Locus 977

Sequence ID 2R_DroMel_CAF1
Location 4,124,822 – 4,124,923
Length 101
Max. P 0.711129
window1739 window1740

overview

Window 9

Location 4,124,822 – 4,124,923
Length 101
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 77.45
Mean single sequence MFE -29.38
Consensus MFE -18.00
Energy contribution -19.45
Covariance contribution 1.45
Combinations/Pair 1.13
Mean z-score -1.35
Structure conservation index 0.61
SVM decision value -0.01
SVM RNA-class probability 0.526565
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4124822 101 + 20766785
----UAUAUCAAUAGUACCCAUCCUUACCUGCGGGAACAGAAGUCGUACCACCAGGCUCCCUGGUGGUGCUCCGCACAGUUCAUGUGCGUGAAGGCGUCAUUGUC
----.....((((.((.(((............))).)).((.((((((((((((((...)))))))))))((((((((.....)))))).)).))).)))))).. ( -39.50)
>DroSec_CAF1 14462 101 + 1
----AACAUCAAUAGUAUUACUCCUUACCUGCGGGAACAGAAGUCGUACCACCAAGCUCCCUGGUGGUGCUCCGCGCAGUUCAUGUGCGUGAAGGCGUCAUUGUC
----.....((((........((((.......))))...((.((((((((((((.......)))))))))((((((((.....)))))).)).))).)))))).. ( -32.00)
>DroSim_CAF1 7875 91 + 1
--------------GUGUAGAUCCUUACCUGCGGGAACAGAAGUCGUACCACCAGGCUCCCUGGUGGUGCUCCGCACAGUUCAUGUGCGUGAAGGCGUCAUUGUC
--------------..((((........))))(....).((.((((((((((((((...)))))))))))((((((((.....)))))).)).))).))...... ( -37.90)
>DroEre_CAF1 6095 94 + 1
G-----------UACUAAUACUCCUUACCUGCGGGAACAGAAGUCGUACCACCAGGCUCCCUGAUGGUGCUCCGCGCAGUUCAUGUGCGUGAAGGCAUCGUGGUC
.-----------.((((....((((.......))))...((.(((((((((.((((...)))).))))))((((((((.....)))))).)).))).)).)))). ( -30.80)
>DroYak_CAF1 4301 105 + 1
AUUUAAGACUAAUACUAAUACUUCCUACCUUCGCGAACAGAAGUCGUACCACCAAGCUCCCUGAUGGUGCUCCGCGCAGUUCAUGUGCGUGAAGGCAUCGUGAUC
...........................(((((((........(..((((((.((.......)).))))))..)(((((.....)))))))))))).......... ( -26.20)
>DroAna_CAF1 3384 92 + 1
---------CUAUAGU----CCCCCUACCUUCUUGAACAAAAAUCAUACCACCACGCCCCGUGAUGAUACUCGGCACAGUUCAUAUGAGUAAACUCAUCGUUGUC
---------.......----.............(((((..............((((...)))).((.....)).....))))).(((((....)))))....... (  -9.90)
>consensus
_________CAAUAGUAAUACUCCUUACCUGCGGGAACAGAAGUCGUACCACCAGGCUCCCUGAUGGUGCUCCGCACAGUUCAUGUGCGUGAAGGCAUCAUUGUC
.......................................((.(((((((((.((((...)))).))))))((((((((.....)))))).)).))).))...... (-18.00 = -19.45 +   1.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,124,822 – 4,124,923
Length 101
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 77.45
Mean single sequence MFE -30.88
Consensus MFE -22.75
Energy contribution -21.95
Covariance contribution -0.80
Combinations/Pair 1.36
Mean z-score -1.10
Structure conservation index 0.74
SVM decision value 0.38
SVM RNA-class probability 0.711129
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4124822 101 - 20766785
GACAAUGACGCCUUCACGCACAUGAACUGUGCGGAGCACCACCAGGGAGCCUGGUGGUACGACUUCUGUUCCCGCAGGUAAGGAUGGGUACUAUUGAUAUA----
..(((((..(((((((......))).(((((.((((((((((((((...)))))))))..(....).))))))))))........))))..))))).....---- ( -35.60)
>DroSec_CAF1 14462 101 - 1
GACAAUGACGCCUUCACGCACAUGAACUGCGCGGAGCACCACCAGGGAGCUUGGUGGUACGACUUCUGUUCCCGCAGGUAAGGAGUAAUACUAUUGAUGUU----
..(((((((.((((.((.(....)..(((((.((((((((((((((...)))))))))..(....).)))))))))))))))).)).....))))).....---- ( -32.50)
>DroSim_CAF1 7875 91 - 1
GACAAUGACGCCUUCACGCACAUGAACUGUGCGGAGCACCACCAGGGAGCCUGGUGGUACGACUUCUGUUCCCGCAGGUAAGGAUCUACAC--------------
.........((((.(..(((((.....)))))((((((((((((((...)))))))))..(....).))))).).))))............-------------- ( -31.60)
>DroEre_CAF1 6095 94 - 1
GACCACGAUGCCUUCACGCACAUGAACUGCGCGGAGCACCAUCAGGGAGCCUGGUGGUACGACUUCUGUUCCCGCAGGUAAGGAGUAUUAGUA-----------C
......((((((((.((.(....)..(((((.((((((((((((((...)))))))))..(....).)))))))))))).))).)))))....-----------. ( -31.70)
>DroYak_CAF1 4301 105 - 1
GAUCACGAUGCCUUCACGCACAUGAACUGCGCGGAGCACCAUCAGGGAGCUUGGUGGUACGACUUCUGUUCGCGAAGGUAGGAAGUAUUAGUAUUAGUCUUAAAU
(((...(((((((((.((((.......)))).)))).(((((((((...)))))))))...((((((....((....)).))))))....))))).)))...... ( -28.80)
>DroAna_CAF1 3384 92 - 1
GACAACGAUGAGUUUACUCAUAUGAACUGUGCCGAGUAUCAUCACGGGGCGUGGUGGUAUGAUUUUUGUUCAAGAAGGUAGGGGG----ACUAUAG---------
..((...(((((....))))).))..((.((((..(((((((((((...)))))))))))..(((((....))))))))).))..----.......--------- ( -25.10)
>consensus
GACAACGACGCCUUCACGCACAUGAACUGCGCGGAGCACCACCAGGGAGCCUGGUGGUACGACUUCUGUUCCCGCAGGUAAGGAGUAAUACUAUUG_________
.........((......)).......(((((.((((((((((((((...)))))))))..(....).))))))))))............................ (-22.75 = -21.95 +  -0.80)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:15 2006