Locus 7210

Sequence ID 3R_DroMel_CAF1
Location 18,974,529 – 18,974,743
Length 214
Max. P 0.837362
window11667 window11668 window11669

overview

Window 7

Location 18,974,529 – 18,974,643
Length 114
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 87.73
Mean single sequence MFE -20.78
Consensus MFE -16.28
Energy contribution -16.48
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.44
Structure conservation index 0.78
SVM decision value -0.05
SVM RNA-class probability 0.509529
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18974529 114 - 27905053
CAAACUGGACUGGACCGUGGCUCCAUGGGCUCCUGCUGCCUGCUGCCUGCUGCCUGCCAUCCUUACCAUUCCUGCCACCUCCACCUCCUAUCUCCU-UCUCUACCUUCUGAUCUU
......(((.((((..(((((...((((......((.((..((.....)).))..))........))))....))))).))))..)))........-.................. ( -23.44)
>DroSec_CAF1 85579 99 - 1
CAAACUGGACUGGACCGUGGCUCCAUGGGCUCCUGCU--------------GCCUGCCAUCCUUACCAUUCCUGCCACCUCCACCUCC-AUCUCCU-GCUCUGCCUUCUGAUCUU
.....((((.((((..(((((...((((......((.--------------....))........))))....))))).))))..)))-)......-.................. ( -20.34)
>DroSim_CAF1 87372 106 - 1
CAAACUGGACUGGACCGUGGCUCCAUGGGCUCCUGCUGCCU-------GCUGCCUGCCAUCCUUACCAUUCCUGCCACCUCCACCUCC-AUCCUCU-GCUCUGCCUUCUGAUCUU
.....((((.((((..(((((...((((((....)).....-------((.....))........))))....))))).))))..)))-)......-.................. ( -22.10)
>DroEre_CAF1 86171 100 - 1
CAAACUGGACUGGACCGUGGCUCCAUGGGCUCCUGCU--------------GCCUGCCAUCCUUACCAUUCCUACCACCUCCACCUCC-AUCUCCUUCCUCUGCCUUCUGAUCUU
......(((.(((...(((((.....((((.......--------------))))))))).....))).)))................-.......................... ( -17.20)
>DroYak_CAF1 88744 101 - 1
CAAACUGGACUGGACCGUGGCUCCAUGGGCUCCUGCUGCCU-------GCUGCCUGCCAUCCUUACCAUUCCAACCACC------UCC-AUCUCCUUCCUCUGCCUUCUGAUCUU
.....((((.(((...(((((..(((((((.......))))-------).))...))))).....))).))))......------...-.......................... ( -20.80)
>consensus
CAAACUGGACUGGACCGUGGCUCCAUGGGCUCCUGCUGCCU_______GCUGCCUGCCAUCCUUACCAUUCCUGCCACCUCCACCUCC_AUCUCCU_CCUCUGCCUUCUGAUCUU
......(((.(((..((((....))))(((....((.((.........)).))..))).......))).)))........................................... (-16.28 = -16.48 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,974,607 – 18,974,723
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.02
Mean single sequence MFE -40.10
Consensus MFE -37.14
Energy contribution -37.50
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -1.03
Structure conservation index 0.93
SVM decision value 0.32
SVM RNA-class probability 0.689018
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18974607 116 - 27905053
CGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCUCAAACUGGACUGGACCGU----GGCUCCAUGGGCUCCUGC
((((((((((((((.......))))).(((..........)))..))))))))).((((..........(((((.((((.......)).)))))))((----(....)))))))...... ( -39.80)
>DroSec_CAF1 85642 116 - 1
CGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCUCAAACUGGACUGGACCGU----GGCUCCAUGGGCUCCUGC
((((((((((((((.......))))).(((..........)))..))))))))).((((..........(((((.((((.......)).)))))))((----(....)))))))...... ( -39.80)
>DroSim_CAF1 87442 116 - 1
CGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCUCAAACUGGACUGGACCGU----GGCUCCAUGGGCUCCUGC
((((((((((((((.......))))).(((..........)))..))))))))).((((..........(((((.((((.......)).)))))))((----(....)))))))...... ( -39.80)
>DroEre_CAF1 86235 116 - 1
CGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCUCAAACUGGACUGGACCGU----GGCUCCAUGGGCUCCUGC
((((((((((((((.......))))).(((..........)))..))))))))).((((..........(((((.((((.......)).)))))))((----(....)))))))...... ( -39.80)
>DroYak_CAF1 88809 116 - 1
CGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCUCAAACUGGACUGGACCGU----GGCUCCAUGGGCUCCUGC
((((((((((((((.......))))).(((..........)))..))))))))).((((..........(((((.((((.......)).)))))))((----(....)))))))...... ( -39.80)
>DroAna_CAF1 88242 120 - 1
CGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGUCUUCAAACUGGACUGGACUGGGAAGGGGACCCUUGGCUCCUUU
((((((((((((((.......))))).(((..........)))..))))))))).(((........(.((((((.((((.......)))).)))))).)((((....)))))))...... ( -41.60)
>consensus
CGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCUCAAACUGGACUGGACCGU____GGCUCCAUGGGCUCCUGC
((((((((((((((.......))))).(((..........)))..))))))))).((((((........(((((.(........).)))))(((((......)).)))))))))...... (-37.14 = -37.50 +   0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,974,643 – 18,974,743
Length 100
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 99.50
Mean single sequence MFE -35.80
Consensus MFE -35.80
Energy contribution -35.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 1.00
SVM decision value 0.74
SVM RNA-class probability 0.837362
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18974643 100 - 27905053
-UGCUGUUGCUGCGAUAUCGCCGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCU
-.((((..((..((((((.((((((((((((((((.......))))).(((..........)))..))))))))).))..)))))...)..))..)))).. ( -35.80)
>DroSec_CAF1 85678 100 - 1
-UGCUGUUGCUGCGAUAUCGCCGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCU
-.((((..((..((((((.((((((((((((((((.......))))).(((..........)))..))))))))).))..)))))...)..))..)))).. ( -35.80)
>DroSim_CAF1 87478 100 - 1
-UGCUGUUGCUGCGAUAUCGCCGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCU
-.((((..((..((((((.((((((((((((((((.......))))).(((..........)))..))))))))).))..)))))...)..))..)))).. ( -35.80)
>DroYak_CAF1 88845 101 - 1
UUGCUGUUGCUGCGAUAUCGCCGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCU
..((((..((..((((((.((((((((((((((((.......))))).(((..........)))..))))))))).))..)))))...)..))..)))).. ( -35.80)
>consensus
_UGCUGUUGCUGCGAUAUCGCCGCGUUCGCGCGUUAAACACAAGCGCAACAAUUUUUAUUCUGUCAGCGAACGCGUGCCUGUAUUUGUGUGGUCCCGGCCU
..((((..((..((((((.((((((((((((((((.......))))).(((..........)))..))))))))).))..)))))...)..))..)))).. (-35.80 = -35.80 +   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 12:40:15 2006