Locus 5750

Sequence ID 3L_DroMel_CAF1
Location 15,627,892 – 15,628,083
Length 191
Max. P 0.980522
window9118 window9119 window9120

overview

Window 8

Location 15,627,892 – 15,628,005
Length 113
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 96.19
Mean single sequence MFE -33.85
Consensus MFE -29.06
Energy contribution -29.88
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -2.56
Structure conservation index 0.86
SVM decision value 0.96
SVM RNA-class probability 0.890118
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15627892 113 + 23771897
AAAUAAAAAUAAAAAUCAAUUUCAGGGCAUUUCCUGGCCACGUUGCACGUGCCACGUGCCAAAACAACAACAAUAACA-ACUCGAGUGGAGUUUGGCUGGCUGGGGGGAUUCCC
........................(((..(..((..(((((((.((....)).))))(((((................-((((.....))))))))).)))..))..)...))) ( -31.59)
>DroSec_CAF1 50139 113 + 1
AAAUAAAAAUAAAAAUCAAUUUCAGGGCAUUUCCUGGCCACGUUGCACGUGCCACGUGCCAAAACAACAACAAUAACAAACUCGAGUGGGGUUUGGCUGGCUGGG-GGAUUCCC
........................(((.((..((..((((.((.(((((.....))))).................(((((((.....)))))))))))))..))-..)).))) ( -37.50)
>DroSim_CAF1 51151 114 + 1
AAAUAAAAAUAAAAAUCAAUUUCAGGGCAUUUCCUGGCCACGUUGCACGUGCCACGUGCCAAAACAACAACAAUAACAAACUCGAGUGGAGUUUGGCUGACUGGGGGGAUUCCC
........................(((.((..((((((.((((.((....)).)))))))................(((((((.....)))))))........)))..)).))) ( -32.10)
>DroYak_CAF1 54719 112 + 1
AAAUAAAAAUAAAAAUCAAUUUCAGGGCAUUUCCUGGCCACGUUGCACGUGCCACGUGCCAAAGGAACAACAAUAACA-ACUCGAGUGGAGUUUCGUUGGCUGGG-GGAUUCCC
........................(((.((..((..((((((..(((((.....)))))..................(-((((.....))))).)).))))..))-..)).))) ( -34.20)
>consensus
AAAUAAAAAUAAAAAUCAAUUUCAGGGCAUUUCCUGGCCACGUUGCACGUGCCACGUGCCAAAACAACAACAAUAACA_ACUCGAGUGGAGUUUGGCUGGCUGGG_GGAUUCCC
........................(((.((((((..(((((...(((((.....))))).................(((((((.....)))))))).))))..)).)))).))) (-29.06 = -29.88 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 15,627,926 – 15,628,043
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.48
Mean single sequence MFE -36.52
Consensus MFE -29.52
Energy contribution -29.24
Covariance contribution -0.28
Combinations/Pair 1.12
Mean z-score -2.28
Structure conservation index 0.81
SVM decision value 1.86
SVM RNA-class probability 0.980522
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15627926 117 + 23771897
UGGCCACGUUGCACGUGCCACGUGCCAAAACAACAACAAUAACA-ACUCGAGUGGAGUUUGGCUGGCUGGGGGGAUUCCCCCAUGUACAUG--UAUAUGCUGAUAGCACUCGAACCCAAA
((((.((((.((....)).)))))))).................-..(((((((....(..((.....(((((....)))))(((((....--)))))))..)...)))))))....... ( -39.20)
>DroSec_CAF1 50173 115 + 1
UGGCCACGUUGCACGUGCCACGUGCCAAAACAACAACAAUAACAAACUCGAGUGGGGUUUGGCUGGCUGGG-GGAUUCCCCCAUACACA----UAUAUGCUGAUAGCACUCGAACCCAAA
((((.((((.((....)).))))))))....................(((((((....(..((((..((((-((...))))))..))..----.....))..)...)))))))....... ( -36.71)
>DroSim_CAF1 51185 116 + 1
UGGCCACGUUGCACGUGCCACGUGCCAAAACAACAACAAUAACAAACUCGAGUGGAGUUUGGCUGACUGGGGGGAUUCCCCCAUACACA----UAUAUGCUGAUAGCACUCGAACCCAAA
