Locus 7143

Sequence ID 2L_DroMel_CAF1
Location 20,010,475 – 20,010,611
Length 136
Max. P 0.999875
window11402 window11403 window11404 window11405

overview

Window 2

Location 20,010,475 – 20,010,573
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.13
Mean single sequence MFE -30.73
Consensus MFE -21.05
Energy contribution -21.38
Covariance contribution 0.33
Combinations/Pair 1.15
Mean z-score -1.80
Structure conservation index 0.68
SVM decision value 0.29
SVM RNA-class probability 0.669352
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20010475 98 + 22407834
GGGUAACUUCACUUGUGGUGGCUGCCGGUCUUCUUUAUUGUCACCCAGCCAUUUGCAGCCAUUAUUUAAAUGGCCCAAAUGAA----------------------AGAGGAGCAGCUGCG
.................(..(((((...((((((((.(((.....))).((((((..((((((.....)))))).))))))))----------------------)))))))))))..). ( -31.20)
>DroSec_CAF1 188216 95 + 1
GGGACACUUCACUUGU---GGCUGCCUGUCUUCUUUAUUGUCACCCAGCCAUUUGCAGCCAUUAUUUAAAUGGCCCAAAUGAA----------------------AGAGGAGCAGCUGCG
..............(.---.(((((...((((((((.(((.....))).((((((..((((((.....)))))).))))))))----------------------)))))))))))..). ( -31.20)
>DroSim_CAF1 190732 95 + 1
GGAACACUUCACUUGU---GGCUGCCGGUCUUCUUUAUUGUCACCCAGCCAUUUGCAGCCAUUAUUUAAAUGGCCCAAAUGAA----------------------AGAGGAGCAGCUGCG
..............(.---.(((((...((((((((.(((.....))).((((((..((((((.....)))))).))))))))----------------------)))))))))))..). ( -31.20)
>DroEre_CAF1 185671 95 + 1
GGGACACUGCACUUGU---GGCUGCCGGUCUGCUUUAUUGUCACCCAACCAUUUGCAGCCAUUACUUAAAUGGCCCAAAUGAA----------------------AGAGGAGCAGCUGCG
..............(.---.(((((((((..((......)).)))....((((((..((((((.....)))))).))))))..----------------------....).)))))..). ( -27.70)
>DroYak_CAF1 186623 95 + 1
UGGACAUUUCACUUGU---GGCUGCUGGCCUUCUUUAUUGUCACCCAACCAUUUGUAGCCAUUAUUUAAAUGGCCCAAAUGAA----------------------AGAAGAGCAGCUGCG
..............(.---.((((((...(((((((.(((.....))).((((((..((((((.....)))))).))))))))----------------------)))))))))))..). ( -31.20)
>DroAna_CAF1 181127 117 + 1
GAGACUCUCCGCUUGU---UGCUGUCACUCUUCUUUAUUGUCGCUCAACAAUUUGCAGCCAUUAUUUAAAAGGCCCAGAUGGAGGAUGGCACUAUGGCAGUAGCCAGAGUAGCAGCUGGG
........(((.((((---((((((((..((((.....(((......)))(((((..(((...........))).)))))))))..))))....((((....)))).)))))))).))). ( -31.90)
>consensus
GGGACACUUCACUUGU___GGCUGCCGGUCUUCUUUAUUGUCACCCAACCAUUUGCAGCCAUUAUUUAAAUGGCCCAAAUGAA______________________AGAGGAGCAGCUGCG
...................((((((...((((((...(((.....))).((((((..((((((.....)))))).))))))........................))))))))))))... (-21.05 = -21.38 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,010,475 – 20,010,573
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.13
Mean single sequence MFE -30.65
Consensus MFE -23.76
Energy contribution -24.18
Covariance contribution 0.42
Combinations/Pair 1.12
Mean z-score -1.88
Structure conservation index 0.78
SVM decision value 0.60
