Locus 4558

Sequence ID 3R_DroMel_CAF1
Location 12,063,321 – 12,063,594
Length 273
Max. P 0.968892
window7444 window7445 window7446 window7447 window7448

overview

Window 4

Location 12,063,321 – 12,063,440
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.06
Mean single sequence MFE -37.13
Consensus MFE -35.79
Energy contribution -35.79
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.96
SVM decision value 0.07
SVM RNA-class probability 0.566606
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12063321 119 + 27905053
GUAGUUUUUGCAAGAGGAAGAGAGCAGGAAGUGAAUGAGAAUUCUCUUUCCUUUUGUUUUGCGGCGAAGCGAUCCGCA-AGCAAUACGUCGAAUUCGCCGCGAACGGAUCGCUUUUGUUU
((.((....(((((((((((((((.................))))).))))))))))...)).))(((((((((((..-.((....((.......))..))...)))))))))))..... ( -36.93)
>DroSec_CAF1 35353 120 + 1
GUAGUUUUUGCAAGAGGAAGAGAGCAGGAAGUGAAUGAGAAUUCUCUUUCCUUUUGUUUUGCGGCGAAGCGAUCCGCAAAGCUAUAUGUCGAAUUCGCCGCGAACGGAUCGCUUUUGUUU
((.((....(((((((((((((((.................))))).))))))))))...)).))(((((((((((....((.....(.((....)).)))...)))))))))))..... ( -35.73)
>DroSim_CAF1 44835 120 + 1
GUAGUUUUUGCAAGAGGAAGAGAGCAGGAAGUGAAUGAGAAUUCUCUUUCCUUUUGUUUUGCGGCGAAGCGAUCCGCAAAGCGAUAUGUCGAAUUCGCCGCGAACGGAUCGCUUUUGUUU
((.((....(((((((((((((((.................))))).))))))))))...)).))(((((((((((....((((..........))))......)))))))))))..... ( -38.73)
>consensus
GUAGUUUUUGCAAGAGGAAGAGAGCAGGAAGUGAAUGAGAAUUCUCUUUCCUUUUGUUUUGCGGCGAAGCGAUCCGCAAAGCAAUAUGUCGAAUUCGCCGCGAACGGAUCGCUUUUGUUU
((.((....(((((((((((((((.................))))).))))))))))...)).))(((((((((((....((.................))...)))))))))))..... (-35.79 = -35.79 +  -0.00)

