Locus 6465

Sequence ID 3L_DroMel_CAF1
Location 17,238,699 – 17,238,937
Length 238
Max. P 0.979639
window10406 window10407 window10408 window10409 window10410 window10411

overview

Window 6

Location 17,238,699 – 17,238,818
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.57
Mean single sequence MFE -29.58
Consensus MFE -24.58
Energy contribution -24.78
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.83
SVM decision value 0.76
SVM RNA-class probability 0.842703
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17238699 119 + 23771897
AAAGUGUAGCAUACUUAUGAGGGCGAAUA-AAAAAGGUGGCGAAAAUAACCACGCUUUGUUGCACGCGUAAUUUGCAUUAUUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCACC
.(((((..(((...(((((...((((...-..((((((((.........)))).)))).))))...)))))..)))..)))))((.((((((((((........)))))))))).))... ( -27.70)
>DroSec_CAF1 122663 119 + 1
AAAGUGUAGCAUACUUAUGAGGGCGAAUG-AAAAAGGUGGCGAAAAUAACCACGCUUUGUUGCACGCCUAAUUUGCAUUAUUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCACC
..((((((((((....))).(((((....-..((((((((.........)))).))))......)))))...)))))))...(((.((((((((((........)))))))))).))).. ( -28.30)
>DroSim_CAF1 116581 119 + 1
AAAGUGUGGCAUACUUAUGAGGGCGAAUG-AAAAAGGUGGCGAAAAUAACCACGCUUUGUUGCACGCGUAAUUUGCAUUAUUUGCUAGUAAUUGAAUAAAGUUUUUGAAUUAUUCGCACC
...(((((.............((((((((-(.....((((.........))))((...(((((....)))))..)).)))))))))(((((((.((........)).)))))))))))). ( -27.40)
>DroEre_CAF1 125891 120 + 1
AAAGUGCAGCAUACUUAUGAGGGCGAAUGCAAAAAGGUGGCGAAAAUAACCACGCUUUGUUGCACGCGUAAUUUGCAUUAUUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCACC
...((((((((.....(((...(((..(((((((((((((.........)))).)))).)))))..)))......)))....))))((((((((((........)))))))))).)))). ( -32.50)
>DroYak_CAF1 129175 120 + 1
AAAGUGCAGCAUACUUAUGAGGGCGAGUGAAAAAAGGUGGCGAAAAUAAGCACGCUUUGUUGCACGCGUAAUUUGCAUUAUUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCUCC
...(((((((.(((((........)))))....((((((((........)).)))))))))))))(((.....))).......((.((((((((((........)))))))))).))... ( -32.00)
>consensus
AAAGUGUAGCAUACUUAUGAGGGCGAAUG_AAAAAGGUGGCGAAAAUAACCACGCUUUGUUGCACGCGUAAUUUGCAUUAUUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCACC
...(((((((...((.....))..........((((((((.........)))).)))))))))))(((.....))).......((.((((((((((........)))))))))).))... (-24.58 = -24.78 +   0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,238,699 – 17,238,818
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.57
Mean single sequence MFE -23.29
Consensus MFE -19.14
Energy contribution -19.54
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.82
SVM decision value 0.02
SVM RNA-class probability 0.545003
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17238699 119 - 23771897
GGUGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAAUAAUGCAAAUUACGCGUGCAACAAAGCGUGGUUAUUUUCGCCACCUUUUU-UAUUCGCCCUCAUAAGUAUGCUACACUUU
((.((((((((........................(((..((((....))))....)))...((((.(((((.......))))))))).)-))))))))).................... ( -22.90)
>DroSec_CAF1 122663 119 - 1
GGUGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAAUAAUGCAAAUUAGGCGUGCAACAAAGCGUGGUUAUUUUCGCCACCUUUUU-CAUUCGCCCUCAUAAGUAUGCUACACUUU
((.((((((..........................(((..((((....))))....)))...((((.(((((.......)))))))))..-.)))))))).................... ( -22.00)
>DroSim_CAF1 116581 119 - 1
GGUGCGAAUAAUUCAAAAACUUUAUUCAAUUACUAGCAAAUAAUGCAAAUUACGCGUGCAACAAAGCGUGGUUAUUUUCGCCACCUUUUU-CAUUCGCCCUCAUAAGUAUGCCACACUUU
(((..((((((..........))))))...((((.(((.....))).......(((......((((.(((((.......)))))))))..-....))).......)))).)))....... ( -22.30)
>DroEre_CAF1 125891 120 - 1
GGUGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAAUAAUGCAAAUUACGCGUGCAACAAAGCGUGGUUAUUUUCGCCACCUUUUUGCAUUCGCCCUCAUAAGUAUGCUGCACUUU
(((((((((((..........)))))....((((.(((.....)))......((.((((((.((((.(((((.......))))))))))))))).))........))))...)))))).. ( -26.80)
>DroYak_CAF1 129175 120 - 1
GGAGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAAUAAUGCAAAUUACGCGUGCAACAAAGCGUGCUUAUUUUCGCCACCUUUUUUCACUCGCCCUCAUAAGUAUGCUGCACUUU
...((((((((..........))))).........(((.....)))......)))(((((.....((((((((((....((...............))....)))))))))))))))... ( -22.46)
>consensus
GGUGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAAUAAUGCAAAUUACGCGUGCAACAAAGCGUGGUUAUUUUCGCCACCUUUUU_CAUUCGCCCUCAUAAGUAUGCUACACUUU
((.((((((..........................(((..((((....))))....)))...((((.(((((.......)))))))))....)))))))).................... (-19.14 = -19.54 +   0.40)

