Locus 4073

Sequence ID 2L_DroMel_CAF1
Location 11,756,231 – 11,756,365
Length 134
Max. P 0.998018
window6417 window6418 window6419 window6420

overview

Window 7

Location 11,756,231 – 11,756,342
Length 111
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.28
Mean single sequence MFE -32.98
Consensus MFE -22.35
Energy contribution -24.38
Covariance contribution 2.03
Combinations/Pair 1.03
Mean z-score -2.70
Structure conservation index 0.68
SVM decision value 0.24
SVM RNA-class probability 0.647108
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11756231 111 + 22407834
G-----GUUGGACGAAGCCAAAAAGGCUGCAGG---CAAACGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGAGAG-GAGGAUGGUGUUGGUGUGCAAU
(-----(((......)))).....(((((((.(---(....))..)).))))).((((((((((((....(((((((....)))))))...(....)-.....))))))))))))..... ( -32.20)
>DroSec_CAF1 14402 112 + 1
G-----GUUGAACGAAGCCAAAAAGGCUGCAGG---CAAACGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGUAGGGUGGGUGGUGUUGGUGUGCAAU
(-----(((......)))).....(((((((.(---(....))..)).))))).((((((((((((...((((((((....))))))).(((......)))).))))))))))))..... ( -34.00)
>DroSim_CAF1 13296 111 + 1
G-----GUUGAACGAAGCCAAAAAGGCUGCAGG---CAAACGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGUAG-GUGGGUGGUGUUGGUGUGCAAU
(-----(((......)))).....(((((((.(---(....))..)).))))).((((((((((((...((((((((....))))))).(((.....-)))).))))))))))))..... ( -33.80)
>DroEre_CAF1 21831 116 + 1
GGUGGUGGUGGGCAAAGCCAAAAAGGCUGCAGG---CAAAUGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGGAG-GAGGGUGGUGUUGGUGUGCAAU
(((..((.....))..)))......((((((..---....))))))....((..((((((((((((...((((((((....)))))))...(....)-..)..))))))))))))))... ( -34.10)
>DroYak_CAF1 15347 115 + 1
GGAGAUGGUGGGAAAAGCCAAAAAGGCUGCAGG---CAAAUGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGGAG-G-GUGUGGUGUUGGUGUGCAAU
...((((.(((......))).....((((((..---....)))))).........)))).(((((((((((((((((....)))))))((((.....-.-)))).))))))))))..... ( -34.40)
>DroAna_CAF1 16817 96 + 1
-----------GCAUUGCCAAAAAGGCUGCAGGCUGCAAAUGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGGGC-AGGGGCGGCA------------
-----------(((..(((.....))))))..(((((...(((.(((...((((....))))........(((((((....))))))).)))...))-)...))))).------------ ( -29.40)
>consensus
G_____GUUGGACAAAGCCAAAAAGGCUGCAGG___CAAACGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGGAG_GAGGGUGGUGUUGGUGUGCAAU
...............((((.....))))((............(((((........)))))(((((((((((((((((....))))))).(((..........)))))))))))))))... (-22.35 = -24.38 +   2.03)

