Locus 5460

Sequence ID 3R_DroMel_CAF1
Location 14,432,013 – 14,432,106
Length 93
Max. P 0.832521
window8884 window8885

overview

Window 4

Location 14,432,013 – 14,432,106
Length 93
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 83.03
Mean single sequence MFE -28.47
Consensus MFE -22.50
Energy contribution -22.70
Covariance contribution 0.20
Combinations/Pair 1.27
Mean z-score -2.17
Structure conservation index 0.79
SVM decision value 0.72
SVM RNA-class probability 0.832521
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14432013 93 + 27905053
UUCAAUUUGGCGUAUUAUGG--CCUAUGGCCACGGUUCCAAUCGAUUUGCGGCGCU--ACAGAAAUCGAGCGAUCUGAUCGAUUCGAUCUGUGGCA--A
........(.((((...(((--((...)))))((((....))))...)))).)(((--(((((..(((((((((...)))).))))))))))))).--. ( -33.40)
>DroSec_CAF1 210463 95 + 1
UUCAAUUUGGUGUAUUUUGG--CCUAUGGCCACGGUUCCAAUCGAUUUGCGGCGCUAUACAGAAAUCGAGCGAUCUGAUCGAUUCGAUCUGUGGCA--A
........(((........)--))....(((((((.((.((((((((.....((((....(....)..))))....)))))))).)).))))))).--. ( -30.10)
>DroSim_CAF1 202660 95 + 1
UUCAAUUUGGUGUAUUAUGG--CCUAUGGCCACGGUUCCAAUCGAUUUGCGGCGCUAUACAGAAAUCGAGCGAUCUGAUCGAUUCGAUCUGUGGCA--A
........(((........)--))....(((((((.((.((((((((.....((((....(....)..))))....)))))))).)).))))))).--. ( -30.10)
>DroEre_CAF1 218826 86 + 1
UUCAAUUUGGUGUAUUA---------UGGCCACGGUUCGAAUCCAUUUGCGGCGUU--ACAGAAAUCGAGCGAUCUGAUCGAUUCGAUCUGUGGCA--A
.................---------..(((((((.(((((((.(((.....((((--...(....).))))....))).))))))).))))))).--. ( -27.10)
>DroYak_CAF1 221603 86 + 1
UUCAAUUUGGUGUAUUA---------UGGCCACGGUUCCAAUCGAUUUGCGGCGCU--ACAGAAAUCGAGCGCUUUGAUCGAUUCGAUCUGUGGCA--A
.................---------..(((((((.((.((((((((...((((((--...(....).))))))..)))))))).)).))))))).--. ( -33.80)
>DroAna_CAF1 195363 89 + 1
UUCAAUUUAG---AUUUUGCUUUUUAUGGCUACGGUUCCGAUCGAUUUGCGGCGCU--ACAGAAAUCGAGCAA-----UCGAUUUAGAUAGUAAUAGUA
..........---....((((.......((..(((.((.....)).)))..))(((--(...(((((((....-----)))))))...))))...)))) ( -16.30)
>consensus
UUCAAUUUGGUGUAUUAUGG__CCUAUGGCCACGGUUCCAAUCGAUUUGCGGCGCU__ACAGAAAUCGAGCGAUCUGAUCGAUUCGAUCUGUGGCA__A
............................(((((((.((.((((((((.....((((.....(....).))))....)))))))).)).))))))).... (-22.50 = -22.70 +   0.20)

alignment

Postscript

secondary structure

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dotplot

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Window 5

Location 14,432,013 – 14,432,106
Length 93
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 83.03
Mean single sequence MFE -22.28
Consensus MFE -16.01
Energy contribution -16.48
Covariance contribution 0.48
Combinations/Pair 1.19
Mean z-score -1.49
Structure conservation index 0.72
SVM decision value -0.03
SVM RNA-class probability 0.516085
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14432013 93 - 27905053
U--UGCCACAGAUCGAAUCGAUCAGAUCGCUCGAUUUCUGU--AGCGCCGCAAAUCGAUUGGAACCGUGGCCAUAGG--CCAUAAUACGCCAAAUUGAA
.--.(((((.(.((.(((((((..(..((((((.....)).--))))...)..))))))).)).).)))))....((--(........)))........ ( -27.90)
>DroSec_CAF1 210463 95 - 1
U--UGCCACAGAUCGAAUCGAUCAGAUCGCUCGAUUUCUGUAUAGCGCCGCAAAUCGAUUGGAACCGUGGCCAUAGG--CCAAAAUACACCAAAUUGAA
.--.(((((.(.((.(((((((..(..((((..((....))..))))...)..))))))).)).).)))))......--.................... ( -23.30)
>DroSim_CAF1 202660 95 - 1
U--UGCCACAGAUCGAAUCGAUCAGAUCGCUCGAUUUCUGUAUAGCGCCGCAAAUCGAUUGGAACCGUGGCCAUAGG--CCAUAAUACACCAAAUUGAA
.--.((.(((((((((..((((...)))).))))..)))))...))........((((((((....((((((...))--))))......)).)))))). ( -23.50)
>DroEre_CAF1 218826 86 - 1
U--UGCCACAGAUCGAAUCGAUCAGAUCGCUCGAUUUCUGU--AACGCCGCAAAUGGAUUCGAACCGUGGCCA---------UAAUACACCAAAUUGAA
.--.(((((.(.(((((((.((.(((((....))))).(((--......))).)).))))))).).)))))..---------................. ( -20.90)
>DroYak_CAF1 221603 86 - 1
U--UGCCACAGAUCGAAUCGAUCAAAGCGCUCGAUUUCUGU--AGCGCCGCAAAUCGAUUGGAACCGUGGCCA---------UAAUACACCAAAUUGAA
.--.(((((.(.((.(((((((....(((((((.....)).--))))).....))))))).)).).)))))..---------................. ( -26.60)
>DroAna_CAF1 195363 89 - 1
UACUAUUACUAUCUAAAUCGA-----UUGCUCGAUUUCUGU--AGCGCCGCAAAUCGAUCGGAACCGUAGCCAUAAAAAGCAAAAU---CUAAAUUGAA
........((((..(((((((-----....)))))))..))--)).........(((((((....))..((........)).....---....))))). ( -11.50)
>consensus
U__UGCCACAGAUCGAAUCGAUCAGAUCGCUCGAUUUCUGU__AGCGCCGCAAAUCGAUUGGAACCGUGGCCAUAGG__CCAUAAUACACCAAAUUGAA
....(((((.(.((.(((((((.....((((..((....))..))))......))))))).)).).)))))............................ (-16.01 = -16.48 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:14 2006