alignment

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secondary structure

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Window 8

Location 17,238,778 – 17,238,897
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.90
Mean single sequence MFE -25.98
Consensus MFE -20.44
Energy contribution -20.88
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.49
Structure conservation index 0.79
SVM decision value 1.84
SVM RNA-class probability 0.979639
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17238778 119 + 23771897
UUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCACCGAAGUCACGCACUCUGCCACAUUGAAACGCAAUUAAGGCAAAAAAAAAUGUAAA-AAAAAAACGUGAGGCGCGUGGAAAA
..(((.((((((((((........)))))))))).)))......((((((.(((((((..((((.....))))...)))).......((((...-......)))))))..)))))).... ( -27.70)
>DroSec_CAF1 122742 120 + 1
UUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCACCGAAGUCACGCACUCUGCCACAUUGAAACGCAAUUAAGGCAAAAAAAAACAUCAAUAAAAAAACGUGAUGCGCGUGGAAAA
..(((.((((((((((........)))))))))).)))......((((((....((((..((((.....))))...))))........(((((...........))))).)))))).... ( -27.30)
>DroSim_CAF1 116660 116 + 1
UUUGCUAGUAAUUGAAUAAAGUUUUUGAAUUAUUCGCACCGAAGUCACGCACUCUGCCACAUUGAAACGCAAUUAAGGCAAAAAAAAAUAAAAA----UAAAUGUGAGGCGCGUGGAAAA
..(((.(((((((.((........)).))))))).)))......((((((.(((((((..((((.....))))...)))).......(((....----....))))))..)))))).... ( -23.80)
>DroEre_CAF1 125971 105 + 1
UUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCACCGAAGUCACGCACUCUGCCACAUUGAAAUGCAAUUAAUGCAAUAA---------------AAACGUGGUGCGCGUGGAAAA
..(((.((((((((((........)))))))))).)))......((((((.(...(((((.((....((((.....))))....---------------.)).)))))).)))))).... ( -27.30)
>DroYak_CAF1 129255 105 + 1
UUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCUCCGAAGUCACGCACUCUGCCACAUUGAAAUGCAAUUAAUGCAAUAA---------------AAACGUGAGGCGCGUGAAAAA
...((.((((((((((........)))))))))).)).......((((((.....(((.(((.....((((.....))))....---------------....))).))))))))).... ( -23.82)
>consensus
UUUGCUAGUAAUUUAAUAAAGUUUUUGAAUUAUUCGCACCGAAGUCACGCACUCUGCCACAUUGAAACGCAAUUAAGGCAAAAAAAAA____AA_____AAACGUGAGGCGCGUGGAAAA
...((.((((((((((........)))))))))).)).......((((((....((((..((((.....))))...)))).......................(.....))))))).... (-20.44 = -20.88 +   0.44)

