Locus 1101

Sequence ID 2L_DroMel_CAF1
Location 3,005,527 – 3,005,752
Length 225
Max. P 0.996064
window1788 window1789 window1790 window1791

overview

Window 8

Location 3,005,527 – 3,005,636
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.22
Mean single sequence MFE -26.10
Consensus MFE -19.01
Energy contribution -19.32
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -1.61
Structure conservation index 0.73
SVM decision value 0.21
SVM RNA-class probability 0.636273
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3005527 109 - 22407834
UGA-----------AUAGGACGUGAGAAGGGCGGUGUGGAAACAAUAAAGAGGCCCGAAAACAAAGCAUUAUGUAAGCAUUAGCACGCUUUAACCUCCCGCACGUCUAGUUAAACAUAAA
..(-----------((.(((((((....(((.(((.((....)).....(((((......(((........)))..((....))..))))).))).))).))))))).)))......... ( -29.00)
>DroSec_CAF1 13063 104 - 1
UGA-----------AAAAGACGUGAAAAGGGCGGCGAGGAAACAAUAAAGAGGCCCGAAAACAAAGCAUUAUGUAAGCAUUAGCACGCUUUAAUCUCCCGCACGUCCAGUUAAAC-----
...-----------....((((((....(((.((...(....)......(((((......(((........)))..((....))..)))))..)).))).)))))).........----- ( -21.80)
>DroEre_CAF1 12991 106 - 1
CGA-----------AAAAUACGUGAGAAGGGCGGGUAGGAAACAAUAACGAGACCCGAAAACAAAGCGUUAUGUAAGCAUUAGCACGCUUUAACCUCCCGCACGUCCAGUUAAAUAU---
...-----------.....(((((....((((((((.(..........)...))))).....(((((((.(((....)))....))))))).....))).)))))............--- ( -25.50)
>DroYak_CAF1 12694 117 - 1
UGAAAAACUCGUGAAAAAUACGUGAGAAGGGCGGGGAGGUAACAAUAAAGAGAGCCGAAAACAAUGCAUUAUGUAAGCAUUAGCACGCUUUAACCUCCCGCACGUCCAGUUAACUAU---
.......((((((.......))))))..((((((((((((.....(((((.(.((.(....)(((((.........))))).)).).))))))))))))...)))))..........--- ( -28.10)
>consensus
UGA___________AAAAGACGUGAGAAGGGCGGGGAGGAAACAAUAAAGAGACCCGAAAACAAAGCAUUAUGUAAGCAUUAGCACGCUUUAACCUCCCGCACGUCCAGUUAAACAU___
..................((((((....(((.((...(....)......................((...(((....)))..)).........)).))).)))))).............. (-19.01 = -19.32 +   0.31)

alignment

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secondary structure

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Window 9

Location 3,005,607 – 3,005,715
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.86
Mean single sequence MFE -39.01
Consensus MFE -30.85
Energy contribution -31.10
Covariance contribution 0.25
Combinations/Pair 1.10
Mean z-score -1.71
Structure conservation index 0.79
SVM decision value 0.46
SVM RNA-class probability 0.745149
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3005607 108 + 22407834
UCCACACCGCCCUUCUCACGUCCUAU-----------UCACCUAUU-UUCACGUCUUUUGUACGUGAGGUAGGCCCAGUUGGGCGGAAGGGCGAGAAAGUCGAGGACAUUUUAGGGCCCU
........(((((((((..(((((.(-----------((..(((((-(.((((((....).)))))))))))((((....))))))))))))))))).(((...)))......))))... ( -38.70)
>DroSec_CAF1 13138 109 + 1
UCCUCGCCGCCCUUUUCACGUCUUUU-----------UCACGUAUUUUUCACGUCUUCUGUACGUGAGGUAGGCCCAGUUGGGCGGAAGGGCGAGAAAGUCGAGGACAUUUUAGGGUCCU
((((((((((((((((.....((.((-----------((((((((..............)))))))))).))((((....))))))))))))).....).)))))).............. ( -39.44)
>DroEre_CAF1 13068 109 + 1
UCCUACCCGCCCUUCUCACGUAUUUU-----------UCGUGUAUUUUCCACGUCUUUUGUACGUGACGUAGGCCCAGUUGGGAGGAAGGGCGAGAAAGUCGAGGACAUUUUAGGGCCUU
(((((..((((((((((((((((...-----------.((((.......))))......))))))))......(((....)))..)))))))).....(((...)))....))))).... ( -37.60)
>DroYak_CAF1 12771 120 + 1
ACCUCCCCGCCCUUCUCACGUAUUUUUCACGAGUUUUUCAUGUAGUUUUCACGUCUCGUGUACGUGAGGUAGGCCCAGUUGGGUGGAAGGGCGAGAGAGUCGAGGACAUUUUAGGGCCCU
....((((((((((((((((((.....((((((......((((.......))))))))))))))))).....((((....)))).)))))))).(((((((...))).)))).))).... ( -40.30)
>consensus
UCCUCCCCGCCCUUCUCACGUAUUUU___________UCACGUAUUUUUCACGUCUUUUGUACGUGAGGUAGGCCCAGUUGGGCGGAAGGGCGAGAAAGUCGAGGACAUUUUAGGGCCCU
.((....(((((((((...............................((((((((....).)))))))....((((....)))))))))))))((((.(((...))).)))).))..... (-30.85 = -31.10 +   0.25)

