Locus 4479

Sequence ID 3L_DroMel_CAF1
Location 12,970,139 – 12,970,379
Length 240
Max. P 0.995883
window6983 window6984 window6985 window6986 window6987 window6988

overview

Window 3

Location 12,970,139 – 12,970,259
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.25
Mean single sequence MFE -44.52
Consensus MFE -35.14
Energy contribution -36.34
Covariance contribution 1.20
Combinations/Pair 1.08
Mean z-score -2.65
Structure conservation index 0.79
SVM decision value 2.01
SVM RNA-class probability 0.985591
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12970139 120 + 23771897
GUUUGUGCGAAGCCAUGGCCGUCCAGACGCCACUUGUCCUGAUAGUGGUGGUGAUGUACUCAAAUAUCGGUGGCACCCUCACGCCAGUGGGUGAUCCACCCAAUGUGAUCAUUGCCACCA
....(((((..(((((.((..((..((((.....))))..))..)).)))))..))))).........(((((((...(((((....((((((...)))))).)))))....))))))). ( -47.20)
>DroSec_CAF1 87483 120 + 1
GUUUGUGUGAAGCCAUGGCCGUGCAGACGCCACUUGUCCUGAUAGUGGUGGUGAUGUACUCAAAUAUCGGUGGAACCCUCACUCCAGUGGGAGAUCCACCCAAUGUGAUCAUUGCCACCA
(((((..((..((....))))..))))).................((((((..(((...(((......((((((.(.(((((....))))).).)))))).....))).)))..)))))) ( -45.50)
>DroSim_CAF1 92349 120 + 1
GUUUGUGCGAAGCCAUGGCCGUCCAGACGCCACUUGUCCUGAUAGUGGUGGUGAUGUACUCAAAUAUCGGUGGCACCCUCACUCCAGUUGGAGAUCCACCCAAUGUGAUCAUUGCCACCA
....(((((..(((((.((..((..((((.....))))..))..)).)))))..))))).........(((((((...((((....(((((........)))))))))....))))))). ( -41.60)
>DroEre_CAF1 92998 120 + 1
GUUUAUGCGAAGCCAUGGCCGUCCGGACACCACUCGUCCUGAUAGCUGUGGUGAUGUACUCCAAUAUCGGUGGCACCCUCACACCGGUGGGUGAUCCACCCAAUGUGAUCAUUGCCACCA
.....((((..((((((((..((.((((.......)))).))..))))))))..))))..........(((((((...(((((....((((((...)))))).)))))....))))))). ( -50.80)
>DroYak_CAF1 91434 120 + 1
GCUUAUGCGAGGCCAUGUCCGUCCAGACACCACUUGUCCUCAUAGCUGUGGUAAUGUACUCCAAUAUCGGUGGCACCCUCACUCCAGUGGGCGAUCCACCCAAUGUGAUCAUUGCCACCA
((....))(((..((((((......)))(((((..((.......)).))))).)))..))).......(((((((..(((((....))))).((((((.....)).))))..))))))). ( -37.50)
>consensus
GUUUGUGCGAAGCCAUGGCCGUCCAGACGCCACUUGUCCUGAUAGUGGUGGUGAUGUACUCAAAUAUCGGUGGCACCCUCACUCCAGUGGGAGAUCCACCCAAUGUGAUCAUUGCCACCA
....(((((..(((((.((..((..((((.....))))..))..)).)))))..))))).........(((((((..(((((....))))).((((((.....)).))))..))))))). (-35.14 = -36.34 +   1.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,970,179 – 12,970,299
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.00
Mean single sequence MFE -44.76
Consensus MFE -36.92
Energy contribution -36.52
Covariance contribution -0.40
Combinations/Pair 1.21
Mean z-score -2.64
Structure conservation index 0.82