alignment

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secondary structure

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Window 9

Location 17,238,778 – 17,238,897
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.90
Mean single sequence MFE -25.27
Consensus MFE -18.01
Energy contribution -17.65
Covariance contribution -0.36
Combinations/Pair 1.11
Mean z-score -1.97
Structure conservation index 0.71
SVM decision value 0.34
SVM RNA-class probability 0.697161
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17238778 119 - 23771897
UUUUCCACGCGCCUCACGUUUUUUU-UUUACAUUUUUUUUUGCCUUAAUUGCGUUUCAAUGUGGCAGAGUGCGUGACUUCGGUGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAA
.......((((((((((((......-...........(((((((...((((.....))))..))))))).))))))....)))))).................................. ( -25.07)
>DroSec_CAF1 122742 120 - 1
UUUUCCACGCGCAUCACGUUUUUUUAUUGAUGUUUUUUUUUGCCUUAAUUGCGUUUCAAUGUGGCAGAGUGCGUGACUUCGGUGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAA
.....(((((((...(((((........))))).....((((((...((((.....))))..)))))))))))))((....))((...(((((.((........)).)))))...))... ( -26.70)
>DroSim_CAF1 116660 116 - 1
UUUUCCACGCGCCUCACAUUUA----UUUUUAUUUUUUUUUGCCUUAAUUGCGUUUCAAUGUGGCAGAGUGCGUGACUUCGGUGCGAAUAAUUCAAAAACUUUAUUCAAUUACUAGCAAA
.....(((((((........((----....))......((((((...((((.....))))..)))))))))))))((....))..((((((..........))))))............. ( -23.10)
>DroEre_CAF1 125971 105 - 1
UUUUCCACGCGCACCACGUUU---------------UUAUUGCAUUAAUUGCAUUUCAAUGUGGCAGAGUGCGUGACUUCGGUGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAA
.....(((((((.(((((((.---------------....((((.....))))....)))))))....)))))))((....))((...(((((.((........)).)))))...))... ( -26.50)
>DroYak_CAF1 129255 105 - 1
UUUUUCACGCGCCUCACGUUU---------------UUAUUGCAUUAAUUGCAUUUCAAUGUGGCAGAGUGCGUGACUUCGGAGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAA
....((((((((((((((((.---------------....((((.....))))....))))))..)).))))))))(....).((...(((((.((........)).)))))...))... ( -25.00)
>consensus
UUUUCCACGCGCCUCACGUUU_____UU____UUUUUUUUUGCCUUAAUUGCGUUUCAAUGUGGCAGAGUGCGUGACUUCGGUGCGAAUAAUUCAAAAACUUUAUUAAAUUACUAGCAAA
.....(((((((.(((((((....................(((.......)))....)))))))....)))))))((....))((...(((((.((........)).)))))...))... (-18.01 = -17.65 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,238,818 – 17,238,937
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.56
Mean single sequence MFE -21.62
Consensus MFE -15.40
Energy contribution -15.64
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.97
Structure conservation index 0.71
SVM decision value 0.36
SVM RNA-class probability 0.705870
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17238818 119 + 23771897
GAAGUCACGCACUCUGCCACAUUGAAACGCAAUUAAGGCAAAAAAAAAUGUAAA-AAAAAAACGUGAGGCGCGUGGAAAAAAUAAUUUAUUGAAUACAAUAAACAAUGUGUUGCCAUAGU
....((((((.(((((((..((((.....))))...)))).......((((...-......)))))))..)))))).........(((((((....)))))))...((((....)))).. ( -21.70)
>DroSec_CAF1 122782 120 + 1
GAAGUCACGCACUCUGCCACAUUGAAACGCAAUUAAGGCAAAAAAAAACAUCAAUAAAAAAACGUGAUGCGCGUGGAAAAAAUAAUUUAUAGAAUACAAUAAACAAUGUGUUGCCAUAGU
....((((((....((((..((((.....))))...))))........(((((...........))))).))))))..........((((.(((((((........)))))).).)))). ( -20.90)
>DroSim_CAF1 116700 116 + 1
