Locus 6389

Sequence ID 2L_DroMel_CAF1
Location 17,922,662 – 17,922,766
Length 104
Max. P 0.916045
window10201 window10202

overview

Window 1

Location 17,922,662 – 17,922,766
Length 104
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 68.59
Mean single sequence MFE -20.06
Consensus MFE -11.78
Energy contribution -13.38
Covariance contribution 1.60
Combinations/Pair 1.25
Mean z-score -1.42
Structure conservation index 0.59
SVM decision value 0.17
SVM RNA-class probability 0.618233
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17922662 104 + 22407834
---AUAUUACUAUUUCAAUUUUAAGACGCAAUAUUGCCCAACUUUGUUGGUAACAUGAAAGUGAAUGUGCAGUGUGAGAGACUGCACUUCACUUUUCU-UUCAUCUAA
---....................(((.(((....)))(((((...)))))......(((((((((.(((((((.(....)))))))))))))))))..-....))).. ( -25.50)
>DroSec_CAF1 140118 104 + 1
---AUAUUACUAUUACAACUUAAAGAUUCUAUAUUGCCCAGCU-UGUUGGUAACAUGAAAUUGAAUGUGCAGUGUGAGAGACUGCACUUCACUUUUCACUUAAUCUAA
---....................(((((.........((((..-..)))).....(((((.((((.(((((((.(....))))))))))))..)))))...))))).. ( -21.80)
>DroSim_CAF1 117839 104 + 1
---AUAUUACUAUUACAAUUUAAAGACGCAAUAUAGCCCAGCU-UAUUGGUUACAUGAAUGUGAAUGUGCAGUGUGAGAGACUGCACUUCACUUUUCACUUAACCUAA
---...................(((..((......))....))-)...(((((..((((.(((((.(((((((.(....)))))))))))))..))))..)))))... ( -26.40)
>DroEre_CAF1 130238 81 + 1
---GUAUAACUAUUAGAAUUUG---------------CUUGCU-UGUUGUUAACACAAAAUAGAACGUGCAGUGGGAGAGACUGCACUUCAAUG-------UAUAU-A
---(((((..............---------------......-..((((....))))....(((.(((((((.......))))))))))..))-------)))..-. ( -13.90)
>DroYak_CAF1 137950 88 + 1
CUCGUAUUACUAUUAGAAUUUG---------------UUUGCU-UGUUGUUAACAUAAAAUGGAACGUGCACAGGU--AGACUGCAUUUUACGUUUUUCU-CAUAU-G
.............((((((..(---------------((((((-(((.((...(((...)))......))))))))--))))...)))))).........-.....-. ( -12.70)
>consensus
___AUAUUACUAUUACAAUUUAAAGA__C_AUAU_GCCCAGCU_UGUUGGUAACAUGAAAUUGAAUGUGCAGUGUGAGAGACUGCACUUCACUUUUCACUUAAUCUAA
........................................................(((((((((.(((((((.......))))))))))))))))............ (-11.78 = -13.38 +   1.60)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,922,662 – 17,922,766
Length 104
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 68.59
Mean single sequence MFE -20.48
Consensus MFE -9.12
Energy contribution -11.36
Covariance contribution 2.24
Combinations/Pair 1.07
Mean z-score -1.97
Structure conservation index 0.45
SVM decision value 1.11
SVM RNA-class probability 0.916045
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17922662 104 - 22407834
UUAGAUGAA-AGAAAAGUGAAGUGCAGUCUCUCACACUGCACAUUCACUUUCAUGUUACCAACAAAGUUGGGCAAUAUUGCGUCUUAAAAUUGAAAUAGUAAUAU---
..(((((..-.((((.((((((((((((.......))))))).)))))))))(((((.(((((...)))))..)))))..)))))....................--- ( -28.10)
>DroSec_CAF1 140118 104 - 1
UUAGAUUAAGUGAAAAGUGAAGUGCAGUCUCUCACACUGCACAUUCAAUUUCAUGUUACCAACA-AGCUGGGCAAUAUAGAAUCUUUAAGUUGUAAUAGUAAUAU---
.........((((((..(((((((((((.......))))))).)))).))))))....(((...-...)))(((((.((((...)))).)))))...........--- ( -22.20)
>DroSim_CAF1 117839 104 - 1
UUAGGUUAAGUGAAAAGUGAAGUGCAGUCUCUCACACUGCACAUUCACAUUCAUGUAACCAAUA-AGCUGGGCUAUAUUGCGUCUUUAAAUUGUAAUAGUAAUAU---
...(((((.(((((..((((((((((((.......))))))).))))).))))).)))))....-(((...))).(((((((.........))))))).......--- ( -29.50)
>DroEre_CAF1 130238 81 - 1
U-AUAUA-------CAUUGAAGUGCAGUCUCUCCCACUGCACGUUCUAUUUUGUGUUAACAACA-AGCAAG---------------CAAAUUCUAAUAGUUAUAC---
.-..(((-------((..((((((((((.......))))))).))).....)))))........-......---------------...................--- ( -13.40)
>DroYak_CAF1 137950 88 - 1
C-AUAUG-AGAAAAACGUAAAAUGCAGUCU--ACCUGUGCACGUUCCAUUUUAUGUUAACAACA-AGCAAA---------------CAAAUUCUAAUAGUAAUACGAG
.-.(((.-((((.(((((((((((..((.(--(....)).))....))))))))))).......-.(....---------------)...)))).))).......... (  -9.20)
>consensus
UUAGAUGAAGAGAAAAGUGAAGUGCAGUCUCUCACACUGCACAUUCAAUUUCAUGUUACCAACA_AGCUGGGC_AUAU_G__UCUUCAAAUUGUAAUAGUAAUAU___
.............(((((((((((((((.......))))))).))))))))......................................................... ( -9.12 = -11.36 +   2.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:51 2006