SVM decision value 2.63
SVM RNA-class probability 0.995883
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12970179 120 + 23771897
GAUAGUGGUGGUGAUGUACUCAAAUAUCGGUGGCACCCUCACGCCAGUGGGUGAUCCACCCAAUGUGAUCAUUGCCACCAAUUCGGAAGUGAUCUCCGCCGGAGUGGAUUUCCUCGAUUU
((...((((((..(((...(((......((((((((((.(......).)))))..))))).....))).)))..))))))..))((((((...((((...))))...))))))....... ( -47.00)
>DroSec_CAF1 87523 120 + 1
GAUAGUGGUGGUGAUGUACUCAAAUAUCGGUGGAACCCUCACUCCAGUGGGAGAUCCACCCAAUGUGAUCAUUGCCACCAAUGCGGAGGUGGUCGCCGCCGGAGUGGAUUUCCUCGAUUU
.....((((((..(((...(((......((((((.(.(((((....))))).).)))))).....))).)))..))))))...(((.(((((...)))))((((.....))))))).... ( -46.60)
>DroSim_CAF1 92389 120 + 1
GAUAGUGGUGGUGAUGUACUCAAAUAUCGGUGGCACCCUCACUCCAGUUGGAGAUCCACCCAAUGUGAUCAUUGCCACCAAUGUGGAGGUGGUCGCCGCCGGAGUGGAUUUCCUCGAUUU
...(((((.((((...((((........)))).)))).)))))......((((((((((((...((((((((..((((....))))..))))))))....)).))))))))))....... ( -47.50)
>DroEre_CAF1 93038 120 + 1
GAUAGCUGUGGUGAUGUACUCCAAUAUCGGUGGCACCCUCACACCGGUGGGUGAUCCACCCAAUGUGAUCAUUGCCACCAAUCCAGAGGUGAUCGCCAAAGGAGUGGAUUUCGUUGUAUU
.(((((.(....(((.((((((......(((((((...(((((....((((((...)))))).)))))....)))))))........(((....)))...)))))).))).))))))... ( -43.30)
>DroYak_CAF1 91474 120 + 1
CAUAGCUGUGGUAAUGUACUCCAAUAUCGGUGGCACCCUCACUCCAGUGGGCGAUCCACCCAAUGUGAUCAUUGCCACCAAUACGGAAGUGAUUGCCAAAGGAGUGGAUUUUCUCAAUUU
......((.((.(((.((((((......(((((((..(((((....))))).((((((.....)).))))..)))))))..(((....))).........)))))).))).)).)).... ( -39.40)
>consensus
GAUAGUGGUGGUGAUGUACUCAAAUAUCGGUGGCACCCUCACUCCAGUGGGAGAUCCACCCAAUGUGAUCAUUGCCACCAAUGCGGAGGUGAUCGCCGCCGGAGUGGAUUUCCUCGAUUU
.....((((((((((.((((....(((.(((((((..(((((....))))).((((((.....)).))))..))))))).)))....))))))))))))))(((........)))..... (-36.92 = -36.52 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,970,179 – 12,970,299
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.00
Mean single sequence MFE -42.92
Consensus MFE -33.82
Energy contribution -34.22
Covariance contribution 0.40
Combinations/Pair 1.13
Mean z-score -2.83
Structure conservation index 0.79
SVM decision value 2.34
SVM RNA-class probability 0.992590
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12970179 120 - 23771897
AAAUCGAGGAAAUCCACUCCGGCGGAGAUCACUUCCGAAUUGGUGGCAAUGAUCACAUUGGGUGGAUCACCCACUGGCGUGAGGGUGCCACCGAUAUUUGAGUACAUCACCACCACUAUC
.....(((........))).((.((.(((.((((....((((((((((....((((..(.(((((.....))))).).))))...))))))))))....))))..))).)).))...... ( -40.70)
>DroSec_CAF1 87523 120 - 1
