Locus 9537

Sequence ID 3R_DroMel_CAF1
Location 25,196,342 – 25,196,479
Length 137
Max. P 0.915419
window15254 window15255 window15256

overview

Window 4

Location 25,196,342 – 25,196,440
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.12
Mean single sequence MFE -27.77
Consensus MFE -15.61
Energy contribution -17.05
Covariance contribution 1.45
Combinations/Pair 1.09
Mean z-score -1.65
Structure conservation index 0.56
SVM decision value 0.45
SVM RNA-class probability 0.741004
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25196342 98 - 27905053
UCUCUGCAGAGAUGCAGCUAAA-------------CGCUGC----UUCCUUGGCUGAAUUCGUAUGCGA-----GGCAGCAUAUGGCAGCCGGAAAUGAAACGUAAAUCAAAUAAGUAAA
((((....)))).(((((....-------------.)))))----((((..(((((...((((((((..-----....)))))))))))))))))......................... ( -31.50)
>DroPse_CAF1 59372 108 - 1
--------UAGUUGCAGCUAAAAUGCCUCUCUGUUCGCUGC----UUCCUUCGCUGAAUUCGUAUGCGAGGCGAGGCAGCAUAUGGCAGCCGGAAAUGAAACGUAAAUCAAAUAAGUAAG
--------..(((((.((......))..........(((((----(((((((((...........)))))).)))))))).....))))).............................. ( -31.60)
>DroWil_CAF1 136479 100 - 1
UCUCAA--------AAACUAAAACACCGCCAU---CGUCUC----UAACAUGACUGAAAUCGCUUGCCA-----GGCAGCAUAUGGCAGCCGGAAAUGAAACGUAAAUCAAAUAAGUAAG
......--------..(((......(((...(---((((..----......))).))....(((.((((-----.........))))))))))...(((........)))....)))... ( -14.90)
>DroYak_CAF1 57432 98 - 1
UCUCUGCAGAUAUGCAGCUAAA-------------CGCUGC----UUCCUUGGCUGAAUUCGUAUGCGA-----GGCAGCAUAUGGCAGCCGGAAAUGAAACGUAAAUCAAAUAAGUAAA
....(((......(((((....-------------.)))))----((((..(((((...((((((((..-----....))))))))))))))))).......)))............... ( -29.70)
>DroAna_CAF1 52721 103 - 1
AACCUGUACAAAUGCAGCUAAAA------------UGCCGCCGUGCUCCUUGGCUGAAUUCGUAUGCGA-----GGCAGCAUAUGGCUGCCGGAAAUGAAACGUAAAUCAAAUAAGUAAG
..((.((((.(((.(((((((..------------.((......))...))))))).))).))))....-----((((((.....))))))))........................... ( -27.30)
>DroPer_CAF1 60332 108 - 1
--------UAGUUGCAGCUAAAAUGCCUCUCUGUUCGCUGC----UUCCUUCGCUGAAUUCGUAUGCGAGGCGAGGCAGCAUAUGGCAGCCGGAAAUGAAACGUAAAUCAAAUAAGUAAG
--------..(((((.((......))..........(((((----(((((((((...........)))))).)))))))).....))))).............................. ( -31.60)
>consensus
UCUCUG__GAGAUGCAGCUAAAA____________CGCUGC____UUCCUUGGCUGAAUUCGUAUGCGA_____GGCAGCAUAUGGCAGCCGGAAAUGAAACGUAAAUCAAAUAAGUAAG
.............(((((..................)))))....((((..(((((...((((((((...........)))))))))))))))))......................... (-15.61 = -17.05 +   1.45)

