Locus 4075

Sequence ID 2R_DroMel_CAF1
Location 13,452,670 – 13,452,791
Length 121
Max. P 0.995300
window6561 window6562 window6563

overview

Window 1

Location 13,452,670 – 13,452,770
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 87.59
Mean single sequence MFE -26.92
Consensus MFE -21.13
Energy contribution -20.88
Covariance contribution -0.25
Combinations/Pair 1.12
Mean z-score -2.46
Structure conservation index 0.79
SVM decision value 0.31
SVM RNA-class probability 0.681425
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13452670 100 - 20766785
AAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGC-------------CGAUAGGC--GCACACACA----AAACGA-
............((.(.((((((((((.(((....))))))))))))).).))......................((-------------(....)))--.........----......- ( -27.50)
>DroSec_CAF1 1390 100 - 1
AAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAUC-------------CGAUAGGC--GCACACACA----AAACGA-
...........(((((.((((((((((.(((....))))))))))))).)..........(((....))).......-------------.....)))--)........----......- ( -24.40)
>DroSim_CAF1 1540 100 - 1
AAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGC-------------CGAUAGGC--GCACACACA----AAACGA-
............((.(.((((((((((.(((....))))))))))))).).))......................((-------------(....)))--.........----......- ( -27.50)
>DroEre_CAF1 2064 100 - 1
AAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGC-------------CGAUAGGC--GCACACACA----AAACGA-
............((.(.((((((((((.(((....))))))))))))).).))......................((-------------(....)))--.........----......- ( -27.50)
>DroYak_CAF1 2182 105 - 1
AAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGCCGC----------CGAUAGGCGCGCACACACA----AAACGA-
............((.(.((((((((((.(((....))))))))))))).).))......................(((((----------(....)))).)).......----......- ( -32.80)
>DroPer_CAF1 1332 120 - 1
AAUUACUUUUACGUCAGUCAUAUGCAAUAGGGUACCUUGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUUGCUGGCAUGAAAAUACAUACAUGCACCCACACACAUAUAAAACCAC
.....((.(((.((.(.(((((((((.((((....))))))))))))).).)).)))..)).................(((((..........)))))...................... ( -21.80)
>consensus
AAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGC_____________CGAUAGGC__GCACACACA____AAACGA_
............((.(.((((((((((.(((....))))))))))))).).))................................................................... (-21.13 = -20.88 +  -0.25)

