Locus 371

Sequence ID X_DroMel_CAF1
Location 1,123,377 – 1,123,503
Length 126
Max. P 0.825778
window556 window557

overview

Window 6

Location 1,123,377 – 1,123,481
Length 104
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 90.31
Mean single sequence MFE -19.53
Consensus MFE -13.92
Energy contribution -13.96
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -2.53
Structure conservation index 0.71
SVM decision value 0.70
SVM RNA-class probability 0.825778
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1123377 104 + 22224390
----AAAACAGCGACAGCAAACAA--AUAUCGCACAAAAUAAAACGGAAACGUGGCCAAAAGCAGGC-------AAACAGUGUUGCCAAAUACUGUCUAACGAAUCUUCCUAAUUAA
----......((((..........--...))))..........(((....))).(((.......)))-------..((((((((....))))))))..................... ( -19.92)
>DroSec_CAF1 20120 104 + 1
----AAAACAGCGACAGCAAACAA--AUAUCGCACAAAAUAAAACGGAAACGUGGCCAAAGGCAAGC-------AAACAGUGUUGCCAAAUACUGUCUUACGAAUCUUCCAAAUUAA
----......((....))......--...((((..........(((....))).(((...)))..))-------..((((((((....)))))))).....)).............. ( -20.20)
>DroSim_CAF1 21066 104 + 1
----AAAACAGCGACAGCAAACAA--AUAUCGCACAAAAUAAAACGGAAACGUGGCCAAAAGCAAGC-------AAACAGUGUUGCCAAAUACUGUCUUACGAAUCUUCCAAAUUAA
----......((....))......--...((((..........(((....))).((.....))..))-------..((((((((....)))))))).....)).............. ( -18.00)
>DroEre_CAF1 21200 104 + 1
---AAAAACAGAGCCAGCAAACAA--AUAUCGCACAAAAUAAAACGGAAACGUGGCCAAAAGCAGAC-------AAACAGUGUUGCCAAAUGCUGUCUUACGAAU-UUCCAAAUUAA
---.......(((.(((((.....--.................(((....)))(((........(((-------(.....)))))))...))))).)))......-........... ( -17.60)
>DroYak_CAF1 20710 116 + 1
ACAAAAAACAGAGCCAGCAAACAAAAAUAUCGCACAAAAUAAAACGGAAACGUGGCCAAAAGCAGGCAAACGGCAAACAGUGUUGCCAAUUACUGUCUUGCGAAU-UUCCAAAUUAA
..........(.(((.((.............))..........(((....)))))))....(((((((...(((((......)))))......)).)))))....-........... ( -21.92)
>consensus
____AAAACAGCGACAGCAAACAA__AUAUCGCACAAAAUAAAACGGAAACGUGGCCAAAAGCAGGC_______AAACAGUGUUGCCAAAUACUGUCUUACGAAUCUUCCAAAUUAA
.............................(((...........(((....))).((.....)).............((((((((....))))))))....))).............. (-13.92 = -13.96 +   0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,123,411 – 1,123,503
Length 92
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 82.74
Mean single sequence MFE -23.30
Consensus MFE -16.74
Energy contribution -16.82
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -1.92
Structure conservation index 0.72
SVM decision value 0.62
SVM RNA-class probability 0.803359
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1123411 92 + 22224390
AAAACGGAAACGUGGCCAAAAGCAGGC-------AAACAGUGUUGCCAAAUACUGUCUAACGAAUCUUCCUAAUUAACAAAAUUCUGCCGAGUUUAGGC------------------
...(((....))).(((..((((.(((-------(..(((((((....)))))))((....))......................))))..)))).)))------------------ ( -23.30)
>DroSec_CAF1 20154 92 + 1
AAAACGGAAACGUGGCCAAAGGCAAGC-------AAACAGUGUUGCCAAAUACUGUCUUACGAAUCUUCCAAAUUAACAAAAUGCUGCCGAGUGCAGGC------------------
...(((....))).((....((((.((-------(.((((((((....)))))))).....((....)).............)))))))....))....------------------ ( -23.20)
>DroSim_CAF1 21100 92 + 1
AAAACGGAAACGUGGCCAAAAGCAAGC-------AAACAGUGUUGCCAAAUACUGUCUUACGAAUCUUCCAAAUUAACAAAAUGCUGCCGAGUGCAGUC------------------
.....((((.((((((.....))....-------..((((((((....))))))))..))))....)))).............(((((.....))))).------------------ ( -19.30)
>DroEre_CAF1 21235 109 + 1
AAAACGGAAACGUGGCCAAAAGCAGAC-------AAACAGUGUUGCCAAAUGCUGUCUUACGAAU-UUCCAAAUUAACAAAAUGCUGCCAAGUGCAGGCGAAUCUACUUCACUUGUC
...(((....)))........((((.(-------(.((((((((....))))))))......(((-(....)))).......))))))((((((.((.........)).)))))).. ( -23.30)
>DroYak_CAF1 20750 102 + 1
AAAACGGAAACGUGGCCAAAAGCAGGCAAACGGCAAACAGUGUUGCCAAUUACUGUCUUGCGAAU-UUCCAAAUUAACAAAGUGCUGCCAACUGCAGGCGAAU--------------
...(((....))).(((...((..((((.((.((((((((((........)))))).)))).(((-(....))))......))..))))..))...)))....-------------- ( -27.40)
>consensus
AAAACGGAAACGUGGCCAAAAGCAGGC_______AAACAGUGUUGCCAAAUACUGUCUUACGAAUCUUCCAAAUUAACAAAAUGCUGCCGAGUGCAGGC__________________
...(((....)))(((....((((............((((((((....)))))))).....((....)).............)))))))............................ (-16.74 = -16.82 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:48 2006