Locus 5103

Sequence ID 2L_DroMel_CAF1
Location 14,530,487 – 14,530,647
Length 160
Max. P 0.999396
window8124 window8125 window8126 window8127 window8128

overview

Window 4

Location 14,530,487 – 14,530,579
Length 92
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 74.45
Mean single sequence MFE -23.32
Consensus MFE -18.50
Energy contribution -18.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 0.79
SVM decision value 1.33
SVM RNA-class probability 0.943093
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14530487 92 - 22407834
GCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAAAUAGC-UUUUUGAUAUUUAAGGGAAAAACCCCUUUCUCAAGGUUAACUUUUUAACAC
(((..(((((.(((.......)))))))).)))....((((-(((..((.....(((((......)))))))..)))))))............ ( -29.00)
>DroSec_CAF1 62589 75 - 1
GCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAGCUUUUUUGAUAAU---------------UUUCUCAAGGUUAACUU--UAACAC
(((..(((((.(((.......)))))))).)))...-(((((((...((....---------------..))..)))))))....--...... ( -22.90)
>DroSim_CAF1 47929 90 - 1
GCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAGAUUUUUUGAUAAUUAAGUUUAUAACGGCUUUCUCAAGGUUAACUU--UAACAA
(((..(((((.(((.......)))))))).)))..(-(((((((..(....)..))))))))...(((((.....))))).....--...... ( -22.10)
>DroEre_CAF1 57723 88 - 1
GCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAUCCUUUUUGAUCUUCUACUUUGAAAGCGUCUUCUCAAUGCUAACUU--UAC--U
...(((((((.(((.......)))))))(((((...-.(((......))).(((......))).)))))........))).....--...--. ( -22.40)
>DroYak_CAF1 52849 76 - 1
GCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UACAUAUUUUGAUUUUUUAGCUUACAAG--UUUUCUCAGGGC--------------
(((..(((((.(((.......)))))))).)))...-......((((((......((((....))--))...)))))).-------------- ( -20.20)
>consensus
GCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA_UAGCUUUUUUGAUAUUUAAGUUUAAAAC__CUUUCUCAAGGUUAACUU__UAACAC
(((..(((((.(((.......)))))))).)))............................................................ (-18.50 = -18.50 +   0.00)