alignment

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secondary structure

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Window 8

Location 11,756,231 – 11,756,342
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.28
Mean single sequence MFE -24.32
Consensus MFE -20.01
Energy contribution -20.35
Covariance contribution 0.33
Combinations/Pair 1.15
Mean z-score -1.67
Structure conservation index 0.82
SVM decision value 0.22
SVM RNA-class probability 0.640401
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11756231 111 - 22407834
AUUGCACACCAACACCAUCCUC-CUCUCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACGUUUG---CCUGCAGCCUUUUUGGCUUCGUCCAAC-----C
.....(((..(((((((.....-..(..((((((((....))))))))..)...)))))))..)))...............(((---..((.((((.....)))).))..))).-----. ( -24.90)
>DroSec_CAF1 14402 112 - 1
AUUGCACACCAACACCACCCACCCUACCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACGUUUG---CCUGCAGCCUUUUUGGCUUCGUUCAAC-----C
.....(((..(((((((.......(((.((((((((....))))))))..))).)))))))..)))...............(((---..((.((((.....)))).))..))).-----. ( -23.80)
>DroSim_CAF1 13296 111 - 1
AUUGCACACCAACACCACCCAC-CUACCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACGUUUG---CCUGCAGCCUUUUUGGCUUCGUUCAAC-----C
.....(((..(((((((.....-.(((.((((((((....))))))))..))).)))))))..)))...............(((---..((.((((.....)))).))..))).-----. ( -24.40)
>DroEre_CAF1 21831 116 - 1
AUUGCACACCAACACCACCCUC-CUCCCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACAUUUG---CCUGCAGCCUUUUUGGCUUUGCCCACCACCACC
..((((....(((((((.....-.....((((((((....))))))))......)))))))(((((...........)))))..---..))))(((.....)))................ ( -23.59)
>DroYak_CAF1 15347 115 - 1
AUUGCACACCAACACCACAC-C-CUCCCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACAUUUG---CCUGCAGCCUUUUUGGCUUUUCCCACCAUCUCC
..((((....(((((((...-.-.....((((((((....))))))))......)))))))(((((...........)))))..---..))))(((.....)))................ ( -24.16)
>DroAna_CAF1 16817 96 - 1
------------UGCCGCCCCU-GCCCCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACAUUUGCAGCCUGCAGCCUUUUUGGCAAUGC-----------
------------(((((...((-((...((((((((....)))))))).......(((((.(((((...........))))).))).)).))))......)))))....----------- ( -25.10)
>consensus
AUUGCACACCAACACCACCCAC_CUCCCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACAUUUG___CCUGCAGCCUUUUUGGCUUCGCCCAAC_____C
..((((....(((((((...........((((((((....))))))))......)))))))(((((...........))))).......))))(((.....)))................ (-20.01 = -20.35 +   0.33)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,756,263 – 11,756,365
Length 102
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 89.34
Mean single sequence MFE -29.82
Consensus MFE -24.70
Energy contribution -24.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.28
Structure conservation index 0.83
SVM decision value 2.08
SVM RNA-class probability 0.987350
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11756263 102 + 22407834
CGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGAGAG-GAGGAUGGUGUUGGUGUGCAAUUGGGAAUUAAAUGUGUGUGUGUG-----------
..((((..(((((.((((((((((((....(((((((....)))))))...(....)-.....))))))))))))..)))))...))))..............----------- ( -28.00)
>DroSec_CAF1 14434 105 + 1
CGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGUAGGGUGGGUGGUGUUGGUGUGCAAUUGGGAAUUAGAUGUGUG--UGUGUGAG-------
..((((..(((((.((((((((((((...((((((((....))))))).(((......)))).))))))))))))..)))))...))))........--........------- ( -29.80)
>DroSim_CAF1 13328 106 + 1
CGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGUAG-GUGGGUGGUGUUGGUGUGCAAUUGGGAAUUAAAUGUGUGUGUGUGUGAG-------
..((((..(((((.((((((((((((...((((((((....))))))).(((.....-)))).))))))))))))..)))))...))))..................------- ( -29.60)
>DroEre_CAF1 21868 101 + 1
UGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGGAG-GAGGGUGGUGUUGGUGUGCAAUUGGGAAUUUAACGUGUGUGUGU------------
........(((((.((((((((((((...((((((((....)))))))...(....)-..)..))))))))))))..)))))....................------------ ( -26.80)
>DroYak_CAF1 15384 112 + 1
UGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGGAG-G-GUGUGGUGUUGGUGUGCAAUUGGGAAUUUAAUGUGUGUGUGUGUGUGUCACACA
.((.((((((....((((..(((((((((((((((((....)))))))((((.....-.-)))).))))))))))((((((((....))))).)))..))))...)))))))). ( -34.90)
>consensus
CGUAGUGACAGUUAACAUUAACACCAAUACAAGCGUAAACAUAUGCUUACACGGGAG_GAGGGUGGUGUUGGUGUGCAAUUGGGAAUUAAAUGUGUGUGUGUGUG_G_______
........(((((.((((((((((((...((((((((....)))))))...(....)...)..))))))))))))..)))))................................ (-24.70 = -24.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,756,263 – 11,756,365
Length 102
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 89.34
Mean single sequence MFE -19.42
Consensus MFE -16.77
Energy contribution -16.77
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.50
Structure conservation index 0.86
SVM decision value 2.98
SVM RNA-class probability 0.998018
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11756263 102 - 22407834
-----------CACACACACACAUUUAAUUCCCAAUUGCACACCAACACCAUCCUC-CUCUCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACG
-----------.....................((.(((.(((..(((((((.....-..(..((((((((....))))))))..)...)))))))..)))))).))........ ( -18.60)
>DroSec_CAF1 14434 105 - 1
-------CUCACACA--CACACAUCUAAUUCCCAAUUGCACACCAACACCACCCACCCUACCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACG
-------........--...............((.(((.(((..(((((((.......(((.((((((((....))))))))..))).)))))))..)))))).))........ ( -17.50)
>DroSim_CAF1 13328 106 - 1
-------CUCACACACACACACAUUUAAUUCCCAAUUGCACACCAACACCACCCAC-CUACCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACG
-------.............(((.(((((.....((((.(((((((..........-.(((.((((((((....))))))))..))))))))))))))))))).)))....... ( -18.20)
>DroEre_CAF1 21868 101 - 1
------------ACACACACACGUUAAAUUCCCAAUUGCACACCAACACCACCCUC-CUCCCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACA
------------......(((.(((((.......((((.(((((((.((.......-.....((((((((....))))))))..)).))))))))))).))))))))....... ( -18.84)
>DroYak_CAF1 15384 112 - 1
UGUGUGACACACACACACACACAUUAAAUUCCCAAUUGCACACCAACACCACAC-C-CUCCCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACA
((((((.....))))))...............((.(((.(((..(((((((...-.-.....((((((((....))))))))......)))))))..)))))).))........ ( -23.96)
>consensus
_______C_CACACACACACACAUUUAAUUCCCAAUUGCACACCAACACCACCCAC_CUCCCGUGUAAGCAUAUGUUUACGCUUGUAUUGGUGUUAAUGUUAACUGUCACUACG
................................((.(((.(((..(((((((...........((((((((....))))))))......)))))))..)))))).))........ (-16.77 = -16.77 +  -0.00)

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 11:08:41 2006