Locus 882

Sequence ID 2L_DroMel_CAF1
Location 2,515,417 – 2,515,539
Length 122
Max. P 0.790681
window1427 window1428 window1429

overview

Window 7

Location 2,515,417 – 2,515,507
Length 90
Sequences 6
Columns 90
Reading direction forward
Mean pairwise identity 77.71
Mean single sequence MFE -19.91
Consensus MFE -9.44
Energy contribution -9.88
Covariance contribution 0.44
Combinations/Pair 1.13
Mean z-score -1.97
Structure conservation index 0.47
SVM decision value 0.03
SVM RNA-class probability 0.549430
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2515417 90 + 22407834
UAAAUUAUUUGCCGGCUUGUGUGACCCACAGGUCAGGCAUAAAUCCAAUCAAAUUGACAGCAAGUCAACGCUGACAGGAUCUACAUACUC
.........((((((((((((.....)))))))).))))...((((..(((..(((((.....)))))...)))..)))).......... ( -25.40)
>DroPse_CAF1 118591 77 + 1
UAAAUUAU-------------UGACCCAUGGCUCAGGCAUAAAUCCAAUCAACUUGACAGCAAGUCAUCGUGGACAGGAUCUGCAUAUUA
.......(-------------(((.(....).))))(((...((((..((.((.((((.....))))..)).))..)))).)))...... ( -13.60)
>DroSec_CAF1 95200 90 + 1
UAAAUUAUUUGCCGGCUUGUGUGACCCACAGGUCGGGCAUAAAUCCAAUCAAAUUGACAGCAAGUCAAUGCUGACAGGAUCUACAUACUC
.........((((((((((((.....)))))))).))))...((((..(((.((((((.....))))))..)))..)))).......... ( -28.10)
>DroEre_CAF1 98562 90 + 1
UAAAUUAUGUGUUGGCUUGUGUGACCCACAGGUCAGGCAUAAAUCCAAUCAAAUUGACAGCAAGUCACGGCAGACAGGAUCUACAUACUC
....((((((.((((((((((.....))))))))))))))))((((..((....((((.....)))).....))..)))).......... ( -22.70)
>DroAna_CAF1 117039 90 + 1
UACAUUAUUUUUCCAAAUGAGGGACCCACGGGUCUCGCAUAAAUCCAAUCAAAUUGACAGCAAGUCAUCAUAAAUGACAUUUCCAUAUUC
..((((..........(((.((((((....)))))).)))..............((((.....)))).....)))).............. ( -17.10)
>DroPer_CAF1 117087 77 + 1
UAAAUUAU-------------UGACCCAUGGCUCAGGCAUAAAUCCAAUCAACCUGACAGCAAGUCAUCGUGGACAGGAUCUCCAUAUUA
........-------------((((.....(((((((...............)))))..))..))))..(((((.......))))).... ( -12.56)
>consensus
UAAAUUAUUUG_CGGCUUGUGUGACCCACAGGUCAGGCAUAAAUCCAAUCAAAUUGACAGCAAGUCAUCGCAGACAGGAUCUACAUACUC
.....................(((((....))))).......((((..((....((((.....)))).....))..)))).......... ( -9.44 =  -9.88 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,515,417 – 2,515,507
Length 90
Sequences 6
Columns 90
Reading direction reverse
Mean pairwise identity 77.71
Mean single sequence MFE -22.49
Consensus MFE -15.07
Energy contribution -15.02
Covariance contribution -0.05
Combinations/Pair 1.24
Mean z-score -1.46
Structure conservation index 0.67
SVM decision value 0.59
SVM RNA-class probability 0.790681
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2515417 90 - 22407834
GAGUAUGUAGAUCCUGUCAGCGUUGACUUGCUGUCAAUUUGAUUGGAUUUAUGCCUGACCUGUGGGUCACACAAGCCGGCAAAUAAUUUA
......((((((((.(((((.((((((.....))))))))))).))))))))(((.(.(.((((.....)))).)).))).......... ( -29.00)
>DroPse_CAF1 118591 77 - 1
UAAUAUGCAGAUCCUGUCCACGAUGACUUGCUGUCAAGUUGAUUGGAUUUAUGCCUGAGCCAUGGGUCA-------------AUAAUUUA
......((((((((.(((.((..((((.....)))).)).))).)))))..))).(((.(....).)))-------------........ ( -18.90)
>DroSec_CAF1 95200 90 - 1
GAGUAUGUAGAUCCUGUCAGCAUUGACUUGCUGUCAAUUUGAUUGGAUUUAUGCCCGACCUGUGGGUCACACAAGCCGGCAAAUAAUUUA
