Locus 6392

Sequence ID 3L_DroMel_CAF1
Location 17,119,411 – 17,119,551
Length 140
Max. P 0.930865
window10235 window10236 window10237

overview

Window 5

Location 17,119,411 – 17,119,526
Length 115
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 95.11
Mean single sequence MFE -35.95
Consensus MFE -31.59
Energy contribution -31.21
Covariance contribution -0.38
Combinations/Pair 1.07
Mean z-score -2.32
Structure conservation index 0.88
SVM decision value 1.21
SVM RNA-class probability 0.930865
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17119411 115 + 23771897
GAAAACGCUUUCGGCCCGGCCUGCCUUCCUCGAAUAUCCUUAAUCGUCCUGUCCUAUCGGUUUCCUGUGAGCCAGAACAAAAACAACCGAAAAACCGACCGGACG-GGGCCGAAAA
........(((((((((((....))...................(((((.(((...((((((...(((........))).....))))))......))).)))))-))))))))). ( -36.90)
>DroSec_CAF1 3768 115 + 1
GAAAACGCUUUCGGCCCGGCCUGCCUUCCUGGAAUAUCCUUAAUCGCCCUGUCCUAUCGGUUUCCUGUGAGCCAGAACAAAAACAACCGAAAAACCGAACGGACA-GGGCCGAAAU
........((((((((((((..........((.....))......))).(((((..(((((((.(((.....)))........(....)..)))))))..)))))-))))))))). ( -34.29)
>DroEre_CAF1 4335 116 + 1
GAAAACGCUUUCGGCCCGGCUUGCCUUCCUGGAAUAUCCUUAAUCGCCCUGUCCUAUCGGUUUCCUGUGAGCCAGAACAAAAACAACCGAAACCCCGACCGGACAAGGGCCGAAAA
........((((((((((((..........((.....))......))).(((((..((((((((.(((..............)))...))))))..))..))))).))))))))). ( -34.23)
>DroYak_CAF1 3754 115 + 1
GAAAACGCUUUCGGCCCGGCUUGCCUUCCUGGAAUAUCCUUAAUCGCCCUGUCCUAUCGGUUUCCUGUGAGCCAGAACAAAAGCAACCGAAAA-CCGACCGGACAAGGGCCGAAAA
........((((((((((((..........((.....))......))).(((((..(((((((.(.((..((..........)).)).).)))-))))..))))).))))))))). ( -38.39)
>consensus
GAAAACGCUUUCGGCCCGGCCUGCCUUCCUGGAAUAUCCUUAAUCGCCCUGUCCUAUCGGUUUCCUGUGAGCCAGAACAAAAACAACCGAAAAACCGACCGGACA_GGGCCGAAAA
........(((((((((((....))........................(((((..((((((((.(((..............)))...))))..))))..))))).))))))))). (-31.59 = -31.21 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,119,411 – 17,119,526
Length 115
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 95.11
Mean single sequence MFE -43.98
Consensus MFE -38.19
Energy contribution -39.00
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -2.06
Structure conservation index 0.87
SVM decision value 0.81
SVM RNA-class probability 0.855552
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17119411 115 - 23771897
UUUUCGGCCC-CGUCCGGUCGGUUUUUCGGUUGUUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGACGAUUAAGGAUAUUCGAGGAAGGCAGGCCGGGCCGAAAGCGUUUUC
((((((((((-.((((.(((((((((..(...(((........)))...)..))))))))).))))....(((.((....)).))).....((....))))))))))))....... ( -41.80)
>DroSec_CAF1 3768 115 - 1
AUUUCGGCCC-UGUCCGUUCGGUUUUUCGGUUGUUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGGCGAUUAAGGAUAUUCCAGGAAGGCAGGCCGGGCCGAAAGCGUUUUC
.(((((((((-(((((..((((((((..(...(((........)))...)..))))))))..))))).(((......((.....)).(.....)..))))))))))))........ ( -42.70)
>DroEre_CAF1 4335 116 - 1
UUUUCGGCCCUUGUCCGGUCGGGGUUUCGGUUGUUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGGCGAUUAAGGAUAUUCCAGGAAGGCAAGCCGGGCCGAAAGCGUUUUC
((((((((((((((((.(((((..((..(...(((........)))...)..))..))))).))))))(((......((.....)).(.....)..)))))))))))))....... ( -42.70)
>DroYak_CAF1 3754 115 - 1
UUUUCGGCCCUUGUCCGGUCGG-UUUUCGGUUGCUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGGCGAUUAAGGAUAUUCCAGGAAGGCAAGCCGGGCCGAAAGCGUUUUC
((((((((((((((((.(((((-(((((.((.(((........)))..)).)))))))))).))))))(((......((.....)).(.....)..)))))))))))))....... ( -48.70)
>consensus
UUUUCGGCCC_UGUCCGGUCGGUUUUUCGGUUGUUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGGCGAUUAAGGAUAUUCCAGGAAGGCAAGCCGGGCCGAAAGCGUUUUC
.(((((((((..((((.(((((((((..(...(((........)))...)..))))))))).)))).........................((....)))))))))))........ (-38.19 = -39.00 +   0.81)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,119,451 – 17,119,551
Length 100
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 93.22
Mean single sequence MFE -31.65
Consensus MFE -26.56
Energy contribution -27.88
Covariance contribution 1.31
Combinations/Pair 1.05
Mean z-score -2.16
Structure conservation index 0.84
SVM decision value 0.98
SVM RNA-class probability 0.894607
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17119451 100 - 23771897
GAUUUAUCCUUAUCCCGCCACCCAUUUUUCGGCCC-CGUCCGGUCGGUUUUUCGGUUGUUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGACGAUUA
...(..((((......(((...........)))..-.((((.(((((((((..(...(((........)))...)..))))))))).))))))))..)... ( -28.40)
>DroSec_CAF1 3808 100 - 1
GAUUUAUCCUUAUCCUGCCACCCACAUUUCGGCCC-UGUCCGUUCGGUUUUUCGGUUGUUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGGCGAUUA
...............................((((-(((((..((((((((..(...(((........)))...)..))))))))..)))))))))..... ( -33.80)
>DroEre_CAF1 4375 101 - 1
GAUUUAUUCUUAUCCUGCCUCCCAUUUUUCGGCCCUUGUCCGGUCGGGGUUUCGGUUGUUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGGCGAUUA
...............................(((((.((((.(((((..((..(...(((........)))...)..))..))))).)))))))))..... ( -29.20)
>DroYak_CAF1 3794 100 - 1
GAUUUAUUCUUAUCCUGCCUCCCAUUUUUCGGCCCUUGUCCGGUCGG-UUUUCGGUUGCUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGGCGAUUA
...............................(((((.((((.(((((-(((((.((.(((........)))..)).)))))))))).)))))))))..... ( -35.20)
>consensus
GAUUUAUCCUUAUCCUGCCACCCAUUUUUCGGCCC_UGUCCGGUCGGUUUUUCGGUUGUUUUUGUUCUGGCUCACAGGAAACCGAUAGGACAGGGCGAUUA
...............................((((.(((((.(((((((((..(...(((........)))...)..))))))))).)))))))))..... (-26.56 = -27.88 +   1.31)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:17 2006