Locus 3566

Sequence ID	2R_DroMel_CAF1
Location	11,883,713 – 11,883,810
Length	97
Max. P	0.686518

overview

Window 6

Location	11,883,713 – 11,883,810
Length	97
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	86.69
Mean single sequence MFE	-37.32
Consensus MFE	-28.66
Energy contribution	-28.86
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.77
SVM decision value	0.05
SVM RNA-class probability	0.557443
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11883713 97 + 20766785
CACCA------------AAAAAGGGGGUUUUUCGCCAAAUGCUGACAGCUGUGUGA---CAGCGCUUGGGGAACGCCCUUAGAAAGGCCUUGGGCACACGGUUGUGUGGGUG----
((((.------------.....((.((....)).))........(((((((((((.---(((.((((((((....)))).....)))).)))..)))))))))))...))))---- ( -35.40)
>DroSec_CAF1 24140 97 + 1
CAGCU------------ACAAAGGGGGUUUUUCGCCAAAUGCUGACAGCUGUGUGA---CAGCGCUUGGGGAACGCCCUUAAAAAGGCCUUGGGCACACGGAUGUGUGGGUG----
((.((------------((((((((.((...((.((((.(((((.((......)).---))))).)))).)))).)))))......(((...))).........))))).))---- ( -32.70)
>DroSim_CAF1 24327 97 + 1
CAGCU------------ACAAAGGGGGUUUUUCGCCAAAUGCUGACAGCUGUGUGA---CAGCGCUUGGGGAACGCCCUUAAAAAGGCCUUGGGCACACGGAUGUGUGGGUG----
((.((------------((((((((.((...((.((((.(((((.((......)).---))))).)))).)))).)))))......(((...))).........))))).))---- ( -32.70)
>DroEre_CAF1 26186 100 + 1
CAACCA-----------CCGAAGGGGG--UUUCGCCAAAUGCUGACAGCUGUGUGA---CAGCGCUUGGGGAACGCCCUUUAAAAGGCCUUGGGCACACGGAUGUGUGGGUGGGUG
...(((-----------((((((((.(--((((.((((.(((((.((......)).---))))).))))))))).)))))).............(((((....))))))))))... ( -43.60)
>DroYak_CAF1 24333 114 + 1
CACCUAUGUAUGUAUGUACAAAGGGGU--UUUCGCCAAAUGCUGACAGCUGUGUGACGACAGCGCUUGGGGAACGCCCUUAAAAAGGCCUUGGGCACACGGAUGUGUGGGUGGGUG
((((((..(((.(.(((....((((((--.(((.((((.(((((....(.....)....))))).)))).))).))))))......(((...)))))).).)))..)))))).... ( -42.20)
>consensus
CACCU____________ACAAAGGGGGUUUUUCGCCAAAUGCUGACAGCUGUGUGA___CAGCGCUUGGGGAACGCCCUUAAAAAGGCCUUGGGCACACGGAUGUGUGGGUG____
....................(((((.(...(((.((((.(((((....(.....)....))))).)))).)))).)))))......((((...(((((....)))))))))..... (-28.66 = -28.86 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	11,883,713 – 11,883,810
Length	97
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	86.69
Mean single sequence MFE	-30.16
Consensus MFE	-22.14
Energy contribution	-22.14
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.80
Structure conservation index	0.73
SVM decision value	0.32
SVM RNA-class probability	0.686518
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11883713 97 - 20766785
----CACCCACACAACCGUGUGCCCAAGGCCUUUCUAAGGGCGUUCCCCAAGCGCUG---UCACACAGCUGUCAGCAUUUGGCGAAAAACCCCCUUUUU------------UGGUG
----....(((((....)))))......(((.....(((((..(((.(((((.((((---.((......)).)))).))))).))).....)))))...------------.))). ( -29.50)
>DroSec_CAF1 24140 97 - 1
----CACCCACACAUCCGUGUGCCCAAGGCCUUUUUAAGGGCGUUCCCCAAGCGCUG---UCACACAGCUGUCAGCAUUUGGCGAAAAACCCCCUUUGU------------AGCUG
----....(((((....))))).....(((..(...(((((..(((.(((((.((((---.((......)).)))).))))).))).....))))).).------------.))). ( -27.80)
>DroSim_CAF1 24327 97 - 1
----CACCCACACAUCCGUGUGCCCAAGGCCUUUUUAAGGGCGUUCCCCAAGCGCUG---UCACACAGCUGUCAGCAUUUGGCGAAAAACCCCCUUUGU------------AGCUG
----....(((((....))))).....(((..(...(((((..(((.(((((.((((---.((......)).)))).))))).))).....))))).).------------.))). ( -27.80)
>DroEre_CAF1 26186 100 - 1
CACCCACCCACACAUCCGUGUGCCCAAGGCCUUUUAAAGGGCGUUCCCCAAGCGCUG---UCACACAGCUGUCAGCAUUUGGCGAAA--CCCCCUUCGG-----------UGGUUG
((.((((((((((....)))))..............(((((.(((.((((((.((((---.((......)).)))).))))).).))--).))))).))-----------))).)) ( -35.10)
>DroYak_CAF1 24333 114 - 1
CACCCACCCACACAUCCGUGUGCCCAAGGCCUUUUUAAGGGCGUUCCCCAAGCGCUGUCGUCACACAGCUGUCAGCAUUUGGCGAAA--ACCCCUUUGUACAUACAUACAUAGGUG
....((((.........(((((..(((((.........(((..(((.(((((.((((.((.(.....).)).)))).))))).))).--.))))))))..))))).......)))) ( -30.59)
>consensus
____CACCCACACAUCCGUGUGCCCAAGGCCUUUUUAAGGGCGUUCCCCAAGCGCUG___UCACACAGCUGUCAGCAUUUGGCGAAAAACCCCCUUUGU____________AGCUG
........(((((....)))))......(((((....))))).(((.(((((.((((....((......)).)))).))))).))).............................. (-22.14 = -22.14 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:40 2006