Locus 6402

Sequence ID 2L_DroMel_CAF1
Location 17,974,861 – 17,975,098
Length 237
Max. P 0.744708
window10216 window10217 window10218

overview

Window 6

Location 17,974,861 – 17,974,981
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.72
Mean single sequence MFE -41.87
Consensus MFE -25.74
Energy contribution -25.17
Covariance contribution -0.58
Combinations/Pair 1.45
Mean z-score -1.66
Structure conservation index 0.61
SVM decision value 0.10
SVM RNA-class probability 0.585417
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17974861 120 - 22407834
GGUAGCAUUAGUCAAUCGGGAAUGAAGUACGAGAAGAUAAUGAGUAAAUUGCCGCAGAUCGAGAAAACGUUGGAGGCGGUGCGAGCAAAGGAUUCCUGUCUGGGGGGCUGGUGCAAGGAA
....(((((((((...(((((((....(((.............)))....(((((...((.((......)).)).)))))...........))))))).......)))))))))...... ( -30.02)
>DroVir_CAF1 247566 120 - 1
GGCAGCAUCAGUCAGUCGGGCAUGAAGUAUGAGAAGAUCAUGAGCGAGCUGCCGCAGAUCAGCAGCACACUGGGGCUGGUGCGUGAGAAGGAUGCCUGCCUGGCGGGCUGGUGCAAGGAG
....(((((((((.(((((((......(((((.....)))))((.(.(((((.........))))).).)).((((.....(....)......))))))))))).)))))))))...... ( -47.60)
>DroGri_CAF1 260672 120 - 1
GGCAGCAUCAGUGAGUCGGGCAUGAAGUAUGAGAAUAUUAUGCGCGAGUUGCCACAGAUCAGUGGCACGUUGGAGUUGGUCCGGCAGAAGGAUGCCUGCUUGGCGGGGUGGUGCAAGGAA
.(((.((((.((.((.(((((((...((((((.....))))))....((.(((((......)))))))((((((.....))))))......))))))).)).))..)))).)))...... ( -44.70)
>DroMoj_CAF1 293595 120 - 1
GGCAGCAUCAGUGAGUCGGGCAUGAAGUACGAGAAGAUCAUGAGCGAGCUGCCACAGAUCAGCAGCACGCUGGAGCUGGUCAGGGCCAAGGAUGCCUGCCUGGCGGGCUGGUGCAAGGAG
....((((((((..(((((((..............((((((.((((.(((((.........))))).)))).)...))))).((((.......)))))))))))..))))))))...... ( -50.70)
>DroAna_CAF1 181534 120 - 1
GGCAGCAUCAGCCAGUCGGGAAUGAAGUACGAAAAGAUAAUGACCGAGCUGCCGCAGAUCGCCAAGACCCUGGACGCUGUGCGAGAGAAGGACGCUUGCCUGGCAGGAUGGUGCAAGGAA
.(((.((((......((((..((................))..)))).(((((((((....(((......)))...))))(((((.(.....).)))))..))))))))).)))...... ( -37.19)
>DroPer_CAF1 281976 120 - 1
GGUAGCAUCAGUCAGUCAGGCAUGAAGUACGAGAAGAUCAUGAGCGAGCUGCCGCAGAUCGGAGAGACACUUGAAGUGGUGAGGGCCAAAGAUGCCUGUCUGGCGGGCUGGUGCAAGGAG
....(((((((((.(((((((..............((((....(((......))).)))).......((((......)))).((((.......))))))))))).)))))))))...... ( -41.00)
>consensus
GGCAGCAUCAGUCAGUCGGGCAUGAAGUACGAGAAGAUCAUGAGCGAGCUGCCGCAGAUCAGCAACACGCUGGAGGUGGUGCGGGAGAAGGAUGCCUGCCUGGCGGGCUGGUGCAAGGAA
....(((((((((.((((((((...(((.((...(.....)...)).)))((((....((((.......))))...))))................)))))))).)))))))))...... (-25.74 = -25.17 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,974,941 – 17,975,058
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.99
Mean single sequence MFE -39.02
Consensus MFE -29.28
Energy contribution -28.27
Covariance contribution -1.02
Combinations/Pair 1.42
Mean z-score -1.35
Structure conservation index 0.75
SVM decision value 0.07
SVM RNA-class probability 0.567702
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17974941 117 - 22407834
UUUUGACGGAUGUGAGUUUAAUCCAGGAAUUCCUACAGAGUGCCCUGCAGUUCCUGCAAAAUGUGCCCAUGGAUGAGGGUAGCAUUAGUCAAUCGGGAAUGAAGUACGAGAAGAUAA
..(((((((((.........))))(((....)))....(((((..(((((...))))).....(((((........)))))))))).)))))(((...........)))........ ( -27.60)
>DroVir_CAF1 247646 117 - 1
UACUCAACGAUGUGGGCGCCGUGCAGGAGUUUCUGCAGAAUGCGCUGCAGUUCCUGCAGAACGUGCCCAUGGACGAGGGCAGCAUCAGUCAGUCGGGCAUGAAGUAUGAGAAGAUCA
..((((((...((((((((..((((((((...((((((......))))))))))))))....)))))))).(((...(((.......))).))).........)).))))....... ( -44.30)
>DroGri_CAF1 260752 117 - 1
UCCUCAACGAUGUACAGGCGGUGCAGGAGUUUUUGCAGAAUGCGUUGCAAUUCCUGCAGAAUGUGCCCAUGGACGAGGGCAGCAUCAGUGAGUCGGGCAUGAAGUAUGAGAAUAUUA
