Locus 4906

Sequence ID 3L_DroMel_CAF1
Location 13,653,703 – 13,653,798
Length 95
Max. P 0.923286
window7743 window7744

overview

Window 3

Location 13,653,703 – 13,653,798
Length 95
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 82.81
Mean single sequence MFE -19.36
Consensus MFE -13.12
Energy contribution -13.16
Covariance contribution 0.04
Combinations/Pair 1.17
Mean z-score -2.35
Structure conservation index 0.68
SVM decision value 1.15
SVM RNA-class probability 0.923286
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13653703 95 + 23771897
ACUUCUAAACGCUUUUAAAUCCAUAAGGA-AAGCGAAUGCAGCUGAUCUGCAUUCGAAAUCUA--------AACAUUUCCAUUCCCUGUCUAAA-A-AUAAAAUUC---
..........((((.....(((....)))-))))((((((((.....))))))))(((((...--------...)))))...............-.-.........--- ( -17.10)
>DroSec_CAF1 61066 98 + 1
UCUUCUAAACGCUUUUAAAGCCAUAAGGA-AAGCGAAUGCAGCUGAUCUGCAUUCGAAAUCUA--------AACGUUUCCAUUCCCUGUCUAAA-A-AUAAAACUCUCU
..........(((.....))).(((.(((-(...((((((((.....))))))))(((((...--------...)))))..)))).))).....-.-............ ( -17.50)
>DroSim_CAF1 71279 100 + 1
ACUUCUAAACACUUUGGAGGCCAUAACGCCCCGCGAAUGCAGCUGAUCUGCAUUCGAAAUCUA--------AACAUUUCCAUUCCCUGUCUAAAAA-AUAAAACUCUCU
..............(((((((......)))...(((((((((.....))))))))).......--------......))))...............-............ ( -19.90)
>DroEre_CAF1 63811 99 + 1
ACUUCUAAACGCUUUUAAAGCCGCACGGA-AAGUGAAUGCAGCUGAUCUGCAUUCGAAAUCUU--------AACAUUUCCAUUCCCUGUCUGCA-AAAAAAGAAUCAUU
...........(((((...((.(((.(((-(...((((((((.....))))))))(((((...--------...)))))..)))).)))..)).-..)))))....... ( -21.70)
>DroYak_CAF1 68926 106 + 1
ACUUCUAAACGCUUUUAAAGCCGCACGGA-GAGUGAAUGCAGCUGAUCUGCAUUCGAAAUCCUAACAUCCUAACAUUUCCAUUCGCUGUCUGAA-A-AUAAAACUCUUA
..........(((.....)))....((((-.(((((((((((.....))))))))(((((..((......))..))))).....))).))))..-.-............ ( -20.60)
>consensus
ACUUCUAAACGCUUUUAAAGCCAUAAGGA_AAGCGAAUGCAGCUGAUCUGCAUUCGAAAUCUA________AACAUUUCCAUUCCCUGUCUAAA_A_AUAAAACUCUCU
..........................(((....(((((((((.....)))))))))...)))............................................... (-13.12 = -13.16 +   0.04)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,653,703 – 13,653,798
Length 95
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 82.81
Mean single sequence MFE -27.32
Consensus MFE -16.04
Energy contribution -16.68
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -2.24
Structure conservation index 0.59
SVM decision value 0.51
SVM RNA-class probability 0.762864
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13653703 95 - 23771897
---GAAUUUUAU-U-UUUAGACAGGGAAUGGAAAUGUU--------UAGAUUUCGAAUGCAGAUCAGCUGCAUUCGCUU-UCCUUAUGGAUUUAAAAGCGUUUAGAAGU
---.......((-(-(((((((........(((((...--------...)))))((((((((.....))))))))((((-(((....))).....)))))))))))))) ( -26.50)
>DroSec_CAF1 61066 98 - 1
AGAGAGUUUUAU-U-UUUAGACAGGGAAUGGAAACGUU--------UAGAUUUCGAAUGCAGAUCAGCUGCAUUCGCUU-UCCUUAUGGCUUUAAAAGCGUUUAGAAGA
...........(-(-(((((((((((((((....))))--------)......(((((((((.....)))))))))...-.)))....(((.....)))))))))))). ( -28.90)
>DroSim_CAF1 71279 100 - 1
AGAGAGUUUUAU-UUUUUAGACAGGGAAUGGAAAUGUU--------UAGAUUUCGAAUGCAGAUCAGCUGCAUUCGCGGGGCGUUAUGGCCUCCAAAGUGUUUAGAAGU
............-((((((((((.......(((((...--------...)))))((((((((.....))))))))(.(((((......))))))....)))))))))). ( -28.80)
>DroEre_CAF1 63811 99 - 1
AAUGAUUCUUUUUU-UGCAGACAGGGAAUGGAAAUGUU--------AAGAUUUCGAAUGCAGAUCAGCUGCAUUCACUU-UCCGUGCGGCUUUAAAAGCGUUUAGAAGU
...(((.(((((..-.((.(.((.((((.((((((...--------...)))))((((((((.....)))))))).).)-))).))).))...))))).)))....... ( -27.40)
>DroYak_CAF1 68926 106 - 1
UAAGAGUUUUAU-U-UUCAGACAGCGAAUGGAAAUGUUAGGAUGUUAGGAUUUCGAAUGCAGAUCAGCUGCAUUCACUC-UCCGUGCGGCUUUAAAAGCGUUUAGAAGU
..........((-(-(..((((.(((....(((((.((((....)))).)))))((((((((.....))))))))....-....))).(((.....)))))))..)))) ( -25.00)
>consensus
AAAGAGUUUUAU_U_UUUAGACAGGGAAUGGAAAUGUU________UAGAUUUCGAAUGCAGAUCAGCUGCAUUCGCUU_UCCUUAUGGCUUUAAAAGCGUUUAGAAGU
...............(((((((........(((((.(..........).)))))((((((((.....))))))))........................)))))))... (-16.04 = -16.68 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:38 2006