Locus 8635

Sequence ID 3L_DroMel_CAF1
Location 22,434,341 – 22,434,526
Length 185
Max. P 0.929823
window14149 window14150 window14151 window14152

overview

Window 9

Location 22,434,341 – 22,434,433
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.74
Mean single sequence MFE -25.84
Consensus MFE -17.97
Energy contribution -18.25
Covariance contribution 0.28
Combinations/Pair 1.05
Mean z-score -1.67
Structure conservation index 0.70
SVM decision value 0.30
SVM RNA-class probability 0.676479
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22434341 92 - 23771897
--UGUUGCUCUUACUGCCAUAUUUCGCUGCACACCGGCUGCCAUUUCCGCACCAAACAAAAGCAAACAGAGCGAAUGGCAGAUACAACAGCCGC--------------------------
--(((((......(((((((...(((((.......((.(((.......)))))........(....)..))))))))))))...))))).....-------------------------- ( -21.50)
>DroPse_CAF1 4158 120 - 1
GCUGUUGCUGUUGCUGCCAUAUUUCGCUGCACACCGGCUGCCAUUUCCGCACCAAACAAAAGCAAACAGACCGAAUGGCAGAUACAGCUACAGCAACUGCCCCUCCACCAUCCCCCCGGC
(((((.(((((..(((((((.....(((.......((.(((.......))))).......)))...(.....).)))))))..))))).)))))....(((................))) ( -33.83)
>DroSim_CAF1 11185 92 - 1
--UGUUGCUGUUACUGCCAUAUUUCGCUGCACACCGGCUGCCAUUUCCGCACCAAACAAAAGCAAACAGAGCGAAUGGCAGAUACAACAGCCGC--------------------------
--.((.((((((.(((((((...(((((.......((.(((.......)))))........(....)..))))))))))))....)))))).))-------------------------- ( -25.90)
>DroPer_CAF1 4231 120 - 1
GCUGUUGCUGUUGCUGCCAUAUUUCGCUGCACACCGGCUGCCAUUUCCGCACCAAACAAAAGCAAACAGACCGAAUGGCAGAUACAGCUACAGCAACUGCCCCUCCACCAUCCCCCCGGC
(((((.(((((..(((((((.....(((.......((.(((.......))))).......)))...(.....).)))))))..))))).)))))....(((................))) ( -33.83)
>DroEre_CAF1 12114 92 - 1
--UGUUGCUCUCACUGCCAUAUUUCGCUGCACACCGGCUGCCAUUUCCGCACCAAACAAAAGCAAACAGAGCGAAUGGAAGAUACAACAGCCGC--------------------------
--..(((((((...(((........((((.....))))(((.......)))..........)))...)))))))..((..(......)..))..-------------------------- ( -16.10)
>DroYak_CAF1 48544 92 - 1
--UGUUGUUUUUACUGCCAUAUUUCGCUGCACACCGGCUGCCAUUUCCGCACCAAACAAAAGCAAACAGAGCGAAUGGCAGAUACAACAGCCGC--------------------------
--((((((.....(((((((...(((((.......((.(((.......)))))........(....)..))))))))))))..)))))).....-------------------------- ( -23.90)
>consensus
__UGUUGCUGUUACUGCCAUAUUUCGCUGCACACCGGCUGCCAUUUCCGCACCAAACAAAAGCAAACAGAGCGAAUGGCAGAUACAACAGCCGC__________________________
...((((......(((((((...(((((.......((.(((.......)))))........(....)..))))))))))))...))))................................ (-17.97 = -18.25 +   0.28)

