Locus 4066

Sequence ID	2R_DroMel_CAF1
Location	13,430,050 – 13,430,176
Length	126
Max. P	0.846297

overview

Window 9

Location	13,430,050 – 13,430,145
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	83.47
Mean single sequence MFE	-36.30
Consensus MFE	-25.83
Energy contribution	-26.80
Covariance contribution	0.97
Combinations/Pair	1.11
Mean z-score	-3.00
Structure conservation index	0.71
SVM decision value	0.77
SVM RNA-class probability	0.846297
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13430050 95 + 20766785
UCGCUCCAUUAGGCAGCACACGCGGCGUAUACGCAACGAGCUGCACCCACGCCGCAUACGCAAUGCGCUGCACAAUUAAGCGCAUUUGUGCGGCU
............(((((...((..(((....)))..)).)))))......((((((((...((((((((.........)))))))))))))))). ( -39.90)
>DroPse_CAF1 27390 86 + 1
UUGCUCCAUUAGGCAGGC---------UCUAUUCAGGGUUCGUCGCACACGGCGUAUACGGAAUGCGCUGCACAAUUAAGCGCAUUUGUGCGGCU
(((((......)))))((---------(((....)))))..(((((((.((.......))(((((((((.........)))))))))))))))). ( -31.90)
>DroSec_CAF1 27328 95 + 1
CCGCUCCAUUAGGCAGCACACGCGGCGUAUACGCAACGAGCUGCACCCACGCCGCAUACGCAAUGCGCUGCACAAUUAAGCGCAUUUGUGCGGCU
............(((((...((..(((....)))..)).)))))......((((((((...((((((((.........)))))))))))))))). ( -39.90)
>DroSim_CAF1 28621 95 + 1
UCGCUCCAUUAGGCAGCACACGCGGCGUAUACGCAACGAGCUGCACCCACGCCGCAUACGCAAUGCGCUGCACAAUUAAGCGCUUUUGUGCGGCU
............(((((...((..(((....)))..)).)))))......((((((((......(((((.........)))))...)))))))). ( -36.10)
>DroYak_CAF1 28640 95 + 1
UCGCUCCAUUAGGCAGCACACGCGGCGUAUACGCAACGAGCUGCACCCACGCCGCAUACGCAAUGCGCUGCACAAUUAAGCGCAUUUGUGCGGCU
............(((((...((..(((....)))..)).)))))......((((((((...((((((((.........)))))))))))))))). ( -39.90)
>DroPer_CAF1 27485 84 + 1
UUGCUCCAUUAGGCAGGC---------UCUAU--GGGGUUCGUCGCACACGGCGUAUACGGAAUGCACUGCACAAUUAAGCGCAUUUGUGCGGCU
..(((((((..((....)---------)..))--)))))..(((((((.((.......))((((((.((.........)).))))))))))))). ( -30.10)
>consensus
UCGCUCCAUUAGGCAGCACACGCGGCGUAUACGCAACGAGCUGCACCCACGCCGCAUACGCAAUGCGCUGCACAAUUAAGCGCAUUUGUGCGGCU
..(((......))).(((..((..(((....)))..))...)))......((((((((...((((((((.........)))))))))))))))). (-25.83 = -26.80 +   0.97)