alignment

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secondary structure

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Window 0

Location 3,005,607 – 3,005,715
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.86
Mean single sequence MFE -40.59
Consensus MFE -32.47
Energy contribution -34.35
Covariance contribution 1.88
Combinations/Pair 1.07
Mean z-score -3.25
Structure conservation index 0.80
SVM decision value 2.65
SVM RNA-class probability 0.996064
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3005607 108 - 22407834
AGGGCCCUAAAAUGUCCUCGACUUUCUCGCCCUUCCGCCCAACUGGGCCUACCUCACGUACAAAAGACGUGAA-AAUAGGUGA-----------AUAGGACGUGAGAAGGGCGGUGUGGA
.((((........))))((.((...(.(((((((((((....(((.(((((..((((((.......)))))).-..)))))..-----------.)))...))).))))))))).)).)) ( -38.50)
>DroSec_CAF1 13138 109 - 1
AGGACCCUAAAAUGUCCUCGACUUUCUCGCCCUUCCGCCCAACUGGGCCUACCUCACGUACAGAAGACGUGAAAAAUACGUGA-----------AAAAGACGUGAAAAGGGCGGCGAGGA
(((((........)))))...((((.((((((((..((((....)))).....((((((.......(((((.....)))))..-----------.....)))))).)))))))).)))). ( -38.74)
>DroEre_CAF1 13068 109 - 1
AAGGCCCUAAAAUGUCCUCGACUUUCUCGCCCUUCCUCCCAACUGGGCCUACGUCACGUACAAAAGACGUGGAAAAUACACGA-----------AAAAUACGUGAGAAGGGCGGGUAGGA
.....((((....(((...)))...((((((((((..(((....)))......(((((((.......((((.......)))).-----------....))))))))))))))))))))). ( -37.80)
>DroYak_CAF1 12771 120 - 1
AGGGCCCUAAAAUGUCCUCGACUCUCUCGCCCUUCCACCCAACUGGGCCUACCUCACGUACACGAGACGUGAAAACUACAUGAAAAACUCGUGAAAAAUACGUGAGAAGGGCGGGGAGGU
(((((........)))))...(((((.((((((((..(((....)))......(((((((((((((.((((.......)))).....)))))).....)))))))))))))))))))).. ( -47.30)
>consensus
AGGGCCCUAAAAUGUCCUCGACUUUCUCGCCCUUCCGCCCAACUGGGCCUACCUCACGUACAAAAGACGUGAAAAAUACAUGA___________AAAAGACGUGAGAAGGGCGGGGAGGA
(((((........)))))...((((((((((((((.((((....)))).....((((((.......)))))).................................)))))))))))))). (-32.47 = -34.35 +   1.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,005,636 – 3,005,752
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.98
Mean single sequence MFE -29.52
Consensus MFE -27.20
Energy contribution -26.82
Covariance contribution -0.38
Combinations/Pair 1.10
Mean z-score -1.34
Structure conservation index 0.92
SVM decision value 0.10
SVM RNA-class probability 0.581688
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3005636 116 - 22407834
UGCCAUGGGAUUACGAAACCCGAGAUGA---UAAUUUAUGAGGGCCCUAAAAUGUCCUCGACUUUCUCGCCCUUCCGCCCAACUGGGCCUACCUCACGUACAAAAGACGUGAA-AAUAGG
..(((((((.....(((...((((((((---....)))(((((((........)))))))....)))))...)))..))))..))).((((..((((((.......)))))).-..)))) ( -31.20)
>DroSec_CAF1 13167 117 - 1
UGCCAUGGGAUUACGAAACCCGAGAUGA---UAAUUUAUGAGGACCCUAAAAUGUCCUCGACUUUCUCGCCCUUCCGCCCAACUGGGCCUACCUCACGUACAGAAGACGUGAAAAAUACG
.(((.((((.....(((...((((((((---....)))(((((((........)))))))....)))))...)))..))))....))).....((((((.......))))))........ ( -30.50)
>DroEre_CAF1 13097 117 - 1
CGCCAUGGGAUUACGAAACCCGAGAUAA---UAAUUUAUGAAGGCCCUAAAAUGUCCUCGACUUUCUCGCCCUUCCUCCCAACUGGGCCUACGUCACGUACAAAAGACGUGGAAAAUACA
.(((.(((((....(((...((((((((---....)))(((.(((........))).)))....)))))...))).)))))....)))(((((((..........)))))))........ ( -26.90)
>DroYak_CAF1 12811 120 - 1
UGCCAUGGGAUUACGAAACCCGAGAUAAUAAUAAUUUAUGAGGGCCCUAAAAUGUCCUCGACUCUCUCGCCCUUCCACCCAACUGGGCCUACCUCACGUACACGAGACGUGAAAACUACA
.(((.((((.....(((...(((((..((((....))))((((((........)))))).....)))))...)))..))))....))).....((((((.......))))))........ ( -29.50)
>consensus
UGCCAUGGGAUUACGAAACCCGAGAUAA___UAAUUUAUGAGGGCCCUAAAAUGUCCUCGACUUUCUCGCCCUUCCGCCCAACUGGGCCUACCUCACGUACAAAAGACGUGAAAAAUACA
.(((.((((.....(((...((((((((.......)))(((((((........)))))))....)))))...)))..))))....))).....((((((.......))))))........ (-27.20 = -26.82 +  -0.38)

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 09:53:41 2006