Locus 6988

Sequence ID X_DroMel_CAF1
Location 17,489,454 – 17,489,623
Length 169
Max. P 0.998636
window11416 window11417 window11418

overview

Window 6

Location 17,489,454 – 17,489,547
Length 93
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 70.39
Mean single sequence MFE -21.83
Consensus MFE -14.12
Energy contribution -13.38
Covariance contribution -0.75
Combinations/Pair 1.35
Mean z-score -1.36
Structure conservation index 0.65
SVM decision value 0.31
SVM RNA-class probability 0.683012
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17489454 93 - 22224390
UUUGUGU----------------------AACAUGUGUUAAGCAAAAGCAAAAGCGAGAAAAUGUUGCUUAGCUAUCUCGCUCUAAUUCGCUAGAGCGAUUGAA-UCUUAUUUGGA
(((((.(----------------------(((....)))).)))))(((..((((((.......)))))).)))...((((((((......)))))))).....-........... ( -23.20)
>DroSec_CAF1 2632 87 - 1
AGUUUA-----------------------AAUAUGAGU------AAAGCAAAAGGGGGAAAUUGCCGCUUAGCUAUCUCCCUCUAAUUCGCUAGCGCGAUUGAUUUCUUAUUUGGA
..((((-----------------------((((.(((.------....(((.(((((((.((.((......)).)).)))))))...((((....)))))))..))).)))))))) ( -21.80)
>DroSim_CAF1 2843 86 - 1
AGUUUA-----------------------AAUAAGCUU------AAAGCAAAAGGGGGAAAUUGCCGCUUAGCUAUCUCCCUCUAAUUCGCUAGCGCGAUUGAA-UCUUAUUUGGA
..((((-----------------------((((((.((------((......(((((((.((.((......)).)).)))))))...((((....)))))))).-.)))))))))) ( -22.70)
>DroEre_CAF1 2642 109 - 1
UUUUUAAAACAUGUGUACAUUUUGACUGAAAUAUGCAU------AAAGCAGAAAGGGGGAAAUGCCGCUUAGCUGUCUCUCUCUAAUUCGCAAAAGCCAACGAA-UCAUAUUUGGA
...........((((((.(((((....))))).)))))------)..((.((((((((((...((......))..)))))))....))))).....((((....-......)))). ( -19.60)
>consensus
AGUUUA_______________________AAUAUGCGU______AAAGCAAAAGGGGGAAAAUGCCGCUUAGCUAUCUCCCUCUAAUUCGCUAGAGCGAUUGAA_UCUUAUUUGGA
................................................(((((((((((....((......))..))))))).....((((....))))...........)))).. (-14.12 = -13.38 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,489,493 – 17,489,587
Length 94
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 69.07
Mean single sequence MFE -16.23
Consensus MFE -7.68
Energy contribution -8.87
Covariance contribution 1.19
Combinations/Pair 1.20
Mean z-score -1.88
Structure conservation index 0.47
SVM decision value 0.41
SVM RNA-class probability 0.723442
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17489493 94 + 22224390
AUAGCUAAGCAACAUUUUCUCGCUUUUGCUUUUGCUUAACACAUGUU----------------------ACACAAAAAUAAGCAGAACUCCAAAUGAAUGGUACUCCAAACAAAAA
..(((.((((...........))))..)))((((((((.....((..----------------------...))....))))))))............(((....)))........ ( -12.80)
>DroSec_CAF1 2672 87 + 1
AUAGCUAAGCGGCAAUUUCCCCCUUUUGCUUU------ACUCAUAUU-----------------------UAAACUAAUAAGCAGAACUACAAAUGAAUGGUUCUGCAAAUAAUAA
..(((.(((.((........)))))..)))..------.........-----------------------...........(((((((((........)))))))))......... ( -16.80)
>DroSim_CAF1 2882 87 + 1
AUAGCUAAGCGGCAAUUUCCCCCUUUUGCUUU------AAGCUUAUU-----------------------UAAACUAAUAAGCAGAACUACAAAUGAAUGGUUCUGCAAAUAAUAA
.(((.((((((((((..........)))))..------..))))).)-----------------------)).........(((((((((........)))))))))......... ( -20.10)
>DroEre_CAF1 2681 110 + 1
ACAGCUAAGCGGCAUUUCCCCCUUUCUGCUUU------AUGCAUAUUUCAGUCAAAAUGUACACAUGUUUUAAAAAGAUAAGCUGAACUAUAAAUGCAUGUUUAUACAAACAGUAC
.....((((((((((((..........((...------..))(((.((((((.....((....))(((((.....))))).)))))).))))))))).))))))............ ( -15.20)
>consensus
AUAGCUAAGCGGCAAUUUCCCCCUUUUGCUUU______ACGCAUAUU_______________________UAAAAAAAUAAGCAGAACUACAAAUGAAUGGUUCUGCAAACAAUAA
......((((((.............))))))..................................................(((((((((........)))))))))......... ( -7.68 =  -8.87 +   1.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,489,529 – 17,489,623
Length 94
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 69.82
Mean single sequence MFE -14.15
Consensus MFE -7.05
Energy contribution -9.30
Covariance contribution 2.25
Combinations/Pair 1.12
Mean z-score -2.86
Structure conservation index 0.50
SVM decision value 3.17
SVM RNA-class probability 0.998636
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17489529 94 + 22224390
UAACACAUGUU----------------------ACACAAAAAUAAGCAGAACUCCAAAUGAAUGGUACUCCAAACAAAAAAGAUCAAUCAACAAAAUAUGAUCAAAAAACAUUUCU
((((....)))----------------------).....................(((((..(((....))).........(((((............)))))......))))).. (  -7.90)
>DroSec_CAF1 2704 91 + 1
--ACUCAUAUU-----------------------UAAACUAAUAAGCAGAACUACAAAUGAAUGGUUCUGCAAAUAAUAAAGAUCAAUCAACAAGAUAUGAUCAAAAAACAUUUCU
--.........-----------------------...........(((((((((........)))))))))..........((((((((.....))).)))))............. ( -19.00)
>DroSim_CAF1 2914 91 + 1
--AAGCUUAUU-----------------------UAAACUAAUAAGCAGAACUACAAAUGAAUGGUUCUGCAAAUAAUAAAGAUCAAACAACAAGAUAUGAUCAAAAAACAUUUCU
--..(((((((-----------------------......)))))))(((((((........)))))))............(((((............)))))............. ( -16.20)
>DroEre_CAF1 2713 113 + 1
--AUGCAUAUUUCAGUCAAAAUGUACACAUGUUUUAAAAAGAUAAGCUGAACUAUAAAUGCAUGUUUAUACAAACAGUACAAAUCAAUUACAAAGGUGUGAUCAUAUAACA-AUCC
--.(((((.((......)).)))))(((((.(((......(((..((((...(((((((....)))))))....))))....)))......))).)))))...........-.... ( -13.50)
>consensus
__ACGCAUAUU_______________________UAAAAAAAUAAGCAGAACUACAAAUGAAUGGUUCUGCAAACAAUAAAGAUCAAUCAACAAGAUAUGAUCAAAAAACAUUUCU
.............................................(((((((((........)))))))))..........((((((((.....))).)))))............. ( -7.05 =  -9.30 +   2.25)

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 12:27:28 2006