AAAUCGAGGAAAUCCACUCCGGCGGCGACCACCUCCGCAUUGGUGGCAAUGAUCACAUUGGGUGGAUCUCCCACUGGAGUGAGGGUUCCACCGAUAUUUGAGUACAUCACCACCACUAUC
..((((.((((..(((((((((.((.(((((((.((((....))))(((((....)))))))))).))..)).)))))))).)..))))..))))...(((.....)))........... ( -43.00)
>DroSim_CAF1 92389 120 - 1
AAAUCGAGGAAAUCCACUCCGGCGGCGACCACCUCCACAUUGGUGGCAAUGAUCACAUUGGGUGGAUCUCCAACUGGAGUGAGGGUGCCACCGAUAUUUGAGUACAUCACCACCACUAUC
.....(((........))).((.((.((....(((...((((((((((....((((.(..(.(((....))).)..).))))...))))))))))....)))....)).)).))...... ( -40.50)
>DroEre_CAF1 93038 120 - 1
AAUACAACGAAAUCCACUCCUUUGGCGAUCACCUCUGGAUUGGUGGCAAUGAUCACAUUGGGUGGAUCACCCACCGGUGUGAGGGUGCCACCGAUAUUGGAGUACAUCACCACAGCUAUC
...................((.(((.(((...(((..(((((((((((....(((((((((.(((.....))))))))))))...)))))))))).)..)))...))).))).))..... ( -46.60)
>DroYak_CAF1 91474 120 - 1
AAAUUGAGAAAAUCCACUCCUUUGGCAAUCACUUCCGUAUUGGUGGCAAUGAUCACAUUGGGUGGAUCGCCCACUGGAGUGAGGGUGCCACCGAUAUUGGAGUACAUUACCACAGCUAUG
.....(((........)))((.(((.(((.(((((.((((((((((((....((((.((.(((((.....))))).))))))...)))))))))))).)))))..))).))).))..... ( -43.80)
>consensus
AAAUCGAGGAAAUCCACUCCGGCGGCGAUCACCUCCGCAUUGGUGGCAAUGAUCACAUUGGGUGGAUCACCCACUGGAGUGAGGGUGCCACCGAUAUUUGAGUACAUCACCACCACUAUC
....................((.((.(((...(((...((((((((((....((((.((.(((((.....))))).))))))...))))))))))....)))...))).)).))...... (-33.82 = -34.22 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,970,219 – 12,970,339
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.83
Mean single sequence MFE -40.18
Consensus MFE -32.56
Energy contribution -32.52
Covariance contribution -0.04
Combinations/Pair 1.19
Mean z-score -1.44
Structure conservation index 0.81
SVM decision value -0.02
SVM RNA-class probability 0.522122
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12970219 120 + 23771897
ACGCCAGUGGGUGAUCCACCCAAUGUGAUCAUUGCCACCAAUUCGGAAGUGAUCUCCGCCGGAGUGGAUUUCCUCGAUUUCACCAUUCACAUGUUGCCUGGCGUUUUAUUGGCGGCUGUA
.((((((((((((...))))).....(((((((.((........)).)))))))..((((((.(((((..........)))))(((....)))....))))))....)))))))...... ( -38.20)
>DroSec_CAF1 87563 120 + 1
ACUCCAGUGGGAGAUCCACCCAAUGUGAUCAUUGCCACCAAUGCGGAGGUGGUCGCCGCCGGAGUGGAUUUCCUCGAUUUCACCAUUCACAUGUUGCCUGGCGUUAUAAUAGCGGCUGUA
....(((((((((((((((((...((((((((..((........))..))))))))....)).)))))))))))........(((..((.....))..)))(((((...))))))))).. ( -39.60)
>DroSim_CAF1 92429 120 + 1
ACUCCAGUUGGAGAUCCACCCAAUGUGAUCAUUGCCACCAAUGUGGAGGUGGUCGCCGCCGGAGUGGAUUUCCUCGAUUUCACCAUUCACAUGUUGCCUGGCGUUGUAAUGGCGGCUGUA
....(((((((((((((((((...((((((((..((((....))))..))))))))....)).)))))))))).........(((((.(((((((....)))).)))))))).))))).. ( -47.00)