alignment

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secondary structure

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Window 0

Location 22,434,395 – 22,434,503
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.77
Mean single sequence MFE -28.87
Consensus MFE -26.49
Energy contribution -26.55
Covariance contribution 0.06
Combinations/Pair 1.07
Mean z-score -1.11
Structure conservation index 0.92
SVM decision value 0.24
SVM RNA-class probability 0.648898
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22434395 108 + 23771897
CAGCCGGUGUGCAGCGAAAUAUGGCAGUAAGAGCAACA---------ACAUCACGCAUACGCCAUGUUGCGCCAUUUGAAGUUGUUGGCGUAUACGUAAUUUUUAUUUUACAAGCAA---
..((..((((((.(((..(((((((.(((...((....---------.......)).)))))))))))))((((...........))))))))))((((........))))..))..--- ( -28.30)
>DroPse_CAF1 4238 120 + 1
CAGCCGGUGUGCAGCGAAAUAUGGCAGCAACAGCAACAGCAAAAACGACAUCACGCAUACGCCAUGUUGCGCCAUUUGAAGUUGUUGGCGUAUACGUAAUUUUUAUUUUACAAGCAAAAG
..((((....(((((.....(((((.((((((((....))..............((....))..))))))))))).....)))))))))......((((........))))......... ( -30.40)
>DroSim_CAF1 11239 108 + 1
CAGCCGGUGUGCAGCGAAAUAUGGCAGUAACAGCAACA---------ACAUCACGCAUACGCCAUGUUGCGCCAUUUGAAGUUGUUGGCGUAUACGUAAUUUUUAUUUUACAAGCAA---
..((..((((((.(((..(((((((.(((...((....---------.......)).)))))))))))))((((...........))))))))))((((........))))..))..--- ( -28.30)
>DroPer_CAF1 4311 120 + 1
CAGCCGGUGUGCAGCGAAAUAUGGCAGCAACAGCAACAGCAAAAACGACAUCACGCAUACGCCAUGUUGCGCCAUUUGAAGUUGUUGGCGUAUACGUAAUUUUUAUUUUACAAGCAAAAG
..((((....(((((.....(((((.((((((((....))..............((....))..))))))))))).....)))))))))......((((........))))......... ( -30.40)
>DroEre_CAF1 12168 108 + 1
CAGCCGGUGUGCAGCGAAAUAUGGCAGUGAGAGCAACA---------ACAUCACGCAUACGCCAUGUUGCGCCAUUUGAAGUUGUUGGCGUAUACGUAAUUUUUAUUUUACAAGCAA---
..((..((((((.(((..(((((((.((((........---------...))))(....)))))))))))((((...........))))))))))((((........))))..))..--- ( -29.30)
>DroYak_CAF1 48598 108 + 1
CAGCCGGUGUGCAGCGAAAUAUGGCAGUAAAAACAACA---------ACAUCACGCAUACGCCAUGUUGCGCCAUUUGAAGUUGUUGGCGUAUACGUAAUUUUUAUUUUACAAGCAA---
..((..((((((.(((..(((((((.(((.........---------..........)))))))))))))((((...........))))))))))((((........))))..))..--- ( -26.51)
>consensus
CAGCCGGUGUGCAGCGAAAUAUGGCAGUAACAGCAACA_________ACAUCACGCAUACGCCAUGUUGCGCCAUUUGAAGUUGUUGGCGUAUACGUAAUUUUUAUUUUACAAGCAA___
..((..((((((.(((..(((((((.((....))....................(....)))))))))))((((...........))))))))))((((........))))..))..... (-26.49 = -26.55 +   0.06)

