Locus 8980

Sequence ID 3R_DroMel_CAF1
Location 24,093,295 – 24,093,431
Length 136
Max. P 0.848488
window14392 window14393 window14394

overview

Window 2

Location 24,093,295 – 24,093,397
Length 102
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 81.90
Mean single sequence MFE -40.84
Consensus MFE -31.92
Energy contribution -33.12
Covariance contribution 1.20
Combinations/Pair 1.16
Mean z-score -1.87
Structure conservation index 0.78
SVM decision value 0.78
SVM RNA-class probability 0.848488
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24093295 102 + 27905053
CGGCUCCACAUGUAGUACAUCCUGCAUGAGCCAAAUGCGGCUGGCUCCUGCCAAGGAUA-------AGCUCGAGCUCAGCCUCUUGGCGCUGCAGCCGGUUGGCCUACA
(((((.(((((((((......))))))).(((((..(.(((((((((..((........-------.))..)))).))))).))))))..)).)))))........... ( -41.10)
>DroSec_CAF1 280624 109 + 1
CGGCUCCACAUGUAGUACAUUCUGCAUGAGUCUAAUGCGGCUGGCUCCUGCCAAGGAUGAGCAAGGAGCUCGAGCUCAGCCUCUUGGCGCUGCAGUCGGUUGGCCUGUA
.((((((.(((((((......))))))).......((((((.(((((((((((....)).)).)))))))........(((....)))))))))...))..)))).... ( -44.40)
>DroSim_CAF1 280337 109 + 1
GGGCUCCACAUGUAGUACAUUCUGCAUGAGUCUAAUGCGGCUGGCUCCUGCCAAGGAUGAACAGGGAGCUCGAGCUCAGCCUCUUGGCGCUGCAGUCGGUUGGCCUGUA
(((((((.(((((((......))))))).......((((((((((....))))............((((....)))).(((....)))))))))...))..)))))... ( -42.90)
>DroEre_CAF1 294032 96 + 1
UGGCUCCACAUA-----CAUUCUGUAUGAACCUAAUGCGGUUGGCCCAUGCCAAGGAUGAGCAGGG------AGCUCAGCCUCUUGGCGCUGCAGCCGGUUGGCCUG--
.((((((.((((-----(.....)))))((((......))))(((.((((((((((.(((((....------.)))))...)))))))).))..)))))..))))..-- ( -38.00)
>DroYak_CAF1 292904 102 + 1
UGGCUCCACAUACA-UACAUGCUGCAAGAACCUAAUGCGGUUGCCUCAUGCCAAGGAUGAGCAGGGA----GAGCUCAGCCUCUUGGCGAUGCAACCGCUUGGCCUG--
.((((.(((((...-...))).))............((((((((.((..(((((((.(((((.....----..)))))...))))))))).))))))))..))))..-- ( -37.80)
>consensus
CGGCUCCACAUGUAGUACAUUCUGCAUGAGCCUAAUGCGGCUGGCUCCUGCCAAGGAUGAGCAGGGAGCUCGAGCUCAGCCUCUUGGCGCUGCAGCCGGUUGGCCUG_A
.((((...(((((((......))))))).........((((((.(...((((((((.(((((...........)))))...))))))))..)))))))...)))).... (-31.92 = -33.12 +   1.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 24,093,295 – 24,093,397
Length 102
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 81.90
Mean single sequence MFE -39.32
Consensus MFE -26.68
Energy contribution -27.20
Covariance contribution 0.52
Combinations/Pair 1.08
Mean z-score -1.80
Structure conservation index 0.68
SVM decision value 0.36
SVM RNA-class probability 0.702472
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24093295 102 - 27905053
UGUAGGCCAACCGGCUGCAGCGCCAAGAGGCUGAGCUCGAGCU-------UAUCCUUGGCAGGAGCCAGCCGCAUUUGGCUCAUGCAGGAUGUACUACAUGUGGAGCCG
....(((...(((.((((((.((((((.(((((.((((..(((-------.......)))..)))))))))...)))))).).))))).(((.....))).))).))). ( -41.80)
>DroSec_CAF1 280624 109 - 1
UACAGGCCAACCGACUGCAGCGCCAAGAGGCUGAGCUCGAGCUCCUUGCUCAUCCUUGGCAGGAGCCAGCCGCAUUAGACUCAUGCAGAAUGUACUACAUGUGGAGCCG
....(((....(((((.((((........)))))).))).((((((.((.((....))))))))))...(((((((((...(((.....)))..))).)))))).))). ( -36.20)
>DroSim_CAF1 280337 109 - 1
UACAGGCCAACCGACUGCAGCGCCAAGAGGCUGAGCUCGAGCUCCCUGUUCAUCCUUGGCAGGAGCCAGCCGCAUUAGACUCAUGCAGAAUGUACUACAUGUGGAGCCC