>DroEre_CAF1 93078 120 + 1
ACACCGGUGGGUGAUCCACCCAAUGUGAUCAUUGCCACCAAUCCAGAGGUGAUCGCCAAAGGAGUGGAUUUCGUUGUAUUCACCCUGCACAUGCUGCCAGGUGUUUUAAUGGCGGCUGUA
.(((((((((((((((((.....)).))))))..)))))..(....)))))...((...(((.((((((........)))))))))))(((.(((((((..........)))))))))). ( -41.20)
>DroYak_CAF1 91514 120 + 1
ACUCCAGUGGGCGAUCCACCCAAUGUGAUCAUUGCCACCAAUACGGAAGUGAUUGCCAAAGGAGUGGAUUUUCUCAAUUUCACAAUUCACAUGCUGCCUGGAGUUUUAAUGGCUGGUGUG
(((((((..((((((((((((...(..((((((.((........)).))))))..)....)).))))))).....((((....)))).....)))..)))))))................ ( -34.90)
>consensus
ACUCCAGUGGGAGAUCCACCCAAUGUGAUCAUUGCCACCAAUGCGGAGGUGAUCGCCGCCGGAGUGGAUUUCCUCGAUUUCACCAUUCACAUGUUGCCUGGCGUUUUAAUGGCGGCUGUA
.((((....))))((((((((...(((((((((.((........)).)))))))))....)).))))))...................(((.((((((............))))))))). (-32.56 = -32.52 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,970,219 – 12,970,339
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.83
Mean single sequence MFE -40.32
Consensus MFE -27.06
Energy contribution -28.06
Covariance contribution 1.00
Combinations/Pair 1.23
Mean z-score -2.02
Structure conservation index 0.67
SVM decision value 0.17
SVM RNA-class probability 0.616105
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12970219 120 - 23771897
UACAGCCGCCAAUAAAACGCCAGGCAACAUGUGAAUGGUGAAAUCGAGGAAAUCCACUCCGGCGGAGAUCACUUCCGAAUUGGUGGCAAUGAUCACAUUGGGUGGAUCACCCACUGGCGU
....(((((((((....(((((..((.....))..)))))...(((.((....)).((((...))))........))))))))))))........((.((((((...)))))).)).... ( -41.10)
>DroSec_CAF1 87563 120 - 1
UACAGCCGCUAUUAUAACGCCAGGCAACAUGUGAAUGGUGAAAUCGAGGAAAUCCACUCCGGCGGCGACCACCUCCGCAUUGGUGGCAAUGAUCACAUUGGGUGGAUCUCCCACUGGAGU
....((((((.......(((((..((.....))..))))).....(((........))).))))))..(((((.((((....))))(((((....))))))))))..((((....)))). ( -42.50)
>DroSim_CAF1 92429 120 - 1
UACAGCCGCCAUUACAACGCCAGGCAACAUGUGAAUGGUGAAAUCGAGGAAAUCCACUCCGGCGGCGACCACCUCCACAUUGGUGGCAAUGAUCACAUUGGGUGGAUCUCCAACUGGAGU
....((((((.......(((((..((.....))..))))).....(((........))).))))))..(((((.((((....))))(((((....))))))))))..((((....)))). ( -46.60)
>DroEre_CAF1 93078 120 - 1
UACAGCCGCCAUUAAAACACCUGGCAGCAUGUGCAGGGUGAAUACAACGAAAUCCACUCCUUUGGCGAUCACCUCUGGAUUGGUGGCAAUGAUCACAUUGGGUGGAUCACCCACCGGUGU
....(((((((......(((((.(((.....))).))))).................(((...((......))...))).)))))))......(((..((((((...))))))...))). ( -38.60)
>DroYak_CAF1 91514 120 - 1
CACACCAGCCAUUAAAACUCCAGGCAGCAUGUGAAUUGUGAAAUUGAGAAAAUCCACUCCUUUGGCAAUCACUUCCGUAUUGGUGGCAAUGAUCACAUUGGGUGGAUCGCCCACUGGAGU