alignment

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secondary structure

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Window 1

Location 22,434,395 – 22,434,503
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.77
Mean single sequence MFE -30.48
Consensus MFE -27.19
Energy contribution -27.05
Covariance contribution -0.14
Combinations/Pair 1.04
Mean z-score -1.68
Structure conservation index 0.89
SVM decision value 1.10
SVM RNA-class probability 0.915703
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22434395 108 - 23771897
---UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU---------UGUUGCUCUUACUGCCAUAUUUCGCUGCACACCGGCUG
---..((..(((((((((..(((((((((((((((...........((......))))))))))))))))).)---------))))....)))).))........((((.....)))).. ( -27.70)
>DroPse_CAF1 4238 120 - 1
CUUUUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGUCGUUUUUGCUGUUGCUGUUGCUGCCAUAUUUCGCUGCACACCGGCUG
.........((((((.....(((((((((((((((...........((......))))))))))))))))).....)))))).((((.(((.((.((........)).))))).)))).. ( -34.50)
>DroSim_CAF1 11239 108 - 1
---UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU---------UGUUGCUGUUACUGCCAUAUUUCGCUGCACACCGGCUG
---..((..((((..(((..(((((((((((((((...........((......)))))))))))))))))..---------..)))...)))).))........((((.....)))).. ( -28.40)
>DroPer_CAF1 4311 120 - 1
CUUUUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGUCGUUUUUGCUGUUGCUGUUGCUGCCAUAUUUCGCUGCACACCGGCUG
.........((((((.....(((((((((((((((...........((......))))))))))))))))).....)))))).((((.(((.((.((........)).))))).)))).. ( -34.50)
>DroEre_CAF1 12168 108 - 1
---UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU---------UGUUGCUCUCACUGCCAUAUUUCGCUGCACACCGGCUG
---.(((..(..(((((...(((((((((((((((...........((......)))))))))))))))))..---------....((.......))..)))))..).)))......... ( -27.40)
>DroYak_CAF1 48598 108 - 1
---UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU---------UGUUGUUUUUACUGCCAUAUUUCGCUGCACACCGGCUG
---..((..(((((((((..(((((((((((((((...........((......)))))))))))))))))..---------..))).)))))).))........((((.....)))).. ( -30.40)
>consensus
___UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU_________UGUUGCUGUUACUGCCAUAUUUCGCUGCACACCGGCUG
....(((..(..(((((...(((((((((((((((...........((......)))))))))))))))))...............((.......))..)))))..).)))......... (-27.19 = -27.05 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,434,433 – 22,434,526
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.54
Mean single sequence MFE -24.43
Consensus MFE -20.90
Energy contribution -20.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.86
SVM decision value 1.20
SVM RNA-class probability 0.929823
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22434433 93 - 23771897
UAUUCCCGUU--------------UUUUCGUUUUUGU------UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU-------
..........--------------.......((((((------((.......))))))))(((((((((((((((...........((......)))))))))))))))))..------- ( -23.80)
>DroSec_CAF1 6287 93 - 1
UAUUCCCGUU--------------UUUUCGUUUUUGU------UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU-------
..........--------------.......((((((------((.......))))))))(((((((((((((((...........((......)))))))))))))))))..------- ( -23.80)
>DroSim_CAF1 11277 93 - 1
UAUUCCCGUU--------------UUUUCGUUUUUGU------UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU-------
..........--------------.......((((((------((.......))))))))(((((((((((((((...........((......)))))))))))))))))..------- ( -23.80)
>DroPer_CAF1 4351 106 - 1
UCUUUCCGUU--------------UUUUAGUUUUUGUUCGCUUUUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGUCGUUUUU
.......(((--------------((..(((....(....)....)))...)))))....(((((((((((((((...........((......)))))))))))))))))......... ( -22.80)
>DroEre_CAF1 12206 107 - 1
UAUUCGCGUUUUCGCGUUUUCGUUUUUUCGUUUUUGU------UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU-------
....((((....))))...............((((((------((.......))))))))(((((((((((((((...........((......)))))))))))))))))..------- ( -28.60)
>DroYak_CAF1 48636 92 - 1
UAUUCCCGUU---------------UUUCGUUUUUGU------UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU-------
..........---------------......((((((------((.......))))))))(((((((((((((((...........((......)))))))))))))))))..------- ( -23.80)
>consensus
UAUUCCCGUU______________UUUUCGUUUUUGU______UUGCUUGUAAAAUAAAAAUUACGUAUACGCCAACAACUUCAAAUGGCGCAACAUGGCGUAUGCGUGAUGU_______
............................................................(((((((((((((((...........((......)))))))))))))))))......... (-20.90 = -20.90 +   0.00)

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 13:21:00 2006