Locus 6486

Sequence ID 3L_DroMel_CAF1
Location 17,254,315 – 17,254,524
Length 209
Max. P 0.955798
window10462 window10463 window10464

overview

Window 2

Location 17,254,315 – 17,254,406
Length 91
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 80.26
Mean single sequence MFE -19.12
Consensus MFE -13.78
Energy contribution -13.22
Covariance contribution -0.56
Combinations/Pair 1.24
Mean z-score -2.18
Structure conservation index 0.72
SVM decision value 1.46
SVM RNA-class probability 0.955798
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17254315 91 + 23771897
UGCCACUUUGCCAGCUUUGACACUUUUUGUGGCUUACAGAAAAUUCCACAAAAAA-AAAAGAAAAUCAACAUAU--------------------ACGCAGAGCAAAAAAGAA
.....((((....((((((.(..(((((((((..(.......)..))))))))).-....(.....).......--------------------..)))))))...)))).. ( -15.60)
>DroSec_CAF1 138097 90 + 1
UGCCACUUUGCCAGCUUUGACACUUUUUGUGGCUUACAGAAAAUUCCACAAAAA--AAACGUAAAUCAACAUAU--------------------ACGCAGGGCAAAAAAGAA
.....((((....((((((....(((((((((..(.......)..)))))))))--...((((.((....)).)--------------------)))))))))...)))).. ( -16.80)
>DroSim_CAF1 132936 89 + 1
UGCCACUUUGCCAGCUUUGACACUUUUUGUGGCUUACAGAAAAUUCCACAAAA---AAAUGUAAAUCAACAUAU--------------------ACGUAGGGCAAAAAAGAA
......((((((...........(((((((((..(.......)..))))))))---).((((......))))..--------------------......))))))...... ( -16.60)
>DroYak_CAF1 145068 108 + 1
UGCCACUUUGCCAGCCCUGACAGUUUUUGUGGCUUACAGCACAUGCCACAAAAAAAAAGAGCAAAUCAACAUAUUCUCGUUUAUGUAGCUUCAAACGUAGGGCAAA----AA
......((((((.((.((.....((((((((((...........))))))))))...)).))......(((((........)))))..............))))))----.. ( -27.50)
>consensus
UGCCACUUUGCCAGCUUUGACACUUUUUGUGGCUUACAGAAAAUUCCACAAAAA__AAAAGUAAAUCAACAUAU____________________ACGCAGGGCAAAAAAGAA
.............((((((.(..(((((((((.............)))))))))......(........)..........................)))))))......... (-13.78 = -13.22 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,254,406 – 17,254,524
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.32
Mean single sequence MFE -22.90
Consensus MFE -20.06
Energy contribution -20.26
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.32
Structure conservation index 0.88
SVM decision value 0.03
SVM RNA-class probability 0.549616
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17254406 118 + 23771897
ACGCAUUACACAAACAUGACCGAAACCAAAGACAGCUUGUUAAUUGGAAAGUUUUAUGCAAUUAUAAAACUUUUUUCAUUAUUCCCUGGUGUUUUUUUCGUG--UGUCCUGUUGAUAUUU
............((((.((((((((...((((((.(....((((.(((((((((((((....)))))))))))))..))))......).)))))))))))..--.))).))))....... ( -22.40)
>DroSec_CAF1 138187 120 + 1
ACGCAUUACACAAACAUGACCAAAACCAAAGACAGCUUGUUAAUUGGAAAGUUUUAUGCAAUUAUAAAACUUUUUUCAUUAUUCCCUGGUGUUUUUUUCGUGUGUGUCCUGUUGAUAUUU
..(((..((((..((((((..(((((......(((.....((((.(((((((((((((....)))))))))))))..))))....)))..)))))..))))))))))..)))........ ( -24.20)
>DroSim_CAF1 133025 120 + 1
ACGCAUUACACAAACAUGACCGAAACCAAAGACAGCUUGUUAAUUGGAAAGUUUUAUGCAAUUAUAAAACUUUUUUCAUUAUUCCCUGGUGUUUUUUUCGUGUGUGUCCUGUUGAUAUUU
..(((..((((..((((((..(((((......(((.....((((.(((((((((((((....)))))))))))))..))))....)))..)))))..))))))))))..)))........ ( -24.60)
