Locus 6787

Sequence ID X_DroMel_CAF1
Location 16,891,150 – 16,891,299
Length 149
Max. P 0.598189
window11115 window11116 window11117

overview

Window 5

Location 16,891,150 – 16,891,265
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.68
Mean single sequence MFE -36.76
Consensus MFE -28.64
Energy contribution -28.92
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.56
Structure conservation index 0.78
SVM decision value -0.00
SVM RNA-class probability 0.532099
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16891150 115 - 22224390
CUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGCAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGUGUGU-----GGACGAGACGAAAGUCAAGUUGCCAUUUAAA
........(((.(((((..(((((.......))))).))))).)))(((.((((((.(((........))).))))))......-----.(((..(((....)))..))))))....... ( -37.10)
>DroSec_CAF1 90121 115 - 1
CUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGCAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGUGUGU-----GGACGAGACGAAAGUCAAGUCGGCAUUUAAA
.....(((.((.(((((..(((((.......))))).))))).)))))..((((((.(((........))).))))))..((((-----.(((..(((....)))..))).))))..... ( -39.70)
>DroSim_CAF1 70568 115 - 1
CUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGUAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGUGUGU-----GGACGAGACGAAAGUCAAGUCGGCAUUUAAA
....((((.((.(((((..(((((.......))))).))))).)))))).((((((.(((........))).))))))..((((-----.(((..(((....)))..))).))))..... ( -41.50)
>DroEre_CAF1 74614 114 - 1
CUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCGACGAGCUGGGCGGCAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGUGUGC-----GGACGCAAGGAAAGUCAA-CUGCCAUUUAAA
........(((.(((((..(((((.......))))).))))).)))((((((((((.(((........))).))))))((((..-----..))))............-.))))....... ( -32.50)
>DroYak_CAF1 76588 120 - 1
CUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGCAUUUUCCGAUUAACUGAUGGGUGGGAAAAGUGUGCGAUACGGACGAAACGAAAGUCAAGCUGGCAUUUAAA
.....((((((..((((..((.((((((((.((......)).)))).(((((((((.(((........))).)))))...)))).....)))).))....))))..))))))........ ( -33.00)
>consensus
CUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGCAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGUGUGU_____GGACGAGACGAAAGUCAAGUUGGCAUUUAAA
.....((.(((.(((((..(((((.......))))).))))).))).(((((((((.(((........))).)).))))))).......))....(((....)))............... (-28.64 = -28.92 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,891,185 – 16,891,299
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.80
Mean single sequence MFE -31.45
Consensus MFE -25.44
Energy contribution -26.56
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -1.40
Structure conservation index 0.81
SVM decision value 0.12
SVM RNA-class probability 0.591484
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16891185 114 + 22224390
ACUUUUCCCACCCAUCAAUUAAUCGGAAAAUGCCGCCCAGCUCGUUGGCAAGGCAAACCAAUUAAGCUCAGCCGGUUAAGCCAAUGGCUUUGGUAAACAUUCUGGGAUAUGGGG------
......((((((((....((((((((....((((..((((....))))...))))................))))))))(((((.....)))))........))))...)))).------ ( -31.45)
>DroSec_CAF1 90156 116 + 1
ACUUUUCCCACCCAUCAAUUAAUCGGAAAAUGCCGCCCAGCUCGUUGGCAAGGCAAACCAAUUAAGCUCAGCCGGUUAAGCCAAUAGCUUUGGUAAACAUACCGGGAUAUGGGAUA----
.....(((((...(((..(((((.((....((((..((((....))))...))))..)).)))))......(((((...(((((.....)))))......)))))))).)))))..---- ( -33.10)
>DroSim_CAF1 70603 120 + 1