......((((((((.(((((.((((((.....))))))))))).))))))))(((.(.(.((((.....)))).)).))).......... ( -29.50)
>DroEre_CAF1 98562 90 - 1
GAGUAUGUAGAUCCUGUCUGCCGUGACUUGCUGUCAAUUUGAUUGGAUUUAUGCCUGACCUGUGGGUCACACAAGCCAACACAUAAUUUA
...(((((((((((.(((.....((((.....))))....))).)))))).((..(((((....)))))..)).......)))))..... ( -23.50)
>DroAna_CAF1 117039 90 - 1
GAAUAUGGAAAUGUCAUUUAUGAUGACUUGCUGUCAAUUUGAUUGGAUUUAUGCGAGACCCGUGGGUCCCUCAUUUGGAAAAAUAAUGUA
..((((.......(((...((((((((.....))))........(((((((((.(....)))))))))).)))).))).......)))). ( -15.84)
>DroPer_CAF1 117087 77 - 1
UAAUAUGGAGAUCCUGUCCACGAUGACUUGCUGUCAGGUUGAUUGGAUUUAUGCCUGAGCCAUGGGUCA-------------AUAAUUUA
......((.(((((.(((.((..((((.....)))).)).))).)))))....))(((.(....).)))-------------........ ( -18.20)
>consensus
GAAUAUGUAGAUCCUGUCAACGAUGACUUGCUGUCAAUUUGAUUGGAUUUAUGCCUGACCCGUGGGUCACACAAGCCG_CAAAUAAUUUA
........((((((.(((.....((((.....))))....))).))))))......((((....))))...................... (-15.07 = -15.02 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,515,445 – 2,515,539
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 80.40
Mean single sequence MFE -29.72
Consensus MFE -14.79
Energy contribution -15.90
Covariance contribution 1.11
Combinations/Pair 1.17
Mean z-score -2.14
Structure conservation index 0.50
SVM decision value -0.06
SVM RNA-class probability 0.505541
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2515445 94 - 22407834
----UCCCUGACUAGGCGCAUUUCA--GAGUGCCUAAUGAGUAUGUAGAUCCUGUCAGCGUUGACUUGCUGUCAAUUUGAUUGGAUUUAUGCCUGACCUG
----...((.(.(((((((......--..))))))).).))...((((((((.(((((.((((((.....))))))))))).)))))))).......... ( -30.90)
>DroPse_CAF1 118606 100 - 1
AUGAUUCAUGGGGAAAUCCAUAUCCGGGAAUGCCUAAUUAAUAUGCAGAUCCUGUCCACGAUGACUUGCUGUCAAGUUGAUUGGAUUUAUGCCUGAGCCA
.((..(((.((.((((((((....(((((.(((.((.....)).)))..)))))((.((..((((.....)))).)).)).))))))).).)))))..)) ( -25.60)
>DroSec_CAF1 95228 94 - 1
----UCCCUGGUUAGGCGCAUUUCA--GAGUGCCUAAUGAGUAUGUAGAUCCUGUCAGCAUUGACUUGCUGUCAAUUUGAUUGGAUUUAUGCCCGACCUG
----...((.(((((((((......--..))))))))).))...((((((((.(((((.((((((.....))))))))))).)))))))).......... ( -35.40)
>DroEre_CAF1 98590 94 - 1
----UCCCUGGCUAGGCGCAUUUCA--GAGUGCCUAAUGAGUAUGUAGAUCCUGUCUGCCGUGACUUGCUGUCAAUUUGAUUGGAUUUAUGCCUGACCUG
----.....((((((((((......--..)))))))........((((((((.(((.....((((.....))))....))).)))))))))))....... ( -30.60)
>DroYak_CAF1 98642 94 - 1
----UCCCUGGUUACGCGCAUUUCA--GGGUGCCUAAUGAGCAUGUAGAUCCUGCUAAAGUUGACUUGACGUCAAUUUGAUUGGAUUUAUGCCUGACCUG
----.....(((((.(((((((...--.)))))...........((((((((.....((((((((.....))))))))....)))))))))).))))).. ( -28.20)
>DroPer_CAF1 117102 100 - 1
AUGAUUCAUGGGUAAAUCCAUAUCCGGGAAUGCCUAAUUAAUAUGGAGAUCCUGUCCACGAUGACUUGCUGUCAGGUUGAUUGGAUUUAUGCCUGAGCCA
.((..(((.(.(((((((((....(((((...((..........))...)))))((.((..((((.....)))).)).)).))))))))).).)))..)) ( -27.60)
>consensus
____UCCCUGGCUAGGCGCAUUUCA__GAGUGCCUAAUGAGUAUGUAGAUCCUGUCAACGUUGACUUGCUGUCAAUUUGAUUGGAUUUAUGCCUGACCUG
.........(((.....((((((....))))))...........((((((((.(((.....((((.....))))....))).)))))))))))....... (-14.79 = -15.90 +   1.11)

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 09:47:53 2006