GAAGUCACGCACUCUGCCACAUUGAAACGCAAUUAAGGCAAAAAAAAAUAAAAA----UAAAUGUGAGGCGCGUGGAAAAAAUAAUUUAUAGAAUACAAUAAACAAUGUGUUGCCAUAGU
....((((((.(((((((..((((.....))))...)))).......(((....----....))))))..))))))..........((((.(((((((........)))))).).)))). ( -19.30)
>DroEre_CAF1 126011 105 + 1
GAAGUCACGCACUCUGCCACAUUGAAAUGCAAUUAAUGCAAUAA---------------AAACGUGGUGCGCGUGGAAAAAAUAUUUUAUUGAAUACAAUAAACAAUGUGUUGCCAUAGU
....((((((.(...(((((.((....((((.....))))....---------------.)).)))))).)))))).........(((((((....)))))))...((((....)))).. ( -21.20)
>DroYak_CAF1 129295 105 + 1
GAAGUCACGCACUCUGCCACAUUGAAAUGCAAUUAAUGCAAUAA---------------AAACGUGAGGCGCGUGAAAAAAAUAAUUUAUGGAAUACAAUAAACAAUGUGUUGCCAUAGU
....((((((.....(((.(((.....((((.....))))....---------------....))).)))))))))..........((((((((((((........)))))).)))))). ( -25.02)
>consensus
GAAGUCACGCACUCUGCCACAUUGAAACGCAAUUAAGGCAAAAAAAAA____AA_____AAACGUGAGGCGCGUGGAAAAAAUAAUUUAUAGAAUACAAUAAACAAUGUGUUGCCAUAGU
....((((((....((((..((((.....))))...)))).......................(.....)))))))..........((((.(((((((........)))))).).)))). (-15.40 = -15.64 +   0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,238,818 – 17,238,937
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.56
Mean single sequence MFE -25.96
Consensus MFE -17.63
Energy contribution -17.39
Covariance contribution -0.24
Combinations/Pair 1.15
Mean z-score -2.96
Structure conservation index 0.68
SVM decision value 1.08
SVM RNA-class probability 0.912469
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17238818 119 - 23771897
ACUAUGGCAACACAUUGUUUAUUGUAUUCAAUAAAUUAUUUUUUCCACGCGCCUCACGUUUUUUU-UUUACAUUUUUUUUUGCCUUAAUUGCGUUUCAAUGUGGCAGAGUGCGUGACUUC
....((....))....((((((((....)))))))).........(((((((.....((......-...)).......((((((...((((.....))))..)))))))))))))..... ( -25.40)
>DroSec_CAF1 122782 120 - 1
ACUAUGGCAACACAUUGUUUAUUGUAUUCUAUAAAUUAUUUUUUCCACGCGCAUCACGUUUUUUUAUUGAUGUUUUUUUUUGCCUUAAUUGCGUUUCAAUGUGGCAGAGUGCGUGACUUC
..(((((.((.(((........))).)))))))............(((((((...(((((........))))).....((((((...((((.....))))..)))))))))))))..... ( -26.60)
>DroSim_CAF1 116700 116 - 1
ACUAUGGCAACACAUUGUUUAUUGUAUUCUAUAAAUUAUUUUUUCCACGCGCCUCACAUUUA----UUUUUAUUUUUUUUUGCCUUAAUUGCGUUUCAAUGUGGCAGAGUGCGUGACUUC
..(((((.((.(((........))).)))))))............(((((((........((----....))......((((((...((((.....))))..)))))))))))))..... ( -21.40)
>DroEre_CAF1 126011 105 - 1
ACUAUGGCAACACAUUGUUUAUUGUAUUCAAUAAAAUAUUUUUUCCACGCGCACCACGUUU---------------UUAUUGCAUUAAUUGCAUUUCAAUGUGGCAGAGUGCGUGACUUC
....((....)).....(((((((....)))))))..........(((((((.(((((((.---------------....((((.....))))....)))))))....)))))))..... ( -28.20)
>DroYak_CAF1 129295 105 - 1
ACUAUGGCAACACAUUGUUUAUUGUAUUCCAUAAAUUAUUUUUUUCACGCGCCUCACGUUU---------------UUAUUGCAUUAAUUGCAUUUCAAUGUGGCAGAGUGCGUGACUUC
..(((((.((.(((........))).)))))))...........((((((((((((((((.---------------....((((.....))))....))))))..)).)))))))).... ( -28.20)
>consensus
ACUAUGGCAACACAUUGUUUAUUGUAUUCAAUAAAUUAUUUUUUCCACGCGCCUCACGUUU_____UU____UUUUUUUUUGCCUUAAUUGCGUUUCAAUGUGGCAGAGUGCGUGACUUC
..(((((.((.(((........))).)))))))............(((((((.(((((((....................(((.......)))....)))))))....)))))))..... (-17.63 = -17.39 +  -0.24)

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 12:20:03 2006