................(((((((.....(((((((((((.(((..(((........))).))).)))))((((........)))).......))))))((((((...))))))))))))) ( -32.80)
>consensus
UACAGCCGCCAUUAAAACGCCAGGCAACAUGUGAAUGGUGAAAUCGAGGAAAUCCACUCCGGCGGCGAUCACCUCCGCAUUGGUGGCAAUGAUCACAUUGGGUGGAUCACCCACUGGAGU
....((((((.......(((((..((.....))..))))).....(((........))).))))))..(((((........)))))(((((....)))))(((((.....)))))..... (-27.06 = -28.06 +   1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,970,259 – 12,970,379
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.67
Mean single sequence MFE -31.47
Consensus MFE -21.64
Energy contribution -21.48
Covariance contribution -0.16
Combinations/Pair 1.32
Mean z-score -1.75
Structure conservation index 0.69
SVM decision value 0.12
SVM RNA-class probability 0.592266
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12970259 120 - 23771897
AAGAUUUCCUCAUGGUCACAUACAUGACAGCAUAGCCCGCUACAGCCGCCAAUAAAACGCCAGGCAACAUGUGAAUGGUGAAAUCGAGGAAAUCCACUCCGGCGGAGAUCACUUCCGAAU
..(((((((((....((((.((((((..(((.......)))...(((...............)))..))))))....))))....)))))))))........(((((.....)))))... ( -34.26)
>DroSec_CAF1 87603 120 - 1
AAGAUUUCCUCAUGGUCACAUACAUGACAGCAUAGCCCGCUACAGCCGCUAUUAUAACGCCAGGCAACAUGUGAAUGGUGAAAUCGAGGAAAUCCACUCCGGCGGCGACCACCUCCGCAU
..(((((((((....((((.((((((..(((.......)))...(((((.........))..)))..))))))....))))....))))))))).......((((.(.....).)))).. ( -36.40)
>DroSim_CAF1 92469 120 - 1
AAGAUUUCCUCAUGGUCACAUACAUGACAGCAUAGCCCGCUACAGCCGCCAUUACAACGCCAGGCAACAUGUGAAUGGUGAAAUCGAGGAAAUCCACUCCGGCGGCGACCACCUCCACAU
............(((((...........(((.......)))...((((((.......(((((..((.....))..))))).....(((........))).)))))))))))......... ( -35.00)
>DroEre_CAF1 93118 120 - 1
AAGAUUUUCUCAUAGUCAGAUAAAUGACACAAUAACCCGAUACAGCCGCCAUUAAAACACCUGGCAGCAUGUGCAGGGUGAAUACAACGAAAUCCACUCCUUUGGCGAUCACCUCUGGAU
..((((((......((((......))))......((((..((((((.((((..........)))).)).))))..)))).........))))))...(((...((......))...))). ( -29.20)
>DroYak_CAF1 91554 120 - 1
GGGAUUUCCUCAUGGUCAGAUAUAUGACACCAUAACCCGCCACACCAGCCAUUAAAACUCCAGGCAGCAUGUGAAUUGUGAAAUUGAGAAAAUCCACUCCUUUGGCAAUCACUUCCGUAU
.((((((.((((..((((......))))..(((((..(((.......(((............))).....)))..)))))....)))).))))))......................... ( -22.50)
>consensus
AAGAUUUCCUCAUGGUCACAUACAUGACAGCAUAGCCCGCUACAGCCGCCAUUAAAACGCCAGGCAACAUGUGAAUGGUGAAAUCGAGGAAAUCCACUCCGGCGGCGAUCACCUCCGCAU
..(((((((((...((((......))))......(((...((((...(((............)))....))))...)))......))))))))).......((((.(.....).)))).. (-21.64 = -21.48 +  -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 11:24:23 2006