Locus 2017

Sequence ID 2L_DroMel_CAF1
Location 5,466,348 – 5,466,530
Length 182
Max. P 0.756653
window3245 window3246 window3247

overview

Window 5

Location 5,466,348 – 5,466,468
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.24
Mean single sequence MFE -56.00
Consensus MFE -38.74
Energy contribution -37.88
Covariance contribution -0.86
Combinations/Pair 1.37
Mean z-score -1.34
Structure conservation index 0.69
SVM decision value 0.04
SVM RNA-class probability 0.554909
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5466348 120 - 22407834
GCUUGAGCGGCGGCAGCUUGCUGAUUGGCGCUGGCCAAAAAGCCGGCGGUAAGUUGGGGCCACUGCUGCUGGAACAUGUGGAAGGCGCCCAGGCCGGGGGGUGGCGGAGGUGGUCCGGCU
.....(((((.(((..((.(((...((.(((((((......))))))).))))).)).))).)))))((((((.(((.(....(.(((((........))))).)..).))).)))))). ( -52.70)
>DroVir_CAF1 125454 108 - 1
GCCUGAGCAGCGGCUGCCUGCUGAUUGGCGCUGGCCAAAAAGCCGGCGGUCAGCUGCGGCCAUUGCUGCUGGAACAUGUGAAAGGCGCCCAGGCCGGGUGGUGG---CGGC---------
(((...((((((((((((.(((..(((((....)))))..))).))))))).))))).(((((..((((........))....(((......))).))..))))---))))--------- ( -56.40)
>DroGri_CAF1 133292 111 - 1
GCUUGGGCGGCUGCCGCCUGCUGAUUGGCGCUGGCCAGAAAGCCGGCGGUUAGCUGCGGCCAUUGCUGCUGGAACAUGUGAAAGGCGCCCAGGCCGGGGGGUGGAUGGGGU---------
((((((((((((((((((.(((..(((((....)))))..))).))))).)))).(((((....)))))................))))))))).................--------- ( -52.60)
>DroWil_CAF1 127166 120 - 1
GCCUGAGCAGCGGCCGCCUGUUGAUUGGCGCUGGCCAAGAAUCCGGCUGUCAAUUGCGGCCAUUGCUGCUGGAACAUAUGAAAAGCUCCCAGACCCGGCGGUGGGGGAGGAGGGCCGGCA
(((..((((((((((((.....((((((((((((........))))).)))))))))))))...))))))((..(...(....).(((((..(((....)))..)))))..)..))))). ( -55.30)
>DroMoj_CAF1 139573 108 - 1
GCCUGGGCGGCAGCGGCCUGCUGAUUGGCGCUGGCCAAAAAGCCGGCCGUCAGCUGCGGCCAUUGCUGCUGGAACAUGUGAAAGGCGCCGAGGCCGGGCGGCGG---UGGU---------
......(((((.((((((.(((..(((((....)))))..))).))))))..))))).((((((((((((((.....(((.....))).....)).))))))))---))))--------- ( -55.70)
>DroAna_CAF1 91048 120 - 1
GCUUGAGCGGCGGCGGCCUGCUGAUUGGCGCUCGCCAAGAAGCCGGCGGUAAGCUGCGGCCACUGCUGCUGGAACAUGUGGAAGGCCCCCAGCCCGGGGGGUGGUGGCGGGGGUCCGGCC
(.((.((((((((.((((.(((..(((((....)))))..)))..((((....)))))))).)))))))).)).)....((..(((((((.((((........).)))))))).))..)) ( -63.30)
>consensus
GCCUGAGCGGCGGCCGCCUGCUGAUUGGCGCUGGCCAAAAAGCCGGCGGUCAGCUGCGGCCAUUGCUGCUGGAACAUGUGAAAGGCGCCCAGGCCGGGGGGUGG_GGAGGU_________
((((.((((((((..(((.((((((...(((((((......)))))))))))))...)))..))))))))....(....)..))))(((....(((.....)))....)))......... (-38.74 = -37.88 +  -0.86)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,466,388 – 5,466,501
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.21
Mean single sequence MFE -61.33
Consensus MFE -50.06
Energy contribution -49.15
Covariance contribution -0.91
Combinations/Pair 1.37
Mean z-score -2.06
Structure conservation index 0.82
SVM decision value 0.49
SVM RNA-class probability 0.756653
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5466388 113 - 22407834
-------GCCGCCUGCGCCUGCGCUUGGGCCUGAGCGGCGGCUUGAGCGGCGGCAGCUUGCUGAUUGGCGCUGGCCAAAAAGCCGGCGGUAAGUUGGGGCCACUGCUGCUGGAACAUGUG
-------((((((.((((((......))))....))))))))((.((((((((..(((..(..((((.(((((((......))))))).).)))..))))..)))))))).))....... ( -54.00)
>DroVir_CAF1 125482 116 - 1
-GCC---GCGGCCUGCGCUUGCGCCUGCGCCUGGGCGGCGGCCUGAGCAGCGGCUGCCUGCUGAUUGGCGCUGGCCAAAAAGCCGGCGGUCAGCUGCGGCCAUUGCUGCUGGAACAUGUG
-(((---((.((((((((........))))..)))).))))).(.((((((((((((..((((((...(((((((......))))))))))))).))))))...)))))).)........ ( -68.10)
>DroGri_CAF1 133323 120 - 1
