGUUUAUAUAGCUGGUUGGGCCGGAAUUAUUCGGCAAUGGAAACUCGAGGAACAA---UAGAUGA
(((((((((....--)))))))))..(((((((((.....)))))((((.((((((....))))))...(....)........)))---).)))). ( -24.40)
>DroEre_CAF1 12018 92 + 1
GAUAUAUGUAGCUAUAUA----UCUGCGUUCGGCUUAUAUAGCUGGCUAGGCCGGAAUUAUUCGGCAGUGGGAACUCGACGAACAAUAAUAGUUGA
........((((((((((----...((.....)).)))))))))).(((.((((((....))))))..)))....(((((...........))))) ( -24.70)
>consensus
GAUAUAUGUACAU__ACAUAUAUCUACGUUCGGUUUAUAUAGCUGGUUGGGCCGGAAUUAUUCGGCAAUGGAAACUCGAGGAACAA___UAGAUGA
(((((((((......)))))))))...((((((((.....))))......((((((....))))))..............))))............ (-18.77 = -19.65 +   0.88)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,222,518 – 5,222,611
Length 93
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 86.02
Mean single sequence MFE -17.94
Consensus MFE -11.85
Energy contribution -13.59
Covariance contribution 1.75
Combinations/Pair 1.09
Mean z-score -1.83
Structure conservation index 0.66
SVM decision value 0.23
SVM RNA-class probability 0.644268
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5222518 93 - 27905053
UCAUCUA---UUGUUCAUCAAGUUCCCAUUGCCGAAUAAUUCCGGGCCAACCAGCUAUAUAAACCGAACAUAGAUAUAUGUGCAUGUACAUAUAUC
.......---.(((((...............(((........)))((......))..........)))))..((((((((((....)))))))))) ( -18.30)
>DroSec_CAF1 5905 91 - 1
UCAUCUA---UUGUUCCUCGAGUUUCCAUUGCCGAAUAAUUCCGGCCCAACCAGCUAUAUAAACCGAACGUAGAUAUAUGU--UUGUACAUAUAUC
...((((---(.((((....((((......((((........))))......)))).........)))))))))(((((((--....))))))).. ( -17.32)
>DroSim_CAF1 11240 91 - 1
UCAUCUA---UUGUUCCUCGAGUUUCCAUUGCCGAAUAAUUCCGGCCCAACCAGCUAUAUAAACCGAACGUAGAUAUAUGU--AUGUACAUAUAUC
...((((---(.((((....((((......((((........))))......)))).........)))))))))(((((((--....))))))).. ( -17.02)
>DroEre_CAF1 12018 92 - 1
UCAACUAUUAUUGUUCGUCGAGUUCCCACUGCCGAAUAAUUCCGGCCUAGCCAGCUAUAUAAGCCGAACGCAGA----UAUAUAGCUACAUAUAUC
.........((((((((.(.(((....)))).))))))))...(((...)))(((((((((.((.....))...----)))))))))......... ( -19.10)
>consensus
UCAUCUA___UUGUUCCUCGAGUUCCCAUUGCCGAAUAAUUCCGGCCCAACCAGCUAUAUAAACCGAACGUAGAUAUAUGU__AUGUACAUAUAUC
...........(((((....((((......((((........))))......)))).........)))))..((((((((((....)))))))))) (-11.85 = -13.59 +   1.75)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:25 2006