>DroEre_CAF1 141341 118 + 1
ACGCAUUACACAAACAUGACCGAAACCAAAGACAGCUUGUUAAUUGGAAAGUUUUAUGCAAUUAUAAAACUUUUUUCAUUAUUCUCUGGUGUUUUUUUCGUU--UGUCCUGUUGAUAUUU
............((((.((((((((...((((((.(....((((.(((((((((((((....)))))))))))))..))))......).)))))))))))..--.))).))))....... ( -22.40)
>DroYak_CAF1 145176 118 + 1
ACGCAUUACACAAACAUGACCAAAACCAAAGACAGCUUGUUAAUUGGAAAGUUUUAUGCAAUUAUAAAACUUUUUUCAUUAUUCCCUGGUGUUCUUUUCGUU--UGUCCUGUUGAUAUUU
............((((.(((..((((.(((((((.(....((((.(((((((((((((....)))))))))))))..))))......).)).)))))..)))--)))).))))....... ( -20.90)
>consensus
ACGCAUUACACAAACAUGACCGAAACCAAAGACAGCUUGUUAAUUGGAAAGUUUUAUGCAAUUAUAAAACUUUUUUCAUUAUUCCCUGGUGUUUUUUUCGUG__UGUCCUGUUGAUAUUU
............((((.(((....((.(((((((.(....((((.(((((((((((((....)))))))))))))..))))......).)))))))...))....))).))))....... (-20.06 = -20.26 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,254,406 – 17,254,524
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.32
Mean single sequence MFE -22.36
Consensus MFE -21.22
Energy contribution -20.82
Covariance contribution -0.40
Combinations/Pair 1.05
Mean z-score -1.26
Structure conservation index 0.95
SVM decision value 0.53
SVM RNA-class probability 0.772362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17254406 118 - 23771897
AAAUAUCAACAGGACA--CACGAAAAAAACACCAGGGAAUAAUGAAAAAAGUUUUAUAAUUGCAUAAAACUUUCCAAUUAACAAGCUGUCUUUGGUUUCGGUCAUGUUUGUGUAAUGCGU
..((((.((((.(((.--..((((......((((((((.((((....((((((((((......))))))))))...))))........))))))))))))))).)))).))))....... ( -22.30)
>DroSec_CAF1 138187 120 - 1
AAAUAUCAACAGGACACACACGAAAAAAACACCAGGGAAUAAUGAAAAAAGUUUUAUAAUUGCAUAAAACUUUCCAAUUAACAAGCUGUCUUUGGUUUUGGUCAUGUUUGUGUAAUGCGU
.........((..(((((.(((..(..((.((((((((.((((....((((((((((......))))))))))...))))........)))))))).))..)..))).)))))..))... ( -23.30)
>DroSim_CAF1 133025 120 - 1
AAAUAUCAACAGGACACACACGAAAAAAACACCAGGGAAUAAUGAAAAAAGUUUUAUAAUUGCAUAAAACUUUCCAAUUAACAAGCUGUCUUUGGUUUCGGUCAUGUUUGUGUAAUGCGU
.........((..(((((.(((........((((((((.((((....((((((((((......))))))))))...))))........))))))))........))).)))))..))... ( -22.49)
>DroEre_CAF1 141341 118 - 1
AAAUAUCAACAGGACA--AACGAAAAAAACACCAGAGAAUAAUGAAAAAAGUUUUAUAAUUGCAUAAAACUUUCCAAUUAACAAGCUGUCUUUGGUUUCGGUCAUGUUUGUGUAAUGCGU
..((((.((((.(((.--..((((......((((((((.((((....((((((((((......))))))))))...))))........))))))))))))))).)))).))))....... ( -23.10)
>DroYak_CAF1 145176 118 - 1
AAAUAUCAACAGGACA--AACGAAAAGAACACCAGGGAAUAAUGAAAAAAGUUUUAUAAUUGCAUAAAACUUUCCAAUUAACAAGCUGUCUUUGGUUUUGGUCAUGUUUGUGUAAUGCGU
...........(.(((--((((....(((.((((((((.((((....((((((((((......))))))))))...))))........))))))))))).....))))))).)....... ( -20.60)
>consensus
AAAUAUCAACAGGACA__CACGAAAAAAACACCAGGGAAUAAUGAAAAAAGUUUUAUAAUUGCAUAAAACUUUCCAAUUAACAAGCUGUCUUUGGUUUCGGUCAUGUUUGUGUAAUGCGU
..((((.((((.(((.....((((......((((((((.((((....((((((((((......))))))))))...))))........))))))))))))))).)))).))))....... (-21.22 = -20.82 +  -0.40)

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 12:20:54 2006