alignment

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secondary structure

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Window 5

Location 25,196,382 – 25,196,479
Length 97
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 80.15
Mean single sequence MFE -28.50
Consensus MFE -23.41
Energy contribution -23.08
Covariance contribution -0.33
Combinations/Pair 1.35
Mean z-score -1.96
Structure conservation index 0.82
SVM decision value 1.10
SVM RNA-class probability 0.915419
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25196382 97 + 27905053
GCUGCCUCGCAUACGAAUUCAGCCAAGGAA----GCAGCG-UUUAGCUGCAUCUCUGCAGAGAGAGAAAAGUGGCAGCAAGUAUCGAGGAAGAUUCAUAAAA
.((.(((((.(((((....).((((.....----(((((.-....))))).(((((......)))))....)))).....))))))))).)).......... ( -32.50)
>DroSec_CAF1 55571 84 + 1
GCUGCCUCGCAUACGAAUUCAGCCAAGGAA----GCAGCG-UUUAGCUGCAUCUCUGCAGAGAGAGAAAAGUGGCAGCAAGUAUCGCGG-------------
(((((((((....))).(((..........----(((((.-....))))).(((((....))))))))....))))))...........------------- ( -28.70)
>DroSim_CAF1 54958 97 + 1
GCUGCCUCGCAUACGAAUUCAGCCAAGGAA----GCAGCG-UUUAGCUGCAUCUCUGCAGAGAGAGAAAAGCGGCAGCAAGUAUCGAGGGAGAUUCAUAAAU
.((.(((((.(((((....).(((......----(((((.-....))))).(((((......))))).....))).....))))))))).)).......... ( -34.00)
>DroEre_CAF1 58064 96 + 1
GCUGCCUCGCAUACGAAUUCAGCCAAGGAA----GCAGCG-UUUAGCUGCAUUUCUGCAGAGAGAGAAAAGUGGCGGCGAUGAUCGAG-GAGAUUCAUAAAU
(((((((((....))).(((.((..(((((----(((((.-....))))).))))))).)))..........)))))).((((((...-..)).)))).... ( -29.40)
>DroYak_CAF1 57472 97 + 1
GCUGCCUCGCAUACGAAUUCAGCCAAGGAA----GCAGCG-UUUAGCUGCAUAUCUGCAGAGAGAGAAAAGUGGCAGCGAUAAUCGAGGGAGAUUCAUAAGU
.((.((((((....(....).((((.....----(((((.-....)))))...(((......)))......)))).))(.....))))).)).......... ( -25.80)
>DroAna_CAF1 52761 84 + 1
GCUGCCUCGCAUACGAAUUCAGCCAAGGAGCACGGCGGCAUUUUAGCUGCAUUUGUACAGGUUCAGAAAAGUAGUACUCUGAAU------------------
((((..(((....)))...))))....(.(((..(((((......)))))...))).)..(((((((..........)))))))------------------ ( -20.60)
>consensus
GCUGCCUCGCAUACGAAUUCAGCCAAGGAA____GCAGCG_UUUAGCUGCAUCUCUGCAGAGAGAGAAAAGUGGCAGCAAGUAUCGAGGGAGAUUCAUAAAU
((((((.(..........................(((((......))))).(((((......)))))...).))))))........................ (-23.41 = -23.08 +  -0.33)

alignment

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secondary structure

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Window 6

Location 25,196,382 – 25,196,479
Length 97
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 80.15
Mean single sequence MFE -26.07
Consensus MFE -17.59
Energy contribution -18.73
Covariance contribution 1.14
Combinations/Pair 1.14
Mean z-score -1.88
Structure conservation index 0.67
SVM decision value 0.74
SVM RNA-class probability 0.838742
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25196382 97 - 27905053
UUUUAUGAAUCUUCCUCGAUACUUGCUGCCACUUUUCUCUCUCUGCAGAGAUGCAGCUAAA-CGCUGC----UUCCUUGGCUGAAUUCGUAUGCGAGGCAGC
..........((.(((((((((...(.((((....(((((......))))).(((((....-.)))))----.....)))).).....)))).))))).)). ( -28.70)
>DroSec_CAF1 55571 84 - 1
-------------CCGCGAUACUUGCUGCCACUUUUCUCUCUCUGCAGAGAUGCAGCUAAA-CGCUGC----UUCCUUGGCUGAAUUCGUAUGCGAGGCAGC
-------------...........((((((...........((.((.(((..(((((....-.)))))----...))).)).))..(((....))))))))) ( -26.80)
>DroSim_CAF1 54958 97 - 1
AUUUAUGAAUCUCCCUCGAUACUUGCUGCCGCUUUUCUCUCUCUGCAGAGAUGCAGCUAAA-CGCUGC----UUCCUUGGCUGAAUUCGUAUGCGAGGCAGC
..........((.(((((((((...(.(((.....(((((......))))).(((((....-.)))))----......))).).....)))).))))).)). ( -28.10)
>DroEre_CAF1 58064 96 - 1
AUUUAUGAAUCUC-CUCGAUCAUCGCCGCCACUUUUCUCUCUCUGCAGAAAUGCAGCUAAA-CGCUGC----UUCCUUGGCUGAAUUCGUAUGCGAGGCAGC
....((((.((..-...)))))).(((((((..((((((.....).))))).(((((....-.)))))----.....)))).....(((....))))))... ( -24.30)
>DroYak_CAF1 57472 97 - 1
ACUUAUGAAUCUCCCUCGAUUAUCGCUGCCACUUUUCUCUCUCUGCAGAUAUGCAGCUAAA-CGCUGC----UUCCUUGGCUGAAUUCGUAUGCGAGGCAGC
.......((((......))))...((((((...........((.((......(((((....-.)))))----.......)).))..(((....))))))))) ( -25.92)
>DroAna_CAF1 52761 84 - 1
------------------AUUCAGAGUACUACUUUUCUGAACCUGUACAAAUGCAGCUAAAAUGCCGCCGUGCUCCUUGGCUGAAUUCGUAUGCGAGGCAGC
------------------.(((((((........))))))).(((((....)))))......((((((((.......)))).....(((....))))))).. ( -22.60)
>consensus
AUUUAUGAAUCUCCCUCGAUACUUGCUGCCACUUUUCUCUCUCUGCAGAGAUGCAGCUAAA_CGCUGC____UUCCUUGGCUGAAUUCGUAUGCGAGGCAGC
........................((((((...........((.((.(((..(((((......)))))....)))....)).))..(((....))))))))) (-17.59 = -18.73 +   1.14)

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 13:36:42 2006