alignment

secondary structure

dotplot

Window 0

Location	13,430,050 – 13,430,145
Length	95
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	83.47
Mean single sequence MFE	-37.79
Consensus MFE	-26.42
Energy contribution	-31.53
Covariance contribution	5.11
Combinations/Pair	1.03
Mean z-score	-2.41
Structure conservation index	0.70
SVM decision value	0.39
SVM RNA-class probability	0.718492
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13430050 95 - 20766785
AGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGCGUGUGCUGCCUAAUGGAGCGA
....(((....)))((((.((((.(((((((((.......((((((((..(((((....)))))..))))))))))))))))).)))).)))).. ( -44.91)
>DroPse_CAF1 27390 86 - 1
AGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUCCGUAUACGCCGUGUGCGACGAACCCUGAAUAGA---------GCCUGCCUAAUGGAGCAA
....(((....)))((((.((((.((((.((....(((((((...))))))).......((....)).---------)))))).)))).)))).. ( -23.10)
>DroSec_CAF1 27328 95 - 1
AGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGCGUGUGCUGCCUAAUGGAGCGG
..((((...((((((((.........))))))))((((((((((((((..(((((....)))))..))))))))))))))..((....)).)))) ( -45.90)
>DroSim_CAF1 28621 95 - 1
AGCCGCACAAAAGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGCGUGUGCUGCCUAAUGGAGCGA
.............(((((.((((.(((((((((.......((((((((..(((((....)))))..))))))))))))))))).)))).))))). ( -44.61)
>DroYak_CAF1 28640 95 - 1
AGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGCGUGUGCUGCCUAAUGGAGCGA
....(((....)))((((.((((.(((((((((.......((((((((..(((((....)))))..))))))))))))))))).)))).)))).. ( -44.91)
>DroPer_CAF1 27485 84 - 1
AGCCGCACAAAUGCGCUUAAUUGUGCAGUGCAUUCCGUAUACGCCGUGUGCGACGAACCCC--AUAGA---------GCCUGCCUAAUGGAGCAA
.((.((((...(((((......)))))))))....(((((((...))))))).......((--((((.---------(....))).)))).)).. ( -23.30)
>consensus
AGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGCGUGUGCUGCCUAAUGGAGCGA
....((......))((((.((((.(((((((((.......((((((((..(((((....)))))..))))))))))))))))).)))).)))).. (-26.42 = -31.53 +   5.11)

alignment

secondary structure

dotplot

Window 1

Location	13,430,071 – 13,430,176
Length	105
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	86.93
Mean single sequence MFE	-39.15
Consensus MFE	-30.80
Energy contribution	-33.72
Covariance contribution	2.92
Combinations/Pair	1.10
Mean z-score	-2.21
Structure conservation index	0.79
SVM decision value	0.17
SVM RNA-class probability	0.618805
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13430071 105 - 20766785
UCACUUCAUUUGCAUGCAUUUCGCGGUUGAGAGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGC
...........((((((.....(((((.....)))))...((((((((.........))))))))..))))))((((((..(((((....)))))..)))))).. ( -44.20)
>DroPse_CAF1 27408 99 - 1
UCGCUUCAUUUGCAUGCAUUACGCGGCUGAGAGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUCCGUAUACGCCGUGUGCGACGAACCCUGAAUAGA------
....(((..((((((((.....(((((.....)))))((.((((((((.........))))))))..)).......)))))))).)))...........------ ( -29.50)
>DroSim_CAF1 28642 105 - 1
UCACUUCAUUUGCAUGCAUUUCGCGGUUGAGAGCCGCACAAAAGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGC
...........((((((.....(((((.....)))))......((((......))))...))).)))....((((((((..(((((....)))))..)))))))) ( -42.40)
>DroEre_CAF1 28980 105 - 1
UCACUUCAUUUGCAUGCAUUUCGCGGUUGAGAGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGC
...........((((((.....(((((.....)))))...((((((((.........))))))))..))))))((((((..(((((....)))))..)))))).. ( -44.20)
>DroYak_CAF1 28661 105 - 1
UCACUUCAUUUGCAUGCAUUUCGCGGUUGAGAGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGC
...........((((((.....(((((.....)))))...((((((((.........))))))))..))))))((((((..(((((....)))))..)))))).. ( -44.20)
>DroPer_CAF1 27503 97 - 1
UCGCUUCAUUUGCAUGCAUUACGCGGCUGAGAGCCGCACAAAUGCGCUUAAUUGUGCAGUGCAUUCCGUAUACGCCGUGUGCGACGAACCCC--AUAGA------
..((.......))(((((((..(((((.....)))))......((((......)))))))))))..(((((((...))))))).........--.....------ ( -30.40)
>consensus
UCACUUCAUUUGCAUGCAUUUCGCGGUUGAGAGCCGCACAAAUGCGCUUAAUUGUGCAGCGCAUUGCGUAUGCGGCGUGGGUGCAGCUCGUUGCGUAUACGCCGC
...........((((((.....(((((.....)))))...((((((((.........))))))))..))))))((((((..(((((....)))))..)))))).. (-30.80 = -33.72 +   2.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:58 2006