ACUUUUCCCACCCAUCAAUUAAUCGGAAAAUACCGCCCAGCUCGUUGGCAAGGCAAACCAAUUAAGCUCAGCCGGUUAAGCCAAUAGCUUUGGUAAACAUACCGGGAUAUGGGAUAUGCU
.....(((((.............(((......)))(((((((.((((((..((....))..((((.(......).))))))))))))))..((((....)))))))...)))))...... ( -32.00)
>DroEre_CAF1 74648 113 + 1
ACUUUUCCCACCCAUCAAUUAAUCGGAAAAUGCCGCCCAGCUCGUCGGCAAGGCAAACCAAUUAAGCUCAGCCGGUUAAGCCAAUAGCUUUGGUAAACAUUUCGGGU-------UUUGGG
......(((((((.....((((((((....(((((.(......).))))).((....))............))))))))(((((.....))))).........))))-------...))) ( -30.60)
>DroYak_CAF1 76628 120 + 1
ACUUUUCCCACCCAUCAGUUAAUCGGAAAAUGCCGCCCAGCUCGUUGGCAAGGCAAACCAAUUAAGCUCAGCCGGUUAAGCCAAUAGCUUUGGUAAACAUUCCGGGAAAUGCGAUAUGGU
.........(((.(((.(((..((((((..((((..((((....))))...)))).(((((...((((.....((.....))...))))))))).....))))))..)))..)))..))) ( -30.10)
>consensus
ACUUUUCCCACCCAUCAAUUAAUCGGAAAAUGCCGCCCAGCUCGUUGGCAAGGCAAACCAAUUAAGCUCAGCCGGUUAAGCCAAUAGCUUUGGUAAACAUUCCGGGAUAUGGGAUAUG__
.....((((((((.....((((((((....(((((.(......).))))).((....))............))))))))(((((.....))))).........)))...)))))...... (-25.44 = -26.56 +   1.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,891,185 – 16,891,299
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.80
Mean single sequence MFE -36.00
Consensus MFE -30.32
Energy contribution -30.28
Covariance contribution -0.04
Combinations/Pair 1.12
Mean z-score -1.32
Structure conservation index 0.84
SVM decision value 0.13
SVM RNA-class probability 0.598189
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16891185 114 - 22224390
------CCCCAUAUCCCAGAAUGUUUACCAAAGCCAUUGGCUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGCAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGU
------.((((...((((....(((((((.(((((...)))))....)).)))))((((((((..((((..(((.........)))))))....))))))))....))))))))...... ( -35.20)
>DroSec_CAF1 90156 116 - 1
----UAUCCCAUAUCCCGGUAUGUUUACCAAAGCUAUUGGCUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGCAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGU
----..(((((...(((((((....)))).(((((...((((.....)))).)))))((((((..((((..(((.........)))))))....)))))).......))))))))..... ( -37.50)
>DroSim_CAF1 70603 120 - 1
AGCAUAUCCCAUAUCCCGGUAUGUUUACCAAAGCUAUUGGCUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGUAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGU
......(((((...(((((((....))))......(((((....((((.((.(((((..(((((.......))))).))))).)))))).....)))))........))))))))..... ( -38.10)
>DroEre_CAF1 74648 113 - 1
CCCAAA-------ACCCGAAAUGUUUACCAAAGCUAUUGGCUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCGACGAGCUGGGCGGCAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGU
(((...-------(((((....(((((((.((((.....))))....)).)))))((((((((..((((..(((.(.....).)))))))....))))))))....))))))))...... ( -33.50)
>DroYak_CAF1 76628 120 - 1
ACCAUAUCGCAUUUCCCGGAAUGUUUACCAAAGCUAUUGGCUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGCAUUUUCCGAUUAACUGAUGGGUGGGAAAAGU
........((.((((((((((((((..(((..(((.(((((......(((.(((((.....))))))))..)))))..))))))..))))))))((.(((....))).)).)))))).)) ( -35.70)
>consensus
__CAUAUCCCAUAUCCCGGAAUGUUUACCAAAGCUAUUGGCUUAACCGGCUGAGCUUAAUUGGUUUGCCUUGCCAACGAGCUGGGCGGCAUUUUCCGAUUAAUUGAUGGGUGGGAAAAGU
.............((((((((((((.....((((.....)))).....(((.(((((..(((((.......))))).))))).)))))))))))((.(((....))).)).))))..... (-30.32 = -30.28 +  -0.04)

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 12:22:57 2006