((((.((((.((....)).))))))))....................(((((((....(..((((..((((((....))))))..))..----.....))..)...)))))))....... ( -36.41)
>DroEre_CAF1 51419 109 + 1
UGGCCACGUUGCACGUGCCACGUGCCAAAACAACAACAAUAACA-ACUCGAGUGGAGCUGCCU-CGCUGGG-GUAUUCCCCCAUA--------UAUAUGCUGAUAGCACUCGAACCCAAA
((((.((((.((....)).)))))))).................-..(((((((.(((.....-.)))(((-(.....))))...--------.............)))))))....... ( -32.70)
>DroYak_CAF1 54753 118 + 1
UGGCCACGUUGCACGUGCCACGUGCCAAAGGAACAACAAUAACA-ACUCGAGUGGAGUUUCGUUGGCUGGG-GGAUUCCCCCAUAUACUCGUAUAUAUGCUGAUAGCACUCGAACCCAAA
((((.((((.((....)).)))))))).................-..((((((((.....)((..((.(((-((...)))))(((((....)))))..))..))..)))))))....... ( -37.60)
>consensus
UGGCCACGUUGCACGUGCCACGUGCCAAAACAACAACAAUAACA_ACUCGAGUGGAGUUUGGCUGGCUGGG_GGAUUCCCCCAUACACA____UAUAUGCUGAUAGCACUCGAACCCAAA
((((.((((.((....)).))))))))....................(((((((.((((.....))))(((.(.....))))........................)))))))....... (-29.52 = -29.24 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 15,627,966 – 15,628,083
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.57
Mean single sequence MFE -33.30
Consensus MFE -22.42
Energy contribution -23.66
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -1.96
Structure conservation index 0.67
SVM decision value 0.43
SVM RNA-class probability 0.733454
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15627966 117 - 23771897
AGAGGGCACAAAACUGCUACCCCCAAAAUGGUAAUGAAAUUUUGGGUUCGAGUGCUAUCAGCAUAUA--CAUGUACAUGGGGGAAUCCCCCCAGCCAGCCAAACUCCACUCGAGU-UGUU
....((((......))))...((((((((.........))))))))((((((((......((((...--.))))...((((((....)))))).............)))))))).-.... ( -34.70)
>DroSec_CAF1 50213 115 - 1
AGAGGGCACAAAACUGCUACCCCCAAAAUGGUAAUGAAAUUUUGGGUUCGAGUGCUAUCAGCAUAUA----UGUGUAUGGGGGAAUCC-CCCAGCCAGCCAAACCCCACUCGAGUUUGUU
....((((......))))...((((((((.........))))))))((((((((......((((...----.)))).((((((...))-)))).............))))))))...... ( -33.60)
>DroSim_CAF1 51225 116 - 1
AGAGGGCACAAAACUGCUACCCCCAAAAUGGUAAUGAAAUUUUGGGUUCGAGUGCUAUCAGCAUAUA----UGUGUAUGGGGGAAUCCCCCCAGUCAGCCAAACUCCACUCGAGUUUGUU
.((..(((((....((((...((((((((.........))))))))...((......))))))....----))))).((((((....)))))).))...(((((((.....))))))).. ( -36.60)
>DroEre_CAF1 51459 90 - 1
------------------ACCCCGAAAA-GGUAAUCAAAUUUUGGGUUCGAGUGCUAUCAGCAUAUA--------UAUGGGGGAAUAC-CCCAGCG-AGGCAGCUCCACUCGAGU-UGUU
------------------..(((((((.-.(....)...)))))))((((.((((.....))))...--------..(((((.....)-)))).))-))(((((((.....))))-))). ( -29.00)
>DroYak_CAF1 54793 117 - 1
AGAGGGCACAAAA-UGCUACCCCAAAAAUGGUAAUGAAAUUUUGGGUUCGAGUGCUAUCAGCAUAUAUACGAGUAUAUGGGGGAAUCC-CCCAGCCAACGAAACUCCACUCGAGU-UGUU
.(..(((.....(-((((..(((((((.(........).))))))).....((((.....)))).......))))).((((((...))-)))))))..)..(((((.....))))-)... ( -32.60)
>consensus
AGAGGGCACAAAACUGCUACCCCCAAAAUGGUAAUGAAAUUUUGGGUUCGAGUGCUAUCAGCAUAUA____UGUAUAUGGGGGAAUCC_CCCAGCCAGCCAAACUCCACUCGAGU_UGUU
....((((......))))...((((((((.........))))))))((((((((.......((((((......))))))(((.......)))..............))))))))...... (-22.42 = -23.66 +   1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:44 2006