AGCCGCAGCUGCCUGAGCUUGCGCUUGCGCCUGAGCGGCAGCUUGGGCGGCUGCCGCCUGCUGAUUGGCGCUGGCCAGAAAGCCGGCGGUUAGCUGCGGCCAUUGCUGCUGGAACAUGUG
.((((((((((((.((((....))))..(((..(((....)))..)))))).((((((.(((..(((((....)))))..))).)))))).))))))))).................... ( -64.60)
>DroWil_CAF1 127206 113 - 1
-------GCAGCUUGAGCCUGCGCCUGCGCCUGGGCAGCUGCCUGAGCAGCGGCCGCCUGUUGAUUGGCGCUGGCCAAGAAUCCGGCUGUCAAUUGCGGCCAUUGCUGCUGGAACAUAUG
-------((((((...(((((((....)))..)))))))))).(.((((((((((((.....((((((((((((........))))).)))))))))))))...)))))).)........ ( -53.40)
>DroMoj_CAF1 139601 116 - 1
-GCC---GCCGCCUGCGCUUGCGCCUGCGCCUGAGCGGCGGCCUGGGCGGCAGCGGCCUGCUGAUUGGCGCUGGCCAAAAAGCCGGCCGUCAGCUGCGGCCAUUGCUGCUGGAACAUGUG
-(((---((((((.((((........))))..).)))))))).(.((((((((.((((.((.(.(((((((((((......))))).))))))).)))))).)))))))).)........ ( -65.80)
>DroAna_CAF1 91088 113 - 1
-------GCGGCCUGGGCCUGCGCCUGCGCUUGGGCGGCUGCUUGAGCGGCGGCGGCCUGCUGAUUGGCGCUCGCCAAGAAGCCGGCGGUAAGCUGCGGCCACUGCUGCUGGAACAUGUG
-------((((((...(((((((....)))..))))))))))((.((((((((.((((.(((..(((((....)))))..)))..((((....)))))))).)))))))).))....... ( -62.10)
>consensus
_______GCCGCCUGCGCCUGCGCCUGCGCCUGAGCGGCGGCCUGAGCGGCGGCCGCCUGCUGAUUGGCGCUGGCCAAAAAGCCGGCGGUCAGCUGCGGCCAUUGCUGCUGGAACAUGUG
.......((((((...(((((((....)))..)))))))))).(.((((((((..(((.((((((...(((((((......)))))))))))))...)))..)))))))).)........ (-50.06 = -49.15 +  -0.91)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 5,466,428 – 5,466,530
Length 102
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 84.27
Mean single sequence MFE -56.83
Consensus MFE -42.62
Energy contribution -41.90
Covariance contribution -0.72
Combinations/Pair 1.33
Mean z-score -1.73
Structure conservation index 0.75
SVM decision value -0.00
SVM RNA-class probability 0.531536
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5466428 102 - 22407834
GCGUCCGGUUGGCGGCCAUCGCUGCGGCU---GCCGCCUGCGCCUGCGCUUGGGCCUGAGCGGCGGCUUGAGCGGCGGCAGCUUGCUGAUUGGCGCUGGCCAAAA
......(((..(((.(((...(.((((((---((((((.((....))(((..((((........))))..)))))))))))).))).)..))))))..))).... ( -59.50)
>DroVir_CAF1 125522 105 - 1
GUGUGCGAUUGGCGGCCAUUGCUGCAGCGGCCGCGGCCUGCGCUUGCGCCUGCGCCUGGGCGGCGGCCUGAGCAGCGGCUGCCUGCUGAUUGGCGCUGGCCAAAA
....(((...(((((((...(((((...((((((.((((((((........))))..)))).))))))...)))))))))))))))...(((((....))))).. ( -59.60)
>DroPse_CAF1 102358 102 - 1
GGGUUCGAUUGGCAGCCAUCGCCGCUGCG---GCGGCCUGCGCCUGCGCUUGGGCCUGGGCUGCAGCCUGGGCGGCGGCCGCCUGUUGAUUGGCGCUGGCCAGAA
....(((((.(((.(((..((((((((((---((((((((((....)))..)))))...))))))))...))))..))).))).)))))(((((....))))).. ( -57.30)
>DroWil_CAF1 127246 102 - 1
GGGUACGAUUGGCGGCGAUGGCAGCGGCG---GCAGCUUGAGCCUGCGCCUGCGCCUGGGCAGCUGCCUGAGCAGCGGCCGCCUGUUGAUUGGCGCUGGCCAAGA
........(((((((((....((((((((---((.......(((((((....)))..)))).(((((....))))).)))))).)))).....)))).))))).. ( -50.10)
>DroYak_CAF1 93762 102 - 1
GCGUCCGGUUGGCGGCCAUUGCUGCGGCG---GCCGCCUGCGCUUGCGCUUGAGCCUGAGCGGCGGCUUGGGCGGCGGCAGCUUGCUGAUUGGCGCUGGCCAGAA
...((.(((..(((.(((...(.(((((.---((((((.(((....)))....(((..(((....)))..))))))))).)).))).)..))))))..))).)). ( -57.20)
>DroPer_CAF1 103075 102 - 1
GGGUUCGAUUGGCAGCCAUCGCCGCUGCG---GCGGCCUGCGCCUGCGCUUGGGCCUGGGCUGCAGCCUGGGCGGCGGCCGCCUGUUGAUUGGCGCUGGCCAGAA
....(((((.(((.(((..((((((((((---((((((((((....)))..)))))...))))))))...))))..))).))).)))))(((((....))))).. ( -57.30)
>consensus
GGGUCCGAUUGGCGGCCAUCGCUGCGGCG___GCGGCCUGCGCCUGCGCUUGGGCCUGGGCGGCGGCCUGAGCGGCGGCCGCCUGCUGAUUGGCGCUGGCCAAAA
.....((((.(((.(((.((((((((((....)))))(((((((((.((....)).))))).))))....))))).))).))).)))).(((((....))))).. (-42.62 = -41.90 +  -0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:13 2006