alignment

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secondary structure

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Window 2

Location 13,452,693 – 13,452,791
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.02
Mean single sequence MFE -30.15
Consensus MFE -25.98
Energy contribution -26.90
Covariance contribution 0.92
Combinations/Pair 1.06
Mean z-score -2.29
Structure conservation index 0.86
SVM decision value 1.14
SVM RNA-class probability 0.921412
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13452693 98 + 20766785
---GCUGAGGGAAAGUUUUCUAAUUAAGUUACUCAUACGCACCGGGUGCCCGAGUGCAUAUGACUGACGUGAAAGUAAUUUUCAUAA--AAGGGAACUUG-----------------GUG
---.........(((((..((......((((.(((((.(((((((....))).)))).))))).))))(((((((...)))))))..--.))..))))).-----------------... ( -31.40)
>DroSec_CAF1 1413 99 + 1
---GAUGAGGGAAAGUUUUCUAAUUAAGUUACUCAUACGCACCGGGUGCCCGAGUGCAUAUGACUGACGUGAAAGUAAUUUUCAUAA--AAGGGAACUUGG----------------GUG
---.........(((((..((......((((.(((((.(((((((....))).)))).))))).))))(((((((...)))))))..--.))..)))))..----------------... ( -31.40)
>DroSim_CAF1 1563 99 + 1
---GCUGAGGGAAAGUUUUCUAAUUAAGUUACUCAUACGCACCGGGUGCCCGAGUGCAUAUGACUGACGUGAAAGUAAUUUUCAUAA--AAGGGAACUUGG----------------GUG
---.........(((((..((......((((.(((((.(((((((....))).)))).))))).))))(((((((...)))))))..--.))..)))))..----------------... ( -31.40)
>DroEre_CAF1 2087 98 + 1
---GCUGAGGGAAAGUUUUCUAAUUAAGUUACUCAUACGCACCGGGUGCCCGAGUGCAUAUGACUGACGUGAAAGUAAUUUUCAUAA--AAGGGAACUUGG-----------------UG
---.........(((((..((......((((.(((((.(((((((....))).)))).))))).))))(((((((...)))))))..--.))..)))))..-----------------.. ( -31.40)
>DroYak_CAF1 2207 104 + 1
GCGGCUGAGGGAAAGUUUUCUAAUUAAGUUACUCAUACGCACCGGGUGCCCGAGUGCAUAUGACUGACGUGAAAGUAAUUUUCAUAA--AAGGCAACUUGGUG--------------GUG
((.((..((((((....))))......((((.(((((.(((((((....))).)))).))))).))))(((((((...)))))))..--.......))..)).--------------)). ( -32.60)
>DroPer_CAF1 1372 120 + 1
GCCAGCAAGGGAAAGUUUUCUAAUUAAGUUACUCAUACGCACAAGGUACCCUAUUGCAUAUGACUGACGUAAAAGUAAUUUUCAUAUCAACCAUAACUCAGAGGAGAGAGGAAAAGGGUG
.((.....))(((((((..((......((((.(((((.(((..(((...)))..))).))))).)))).....)).)))))))......(((....(((........)))......))). ( -22.70)
>consensus
___GCUGAGGGAAAGUUUUCUAAUUAAGUUACUCAUACGCACCGGGUGCCCGAGUGCAUAUGACUGACGUGAAAGUAAUUUUCAUAA__AAGGGAACUUGG________________GUG
............(((((((((......((((.(((((.(((((((....))).)))).))))).))))(((((((...))))))).....)))))))))..................... (-25.98 = -26.90 +   0.92)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,452,693 – 13,452,791
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 86.02
Mean single sequence MFE -26.18
Consensus MFE -24.09
Energy contribution -23.57
Covariance contribution -0.53
Combinations/Pair 1.15
Mean z-score -2.93
Structure conservation index 0.92
SVM decision value 2.56
SVM RNA-class probability 0.995300
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13452693 98 - 20766785
CAC-----------------CAAGUUCCCUU--UUAUGAAAAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGC---
...-----------------.(((((..((.--((((((((.....))))).((.(.((((((((((.(((....))))))))))))).).)).)))..))..))))).........--- ( -25.70)
>DroSec_CAF1 1413 99 - 1
CAC----------------CCAAGUUCCCUU--UUAUGAAAAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAUC---
...----------------..(((((..((.--((((((((.....))))).((.(.((((((((((.(((....))))))))))))).).)).)))..))..))))).........--- ( -25.70)
>DroSim_CAF1 1563 99 - 1
CAC----------------CCAAGUUCCCUU--UUAUGAAAAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGC---
...----------------..(((((..((.--((((((((.....))))).((.(.((((((((((.(((....))))))))))))).).)).)))..))..))))).........--- ( -25.70)
>DroEre_CAF1 2087 98 - 1
CA-----------------CCAAGUUCCCUU--UUAUGAAAAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGC---
..-----------------..(((((..((.--((((((((.....))))).((.(.((((((((((.(((....))))))))))))).).)).)))..))..))))).........--- ( -25.70)
>DroYak_CAF1 2207 104 - 1
CAC--------------CACCAAGUUGCCUU--UUAUGAAAAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGCCGC
...--------------....(((((((...--...(((((.....)))))......((((((((((.(((....))))))))))))))))))))......................... ( -28.40)
>DroPer_CAF1 1372 120 - 1
CACCCUUUUCCUCUCUCCUCUGAGUUAUGGUUGAUAUGAAAAUUACUUUUACGUCAGUCAUAUGCAAUAGGGUACCUUGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUUGCUGGC
.............(((....((((((((..((((..(((((.....)))))..))))(((((((((.((((....)))))))))))))))))))))...)))........((.....)). ( -25.90)
>consensus
CAC________________CCAAGUUCCCUU__UUAUGAAAAUUACUUUCACGUCAGUCAUAUGCACUCGGGCACCCGGUGCGUAUGAGUAACUUAAUUAGAAAACUUUCCCUCAGC___
.....................(((((..........(((((.....))))).((.(.((((((((((.(((....))))))))))))).).))..........)))))............ (-24.09 = -23.57 +  -0.53)

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 11:11:09 2006