Locus 1362

Sequence ID 2R_DroMel_CAF1
Location 5,251,661 – 5,251,779
Length 118
Max. P 0.791583
window2349 window2350

overview

Window 9

Location 5,251,661 – 5,251,779
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.53
Mean single sequence MFE -26.52
Consensus MFE -6.50
Energy contribution -6.50
Covariance contribution -0.00
Combinations/Pair 1.20
Mean z-score -1.88
Structure conservation index 0.25
SVM decision value 0.59
SVM RNA-class probability 0.791583
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5251661 118 + 20766785
UACAGAAGAUUGAA-UUACAAGGAUGCAAUUGCCUGGACAAGAGAUAUCUCCCAUCUUUAUGGCAUACCAUCCAAGCGUUUAAUCUUUAAGUGAUCAGG-ACUUCUUCCUGUGCACUACG
....((((((((((-(.....(((((....((((.(((...(((....)))...)))....))))...)))))....))))))))))).((((..((((-(.....)))))..))))... ( -35.90)
>DroSec_CAF1 119772 113 + 1
UACAGAAAUAUAGA-U-----CCAGGCAAUUGCCUGGACAAGAGAUAUCUCCCAUCUUUACGGCAUACCAUCCAACCGUUUAAUCUUUAAGUGAUCAGG-ACUUUUUCCUGUGCACUUCG
...(((.....(((-(-----((((((....)))))))...(((....)))...)))..((((............))))....)))..(((((..((((-(.....)))))..))))).. ( -28.40)
>DroSim_CAF1 107165 113 + 1
UACAGAAAUAUAGA-U-----CCAGGCAAUUGCCUGGACAAGAGAUAUCUCCCAUCUUUACGGCAUACCAUCCAACCGUUUAAUCUUUAAGUGAUCAGG-ACUUCUUCCUGUGCACGUCG
....((..((.(((-(-----((((((....)))))))..((((((.......))))))((((............))))....))).)).(((..((((-(.....)))))..))).)). ( -27.90)
>DroEre_CAF1 120396 99 + 1
UUUACA---AUAGAAGUACGUG-------------GUACAAGUGAUAUCUCCCAUCUUUAUGGCAUCG----CAACCGUUUAAUCCUCAAGUGAUCAGG-ACUUCUUCCUGUGCACUCUG
......---...((..((..((-------------((....(((((.....((((....)))).))))----).))))..))....)).((((..((((-(.....)))))..))))... ( -17.70)
>DroYak_CAF1 121558 97 + 1
UACACAC-UAUAGAAGUACGAGAAUGCAAUUGCUUGCACAAGUGGUAUCACCCAUCUU----------------------UGAUCUUCAAGGGAUCAGGCAUUUUUUUCUGUGCACUCUG
.......-(((((((....((((((((.((..(((....)))..))...........(----------------------((((((.....))))))))))))))))))))))....... ( -22.70)
>consensus
UACAGAA_UAUAGA_UUAC__GCAGGCAAUUGCCUGGACAAGAGAUAUCUCCCAUCUUUACGGCAUACCAUCCAACCGUUUAAUCUUUAAGUGAUCAGG_ACUUCUUCCUGUGCACUCCG
.........................................(((....))).......................................(((..((((........))))..))).... ( -6.50 =  -6.50 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 5,251,661 – 5,251,779
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.53
Mean single sequence MFE -29.92
Consensus MFE -11.44
Energy contribution -12.44
Covariance contribution 1.00
Combinations/Pair 1.13
Mean z-score -1.76
Structure conservation index 0.38
SVM decision value 0.21
SVM RNA-class probability 0.637053
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5251661 118 - 20766785
CGUAGUGCACAGGAAGAAGU-CCUGAUCACUUAAAGAUUAAACGCUUGGAUGGUAUGCCAUAAAGAUGGGAGAUAUCUCUUGUCCAGGCAAUUGCAUCCUUGUAA-UUCAAUCUUCUGUA
...((((..(((((.....)-))))..))))..((((((....(((((.((((....))))...((..((((....))))..)))))))(((((((....)))))-)).))))))..... ( -35.90)
>DroSec_CAF1 119772 113 - 1
CGAAGUGCACAGGAAAAAGU-CCUGAUCACUUAAAGAUUAAACGGUUGGAUGGUAUGCCGUAAAGAUGGGAGAUAUCUCUUGUCCAGGCAAUUGCCUGG-----A-UCUAUAUUUCUGUA
..(((((..(((((.....)-))))..)))))..(((((..(((((..........)))))...((..((((....))))..))(((((....))))))-----)-)))........... ( -36.50)
>DroSim_CAF1 107165 113 - 1
CGACGUGCACAGGAAGAAGU-CCUGAUCACUUAAAGAUUAAACGGUUGGAUGGUAUGCCGUAAAGAUGGGAGAUAUCUCUUGUCCAGGCAAUUGCCUGG-----A-UCUAUAUUUCUGUA
....(((..(((((.....)-))))..)))....(((((..(((((..........)))))...((..((((....))))..))(((((....))))))-----)-)))........... ( -34.40)
>DroEre_CAF1 120396 99 - 1
CAGAGUGCACAGGAAGAAGU-CCUGAUCACUUGAGGAUUAAACGGUUG----CGAUGCCAUAAAGAUGGGAGAUAUCACUUGUAC-------------CACGUACUUCUAU---UGUAAA
.....((((..(((((.(((-(((.(.....).))))))....(((.(----(((..((((....))))((....))..))))))-------------).....)))))..---)))).. ( -21.80)
>DroYak_CAF1 121558 97 - 1
CAGAGUGCACAGAAAAAAAUGCCUGAUCCCUUGAAGAUCA----------------------AAGAUGGGUGAUACCACUUGUGCAAGCAAUUGCAUUCUCGUACUUCUAUA-GUGUGUA
..((((((..((((.........(((((.......)))))----------------------...(..((((....))))..)((((....)))).)))).)))))).....-....... ( -21.00)
>consensus
CGAAGUGCACAGGAAGAAGU_CCUGAUCACUUAAAGAUUAAACGGUUGGAUGGUAUGCCAUAAAGAUGGGAGAUAUCUCUUGUCCAGGCAAUUGCAUGC__GUAA_UCUAUA_UUCUGUA
..(((((..((((........))))..)))))................................((..((((....))))..)).................................... (-11.44 = -12.44 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:06 2006