.....(((((......((((.(((....))).((((....)))).))))......))))).((.((...(((((((((...(((.....)))..))).)))))).)))) ( -32.80)
>DroEre_CAF1 294032 96 - 1
--CAGGCCAACCGGCUGCAGCGCCAAGAGGCUGAGCU------CCCUGCUCAUCCUUGGCAUGGGCCAACCGCAUUAGGUUCAUACAGAAUG-----UAUGUGGAGCCA
--..(((.....((((.((..((((((.((.(((((.------....))))))))))))).))))))..((((((.(.((((.....)))).-----))))))).))). ( -41.50)
>DroYak_CAF1 292904 102 - 1
--CAGGCCAAGCGGUUGCAUCGCCAAGAGGCUGAGCUC----UCCCUGCUCAUCCUUGGCAUGAGGCAACCGCAUUAGGUUCUUGCAGCAUGUA-UGUAUGUGGAGCCA
--........((((((((.((((((((.((.(((((..----.....)))))))))))))..)).))))))))....((((((....(((((..-..))))))))))). ( -44.30)
>consensus
U_CAGGCCAACCGGCUGCAGCGCCAAGAGGCUGAGCUCGAGCUCCCUGCUCAUCCUUGGCAGGAGCCAGCCGCAUUAGGCUCAUGCAGAAUGUACUACAUGUGGAGCCA
....(((..............((((((.((.(((((...........))))))))))))).........((((((......(((.....)))......)))))).))). (-26.68 = -27.20 +   0.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,093,324 – 24,093,431
Length 107
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 74.42
Mean single sequence MFE -40.22
Consensus MFE -19.51
Energy contribution -22.54
Covariance contribution 3.03
Combinations/Pair 1.26
Mean z-score -1.73
Structure conservation index 0.49
SVM decision value 0.09
SVM RNA-class probability 0.580272
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24093324 107 - 27905053
AAUGCGGCUCAUUAGGCCCGGUCAGAGUUCAGAGUGUAGGCCAACCGGCUGCAGCGCCAAGAGGCUGAGCUCGAGCU-------UAUCCUUGGCAGGAGCCAGCCGCAUUUGGC
(((((((((.....(((((.((((((((((.((((...((((....(((......)))....))))..)))))))))-------).....)))).)).)))))))))))).... ( -46.20)
>DroSec_CAF1 280653 114 - 1
AAUGCUUCUCAUUAGGCCCGGUCUGAGUUCAGAGUACAGGCCAACCGACUGCAGCGCCAAGAGGCUGAGCUCGAGCUCCUUGCUCAUCCUUGGCAGGAGCCAGCCGCAUUAGAC
(((((.........((((.(.((((....))))...).))))....................(((((.((((((((.....))))...((....)))))))))))))))).... ( -38.70)
>DroSim_CAF1 280366 114 - 1
AAUGCGGCUCAUUAGGCCCGGUCAGAGUUCAGAGUACAGGCCAACCGACUGCAGCGCCAAGAGGCUGAGCUCGAGCUCCCUGUUCAUCCUUGGCAGGAGCCAGCCGCAUUAGAC
(((((((((.....(((((.(((((((((((.(((...((....)).))).....(((....))))))))))((((.....)))).....)))).)).)))))))))))).... ( -45.80)
>DroEre_CAF1 294056 103 - 1
AAUGCGCCUCAUUAGGUCCGGUCAGAGUUCA-----CAGGCCAACCGGCUGCAGCGCCAAGAGGCUGAGCU------CCCUGCUCAUCCUUGGCAUGGGCCAACCGCAUUAGGU
((((((........(((..((((........-----..)))).)))((((.((..((((((.((.(((((.------....))))))))))))).))))))...)))))).... ( -39.40)
>DroYak_CAF1 292932 105 - 1
AAUGCGCCUCAUUAGGCCCGGUCAGAGUUCA-----CAGGCCAAGCGGUUGCAUCGCCAAGAGGCUGAGCUC----UCCCUGCUCAUCCUUGGCAUGAGGCAACCGCAUUAGGU
.....((((.....((((.(...........-----).))))..((((((((.((((((((.((.(((((..----.....)))))))))))))..)).))))))))...)))) ( -44.80)
>DroAna_CAF1 289885 89 - 1
AGUGCGGCUCAUUAGGCCAGGCCGGAGACCU-----CAG-----AAGGCUGCAACGCCAAAAGACAGAGGCCGAG--------------UAGGCAUU-UCCAGCAAUAUUGCAA
(((((((((.....)))).(((((....)..-----...-----..(((......)))..........))))...--------------...)))))-....(((....))).. ( -26.40)
>consensus
AAUGCGGCUCAUUAGGCCCGGUCAGAGUUCA_____CAGGCCAACCGGCUGCAGCGCCAAGAGGCUGAGCUCGAG_UCCCUGCUCAUCCUUGGCAGGAGCCAGCCGCAUUAGAC
((((((((((....((((.((((...............))))....)))).....((((((.((.(((((...........)))))))))))))..)))))....))))).... (-19.51 = -22.54 +   3.03)

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 13:24:06 2006