Locus 1548

Sequence ID 2L_DroMel_CAF1
Location 4,168,347 – 4,168,450
Length 103
Max. P 0.961706
window2502 window2503

overview

Window 2

Location 4,168,347 – 4,168,450
Length 103
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 68.88
Mean single sequence MFE -43.85
Consensus MFE -23.04
Energy contribution -25.60
Covariance contribution 2.56
Combinations/Pair 1.28
Mean z-score -1.94
Structure conservation index 0.53
SVM decision value 1.53
SVM RNA-class probability 0.961706
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4168347 103 + 22407834
---AUGGCGCCCAUUGUCGAACGCCCCA--GGUCACGGG-GGCGUGGCAGUGGCAAAAGAGGCUG----AGGGGCGUGGCCGAGUGGUAUAAUGGCCACAGAG---AAAUGGGGC---U
---..(((.((((((.(((.(((((((.--.((((((..-..))))))...(((.......))).----.)))))))...)))(((((......)))))....---.))))))))---) ( -46.30)
>DroSec_CAF1 3218 103 + 1
---A-GGCGCCCAUUGUCGAACGCCCCA--GGUCACGGGGGGCGUGGCAGGGGCAAAAGGGGCUG----AGGGGCGUGGCCGAGUGGUAUAAUGGCCACGGAG---AAAUGGGGC---U
---.-(((.((((((.(((.(((((((.--.((((((.....))))))...(((.......))).----.)))))))...)))(((((......)))))....---.))))))))---) ( -46.60)
>DroSim_CAF1 3372 103 + 1
---A-GGCGCCCAUUGUCGAACGCCCCA--GGUCACGGGGGGCGUGGCAGGGGCAAAGGGGGCUG----AGGGGCGUGGCCGAGUGGUAUAAUGGCCACGGAG---AAAUGGGGC---U
---.-(((.((((((.(((.(((((((.--.((((((.....))))))...(((.......))).----.)))))))...)))(((((......)))))....---.))))))))---) ( -46.60)
>DroEre_CAF1 3457 95 + 1
---A-GACGCCCAUUG-------CCACA--GGUCACGAG-GUCGUGGCAGGGGCAAGAGAGGCUG----AGGGGCGUGGCCGAGUGCUAUAAUGGCCACAGAG---AGUUGGGGC---G
---.-..(((((.(((-------((.(.--.((((((..-..))))))..)))))).....(((.----...)))(((((((..........)))))))....---.....))))---) ( -40.20)
>DroAna_CAF1 3877 111 + 1
CGCA-GGCUCCCAUUGUCAAGCGCUCCA--GGUCAUGGCAGACCC---GUGGGCUAUUGGGCGUG--GCAGGGGCGUGGUCGAGUGGUAUAAUGGCCGCGGAGGUGAGUCGAGGCACCU
.((.-(((((((.(((....(((((((.--.((((((.(((.((.---...))))....).))))--)).)))))))...)))(((((......)))))...)).)))))...)).... ( -44.80)
>DroPer_CAF1 69450 90 + 1
---A-GCCCACCAUUGU-GUCCGCCCCGAGGGCCAUGGG--GCA-GGCUUUUCCAGGUGGGGCCUGGGCCGGUGUCUGGAUGAGUGGGAUAAUGGCCA---------------------
---.-.....(((((((-.(((((((((.......))))--)).-.((((.(((((..(.(((....)))..)..))))).))))))))))))))...--------------------- ( -38.60)
>consensus
___A_GGCGCCCAUUGUCGAACGCCCCA__GGUCACGGG_GGCGUGGCAGGGGCAAAAGGGGCUG____AGGGGCGUGGCCGAGUGGUAUAAUGGCCACGGAG___AAAUGGGGC___U
........((((..........(((((....((((((.....))))))...(((.......)))......)))))(((((((..........)))))))............)))).... (-23.04 = -25.60 +   2.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,168,347 – 4,168,450
Length 103
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 68.88
Mean single sequence MFE -34.68
Consensus MFE -15.81
Energy contribution -17.81
Covariance contribution 2.00
Combinations/Pair 1.23
Mean z-score -2.04
Structure conservation index 0.46
SVM decision value 1.43
SVM RNA-class probability 0.953452
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4168347 103 - 22407834
A---GCCCCAUUU---CUCUGUGGCCAUUAUACCACUCGGCCACGCCCCU----CAGCCUCUUUUGCCACUGCCACGCC-CCCGUGACC--UGGGGCGUUCGACAAUGGGCGCCAU---
.---(((((((((---(...((((((............))))))(((((.----...........((....))((((..-..))))...--.)))))....)).)))))).))...--- ( -36.30)
>DroSec_CAF1 3218 103 - 1
A---GCCCCAUUU---CUCCGUGGCCAUUAUACCACUCGGCCACGCCCCU----CAGCCCCUUUUGCCCCUGCCACGCCCCCCGUGACC--UGGGGCGUUCGACAAUGGGCGCC-U---
.---(((((((((---(..(((((((............))))))).....----...........(((((.(.((((.....)))).).--.)))))....)).)))))).)).-.--- ( -38.30)
>DroSim_CAF1 3372 103 - 1
A---GCCCCAUUU---CUCCGUGGCCAUUAUACCACUCGGCCACGCCCCU----CAGCCCCCUUUGCCCCUGCCACGCCCCCCGUGACC--UGGGGCGUUCGACAAUGGGCGCC-U---
.---(((((((((---(..(((((((............))))))).....----...........(((((.(.((((.....)))).).--.)))))....)).)))))).)).-.--- ( -38.30)
>DroEre_CAF1 3457 95 - 1
C---GCCCCAACU---CUCUGUGGCCAUUAUAGCACUCGGCCACGCCCCU----CAGCCUCUCUUGCCCCUGCCACGAC-CUCGUGACC--UGUGG-------CAAUGGGCGUC-U---
(---((((.....---....((((((............))))))(((...----(((........((....))((((..-..))))..)--)).))-------)...)))))..-.--- ( -31.00)
>DroAna_CAF1 3877 111 - 1
AGGUGCCUCGACUCACCUCCGCGGCCAUUAUACCACUCGACCACGCCCCUGC--CACGCCCAAUAGCCCAC---GGGUCUGCCAUGACC--UGGAGCGCUUGACAAUGGGAGCC-UGCG
(((((........))))).((((((...................((....))--....((((..((((..(---(((((......))))--))..).)))......)))).)))-.))) ( -30.40)
>DroPer_CAF1 69450 90 - 1
---------------------UGGCCAUUAUCCCACUCAUCCAGACACCGGCCCAGGCCCCACCUGGAAAAGCC-UGC--CCCAUGGCCCUCGGGGCGGAC-ACAAUGGUGGGC-U---
---------------------..........(((((.(((((((.....(((....)))....)))))...(.(-(((--(((.........))))))).)-....))))))).-.--- ( -33.80)
>consensus
A___GCCCCAUUU___CUCCGUGGCCAUUAUACCACUCGGCCACGCCCCU____CAGCCCCUUUUGCCCCUGCCACGCC_CCCGUGACC__UGGGGCGUUCGACAAUGGGCGCC_U___
....................((((((............))))))(((((.......(((((....((....))((((.....))))......)))))..........))).))...... (-15.81 = -17.81 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:15 2006