Locus 6748

Sequence ID 3R_DroMel_CAF1
Location 17,781,534 – 17,781,651
Length 117
Max. P 0.976678
window10959 window10960 window10961

overview

Window 9

Location 17,781,534 – 17,781,625
Length 91
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 73.82
Mean single sequence MFE -26.09
Consensus MFE -15.54
Energy contribution -16.71
Covariance contribution 1.17
Combinations/Pair 1.29
Mean z-score -2.07
Structure conservation index 0.60
SVM decision value 1.75
SVM RNA-class probability 0.975635
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17781534 91 + 27905053
GCUUU--UGCUAUUUCUGCUGCCAAAAUGCUCAACAAAACAUGUCGAAAAUGUGCCACAUGCCAGUAGCAGGAGCAGCAGGAGCUGUAGGAGC------
(((((--(((..(((((((((((....((((..((....(((((.(........).)))))...)))))).).))))))))))..))))))))------ ( -32.20)
>DroGri_CAF1 65865 86 + 1
GGUUU--UGUUGCUGUUGUUGCCAAAUUGCAC-ACAAAACAUGUCGAAAAUGUGCCAUAUGCCAGCAGCAAAUGAAAUC---GU-UGUCUGUU------
(((((--..(((((((((..((...((.((((-(................))))).))..))))))))).))..)))))---..-........------ ( -21.39)
>DroSec_CAF1 70180 91 + 1
GCUUU--UGCUAUUUCUGCUGCCAAAAUGCUCAACAAAACAUGUCGAAAAUGUGCCACAUGCCAGAAGCAGGAGCAGCACGAGCUGUAGGAGC------
(((((--(((..(((.(((((((....((((........(((((.(........).))))).....)))).).)))))).)))..))))))))------ ( -26.22)
>DroEre_CAF1 75722 82 + 1
GCUUU--UGCUAUUUCUGCUGCCAAAAUGCUCAACAAAACAUGUCGAAAAUGUGCCACAUGCCAGUAGCAGGAGCAGCAGGAGC---------------
(((((--((((.((((((((((........((.(((.....))).))...((.((.....)))))))))))))).)))))))))--------------- ( -28.30)
>DroYak_CAF1 75729 99 + 1
GCUUUUCUGCUAUUUCUGCUGCCAAAAUGCUCAACAAAACAUGUCGAAAAUGUGCCACAUGCCAGUAGCAGGAGCAGCAGGAGCUGUAGGAGCUGUUGU
((((..((((..(((((((((((....((((..((....(((((.(........).)))))...)))))).).))))))))))..))))))))...... ( -31.10)
>DroMoj_CAF1 81984 77 + 1
-----------GUUAUUGUUGCCAAAAUGCAC-ACAAAACAUGUCGAAAAUGUGCCAUGUGCCAGCAGCAAAUGGAAUC---GU-UGUCUGCU------
-----------(((.(((((((......))).-)))))))..((.((.((((..((((.(((.....))).))))...)---))-).)).)).------ ( -17.30)
>consensus
GCUUU__UGCUAUUUCUGCUGCCAAAAUGCUCAACAAAACAUGUCGAAAAUGUGCCACAUGCCAGUAGCAGGAGCAGCAGGAGC_GUAGGAGC______
((((...((((.((((((((((......((........((((.......)))).......))..)))))))))).)))).))))............... (-15.54 = -16.71 +   1.17)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,781,534 – 17,781,625
Length 91
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 73.82
Mean single sequence MFE -26.22
Consensus MFE -13.81
Energy contribution -15.20
Covariance contribution 1.39
Combinations/Pair 1.10
Mean z-score -2.25
Structure conservation index 0.53
SVM decision value 1.78
SVM RNA-class probability 0.976678
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17781534 91 - 27905053
------GCUCCUACAGCUCCUGCUGCUCCUGCUACUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCAGCAGAAAUAGCA--AAAGC
------.........(((.((((((((..((((((......))))))....(((((((.....)))))))......))))))))....))).--..... ( -29.10)
>DroGri_CAF1 65865 86 - 1
------AACAGACA-AC---GAUUUCAUUUGCUGCUGGCAUAUGGCACAUUUUCGACAUGUUUUGU-GUGCAAUUUGGCAACAACAGCAACA--AAACC
------........-..---.......((((.((((((((((..(.((((.......)))).)..)-))))...(((....)))))))).))--))... ( -22.80)
>DroSec_CAF1 70180 91 - 1
------GCUCCUACAGCUCGUGCUGCUCCUGCUUCUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCAGCAGAAAUAGCA--AAAGC
------(((((....((((((((..(...(((.....))).)..))))......((((.....)))))))).....)).)))..........--..... ( -26.60)
>DroEre_CAF1 75722 82 - 1
---------------GCUCCUGCUGCUCCUGCUACUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCAGCAGAAAUAGCA--AAAGC
---------------(((.((((((((..((((((......))))))....(((((((.....)))))))......))))))))....))).--..... ( -28.90)
>DroYak_CAF1 75729 99 - 1
ACAACAGCUCCUACAGCUCCUGCUGCUCCUGCUACUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCAGCAGAAAUAGCAGAAAAGC
.....((((.....)))).((((((((..((((((......))))))....(((((((.....)))))))......))))))))............... ( -29.10)
>DroMoj_CAF1 81984 77 - 1
------AGCAGACA-AC---GAUUCCAUUUGCUGCUGGCACAUGGCACAUUUUCGACAUGUUUUGU-GUGCAUUUUGGCAACAAUAAC-----------
------(((((.((-(.---........)))))))).(((((..(.((((.......)))).)..)-))))...(((....)))....----------- ( -20.80)
>consensus
______GCUCCUAC_GCUCCUGCUGCUCCUGCUACUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCAGCAGAAAUAGCA__AAAGC
....................((((((...((((((......))))))......(((.((((((....)))))).)))))))))................ (-13.81 = -15.20 +   1.39)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,781,551 – 17,781,651
Length 100
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 74.63
Mean single sequence MFE -27.65
Consensus MFE -13.28
Energy contribution -15.46
Covariance contribution 2.18
Combinations/Pair 1.05
Mean z-score -1.77
Structure conservation index 0.48
SVM decision value 0.17
SVM RNA-class probability 0.615397
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17781551 100 - 27905053
UUGUCCCUGCCCCAGCUGCACCAACU------------------GCUCCUACAGCUCCUGCUGCUCCUGCUACUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCA
........(((...((..(((((...------------------((.....((((....)))).....))...)))..))..)).....(((((((.....)))))))......))). ( -27.80)
>DroSec_CAF1 70197 100 - 1
UUGUCCCUGCCCCAGCUGCACCUACU------------------GCUCCUACAGCUCGUGCUGCUCCUGCUUCUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCA
........(((..((..(((.....)------------------))..))...((((((((..(...(((.....))).)..))))......((((.....)))))))).....))). ( -28.60)
>DroEre_CAF1 75739 91 - 1
UUGUCCCUGCCCCAGCUGCCCCAGCU---------------------------GCUCCUGCUGCUCCUGCUACUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCA
........(((.((((((...)))))---------------------------).......(((((.((((((......)))))).......((((.....)))))))))....))). ( -26.90)
>DroWil_CAF1 90382 75 - 1
-----------------GCAGCAACC------------------GGUAGAACA-----U--GGCUCUGGCUGCUGGCAUGUGGCACAUUUUCGACAUGUUUUGU-GCACAUUUUGGCA
-----------------.(((((.((------------------((.((....-----.--..)))))).)))))((..((((((((..............)))-)).)))....)). ( -23.24)
>DroYak_CAF1 75748 118 - 1
UUGUCCCUGCCCCAGCUGCCCCAACUUCCCCAGCUGCCACAACAGCUCCUACAGCUCCUGCUGCUCCUGCUACUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCA
........(((..(((((............)))))((((((..........((((....))))....(((.....))))))))).....(((((((.....)))))))......))). ( -31.70)
>consensus
UUGUCCCUGCCCCAGCUGCACCAACU__________________GCUCCUACAGCUCCUGCUGCUCCUGCUACUGGCAUGUGGCACAUUUUCGACAUGUUUUGUUGAGCAUUUUGGCA
........(((.....(((................................((((....)))).....(((((......)))))......((((((.....)))))))))....))). (-13.28 = -15.46 +   2.18)

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 12:29:00 2006