SVM RNA-class probability 0.795570
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20010475 98 - 22407834
CGCAGCUGCUCCUCU----------------------UUCAUUUGGGCCAUUUAAAUAAUGGCUGCAAAUGGCUGGGUGACAAUAAAGAAGACCGGCAGCCACCACAAGUGAAGUUACCC
....((((((..(((----------------------(((((((((((((((.....))))))).))))))....(....)......)))))..))))))(((.....)))......... ( -30.50)
>DroSec_CAF1 188216 95 - 1
CGCAGCUGCUCCUCU----------------------UUCAUUUGGGCCAUUUAAAUAAUGGCUGCAAAUGGCUGGGUGACAAUAAAGAAGACAGGCAGCC---ACAAGUGAAGUGUCCC
(((.((((((..(((----------------------(((((((((((((((.....))))))).))))))....(....)......)))))..))))))(---(....))..))).... ( -31.10)
>DroSim_CAF1 190732 95 - 1
CGCAGCUGCUCCUCU----------------------UUCAUUUGGGCCAUUUAAAUAAUGGCUGCAAAUGGCUGGGUGACAAUAAAGAAGACCGGCAGCC---ACAAGUGAAGUGUUCC
(((.((((((..(((----------------------(((((((((((((((.....))))))).))))))....(....)......)))))..))))))(---(....))..))).... ( -30.60)
>DroEre_CAF1 185671 95 - 1
CGCAGCUGCUCCUCU----------------------UUCAUUUGGGCCAUUUAAGUAAUGGCUGCAAAUGGUUGGGUGACAAUAAAGCAGACCGGCAGCC---ACAAGUGCAGUGUCCC
.(((((((((..(((----------------------..(((((((((((((.....))))))).))))))(((.(....).....))))))..)))))).---.....)))........ ( -29.40)
>DroYak_CAF1 186623 95 - 1
CGCAGCUGCUCUUCU----------------------UUCAUUUGGGCCAUUUAAAUAAUGGCUACAAAUGGUUGGGUGACAAUAAAGAAGGCCAGCAGCC---ACAAGUGAAAUGUCCA
.((.((((..(((((----------------------(((((((((((((((.....))))))).))))))((((.....)))))))))))..)))).)).---................ ( -32.10)
>DroAna_CAF1 181127 117 - 1
CCCAGCUGCUACUCUGGCUACUGCCAUAGUGCCAUCCUCCAUCUGGGCCUUUUAAAUAAUGGCUGCAAAUUGUUGAGCGACAAUAAAGAAGAGUGACAGCA---ACAAGCGGAGAGUCUC
.....((((((((.((((....)))).)))((..(((((..(((.((((...........))))....((((((....))))))..))).))).))..)).---...)))))........ ( -30.20)
>consensus
CGCAGCUGCUCCUCU______________________UUCAUUUGGGCCAUUUAAAUAAUGGCUGCAAAUGGCUGGGUGACAAUAAAGAAGACCGGCAGCC___ACAAGUGAAGUGUCCC
....((((((..(((.......................((((((((((((((.....))))))).)))))))...(....)........)))..)))))).................... (-23.76 = -24.18 +   0.42)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,010,515 – 20,010,611
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 94.27
Mean single sequence MFE -34.00
Consensus MFE -27.70
Energy contribution -28.66
Covariance contribution 0.96
Combinations/Pair 1.03
Mean z-score -2.26
Structure conservation index 0.81
SVM decision value 1.76
SVM RNA-class probability 0.976018
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20010515 96 + 22407834
UCACCCAGCCAUUUGCAGCCAUUAUUUAAAUGGCCCAAAUGAAAGAGGAGCAGCUGCGUCUGCGAAAGCCUCCGUUUUGGGCGACGGGCUGUGGAU
...(((((((..((((.((((((.....))))))(((((.....((((.((((......)))).....))))...)))))))))..))))).)).. ( -37.70)
>DroSec_CAF1 188253 96 + 1
UCACCCAGCCAUUUGCAGCCAUUAUUUAAAUGGCCCAAAUGAAAGAGGAGCAGCUGCGUCUGCGGAAGCCUCCGUUUUGGCUGACUGGUUGUGCAU