alignment

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secondary structure

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Window 5

Location 14,530,513 – 14,530,619
Length 106
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 87.01
Mean single sequence MFE -33.04
Consensus MFE -32.20
Energy contribution -32.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.97
SVM decision value 0.44
SVM RNA-class probability 0.736091
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14530513 106 + 22407834
GGGUUUUUCCCUUAAAUAUCAAAAA-GCUAUUUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGU
(((.....)))..............-........((((((((((((.......)))))((((((.((...)).)))).)).................)))))))... ( -35.90)
>DroSec_CAF1 62612 92 + 1
--------------AUUAUCAAAAAAGCUA-UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGU
--------------................-...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))... ( -32.20)
>DroSim_CAF1 47953 106 + 1
CCGUUAUAAACUUAAUUAUCAAAAAAUCUA-UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGU
..............................-...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))... ( -32.20)
>DroEre_CAF1 57745 106 + 1
CGCUUUCAAAGUAGAAGAUCAAAAAGGAUA-UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGU
...((((......))))(((......))).-...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))... ( -32.70)
>DroYak_CAF1 52861 104 + 1
--CUUGUAAGCUAAAAAAUCAAAAUAUGUA-UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGU
--............................-...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))... ( -32.20)
>consensus
__CUUUUAAACUAAAAUAUCAAAAAAGCUA_UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGU
..................................((((((((((((.......)))))((((((.((...)).)))).)).................)))))))... (-32.20 = -32.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,530,513 – 14,530,619
Length 106
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 87.01
Mean single sequence MFE -37.16
Consensus MFE -35.90
Energy contribution -35.90
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.97
SVM decision value 0.94
SVM RNA-class probability 0.885669
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14530513 106 - 22407834
ACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAAAUAGC-UUUUUGAUAUUUAAGGGAAAAACCC
...(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))........-..............(((.....))) ( -38.20)
>DroSec_CAF1 62612 92 - 1
ACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAGCUUUUUUGAUAAU--------------
...(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))...-................-------------- ( -35.90)
>DroSim_CAF1 47953 106 - 1
ACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAGAUUUUUUGAUAAUUAAGUUUAUAACGG
...(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))..(-(((((((..(....)..))))))))..... ( -38.60)
>DroEre_CAF1 57745 106 - 1
ACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAUCCUUUUUGAUCUUCUACUUUGAAAGCG
.........((..(((((.((((((((((((((((((...))))))((((.(((.......))))))))).)))..-.(((......))).)))))))))))).)). ( -37.20)
>DroYak_CAF1 52861 104 - 1
ACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UACAUAUUUUGAUUUUUUAGCUUACAAG--
...(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))...-............................-- ( -35.90)
>consensus
ACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA_UAGCUUUUUUGAUAUUUAAGUUUAAAAC__
...(((((((..((((.......))))((.(((((((...)))))))))(((((.......)))))))))))).................................. (-35.90 = -35.90 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,530,539 – 14,530,647
Length 108
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 93.53
Mean single sequence MFE -37.48
Consensus MFE -36.58
Energy contribution -37.30
Covariance contribution 0.72
Combinations/Pair 1.07
Mean z-score -1.85
Structure conservation index 0.98
SVM decision value 3.23
SVM RNA-class probability 0.998805
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14530539 108 + 22407834
CUAUUUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGUUGGAAAAGUUAGGUUUUCC-GCAUAA-AAU
.......((((((((((((.......)))))((((((.((...)).)))).)).................)))))))(((.((((((......))))))-)))...-... ( -37.80)
>DroSec_CAF1 62625 108 + 1
CUA-UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGUUGGAAAAGUCAGUUUUUCC-GCAUAAAAAU
...-...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))(((.(((((((....)))))))-)))....... ( -38.40)
>DroSim_CAF1 47980 107 + 1
CUA-UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGUUGGAAAAGCUAGUUUUUCC-GCAUAA-AAU
...-...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))(((.(((((((....)))))))-)))...-... ( -39.50)
>DroEre_CAF1 57772 108 + 1
AUA-UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGUUAGUUAAAUAGAUUUUUCCUGCAUAA-AAU
...-...((((((((((((.......)))))((((((.((...)).)))).)).................)))))))(((.((..(((.....)))..)))))...-... ( -33.60)
>DroYak_CAF1 52886 107 + 1
GUA-UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGUUAGGAAAAUAGAUUUUUCC-GCAUAA-AAU
((.-...((((((((((((.......)))))((((((.((...)).)))).)).................))))))).....((((((.....))))))-))....-... ( -38.10)
>consensus
CUA_UUUGCAUCGGCCGGGAAUCGAACCCGGGCCGCCCGCGUGGCAGGCGAGCAUUCUACCACUGAACCACCGAUGCUGUUGGAAAAGUAAGUUUUUCC_GCAUAA_AAU
.......((((((((((((.......)))))((((((.((...)).)))).)).................)))))))(((.(((((((....))))))).)))....... (-36.58 = -37.30 +   0.72)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,530,539 – 14,530,647
Length 108
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 93.53
Mean single sequence MFE -40.06
Consensus MFE -38.08
Energy contribution -38.44
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -2.05
Structure conservation index 0.95
SVM decision value 3.57
SVM RNA-class probability 0.999396
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14530539 108 - 22407834
AUU-UUAUGC-GGAAAACCUAACUUUUCCAACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAAAUAG
...-......-((((((......))))))....(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))....... ( -41.10)
>DroSec_CAF1 62625 108 - 1
AUUUUUAUGC-GGAAAAACUGACUUUUCCAACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAG
..........-((((((......))))))....(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))...-... ( -41.40)
>DroSim_CAF1 47980 107 - 1
AUU-UUAUGC-GGAAAAACUAGCUUUUCCAACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAG
...-......-((((((......))))))....(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))...-... ( -41.40)
>DroEre_CAF1 57772 108 - 1
AUU-UUAUGCAGGAAAAAUCUAUUUAACUAACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAU
...-.............................(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))...-... ( -35.90)
>DroYak_CAF1 52886 107 - 1
AUU-UUAUGC-GGAAAAAUCUAUUUUCCUAACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA-UAC
...-......-((((((.....)))))).....(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))...-... ( -40.50)
>consensus
AUU_UUAUGC_GGAAAAACUAACUUUUCCAACAGCAUCGGUGGUUCAGUGGUAGAAUGCUCGCCUGCCACGCGGGCGGCCCGGGUUCGAUUCCCGGCCGAUGCAAA_UAG
...........((((((......))))))....(((((((..((((.......))))((.(((((((...)))))))))(((((.......))))))))))))....... (-38.08 = -38.44 +   0.36)

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 11:36:07 2006