alignment

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secondary structure

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Window 5

Location 12,063,321 – 12,063,440
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.06
Mean single sequence MFE -31.71
Consensus MFE -30.42
Energy contribution -30.64
Covariance contribution 0.22
Combinations/Pair 1.03
Mean z-score -2.68
Structure conservation index 0.96
SVM decision value 1.63
SVM RNA-class probability 0.968892
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12063321 119 - 27905053
AAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACGUAUUGCU-UGCGGAUCGCUUCGCCGCAAAACAAAAGGAAAGAGAAUUCUCAUUCACUUCCUGCUCUCUUCCUCUUGCAAAAACUAC
......(((((((((((..((.(((.......)))...)).-.)))))))))))....((((......(((((.((((...................))))))))).))))......... ( -32.31)
>DroSec_CAF1 35353 120 - 1
AAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACAUAUAGCUUUGCGGAUCGCUUCGCCGCAAAACAAAAGGAAAGAGAAUUCUCAUUCACUUCCUGCUCUCUUCCUCUUGCAAAAACUAC
......(((((((((((..((.(((....)).).....))...)))))))))))....((((......(((((.((((...................))))))))).))))......... ( -30.11)
>DroSim_CAF1 44835 120 - 1
AAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACAUAUCGCUUUGCGGAUCGCUUCGCCGCAAAACAAAAGGAAAGAGAAUUCUCAUUCACUUCCUGCUCUCUUCCUCUUGCAAAAACUAC
......(((((((((((....(((((..........)))))..)))))))))))....((((......(((((.((((...................))))))))).))))......... ( -32.71)
>consensus
AAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACAUAUAGCUUUGCGGAUCGCUUCGCCGCAAAACAAAAGGAAAGAGAAUUCUCAUUCACUUCCUGCUCUCUUCCUCUUGCAAAAACUAC
......(((((((((((....(((((..........)))))..)))))))))))....((((......(((((.((((...................))))))))).))))......... (-30.42 = -30.64 +   0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,063,361 – 12,063,475
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.65
Mean single sequence MFE -34.10
Consensus MFE -31.38
Energy contribution -31.60
Covariance contribution 0.22
Combinations/Pair 1.04
Mean z-score -2.56
Structure conservation index 0.92
SVM decision value 1.35
SVM RNA-class probability 0.944820
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12063361 114 - 27905053
-----CCUUGAAAAGCGAGCAAACCCAAAGUGGCAGCAAUAAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACGUAUUGCU-UGCGGAUCGCUUCGCCGCAAAACAAAAGGAAAGAGAAU
-----((((.....(((.((....((.....)).............(((((((((((..((.(((.......)))...)).-.))))))))))).))))).......))))......... ( -33.20)
>DroSec_CAF1 35393 115 - 1
-----CCUUGAAAAGCGAGCAAGCCCAAAGUGGCAGCAAUAAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACAUAUAGCUUUGCGGAUCGCUUCGCCGCAAAACAAAAGGAAAGAGAAU
-----((((.....(((.((..(((......)))............(((((((((((..((.(((....)).).....))...))))))))))).))))).......))))......... ( -34.80)
>DroSim_CAF1 44875 120 - 1
GAUUGCCUUGAAAAGCGAGCAAACCCAAAGUGGCAGCAAUAAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACAUAUCGCUUUGCGGAUCGCUUCGCCGCAAAACAAAAGGAAAGAGAAU
..((((.(((.....))))))).......((((((....)......(((((((((((....(((((..........)))))..))))))))))).))))).................... ( -34.30)
>consensus
_____CCUUGAAAAGCGAGCAAACCCAAAGUGGCAGCAAUAAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACAUAUAGCUUUGCGGAUCGCUUCGCCGCAAAACAAAAGGAAAGAGAAU
.....((((.....(((.((....((.....)).............(((((((((((....(((((..........)))))..))))))))))).))))).......))))......... (-31.38 = -31.60 +   0.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,063,370 – 12,063,475
Length 105
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.31
Mean single sequence MFE -33.97
Consensus MFE -30.28
Energy contribution -30.50
Covariance contribution 0.22
Combinations/Pair 1.04
Mean z-score -2.43
Structure conservation index 0.89
SVM decision value 1.21
SVM RNA-class probability 0.931676
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12063370 105 - 27905053
--------------CCUUGAAAAGCGAGCAAACCCAAAGUGGCAGCAAUAAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACGUAUUGCU-UGCGGAUCGCUUCGCCGCAAAACAAAAGG
--------------((((.....(((.((....((.....)).............(((((((((((..((.(((.......)))...)).-.))))))))))).))))).......)))) ( -32.10)
>DroSec_CAF1 35402 106 - 1
--------------CCUUGAAAAGCGAGCAAGCCCAAAGUGGCAGCAAUAAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACAUAUAGCUUUGCGGAUCGCUUCGCCGCAAAACAAAAGG
--------------((((.....(((.((..(((......)))............(((((((((((..((.(((....)).).....))...))))))))))).))))).......)))) ( -33.70)
>DroSim_CAF1 44884 120 - 1
AUUGCACCUGAUUGCCUUGAAAAGCGAGCAAACCCAAAGUGGCAGCAAUAAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACAUAUCGCUUUGCGGAUCGCUUCGCCGCAAAACAAAAGG
......(((..((((.(((.....))))))).......((((((....)......(((((((((((....(((((..........)))))..))))))))))).)))))........))) ( -36.10)
>consensus
______________CCUUGAAAAGCGAGCAAACCCAAAGUGGCAGCAAUAAACAAAAGCGAUCCGUUCGCGGCGAAUUCGACAUAUAGCUUUGCGGAUCGCUUCGCCGCAAAACAAAAGG
..............((((.....(((.((....((.....)).............(((((((((((....(((((..........)))))..))))))))))).))))).......)))) (-30.28 = -30.50 +   0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,063,475 – 12,063,594
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.12
Mean single sequence MFE -39.44
Consensus MFE -28.82
Energy contribution -29.46
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -1.91
Structure conservation index 0.73
SVM decision value 0.20
SVM RNA-class probability 0.630675
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12063475 119 - 27905053
UCAUUUCCGCUUUGGG-CCGGAGUUUGUUGUUGCUUCGGGGCAGCAACAAUAACAACAGCAACUCUGCCACAAAGGCGACCAUUCGGAACCGCCGAGCGAGAAACUAUUGCACCUGAUUG
...(((((((((((((-(.((((((((((((((((....))))))))))...........))))))))).))..((((.((....))...))))))))).))))................ ( -39.10)
>DroSec_CAF1 1 119 - 1
UCAUUUCCGCUUUAGG-CCGGAGUUGGUUGUUGCUUCGGGGCAGCAACAAUAACAACAGCAACUCUGCCACAAAGGCGACCAUUCGGAACCGCCGAGCGAGAAACUAUUGCACCUGAUUG
...(((((((((..((-(.((((((((((((((((....))))))))).....(....))))))))))).....((((.((....))...))))))))).))))................ ( -40.30)
>DroSim_CAF1 1 105 - 1
UCAUUUCCGCUUUAGG-CCGGAGUUGGUUGUUGCUUCGGGGCAGCAACAAUAACAACAGCAACUCUGCCACAAAGGCGACCAUUCGGAACCGCCGAGCGAGAAACU--------------
...(((((((((..((-(.((((((((((((((((....))))))))).....(....))))))))))).....((((.((....))...))))))))).))))..-------------- ( -40.30)
>DroEre_CAF1 1985 119 - 1
UCAUUUCCGCUUUGGG-CCGGAGCUUGUUGUUGUUUCGGGGGAGCAACAAUAACAACAGCAACUCUGCCACAAAGCCGACCAUUCGGAACCGCCGAGCGAGAAACUAUUGCACCUGAUUG
.....((.((((((((-(.((((.(((((((((((...(........)...)))))))))))))))))).)))))).))....((((.....))))((((.......))))......... ( -40.30)
>DroYak_CAF1 2038 120 - 1
UCAUUUCCGCUUUGGGUCCGGUGCUUGUUGUUGUUUCAGGGGAGCAACAAUAAUAACAGCAACUCUGCCACAAAGGCGACCAUUCGGAACCGCCGAGCGAGAAACUAUUGCACCUGAUUG
...(((((((((.(((((((((((((((((((((((.....))))))))))).....))))....((((.....)))).....)))).))).).))))).))))................ ( -37.20)
>consensus
UCAUUUCCGCUUUGGG_CCGGAGUUUGUUGUUGCUUCGGGGCAGCAACAAUAACAACAGCAACUCUGCCACAAAGGCGACCAUUCGGAACCGCCGAGCGAGAAACUAUUGCACCUGAUUG
...(((((((((..((..(((((.(((((((((.....(........).....)))))))))))))))).....((((.((....))...))))))))).))))................ (-28.82 = -29.46 +   0.64)

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 11:32:21 2006