.......((((((((..((((((.....)))))).))))))........(((((((.(((.((.(((((....))))).)).)))))))))))).. ( -31.00)
>DroSim_CAF1 190769 96 + 1
UCACCCAGCCAUUUGCAGCCAUUAUUUAAAUGGCCCAAAUGAAAGAGGAGCAGCUGCGUCUGCGGAAGCCUCCGUUUUGGCUGACUGGUUGUGGAU
...((((((((...(((((((((.....))))((((..........)).)).)))))(((.((.(((((....))))).)).))))))))).)).. ( -33.90)
>DroEre_CAF1 185708 96 + 1
UCACCCAACCAUUUGCAGCCAUUACUUAAAUGGCCCAAAUGAAAGAGGAGCAGCUGCGUCUGCGGAAGCCUCCGUUUUGGGUGACUGGUGGUGGAU
((((((((.((((((..((((((.....)))))).)))))).....(((((..((((....))))..).))))...))))))))............ ( -35.20)
>DroYak_CAF1 186660 96 + 1
UCACCCAACCAUUUGUAGCCAUUAUUUAAAUGGCCCAAAUGAAAGAAGAGCAGCUGCGUCUGCGGAAGCCUCCGUUUUCGGUGACAGGUUGUGGAU
...((((((((((((..((((((.....)))))).)))))(((((..((((..((((....))))..).)))..)))))(....).))))).)).. ( -32.20)
>consensus
UCACCCAGCCAUUUGCAGCCAUUAUUUAAAUGGCCCAAAUGAAAGAGGAGCAGCUGCGUCUGCGGAAGCCUCCGUUUUGGGUGACUGGUUGUGGAU
((((((((.((((((..((((((.....)))))).)))))).....(((((..((((....))))..).))))...))))))))............ (-27.70 = -28.66 +   0.96)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,010,515 – 20,010,611
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 94.27
Mean single sequence MFE -33.76
Consensus MFE -30.70
Energy contribution -30.98
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -2.73
Structure conservation index 0.91
SVM decision value 4.34
SVM RNA-class probability 0.999875
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20010515 96 - 22407834
AUCCACAGCCCGUCGCCCAAAACGGAGGCUUUCGCAGACGCAGCUGCUCCUCUUUCAUUUGGGCCAUUUAAAUAAUGGCUGCAAAUGGCUGGGUGA
............(((((((....(((((.....((((......)))).))))).((((((((((((((.....))))))).))))))).))))))) ( -34.40)
>DroSec_CAF1 188253 96 - 1
AUGCACAACCAGUCAGCCAAAACGGAGGCUUCCGCAGACGCAGCUGCUCCUCUUUCAUUUGGGCCAUUUAAAUAAUGGCUGCAAAUGGCUGGGUGA
.........((.((((((.....(((((.....((((......)))).)))))...((((((((((((.....))))))).))))))))))).)). ( -34.00)
>DroSim_CAF1 190769 96 - 1
AUCCACAACCAGUCAGCCAAAACGGAGGCUUCCGCAGACGCAGCUGCUCCUCUUUCAUUUGGGCCAUUUAAAUAAUGGCUGCAAAUGGCUGGGUGA
.........((.((((((.....(((((.....((((......)))).)))))...((((((((((((.....))))))).))))))))))).)). ( -34.00)
>DroEre_CAF1 185708 96 - 1
AUCCACCACCAGUCACCCAAAACGGAGGCUUCCGCAGACGCAGCUGCUCCUCUUUCAUUUGGGCCAUUUAAGUAAUGGCUGCAAAUGGUUGGGUGA
............((((((((...(((((.....((((......)))).))))).((((((((((((((.....))))))).))))))))))))))) ( -35.90)
>DroYak_CAF1 186660 96 - 1
AUCCACAACCUGUCACCGAAAACGGAGGCUUCCGCAGACGCAGCUGCUCUUCUUUCAUUUGGGCCAUUUAAAUAAUGGCUACAAAUGGUUGGGUGA
..((.(((((.(((.(((....))).)))....((((......)))).........((((((((((((.....))))))).))))))))))))... ( -30.50)
>consensus
AUCCACAACCAGUCACCCAAAACGGAGGCUUCCGCAGACGCAGCUGCUCCUCUUUCAUUUGGGCCAUUUAAAUAAUGGCUGCAAAUGGCUGGGUGA
............(((((((....(((((.....((((......)))).))))).((((((((((((((.....))))))).))))))).))))))) (-30.70 = -30.98 +   0.28)

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 12:28:32 2006