..((((((.((((...(((..(((((((((...(((((......))))))))))))))((.(((((((........))))).)))).....)))..))))...)).))))....... ( -38.10)
>DroMoj_CAF1 293675 117 - 1
UACUGAACGACGUGAGCGCCGUGCAGGAGUUUCUGCAGAACGCGCUGCAGUUCCUGCAGAACGUGCCCAUGGACGAGGGCAGCAUCAGUGAGUCGGGCAUGAAGUACGAGAAGAUCA
((((((..(.(....))((..((((((((...((((((......)))))))))))))).....(((((........))))))).))))))..(((..(.....)..)))........ ( -41.20)
>DroAna_CAF1 181614 117 - 1
UCCUGGCGGACGUCAGUCUGAUCCAGGAGUUCCUGCAGAGCGCACUGCAGUUCCUACAAAACGUUCCUAUGGACGAGGGCAGCAUCAGCCAGUCGGGAAUGAAGUACGAAAAGAUAA
(((((((((((....)))))..))))))....((((((......))))))(((.(((....(((((((...(((...(((.......))).))))))))))..))).)))....... ( -41.20)
>DroPer_CAF1 282056 117 - 1
UCCUCACGGAUGUGGGAGUGGUGCAGGAAUUUCUGCAGAAUGCCCUGCAGUUUCUGCAGAACGUGCCCAUGGACGAGGGUAGCAUCAGUCAGUCAGGCAUGAAGUACGAGAAGAUCA
..(((.((..((((((.((..((((((((...((((((......))))))))))))))..))...))))))..))...(((.(.((((((.....))).))).)))))))....... ( -41.70)
>consensus
UCCUCAACGAUGUGAGCGCGGUGCAGGAGUUUCUGCAGAAUGCGCUGCAGUUCCUGCAGAACGUGCCCAUGGACGAGGGCAGCAUCAGUCAGUCGGGCAUGAAGUACGAGAAGAUCA
..........((((.......((((((((...((((((......))))))))))))))...(((((((...(((...(((.......))).))))))))))...))))......... (-29.28 = -28.27 +  -1.02)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,974,981 – 17,975,098
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 78.75
Mean single sequence MFE -47.15
Consensus MFE -29.02
Energy contribution -28.67
Covariance contribution -0.36
Combinations/Pair 1.48
Mean z-score -1.69
Structure conservation index 0.62
SVM decision value 0.46
SVM RNA-class probability 0.744708
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17974981 117 - 22407834
CGGUAUUGGGAGUCUCUGGCGAAUAGCCUGCGAACUGCCAUUUUGACGGAUGUGAGUUUAAUCCAGGAAUUCCUACAGAGUGCCCUGCAGUUCCUGCAAAAUGUGCCCAUGGAUGAG
.(((((.(((...(((((..((((..((((.(((((..((((......))))..)))))....)))).))))...)))))..)))(((((...)))))....))))).......... ( -34.60)
>DroVir_CAF1 247686 117 - 1
CGCUAUUGGGAGGCGCUCGCGAAUAGUCUGCGUGCAUCGAUACUCAACGAUGUGGGCGCCGUGCAGGAGUUUCUGCAGAAUGCGCUGCAGUUCCUGCAGAACGUGCCCAUGGACGAG
((((((.(((.((((((((((.......)))..((((((........))))))))))))).((((((((...((((((......)))))))))))))).......))))))).)).. ( -52.30)
>DroPse_CAF1 280693 117 - 1
CGGUACUGGGAGUCGCUGUCCAACAGCUUACGCUCCUCCAUCCUCACGGAUGUGGGAGUGGUGCAGGAAUUUCUGCAGAAUGCCCUGCAGUUUCUGCAGAACGUGCCCAUGGAUGAG
.(((((........((((.....))))...((((((..(((((....)))))..)))))).((((((((...((((((......))))))))))))))....))))).......... ( -49.90)
>DroMoj_CAF1 293715 117 - 1
CGCUACUGGGAGGCGCUCGCGACGAGCCUGCGCGCGUCCAUACUGAACGACGUGAGCGCCGUGCAGGAGUUUCUGCAGAACGCGCUGCAGUUCCUGCAGAACGUGCCCAUGGACGAG
(((((.((((.(((((((((((((.((....)).))))(.....)......))))))))).((((((((...((((((......)))))))))))))).......))))))).)).. ( -54.10)
>DroAna_CAF1 181654 117 - 1
CGCUACUGGGAGGCGUUGGCCAGCAGUCUCCGGUCCUCGAUCCUGGCGGACGUCAGUCUGAUCCAGGAGUUCCUGCAGAGCGCACUGCAGUUCCUACAAAACGUUCCUAUGGACGAG
........(((((((((....))).)))))).((((....(((((((((((....)))))..))))))....((((((......))))))....................))))... ( -41.10)
>DroPer_CAF1 282096 117 - 1
CGGUACUGGGAGUCGCUGUCCAACAGCUUACGCUCCUCCAUCCUCACGGAUGUGGGAGUGGUGCAGGAAUUUCUGCAGAAUGCCCUGCAGUUUCUGCAGAACGUGCCCAUGGACGAG
((...(((((.(((((((.....))))...((((((..(((((....)))))..)))))).((((((((...((((((......))))))))))))))).))...)))).)..)).. ( -50.90)
>consensus
CGCUACUGGGAGGCGCUGGCCAACAGCCUGCGCUCCUCCAUCCUCACGGAUGUGAGAGUGGUGCAGGAAUUUCUGCAGAAUGCCCUGCAGUUCCUGCAGAACGUGCCCAUGGACGAG
((....((((....((((.....))))....((((...(((((....)))))...))))..((((((((...((((((......)))))))))))))).......))))....)).. (-29.02 = -28.67 +  -0.36)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:08 2006