Locus 1707

Sequence ID 2R_DroMel_CAF1
Location 6,452,872 – 6,452,993
Length 121
Max. P 0.644473
window2851 window2852 window2853

overview

Window 1

Location 6,452,872 – 6,452,969
Length 97
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 81.48
Mean single sequence MFE -29.48
Consensus MFE -21.34
Energy contribution -21.45
Covariance contribution 0.11
Combinations/Pair 1.21
Mean z-score -1.22
Structure conservation index 0.72
SVM decision value -0.04
SVM RNA-class probability 0.514599
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6452872 97 + 20766785
---UUGUGAUGGAUUAACCGGCGCUUAAGCUGCAGUCGAGCGAUAAGUGCCGCUCAUGGCAGGCCAUUUUGUGUGAUGCCGUUCCCUUUCUGAAUCACCU
---..((((((((.....(((((((((.(((.......)))..)))))))))...((((((...(((.....))).))))))......)))..))))).. ( -29.40)
>DroVir_CAF1 19347 85 + 1
GUCGCGUGAUGGAUUAAACGGCUCUUAAGCUGCAGCUGAGCGAUAAGCGGCGCUCAUGGCCUGCUAUUUU-UGAGCUGCCACAGCU--------------
...(((((...........((((....))))((((((.((.((((.((((.((.....)))))))))).)-).))))))))).)).-------------- ( -28.50)
>DroPse_CAF1 30698 85 + 1
---UUGUGAUGGAUUAACCGGCGCUUAAGCUGCAGUCGAGCGAUAAGUGCCGCUCAUGGCAGGCCAUUUUGUGUGCUGCCGCUCACUC------------
---..(((((((......(((((((((.(((.......)))..))))))))).....((((.((......)).)))).))).))))..------------ ( -29.70)
>DroMoj_CAF1 24783 87 + 1
GUCGUGUGAUGGAUUAAACGGCUCUUAAGCUGCAGCCGAGCGAUAAGCGACGCUCAUGGCAAGCUAUUUU-UGAGCUGCCAGUGGCAU------------
(((((.(((....))).)))))......((..(....(((((........))))).(((((.(((.....-..)))))))))..))..------------ ( -29.90)
>DroAna_CAF1 25142 85 + 1
---UUGUGAUGGAUUAACCGGCGCUUAAGCUGCAGUCGAGCGAUAAGUGCCGCUCAUGGCAGGCCAUUUUGUGUGCUGCCGCUCACUC------------
---..(((((((......(((((((((.(((.......)))..))))))))).....((((.((......)).)))).))).))))..------------ ( -29.70)
>DroPer_CAF1 29216 85 + 1
---UUGUGAUGGAUUAACCGGCGCUUAAGCUGCAGUCGAGCGAUAAGUGCCGCUCAUGGCAGGCCAUUUUGUGUGCUGCCGCUCACUC------------
---..(((((((......(((((((((.(((.......)))..))))))))).....((((.((......)).)))).))).))))..------------ ( -29.70)
>consensus
___UUGUGAUGGAUUAACCGGCGCUUAAGCUGCAGUCGAGCGAUAAGUGCCGCUCAUGGCAGGCCAUUUUGUGUGCUGCCGCUCACUC____________
.....(((((((......((((......))))((((.(((((........)))))((((....)))).......))))))).)))).............. (-21.34 = -21.45 +   0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,452,872 – 6,452,969
Length 97
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 81.48
Mean single sequence MFE -26.90
Consensus MFE -17.80
Energy contribution -17.83
Covariance contribution 0.03
Combinations/Pair 1.19
Mean z-score -1.51
Structure conservation index 0.66
SVM decision value 0.07
SVM RNA-class probability 0.568910
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6452872 97 - 20766785
AGGUGAUUCAGAAAGGGAACGGCAUCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAAGCGCCGGUUAAUCCAUCACAA---
..(((((........(((..((((...((.....))...)))).(((.((((.((((..(((.......))).)))).)))).))).))))))))..--- ( -26.70)
>DroVir_CAF1 19347 85 - 1
--------------AGCUGUGGCAGCUCA-AAAAUAGCAGGCCAUGAGCGCCGCUUAUCGCUCAGCUGCAGCUUAAGAGCCGUUUAAUCCAUCACGCGAC
--------------(((((..((.(((..-.....)))......((((((........))))))))..)))))........................... ( -23.80)
>DroPse_CAF1 30698 85 - 1
------------GAGUGAGCGGCAGCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAAGCGCCGGUUAAUCCAUCACAA---
------------..((((..(((((..((.....))..))))).(((.((((.((((..(((.......))).)))).)))).))).....))))..--- ( -28.80)
>DroMoj_CAF1 24783 87 - 1
------------AUGCCACUGGCAGCUCA-AAAAUAGCUUGCCAUGAGCGUCGCUUAUCGCUCGGCUGCAGCUUAAGAGCCGUUUAAUCCAUCACACGAC
------------..(((..((((((((..-.....))).))))).(((((........)))))))).((.(((....))).))................. ( -24.50)
>DroAna_CAF1 25142 85 - 1
------------GAGUGAGCGGCAGCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAAGCGCCGGUUAAUCCAUCACAA---
------------..((((..(((((..((.....))..))))).(((.((((.((((..(((.......))).)))).)))).))).....))))..--- ( -28.80)
>DroPer_CAF1 29216 85 - 1
------------GAGUGAGCGGCAGCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAAGCGCCGGUUAAUCCAUCACAA---
------------..((((..(((((..((.....))..))))).(((.((((.((((..(((.......))).)))).)))).))).....))))..--- ( -28.80)
>consensus
____________GAGUGAGCGGCAGCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAAGCGCCGGUUAAUCCAUCACAA___
...................((((.((..........))((((..((((((........))))))...)))).......)))).................. (-17.80 = -17.83 +   0.03)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,452,893 – 6,452,993
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 88.30
Mean single sequence MFE -36.08
Consensus MFE -28.42
Energy contribution -28.58
Covariance contribution 0.16
Combinations/Pair 1.18
Mean z-score -1.56
Structure conservation index 0.79
SVM decision value 0.23
SVM RNA-class probability 0.644473
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6452893 100 - 20766785
GCGGCAUGCGUGCCAUUUCGGGGCAGGUGAUUCAGAAAGGGAACGGCAUCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAA
((((((....))))....((((((((((.(((..(...(....)(......).)..))).))))))).(((((((......))))))).)))..)).... ( -32.80)
>DroSec_CAF1 28625 100 - 1
GCGGCAGGCGUGCCAUUUCGGGGCAGGUGAUUCGGAAAGGGAACGGCAUCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAA
(((((((((.((((.......)))).((((((((.........))).)))))........))))))).(((((((......)))))))...))....... ( -39.10)
>DroEre_CAF1 27137 100 - 1
GCGGCAGGCGUGCCAUUUCGGGGCAGGUGAUUCGGAAAGGGAACGGCAUCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAA
(((((((((.((((.......)))).((((((((.........))).)))))........))))))).(((((((......)))))))...))....... ( -39.10)
>DroYak_CAF1 30343 100 - 1
GCGGCAGGCGUGCCAUUUCGGGGCAGGUGAUUCGGAAAGGGAGCGGCAUCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAA
(((((((((.((((.......)))).((((((((.........))).)))))........))))))).(((((((......)))))))...))....... ( -38.10)
>DroAna_CAF1 25163 82 - 1
GUUGCAGGUGUGGCAUCU------------------GAGUGAGCGGCAGCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAA
((((((((((((((.((.------------------....))...))..)))))...((((....))))((((((......))))))..))))))).... ( -31.30)
>consensus
GCGGCAGGCGUGCCAUUUCGGGGCAGGUGAUUCGGAAAGGGAACGGCAUCACACAAAAUGGCCUGCCAUGAGCGGCACUUAUCGCUCGACUGCAGCUUAA
(((((((((((.((.(((((((........))))))).))..))(......)........))))))).(((((((......)))))))...))....... (-28.42 = -28.58 +   0.16)

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 10:11:18 2006